PATH=C:\Program Files\Microsoft Platform SDK\Bin;C:\Program Files\Microsoft Platform SDK\Bin\WinNT;C:\Program Files\Microsoft Visual Studio\VC98\Bin;C:\Program Files\Microsoft Visual Studio\Common\MSDev98\Bin;C:\cygwin\bin;C:\cpanfly-5.16\var\megalib\bin;C:\Perl-5.16\site\bin;C:\Perl-5.16\bin;C:\cygwin\bin;C:\Program Files\Perforce;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\instantclient_11_2;C:\cygwin\bin;C:\Program Files\Perforce;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\mysql\bin
Start 2013-09-08T03:03:53
ActivePerl-1600 CPAN-2.00
LIB=C:\PROGRA~1\MICROS~3\VC98\Lib\PSDK;C:\PROGRA~1\MICROS~2\Lib;C:\PROGRA~1\MICROS~3\VC98\Lib;C:\PROGRA~1\MICROS~3\VC98\MFC\Lib
INCLUDE=C:\PROGRA~1\MICROS~2\Include;C:\PROGRA~1\MICROS~3\VC98\ATL\Include;C:\PROGRA~1\MICROS~3\VC98\Include;C:\PROGRA~1\MICROS~3\VC98\MFC\Include
PATH=C:/CPANFL~1.16/var/libs/bin;C:\PROGRA~1\MICROS~2\Bin;C:\PROGRA~1\MICROS~2\Bin\WinNT;C:\PROGRA~1\MICROS~3\VC98\Bin;C:\PROGRA~1\MICROS~3\Common\MSDev98\Bin;C:\cygwin\bin;C:\CPANFL~1.16\var\megalib\bin;C:\Perl-5.16\site\bin;C:\Perl-5.16\bin;C:\cygwin\bin;C:\PROGRA~1\Perforce;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WINDOW~2\v1.0;C:\WINDOWS\system32\WINDOW~2\v1.0;C:\INSTAN~1;C:\cygwin\bin;C:\PROGRA~1\Perforce;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WINDOW~2\v1.0;C:\WINDOWS\system32\WINDOW~2\v1.0;C:\mysql\bin
Reading 'C:\cpanfly-5.16\var\cpan\Metadata'
  Database was generated on Sun, 08 Sep 2013 09:08:10 GMT
Running make for C/CJ/CJFIELDS/BioPerl-1.6.920.tar.gz
Fetching with LWP:
http://cpan.nas.activestate.com/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.920.tar.gz
Fetching with LWP:
http://cpan.nas.activestate.com/authors/id/C/CJ/CJFIELDS/CHECKSUMS
Checksum for C:\cpanfly-5.16\var\cpan\sources\authors\id\C\CJ\CJFIELDS\BioPerl-1.6.920.tar.gz ok
BioPerl-1.6.920
BioPerl-1.6.920/.travis.yml
BioPerl-1.6.920/AUTHORS
BioPerl-1.6.920/BioPerl.pm
BioPerl-1.6.920/BUGS
BioPerl-1.6.920/Build.PL
BioPerl-1.6.920/Changes
BioPerl-1.6.920/DEPENDENCIES
BioPerl-1.6.920/DEPRECATED
BioPerl-1.6.920/INSTALL
BioPerl-1.6.920/INSTALL.SKIP
BioPerl-1.6.920/INSTALL.WIN
BioPerl-1.6.920/LICENSE
BioPerl-1.6.920/MANIFEST
BioPerl-1.6.920/META.json
BioPerl-1.6.920/META.yml
BioPerl-1.6.920/README
BioPerl-1.6.920/README.md
BioPerl-1.6.920/Bio
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BioPerl-1.6.920/Bio/Annotation/Target.pm
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BioPerl-1.6.920/Bio/Assembly
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BioPerl-1.6.920/Bio/ClusterIO/unigene.pm
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BioPerl-1.6.920/Bio/DB/DBFetch.pm
BioPerl-1.6.920/Bio/DB/EMBL.pm
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BioPerl-1.6.920/Bio/DB/GFF/Adaptor/dbi
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BioPerl-1.6.920/Bio/DB/GFF/Aggregator/coding.pm
BioPerl-1.6.920/Bio/DB/GFF/Aggregator/gene.pm
BioPerl-1.6.920/Bio/DB/GFF/Aggregator/match.pm
BioPerl-1.6.920/Bio/DB/GFF/Aggregator/none.pm
BioPerl-1.6.920/Bio/DB/GFF/Aggregator/orf.pm
BioPerl-1.6.920/Bio/DB/GFF/Aggregator/processed_transcript.pm
BioPerl-1.6.920/Bio/DB/GFF/Aggregator/so_transcript.pm
BioPerl-1.6.920/Bio/DB/GFF/Aggregator/transcript.pm
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BioPerl-1.6.920/Bio/DB/HIV/HIVAnnotProcessor.pm
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BioPerl-1.6.920/Bio/DB/SeqFeature/Segment.pm
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BioPerl-1.6.920/Bio/DB/SeqFeature/Store/DBI/Iterator.pm
BioPerl-1.6.920/Bio/DB/SeqFeature/Store/DBI/mysql.pm
BioPerl-1.6.920/Bio/DB/SeqFeature/Store/DBI/Pg.pm
BioPerl-1.6.920/Bio/DB/SeqFeature/Store/DBI/SQLite.pm
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BioPerl-1.6.920/Bio/Index
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BioPerl-1.6.920/Bio/Index/Blast.pm
BioPerl-1.6.920/Bio/Index/BlastTable.pm
BioPerl-1.6.920/Bio/Index/EMBL.pm
BioPerl-1.6.920/Bio/Index/Fasta.pm
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BioPerl-1.6.920/Bio/Index/SwissPfam.pm
BioPerl-1.6.920/Bio/Index/Swissprot.pm
BioPerl-1.6.920/Bio/LiveSeq
BioPerl-1.6.920/Bio/LiveSeq/AARange.pm
BioPerl-1.6.920/Bio/LiveSeq/Chain.pm
BioPerl-1.6.920/Bio/LiveSeq/ChainI.pm
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BioPerl-1.6.920/examples
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BioPerl-1.6.920/examples/longorf.pl
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BioPerl-1.6.920/examples/align
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BioPerl-1.6.920/examples/Bio-DB-GFF
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BioPerl-1.6.920/examples/cluster
BioPerl-1.6.920/examples/cluster/dbsnp.pl
BioPerl-1.6.920/examples/contributed
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BioPerl-1.6.920/examples/db
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BioPerl-1.6.920/examples/liveseq
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BioPerl-1.6.920/examples/popgen
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BioPerl-1.6.920/examples/quality
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BioPerl-1.6.920/examples/root
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BioPerl-1.6.920/examples/root/lib/TestInterface.pm
BioPerl-1.6.920/examples/root/lib/TestObject.pm
BioPerl-1.6.920/examples/searchio
BioPerl-1.6.920/examples/searchio/blast_example.pl
BioPerl-1.6.920/examples/searchio/custom_writer.pl
BioPerl-1.6.920/examples/searchio/hitwriter.pl
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BioPerl-1.6.920/examples/searchio/waba2gff.pl
BioPerl-1.6.920/examples/searchio/waba2gff3.pl
BioPerl-1.6.920/examples/sirna
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BioPerl-1.6.920/examples/sirna/TAG
BioPerl-1.6.920/examples/structure
BioPerl-1.6.920/examples/structure/structure-io.pl
BioPerl-1.6.920/examples/tk
BioPerl-1.6.920/examples/tk/gsequence.pl
BioPerl-1.6.920/examples/tk/hitdisplay.pl
BioPerl-1.6.920/examples/tools
BioPerl-1.6.920/examples/tools/extract_genes.pl
BioPerl-1.6.920/examples/tools/gb_to_gff.pl
BioPerl-1.6.920/examples/tools/gff2ps.pl
BioPerl-1.6.920/examples/tools/parse_codeml.pl
BioPerl-1.6.920/examples/tools/psw.pl
BioPerl-1.6.920/examples/tools/reverse-translate.pl
BioPerl-1.6.920/examples/tools/run_genscan.pl
BioPerl-1.6.920/examples/tools/run_primer3.pl
BioPerl-1.6.920/examples/tools/seq_pattern.pl
BioPerl-1.6.920/examples/tools/standaloneblast.pl
BioPerl-1.6.920/examples/tree
BioPerl-1.6.920/examples/tree/paup2phylip.pl
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BioPerl-1.6.920/maintenance
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BioPerl-1.6.920/maintenance/check_URLs.pl
BioPerl-1.6.920/maintenance/cvs2cl_by_file.pl
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BioPerl-1.6.920/maintenance/symlink_script.pl
BioPerl-1.6.920/maintenance/version.pl
BioPerl-1.6.920/maintenance/big_split
BioPerl-1.6.920/maintenance/big_split/file_classification.csv
BioPerl-1.6.920/maintenance/big_split/rbuels_notes.txt
BioPerl-1.6.920/models
BioPerl-1.6.920/models/biblio.dia
BioPerl-1.6.920/models/bio_liveseq_variation.dia
BioPerl-1.6.920/models/bio_map.dia
BioPerl-1.6.920/models/bio_restriction.dia
BioPerl-1.6.920/models/bioperl.dia
BioPerl-1.6.920/models/coordinatemapper.dia
BioPerl-1.6.920/models/map_proposal.txt
BioPerl-1.6.920/models/maps_and_markers.dia
BioPerl-1.6.920/models/popgen.dia
BioPerl-1.6.920/models/population_proposal.txt
BioPerl-1.6.920/models/README
BioPerl-1.6.920/scripts
BioPerl-1.6.920/scripts/README
BioPerl-1.6.920/scripts/Bio-DB-GFF
BioPerl-1.6.920/scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
BioPerl-1.6.920/scripts/Bio-DB-GFF/bp_fast_load_gff.pl
BioPerl-1.6.920/scripts/Bio-DB-GFF/bp_genbank2gff.pl
BioPerl-1.6.920/scripts/Bio-DB-GFF/bp_genbank2gff3.pl
BioPerl-1.6.920/scripts/Bio-DB-GFF/bp_generate_histogram.pl
BioPerl-1.6.920/scripts/Bio-DB-GFF/bp_load_gff.pl
BioPerl-1.6.920/scripts/Bio-DB-GFF/bp_meta_gff.pl
BioPerl-1.6.920/scripts/Bio-DB-GFF/bp_process_gadfly.pl
BioPerl-1.6.920/scripts/Bio-DB-GFF/bp_process_sgd.pl
BioPerl-1.6.920/scripts/Bio-DB-GFF/bp_process_wormbase.pl
BioPerl-1.6.920/scripts/Bio-DB-GFF/README
BioPerl-1.6.920/scripts/Bio-DB-SeqFeature-Store
BioPerl-1.6.920/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl
BioPerl-1.6.920/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl
BioPerl-1.6.920/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
BioPerl-1.6.920/scripts/das
BioPerl-1.6.920/scripts/das/bp_das_server.pl
BioPerl-1.6.920/scripts/das/README
BioPerl-1.6.920/scripts/das/TAG
BioPerl-1.6.920/scripts/DB
BioPerl-1.6.920/scripts/DB/bp_biofetch_genbank_proxy.pl
BioPerl-1.6.920/scripts/DB/bp_bioflat_index.pl
BioPerl-1.6.920/scripts/DB/bp_biogetseq.pl
BioPerl-1.6.920/scripts/DB/bp_flanks.pl
BioPerl-1.6.920/scripts/DB/TAG
BioPerl-1.6.920/scripts/DB-HIV
BioPerl-1.6.920/scripts/DB-HIV/bp_hivq.pl
BioPerl-1.6.920/scripts/index
BioPerl-1.6.920/scripts/index/bp_fetch.pl
BioPerl-1.6.920/scripts/index/bp_index.pl
BioPerl-1.6.920/scripts/index/bp_seqret.pl
BioPerl-1.6.920/scripts/index/TAG
BioPerl-1.6.920/scripts/popgen
BioPerl-1.6.920/scripts/popgen/bp_composite_LD.pl
BioPerl-1.6.920/scripts/popgen/bp_heterogeneity_test.pl
BioPerl-1.6.920/scripts/searchio
BioPerl-1.6.920/scripts/searchio/bp_fastam9_to_table.pl
BioPerl-1.6.920/scripts/searchio/bp_filter_search.pl
BioPerl-1.6.920/scripts/searchio/bp_hmmer_to_table.pl
BioPerl-1.6.920/scripts/searchio/bp_parse_hmmsearch.pl
BioPerl-1.6.920/scripts/searchio/bp_search2table.pl
BioPerl-1.6.920/scripts/searchio/README
BioPerl-1.6.920/scripts/searchio/TAG
BioPerl-1.6.920/scripts/seq
BioPerl-1.6.920/scripts/seq/bp_extract_feature_seq.pl
BioPerl-1.6.920/scripts/seq/bp_make_mrna_protein.pl
BioPerl-1.6.920/scripts/seq/bp_seqconvert.pl
BioPerl-1.6.920/scripts/seq/bp_seqcut.pl
BioPerl-1.6.920/scripts/seq/bp_seqpart.pl
BioPerl-1.6.920/scripts/seq/bp_seqretsplit.pl
BioPerl-1.6.920/scripts/seq/bp_split_seq.pl
BioPerl-1.6.920/scripts/seq/bp_translate_seq.pl
BioPerl-1.6.920/scripts/seq/bp_unflatten_seq.pl
BioPerl-1.6.920/scripts/seq/TAG
BioPerl-1.6.920/scripts/seqstats
BioPerl-1.6.920/scripts/seqstats/bp_aacomp.pl
BioPerl-1.6.920/scripts/seqstats/bp_chaos_plot.pl
BioPerl-1.6.920/scripts/seqstats/bp_gccalc.pl
BioPerl-1.6.920/scripts/seqstats/bp_oligo_count.pl
BioPerl-1.6.920/scripts/seqstats/TAG
BioPerl-1.6.920/scripts/taxa
BioPerl-1.6.920/scripts/taxa/bp_classify_hits_kingdom.pl
BioPerl-1.6.920/scripts/taxa/bp_local_taxonomydb_query.pl
BioPerl-1.6.920/scripts/taxa/bp_query_entrez_taxa.pl
BioPerl-1.6.920/scripts/taxa/bp_taxid4species.pl
BioPerl-1.6.920/scripts/taxa/bp_taxonomy2tree.pl
BioPerl-1.6.920/scripts/taxa/TAG
BioPerl-1.6.920/scripts/tree
BioPerl-1.6.920/scripts/tree/bp_blast2tree.pl
BioPerl-1.6.920/scripts/tree/bp_nexus2nh.pl
BioPerl-1.6.920/scripts/tree/bp_tree2pag.pl
BioPerl-1.6.920/scripts/tree/TAG
BioPerl-1.6.920/scripts/utilities
BioPerl-1.6.920/scripts/utilities/bp_dbsplit.pl
BioPerl-1.6.920/scripts/utilities/bp_download_query_genbank.pl
BioPerl-1.6.920/scripts/utilities/bp_mask_by_search.pl
BioPerl-1.6.920/scripts/utilities/bp_mrtrans.pl
BioPerl-1.6.920/scripts/utilities/bp_mutate.pl
BioPerl-1.6.920/scripts/utilities/bp_netinstall.pl
BioPerl-1.6.920/scripts/utilities/bp_nrdb.pl
BioPerl-1.6.920/scripts/utilities/bp_pairwise_kaks.pl
BioPerl-1.6.920/scripts/utilities/bp_remote_blast.pl
BioPerl-1.6.920/scripts/utilities/bp_revtrans-motif.pl
BioPerl-1.6.920/scripts/utilities/bp_search2alnblocks.pl
BioPerl-1.6.920/scripts/utilities/bp_search2BSML.pl
BioPerl-1.6.920/scripts/utilities/bp_search2gff.pl
BioPerl-1.6.920/scripts/utilities/bp_search2tribe.pl
BioPerl-1.6.920/scripts/utilities/bp_seq_length.pl
BioPerl-1.6.920/scripts/utilities/bp_sreformat.pl
BioPerl-1.6.920/scripts/utilities/README
BioPerl-1.6.920/scripts/utilities/TAG
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BioPerl-1.6.920/t/Alphabet.t
BioPerl-1.6.920/t/nexml.t
BioPerl-1.6.920/t/Perl.t
BioPerl-1.6.920/t/PodSyntax.t
BioPerl-1.6.920/t/SearchDist.t
BioPerl-1.6.920/t/SeqEvolution.t
BioPerl-1.6.920/t/Species.t
BioPerl-1.6.920/t/Symbol.t
BioPerl-1.6.920/t/TaxonTree.t
BioPerl-1.6.920/t/Align
BioPerl-1.6.920/t/Align/AlignStats.t
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BioPerl-1.6.920/t/Align/Graphics.t
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BioPerl-1.6.920/t/Align/TreeBuild.t
BioPerl-1.6.920/t/Align/Utilities.t
BioPerl-1.6.920/t/AlignIO
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BioPerl-1.6.920/t/AlignIO/arp.t
BioPerl-1.6.920/t/AlignIO/bl2seq.t
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BioPerl-1.6.920/t/Annotation
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BioPerl-1.6.920/t/Assembly
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BioPerl-1.6.920/t/SearchIO/cross_match.t
BioPerl-1.6.920/t/SearchIO/erpin.t
BioPerl-1.6.920/t/SearchIO/exonerate.t
BioPerl-1.6.920/t/SearchIO/fasta.t
BioPerl-1.6.920/t/SearchIO/gmap_f9.t
BioPerl-1.6.920/t/SearchIO/hmmer.t
BioPerl-1.6.920/t/SearchIO/hmmer_pull.t
BioPerl-1.6.920/t/SearchIO/infernal.t
BioPerl-1.6.920/t/SearchIO/megablast.t
BioPerl-1.6.920/t/SearchIO/psl.t
BioPerl-1.6.920/t/SearchIO/rnamotif.t
BioPerl-1.6.920/t/SearchIO/SearchIO.t
BioPerl-1.6.920/t/SearchIO/sim4.t
BioPerl-1.6.920/t/SearchIO/SimilarityPair.t
BioPerl-1.6.920/t/SearchIO/Tiling.t
BioPerl-1.6.920/t/SearchIO/waba.t
BioPerl-1.6.920/t/SearchIO/wise.t
BioPerl-1.6.920/t/SearchIO/Writer
BioPerl-1.6.920/t/SearchIO/Writer/GbrowseGFF.t
BioPerl-1.6.920/t/SearchIO/Writer/HitTableWriter.t
BioPerl-1.6.920/t/SearchIO/Writer/HSPTableWriter.t
BioPerl-1.6.920/t/SearchIO/Writer/HTMLWriter.t
BioPerl-1.6.920/t/SearchIO/Writer/TextWriter.t
BioPerl-1.6.920/t/Seq
BioPerl-1.6.920/t/Seq/DBLink.t
BioPerl-1.6.920/t/Seq/EncodedSeq.t
BioPerl-1.6.920/t/Seq/LargeLocatableSeq.t
BioPerl-1.6.920/t/Seq/LargePSeq.t
BioPerl-1.6.920/t/Seq/LocatableSeq.t
BioPerl-1.6.920/t/Seq/MetaSeq.t
BioPerl-1.6.920/t/Seq/PrimaryQual.t
BioPerl-1.6.920/t/Seq/PrimarySeq.t
BioPerl-1.6.920/t/Seq/PrimedSeq.t
BioPerl-1.6.920/t/Seq/Quality.t
BioPerl-1.6.920/t/Seq/Seq.t
BioPerl-1.6.920/t/Seq/SimulatedRead.t
BioPerl-1.6.920/t/Seq/WithQuality.t
BioPerl-1.6.920/t/SeqFeature
BioPerl-1.6.920/t/SeqFeature/Amplicon.t
BioPerl-1.6.920/t/SeqFeature/Clone.t
BioPerl-1.6.920/t/SeqFeature/Collection.t
BioPerl-1.6.920/t/SeqFeature/Computation.t
BioPerl-1.6.920/t/SeqFeature/FeaturePair.t
BioPerl-1.6.920/t/SeqFeature/Gene.t
BioPerl-1.6.920/t/SeqFeature/Generic.t
BioPerl-1.6.920/t/SeqFeature/Location.t
BioPerl-1.6.920/t/SeqFeature/LocationFactory.t
BioPerl-1.6.920/t/SeqFeature/Primer.t
BioPerl-1.6.920/t/SeqFeature/Range.t
BioPerl-1.6.920/t/SeqFeature/RangeI.t
BioPerl-1.6.920/t/SeqFeature/SeqAnalysisParser.t
BioPerl-1.6.920/t/SeqFeature/SubSeq.t
BioPerl-1.6.920/t/SeqFeature/Unflattener.t
BioPerl-1.6.920/t/SeqFeature/Unflattener2.t
BioPerl-1.6.920/t/SeqIO
BioPerl-1.6.920/t/SeqIO/abi.t
BioPerl-1.6.920/t/SeqIO/ace.t
BioPerl-1.6.920/t/SeqIO/agave.t
BioPerl-1.6.920/t/SeqIO/alf.t
BioPerl-1.6.920/t/SeqIO/asciitree.t
BioPerl-1.6.920/t/SeqIO/bsml.t
BioPerl-1.6.920/t/SeqIO/bsml_sax.t
BioPerl-1.6.920/t/SeqIO/chadoxml.t
BioPerl-1.6.920/t/SeqIO/chaos.t
BioPerl-1.6.920/t/SeqIO/chaosxml.t
BioPerl-1.6.920/t/SeqIO/ctf.t
BioPerl-1.6.920/t/SeqIO/embl.t
BioPerl-1.6.920/t/SeqIO/entrezgene.t
BioPerl-1.6.920/t/SeqIO/excel.t
BioPerl-1.6.920/t/SeqIO/exp.t
BioPerl-1.6.920/t/SeqIO/fasta.t
BioPerl-1.6.920/t/SeqIO/fastq.t
BioPerl-1.6.920/t/SeqIO/flybase_chadoxml.t
BioPerl-1.6.920/t/SeqIO/game.t
BioPerl-1.6.920/t/SeqIO/gbxml.t
BioPerl-1.6.920/t/SeqIO/gcg.t
BioPerl-1.6.920/t/SeqIO/genbank.t
BioPerl-1.6.920/t/SeqIO/Handler.t
BioPerl-1.6.920/t/SeqIO/interpro.t
BioPerl-1.6.920/t/SeqIO/kegg.t
BioPerl-1.6.920/t/SeqIO/largefasta.t
BioPerl-1.6.920/t/SeqIO/lasergene.t
BioPerl-1.6.920/t/SeqIO/locuslink.t
BioPerl-1.6.920/t/SeqIO/mbsout.t
BioPerl-1.6.920/t/SeqIO/metafasta.t
BioPerl-1.6.920/t/SeqIO/msout.t
BioPerl-1.6.920/t/SeqIO/MultiFile.t
BioPerl-1.6.920/t/SeqIO/Multiple_fasta.t
BioPerl-1.6.920/t/SeqIO/nexml.t
BioPerl-1.6.920/t/SeqIO/phd.t
BioPerl-1.6.920/t/SeqIO/pir.t
BioPerl-1.6.920/t/SeqIO/pln.t
BioPerl-1.6.920/t/SeqIO/qual.t
BioPerl-1.6.920/t/SeqIO/raw.t
BioPerl-1.6.920/t/SeqIO/scf.t
BioPerl-1.6.920/t/SeqIO/SeqBuilder.t
BioPerl-1.6.920/t/SeqIO/SeqIO.t
BioPerl-1.6.920/t/SeqIO/seqxml.t
BioPerl-1.6.920/t/SeqIO/Splicedseq.t
BioPerl-1.6.920/t/SeqIO/strider.t
BioPerl-1.6.920/t/SeqIO/swiss.t
BioPerl-1.6.920/t/SeqIO/tab.t
BioPerl-1.6.920/t/SeqIO/table.t
BioPerl-1.6.920/t/SeqIO/tigr.t
BioPerl-1.6.920/t/SeqIO/tigrxml.t
BioPerl-1.6.920/t/SeqIO/tinyseq.t
BioPerl-1.6.920/t/SeqIO/ztr.t
BioPerl-1.6.920/t/SeqTools
BioPerl-1.6.920/t/SeqTools/Backtranslate.t
BioPerl-1.6.920/t/SeqTools/CodonTable.t
BioPerl-1.6.920/t/SeqTools/ECnumber.t
BioPerl-1.6.920/t/SeqTools/GuessSeqFormat.t
BioPerl-1.6.920/t/SeqTools/OddCodes.t
BioPerl-1.6.920/t/SeqTools/SeqPattern.t
BioPerl-1.6.920/t/SeqTools/SeqStats.t
BioPerl-1.6.920/t/SeqTools/SeqUtils.t
BioPerl-1.6.920/t/SeqTools/SeqWords.t
BioPerl-1.6.920/t/Structure
BioPerl-1.6.920/t/Structure/IO.t
BioPerl-1.6.920/t/Structure/Structure.t
BioPerl-1.6.920/t/Tools
BioPerl-1.6.920/t/Tools/AmpliconSearch.t
BioPerl-1.6.920/t/Tools/ePCR.t
BioPerl-1.6.920/t/Tools/Est2Genome.t
BioPerl-1.6.920/t/Tools/FootPrinter.t
BioPerl-1.6.920/t/Tools/Geneid.t
BioPerl-1.6.920/t/Tools/Genewise.t
BioPerl-1.6.920/t/Tools/Genomewise.t
BioPerl-1.6.920/t/Tools/Genpred.t
BioPerl-1.6.920/t/Tools/GFF.t
BioPerl-1.6.920/t/Tools/GuessSeqFormat.t
BioPerl-1.6.920/t/Tools/Hmmer.t
BioPerl-1.6.920/t/Tools/IUPAC.t
BioPerl-1.6.920/t/Tools/Lucy.t
BioPerl-1.6.920/t/Tools/Match.t
BioPerl-1.6.920/t/Tools/pICalculator.t
BioPerl-1.6.920/t/Tools/Primer3.t
BioPerl-1.6.920/t/Tools/Promoterwise.t
BioPerl-1.6.920/t/Tools/Pseudowise.t
BioPerl-1.6.920/t/Tools/QRNA.t
BioPerl-1.6.920/t/Tools/RandDistFunctions.t
BioPerl-1.6.920/t/Tools/RepeatMasker.t
BioPerl-1.6.920/t/Tools/rnamotif.t
BioPerl-1.6.920/t/Tools/Seg.t
BioPerl-1.6.920/t/Tools/Sigcleave.t
BioPerl-1.6.920/t/Tools/Signalp.t
BioPerl-1.6.920/t/Tools/Sim4.t
BioPerl-1.6.920/t/Tools/SiRNA.t
BioPerl-1.6.920/t/Tools/TandemRepeatsFinder.t
BioPerl-1.6.920/t/Tools/TargetP.t
BioPerl-1.6.920/t/Tools/Tmhmm.t
BioPerl-1.6.920/t/Tools/tRNAscanSE.t
BioPerl-1.6.920/t/Tools/Alignment
BioPerl-1.6.920/t/Tools/Alignment/Consed.t
BioPerl-1.6.920/t/Tools/Analysis
BioPerl-1.6.920/t/Tools/Analysis/DNA
BioPerl-1.6.920/t/Tools/Analysis/DNA/ESEfinder.t
BioPerl-1.6.920/t/Tools/Analysis/Protein
BioPerl-1.6.920/t/Tools/Analysis/Protein/Domcut.t
BioPerl-1.6.920/t/Tools/Analysis/Protein/ELM.t
BioPerl-1.6.920/t/Tools/Analysis/Protein/GOR4.t
BioPerl-1.6.920/t/Tools/Analysis/Protein/HNN.t
BioPerl-1.6.920/t/Tools/Analysis/Protein/Mitoprot.t
BioPerl-1.6.920/t/Tools/Analysis/Protein/NetPhos.t
BioPerl-1.6.920/t/Tools/Analysis/Protein/Scansite.t
BioPerl-1.6.920/t/Tools/Analysis/Protein/Sopma.t
BioPerl-1.6.920/t/Tools/EMBOSS
BioPerl-1.6.920/t/Tools/EMBOSS/Palindrome.t
BioPerl-1.6.920/t/Tools/Phylo
BioPerl-1.6.920/t/Tools/Phylo/Gerp.t
BioPerl-1.6.920/t/Tools/Phylo/Molphy.t
BioPerl-1.6.920/t/Tools/Phylo/PAML.t
BioPerl-1.6.920/t/Tools/Phylo/Phylip
BioPerl-1.6.920/t/Tools/Phylo/Phylip/ProtDist.t
BioPerl-1.6.920/t/Tools/Run
BioPerl-1.6.920/t/Tools/Run/Dummy.pm
BioPerl-1.6.920/t/Tools/Run/RemoteBlast.t
BioPerl-1.6.920/t/Tools/Run/RemoteBlast_rpsblast.t
BioPerl-1.6.920/t/Tools/Run/StandAloneBlast.t
BioPerl-1.6.920/t/Tools/Run/WBCommandExts.t
BioPerl-1.6.920/t/Tools/Run/WrapperBase.t
BioPerl-1.6.920/t/Tools/Run/Dummy
BioPerl-1.6.920/t/Tools/Run/Dummy/Config.pm
BioPerl-1.6.920/t/Tools/Signalp
BioPerl-1.6.920/t/Tools/Signalp/ExtendedSignalp.t
BioPerl-1.6.920/t/Tools/Spidey
BioPerl-1.6.920/t/Tools/Spidey/Spidey.t
BioPerl-1.6.920/t/Tree
BioPerl-1.6.920/t/Tree/Compatible.t
BioPerl-1.6.920/t/Tree/Node.t
BioPerl-1.6.920/t/Tree/RandomTreeFactory.t
BioPerl-1.6.920/t/Tree/Tree.t
BioPerl-1.6.920/t/Tree/TreeIO.t
BioPerl-1.6.920/t/Tree/TreeStatistics.t
BioPerl-1.6.920/t/Tree/PhyloNetwork
BioPerl-1.6.920/t/Tree/PhyloNetwork/Factory.t
BioPerl-1.6.920/t/Tree/PhyloNetwork/GraphViz.t
BioPerl-1.6.920/t/Tree/PhyloNetwork/MuVector.t
BioPerl-1.6.920/t/Tree/PhyloNetwork/PhyloNetwork.t
BioPerl-1.6.920/t/Tree/PhyloNetwork/RandomFactory.t
BioPerl-1.6.920/t/Tree/PhyloNetwork/TreeFactory.t
BioPerl-1.6.920/t/Tree/TreeIO
BioPerl-1.6.920/t/Tree/TreeIO/lintree.t
BioPerl-1.6.920/t/Tree/TreeIO/newick.t
BioPerl-1.6.920/t/Tree/TreeIO/nexml.t
BioPerl-1.6.920/t/Tree/TreeIO/nexus.t
BioPerl-1.6.920/t/Tree/TreeIO/nhx.t
BioPerl-1.6.920/t/Tree/TreeIO/phyloxml.t
BioPerl-1.6.920/t/Tree/TreeIO/svggraph.t
BioPerl-1.6.920/t/Tree/TreeIO/tabtree.t
BioPerl-1.6.920/t/Variation
BioPerl-1.6.920/t/Variation/AAChange.t
BioPerl-1.6.920/t/Variation/AAReverseMutate.t
BioPerl-1.6.920/t/Variation/Allele.t
BioPerl-1.6.920/t/Variation/DNAMutation.t
BioPerl-1.6.920/t/Variation/RNAChange.t
BioPerl-1.6.920/t/Variation/SeqDiff.t
BioPerl-1.6.920/t/Variation/SNP.t
BioPerl-1.6.920/t/Variation/Variation_IO.t
BioPerl-1.6.920/travis_scripts
BioPerl-1.6.920/travis_scripts/dependency_installs

  CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-1.6.920.tar.gz

>>> C:\Perl-5.16\bin\perl.exe Build.PL
could not find ParserDetails.ini in C:/cpanfly-5.16/var/megalib/XML/SAX
Checking prerequisites...
  requires:
    !  DB_File is not installed
  recommends:
    *  Convert::Binary::C is not installed
    *  GraphViz is not installed

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

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

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

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

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

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

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

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

Do you want to run tests that require connection to servers across the internet
(likely to cause some failures)? y/n [n]   - will not run internet-requiring tests
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'BioPerl' version '1.006920'
---- Unsatisfied dependencies detected during ----
----      CJFIELDS/BioPerl-1.6.920.tar.gz     ----
    DB_File [requires]
Running Build test
  Delayed until after prerequisites
Running test for module 'DB_File'

______________________ D i s t r o P r e f s ______________________
                           DB_File.yml[0]                           
Running make for P/PM/PMQS/DB_File-1.829.tar.gz
Disabled via prefs file 'C:\cpanfly-5.16\etc\distroprefs\DB_File.yml' doc 0
  PMQS/DB_File-1.829.tar.gz
  [disabled] -- NA Disabled via prefs file 'C:\cpanfly-5.16\etc\distroprefs\DB_File.yml' doc 0
Running Build for C/CJ/CJFIELDS/BioPerl-1.6.920.tar.gz
  Has already been unwrapped into directory C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv

  CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-1.6.920.tar.gz

Warning: Prerequisite 'DB_File => 0' for 'CJFIELDS/BioPerl-1.6.920.tar.gz' failed when processing 'PMQS/DB_File-1.829.tar.gz' with 'unwrapped => NO Disabled via prefs file 'C:\cpanfly-5.16\etc\distroprefs\DB_File.yml' doc 0'. Continuing, but chances to succeed are limited.
>>> C:\Perl-5.16\bin\perl.exe ./Build
Building BioPerl
  CJFIELDS/BioPerl-1.6.920.tar.gz
  C:\Perl-5.16\bin\perl.exe ./Build -- OK
Running Build test
>>> C:\Perl-5.16\bin\perl.exe ./Build test verbose=1
t/Align/AlignStats.t ................... 
1..45
ok 1 - use Bio::Align::DNAStatistics;
ok 2 - use Bio::Align::ProteinStatistics;
ok 3 - use Bio::AlignIO;
ok 4 - The object isa Bio::Align::AlignI
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17 - The object isa Bio::Align::AlignI
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31 - The object isa Bio::Align::AlignI
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - The object isa Bio::Align::AlignI
ok 38 - The object isa Bio::Matrix::PhylipDist
ok 39
ok 40
ok 41
ok 42 - The object isa Bio::PrimarySeqI
ok 43
ok 44 - Warn if seqs don't overlap
ok 45
ok
t/Align/AlignUtil.t .................... 
1..47
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 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/Align/Graphics.t ..................... 
1..41
ok 1 - use Bio::Align::Graphics;
ok 2 - require Bio::Align::Graphics;
ok 3 - Bio::Align::Graphics->can(...)
ok 4 - input is defined
ok 5 - AlignIO object is defined
ok 6 - The object isa Bio::AlignIO
ok 7 - alignment is there and defined
ok 8 - all starts are present
ok 9 - all ends are present
ok 10 - all colors are present
ok 11 - first end is further than first start
ok 12 - second end is further than second start
ok 13 - third end is further than third start
ok 14 - domain labels are present
ok 15 - domain starts are present
ok 16 - domain ends are present
ok 17 - domain colors are present
ok 18 - label - first end is further than first start
ok 19 - label - second end is further than second start
ok 20 - label - third end is further than third start
ok 21 - first label start is within domain range
ok 22 - second label start is within domain range
ok 23 - third label start is within domain range
ok 24 - first label end is within domain range
ok 25 - second label end is within domain range
ok 26 - third label end is within domain range
ok 27 - individual labels work
ok 28 - The object isa Bio::Align::Graphics
ok 29 - new object is defined
ok 30 -   pad_bottom is right
ok 31 -   default pad_top is right
ok 32 -   start point loaded
ok 33 -   end point loaded
ok 34 -   color of domain loaded
ok 35 -   domain labels loaded
ok 36 -   label starts loaded
ok 37 -   label ends loaded
ok 38 -   label colors loaded
ok 39 -   labels loaded
ok 40 -   output file is png
ok 41 -   wrapping length is not zero
ok
t/Align/SimpleAlign.t .................. 
1..206
ok 1 - use Bio::SimpleAlign;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::SeqFeature::Generic;
ok 4 - use Bio::Location::Simple;
ok 5 - use Bio::Location::Split;
ok 6 - The object isa Bio::AlignIO
ok 7 - pfam input test
ok 8 - match_line
ok 9 - The object isa Bio::Align::AlignI
ok 10 - num_sequences
ok 11 - num_sequences
ok 12 - select_noncont
ok 13 - select_noncont
ok 14 - num_sequences
ok 15 - select_noncont
ok 16 - select_noncont
ok 17 - select_noncont_by_name
ok 18 - select_noncont_by_name
ok 19 - select_noncont_by_name
ok 20 - select_noncont_by_name
ok 21 - each_seq
ok 22 - get_nse
ok 23 - id
ok 24 - num_gaps
ok 25 - each_alphabetically
ok 26 - column_from_residue_number
ok 27 - display_name get/set
ok 28 - display_name get
ok 29 - consensus_string
ok 30 - consensus_string
ok 31 - consensus_string
ok 32
ok 33 - each_seq_with_id
ok 34 - is_flush
ok 35 - id get/set
ok 36 - length
ok 37 - num_residues
ok 38 - num_sequences
ok 39 - overall_percentage_identity
ok 40 - overall_percentage_identity (align)
ok 41 - overall_percentage_identity (short)
ok 42 - overall_percentage_identity (long)
ok 43 - average_percentage_identity
ok 44
ok 45 - set_displayname_count
ok 46
ok 47 - set_displayname_flat
ok 48
ok 49 - set_displayname_normal
ok 50
ok 51
ok 52 - uppercase, map_chars
ok 53 - match_line
ok 54 - remove_seqs
ok 55 - remove_seqs
ok 56 - add_seq
ok 57 - add_seq
ok 58 - get_seq_by_pos
ok 59 - get_seq_by_pos
ok 60
ok 61
ok 62
ok 63 - purge
ok 64 - purge
ok 65 - IO::String consensus_iupac
ok 66 - IO::String write_aln normal
ok 67 - IO::String write_aln slice
ok 68 - IO::String write_aln slice
ok 69 - IO::String write_aln slice
ok 70 - IO::String write_aln slice
ok 71 - IO::String write_aln slice
ok 72
ok 73 - remove_columns by position
ok 74 - remove_columns by position (wrong order)
ok 75 - cigar_line
ok 76 - cigar_line
ok 77 - cigar_line
ok 78 - cigar_line
ok 79 - sort_alphabetically - before
ok 80
ok 81 - sort_alphabetically - after
ok 82 - remove_gaps
ok 83 - remove_gaps all_gaps_only
ok 84 - set_new_reference
ok 85 - set_new_reference
ok 86 - uniq_seq
ok 87 - bug 2099
ok 88 - bug 2099
ok 89 - bug 2793
ok 90 - bug 2793
ok 91 - bug 2793
ok 92 - bug 2793
ok 93 - Bad sequence, bad!
ok 94 - The object isa Bio::AnnotatableI
ok 95 - added 3 seqs
ok 96 - first 2 features added
ok 97 - 3rd feature added
not ok 98 # TODO This should pass but dies; see bug 2842

#   Failed (TODO) test at t/Align/SimpleAlign.t line 432.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 1.  
# Overriding value [0] with value 1 for Bio::LocatableSeq::end().
# ?
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:201
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1167
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:432
# STACK: t/Align/SimpleAlign.t:432
# -----------------------------------------------------------
# )
ok 99 - slice 1 len
ok 100 - correct masked seq
ok 101 - correct masked seq
ok 102 - correct masked seq
not ok 103 # TODO This should pass but dies; see bug 2842

#   Failed (TODO) test at t/Align/SimpleAlign.t line 432.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 3.  
# Overriding value [2] with value 3 for Bio::LocatableSeq::end().
# ?
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:201
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1167
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:432
# STACK: t/Align/SimpleAlign.t:432
# -----------------------------------------------------------
# )
ok 104 - slice 2 len
ok 105 - correct masked seq
ok 106 - correct masked seq
ok 107 - correct masked seq
not ok 108 # TODO This should pass but dies; see bug 2842

#   Failed (TODO) test at t/Align/SimpleAlign.t line 432.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 3.  
# Overriding value [1] with value 3 for Bio::LocatableSeq::end().
# ??
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:201
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1167
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:432
# STACK: t/Align/SimpleAlign.t:432
# -----------------------------------------------------------
# )
ok 109 - slice 3 len
ok 110 - correct masked seq
ok 111 - correct masked seq
ok 112 - correct masked seq
not ok 113 # TODO This should pass but dies; see bug 2842

#   Failed (TODO) test at t/Align/SimpleAlign.t line 432.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 6.  
# Overriding value [4] with value 6 for Bio::LocatableSeq::end().
# ??
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:201
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1167
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:432
# STACK: t/Align/SimpleAlign.t:432
# -----------------------------------------------------------
# )
ok 114 - slice 4 len
ok 115 - correct masked seq
ok 116 - correct masked seq
ok 117 - correct masked seq
ok 118 - initial display id ok
ok 119 - safe display id ok
ok 120 - restored display id ok
ok 121 - sort by list ok
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128 - BIC:GGATCCATT[C/C]CTACT
ok 129 - BIC:GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT
ok 130 - BIC:G[G/C]ATCCATT[C/G]CTACT
ok 131 - BIC:GGATCCATT[C/G]CTACT
ok 132 - BIC:GGATCCATT[C/G]CTAC[T/A]
ok 133 - BIC:GGATCCATT[C/G]CTA[C/G][T/A]
ok 134 - BIC:GGATCCATT[C/G]CTACT
ok 135 - BIC:GGATCCATT{C.C}CTACT
ok 136 - BIC:GGAT{C.-}{C.-}ATT{C.C}CT{A.C}CT
ok 137 - BIC:G{G.C}ATCCATT{C.G}CTACT
ok 138 - BIC:GGATCCATT{C.G}CTACT
ok 139 - BIC:GGATCCATT{C.G}CTAC{T.A}
ok 140 - BIC:GGATCCATT{C.G}CTA{C.G}{T.A}
ok 141 - BIC:GGATCCATT{C.G}CTACT
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 - The object isa Bio::SimpleAlign
ok 200 - consensus string looks ok
ok 201 - conservation length
ok 202 - conservation scores
ok 203 - looks like correct unmasked alignment (from clustalw)
ok 204 - looks like correct masked alignment (from clustalw)
ok 205
ok 206 - align after looks ok
ok
t/Align/TreeBuild.t .................... 
1..13
ok 1 - use Bio::Align::DNAStatistics;
ok 2 - use Bio::Align::ProteinStatistics;
ok 3 - use Bio::Align::Utilities;
ok 4 - use Bio::AlignIO;
ok 5 - use Bio::Tree::DistanceFactory;
ok 6 - use Bio::TreeIO;
ok 7 - SimpleAlign object parsed out isa Bio::SimpleAlign
ok 8 - Protein distance matrix retrieved isa Bio::Matrix::MatrixI
ok 9 - Tree object gotten back isa Bio::Tree::TreeI
ok 10 - NJ calculated Branch length
ok 11 - NJ calculated Branch length
ok 12 - Make sure two nodes are sister
ok 13 - 10 replicates formulated
ok
t/Align/Utilities.t .................... 
1..13
ok 1 - use Bio::Align::Utilities;
ok 2 - use Bio::SimpleAlign;
ok 3 - use Bio::PrimarySeq;
ok 4 - use Bio::LocatableSeq;
ok 5 - use Bio::AlignIO;
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok
Subroutine new redefined at Bio\Annotation\SimpleValue.pm line 96, <GEN25> line 86.
Subroutine as_text redefined at Bio\Annotation\SimpleValue.pm line 128, <GEN25> line 86.
Subroutine display_text redefined at Bio\Annotation\SimpleValue.pm line 153, <GEN25> line 86.
Subroutine hash_tree redefined at Bio\Annotation\SimpleValue.pm line 174, <GEN25> line 86.
Subroutine tagname redefined at Bio\Annotation\SimpleValue.pm line 199, <GEN25> line 86.
Subroutine value redefined at Bio\Annotation\SimpleValue.pm line 229, <GEN25> line 86.
Subroutine tag_term redefined at Bio\Annotation\SimpleValue.pm line 265, <GEN25> line 86.
Subroutine new redefined at Bio\Seq\Meta.pm line 225, <GEN53> line 64.
Subroutine meta redefined at Bio\Seq\Meta.pm line 269, <GEN53> line 64.
Subroutine meta_text redefined at Bio\Seq\Meta.pm line 284, <GEN53> line 64.
Subroutine named_meta redefined at Bio\Seq\Meta.pm line 300, <GEN53> line 64.
Subroutine _test_gap_positions redefined at Bio\Seq\Meta.pm line 347, <GEN53> line 64.
Subroutine named_meta_text redefined at Bio\Seq\Meta.pm line 377, <GEN53> line 64.
Subroutine submeta redefined at Bio\Seq\Meta.pm line 409, <GEN53> line 64.
Subroutine submeta_text redefined at Bio\Seq\Meta.pm line 425, <GEN53> line 64.
Subroutine named_submeta redefined at Bio\Seq\Meta.pm line 444, <GEN53> line 64.
Subroutine named_submeta_text redefined at Bio\Seq\Meta.pm line 503, <GEN53> line 64.
Subroutine meta_names redefined at Bio\Seq\Meta.pm line 518, <GEN53> line 64.
Subroutine meta_length redefined at Bio\Seq\Meta.pm line 540, <GEN53> line 64.
Subroutine named_meta_length redefined at Bio\Seq\Meta.pm line 556, <GEN53> line 64.
Subroutine force_flush redefined at Bio\Seq\Meta.pm line 577, <GEN53> line 64.
Subroutine _do_flush redefined at Bio\Seq\Meta.pm line 605, <GEN53> line 64.
Subroutine is_flush redefined at Bio\Seq\Meta.pm line 637, <GEN53> line 64.
Subroutine revcom redefined at Bio\Seq\Meta.pm line 679, <GEN53> line 64.
Subroutine trunc redefined at Bio\Seq\Meta.pm line 702, <GEN53> line 64.
Subroutine to_string redefined at Bio\Seq\Meta.pm line 726, <GEN53> line 64.
t/AlignIO/AlignIO.t .................... 
1..29
ok 1 - use Bio::AlignIO;
ok 2 - The object isa Bio::AnnotatableI
ok 3 - input filehandle method test : metafasta
ok 4 - input filehandle method test : po
ok 5 - input filehandle method test : nexus
ok 6 - input filehandle method test : clustalw
ok 7 - input filehandle method test : prodom
ok 8 - input filehandle method test : fasta
ok 9 - input filehandle method test : arp
ok 10 - input filehandle method test : xmfa
ok 11 - input filehandle method test : mase
ok 12 - input filehandle method test : psi
ok 13 - input filehandle method test : phylip
ok 14 - input filehandle method test : pfam
ok 15 - input filehandle method test : selex
ok 16 - input filehandle method test : stockholm
ok 17 - input filehandle method test : msf
ok 18 - filehandle output test : metafasta
ok 19 - filehandle output test : po
ok 20 - filehandle output test : nexus
ok 21 - filehandle output test : clustalw
ok 22 - filehandle output test : fasta
ok 23 - filehandle output test : xmfa
ok 24 - filehandle output test : psi
ok 25 - filehandle output test : phylip
ok 26 - filehandle output test : pfam
ok 27 - filehandle output test : selex
ok 28 - filehandle output test : stockholm
ok 29 - filehandle output test : msf
ok
Subroutine next_aln redefined at Bio\AlignIO\arp.pm line 116.
Subroutine write_aln redefined at Bio\AlignIO\arp.pm line 199.
Subroutine _process_sequence redefined at Bio\AlignIO\arp.pm line 206.
Subroutine _process_annotation redefined at Bio\AlignIO\arp.pm line 218.
Subroutine new redefined at Bio\Annotation\SimpleValue.pm line 96, <GEN0> line 86.
Subroutine as_text redefined at Bio\Annotation\SimpleValue.pm line 128, <GEN0> line 86.
Subroutine display_text redefined at Bio\Annotation\SimpleValue.pm line 153, <GEN0> line 86.
Subroutine hash_tree redefined at Bio\Annotation\SimpleValue.pm line 174, <GEN0> line 86.
Subroutine tagname redefined at Bio\Annotation\SimpleValue.pm line 199, <GEN0> line 86.
Subroutine value redefined at Bio\Annotation\SimpleValue.pm line 229, <GEN0> line 86.
Subroutine tag_term redefined at Bio\Annotation\SimpleValue.pm line 265, <GEN0> line 86.
t/AlignIO/arp.t ........................ 
1..48
ok 1 - use Bio::AlignIO::arp;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4 - ARP get_nse()
ok 5
ok 6 - ARP num_sequences()
ok 7 - ARP id()
ok 8 - ARP description()
ok 9 - The object isa Bio::AnnotationCollectionI
ok 10 - The object isa Bio::AnnotationI
ok 11
ok 12
ok 13
ok 14
ok 15 - The object isa Bio::AlignIO
ok 16 - The object isa Bio::Align::AlignI
ok 17 - ARP get_nse()
ok 18 - ARP num_sequences()
ok 19 - ARP id()
ok 20 - ARP description()
ok 21 - The object isa Bio::AnnotationCollectionI
ok 22 - The object isa Bio::AnnotationI
ok 23
ok 24
ok 25
ok 26
ok 27 - The object isa Bio::Align::AlignI
ok 28 - ARP get_nse()
ok 29 - ARP num_sequences()
ok 30 - ARP id()
ok 31 - ARP description()
ok 32 - The object isa Bio::AnnotationCollectionI
ok 33 - The object isa Bio::AnnotationI
ok 34
ok 35
ok 36
ok 37
ok 38 - The object isa Bio::Align::AlignI
ok 39 - ARP get_nse()
ok 40 - ARP num_sequences()
ok 41 - ARP id()
ok 42 - ARP description()
ok 43 - The object isa Bio::AnnotationCollectionI
ok 44 - The object isa Bio::AnnotationI
ok 45
ok 46
ok 47
ok 48
ok
Subroutine _initialize redefined at Bio\AlignIO\bl2seq.pm line 124.
Subroutine next_aln redefined at Bio\AlignIO\bl2seq.pm line 142.
Subroutine write_aln redefined at Bio\AlignIO\bl2seq.pm line 184.
Subroutine report_type redefined at Bio\AlignIO\bl2seq.pm line 200.
Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175.
Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264.
Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284.
Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311.
Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337.
Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357.
Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378.
Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399.
Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420.
Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442.
Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465.
Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487.
Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508.
Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523.
Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540.
Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555.
Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574.
Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599.
Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616.
Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629.
Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646.
Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663.
Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680.
Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700.
Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728.
Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747.
Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763.
Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777.
Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794.
Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815.
Subroutine new redefined at Bio/Search/Hit/GenericHit.pm line 127.
Subroutine add_hsp redefined at Bio/Search/Hit/GenericHit.pm line 204.
Subroutine hsp_factory redefined at Bio/Search/Hit/GenericHit.pm line 228.
Subroutine name redefined at Bio/Search/Hit/GenericHit.pm line 248.
Subroutine accession redefined at Bio/Search/Hit/GenericHit.pm line 268.
Subroutine description redefined at Bio/Search/Hit/GenericHit.pm line 288.
Subroutine length redefined at Bio/Search/Hit/GenericHit.pm line 308.
Subroutine algorithm redefined at Bio/Search/Hit/GenericHit.pm line 333.
Subroutine raw_score redefined at Bio/Search/Hit/GenericHit.pm line 355.
Subroutine score redefined at Bio/Search/Hit/GenericHit.pm line 385.
Subroutine significance redefined at Bio/Search/Hit/GenericHit.pm line 400.
Subroutine bits redefined at Bio/Search/Hit/GenericHit.pm line 430.
Subroutine next_hsp redefined at Bio/Search/Hit/GenericHit.pm line 458.
Subroutine hsps redefined at Bio/Search/Hit/GenericHit.pm line 494.
Subroutine num_hsps redefined at Bio/Search/Hit/GenericHit.pm line 517.
Subroutine rewind redefined at Bio/Search/Hit/GenericHit.pm line 538.
Subroutine ambiguous_aln redefined at Bio/Search/Hit/GenericHit.pm line 564.
Subroutine overlap redefined at Bio/Search/Hit/GenericHit.pm line 576.
Subroutine n redefined at Bio/Search/Hit/GenericHit.pm line 605.
Subroutine p redefined at Bio/Search/Hit/GenericHit.pm line 652.
Subroutine hsp redefined at Bio/Search/Hit/GenericHit.pm line 694.
Subroutine logical_length redefined at Bio/Search/Hit/GenericHit.pm line 740.
Subroutine length_aln redefined at Bio/Search/Hit/GenericHit.pm line 786.
Subroutine gaps redefined at Bio/Search/Hit/GenericHit.pm line 849.
Subroutine matches redefined at Bio/Search/Hit/GenericHit.pm line 887.
Subroutine start redefined at Bio/Search/Hit/GenericHit.pm line 948.
Subroutine end redefined at Bio/Search/Hit/GenericHit.pm line 1025.
Subroutine range redefined at Bio/Search/Hit/GenericHit.pm line 1093.
Subroutine frac_identical redefined at Bio/Search/Hit/GenericHit.pm line 1150.
Subroutine frac_conserved redefined at Bio/Search/Hit/GenericHit.pm line 1226.
Subroutine frac_aligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1274.
Subroutine frac_aligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1310.
Subroutine num_unaligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1364.
Subroutine num_unaligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1400.
Subroutine seq_inds redefined at Bio/Search/Hit/GenericHit.pm line 1442.
Subroutine strand redefined at Bio/Search/Hit/GenericHit.pm line 1473.
Subroutine frame redefined at Bio/Search/Hit/GenericHit.pm line 1535.
Subroutine rank redefined at Bio/Search/Hit/GenericHit.pm line 1574.
Subroutine locus redefined at Bio/Search/Hit/GenericHit.pm line 1590.
Subroutine each_accession_number redefined at Bio/Search/Hit/GenericHit.pm line 1618.
Subroutine tiled_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1666.
Subroutine query_length redefined at Bio/Search/Hit/GenericHit.pm line 1683.
Subroutine ncbi_gi redefined at Bio/Search/Hit/GenericHit.pm line 1701.
Subroutine sort_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1732.
Subroutine iteration redefined at Bio/Search/Hit/GenericHit.pm line 1772.
Subroutine found_again redefined at Bio/Search/Hit/GenericHit.pm line 1807.
Subroutine Bio::Search::Hit::GenericHit::frac_aligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1333.
Subroutine Bio::Search::Hit::GenericHit::num_unaligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1341.
Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, <GEN0> line 64.
Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, <GEN0> line 64.
Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, <GEN0> line 64.
Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, <GEN0> line 64.
Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, <GEN0> line 64.
Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, <GEN0> line 64.
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
Subroutine _initialize redefined at Bio\AlignIO\clustalw.pm line 100.
Subroutine next_aln redefined at Bio\AlignIO\clustalw.pm line 121.
Subroutine write_aln redefined at Bio\AlignIO\clustalw.pm line 233.
Subroutine percentages redefined at Bio\AlignIO\clustalw.pm line 332.
Subroutine line_length redefined at Bio\AlignIO\clustalw.pm line 351.
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
Subroutine _initialize redefined at Bio\AlignIO\emboss.pm line 92.
Subroutine next_aln redefined at Bio\AlignIO\emboss.pm line 109.
Subroutine write_aln redefined at Bio\AlignIO\emboss.pm line 252.
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
Subroutine next_aln redefined at Bio\AlignIO\fasta.pm line 80.
Subroutine write_aln redefined at Bio\AlignIO\fasta.pm line 181.
Subroutine _get_len redefined at Bio\AlignIO\fasta.pm line 224.
Subroutine width redefined at Bio\AlignIO\fasta.pm line 243.
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
Subroutine _initialize redefined at Bio\AlignIO\largemultifasta.pm line 81.
Subroutine next_seq redefined at Bio\AlignIO\largemultifasta.pm line 103.
Subroutine next_aln redefined at Bio\AlignIO\largemultifasta.pm line 145.
Subroutine write_aln redefined at Bio\AlignIO\largemultifasta.pm line 178.
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
Subroutine _initialize redefined at Bio\AlignIO\maf.pm line 102.
Subroutine next_aln redefined at Bio\AlignIO\maf.pm line 121.
Subroutine write_aln redefined at Bio\AlignIO\maf.pm line 187.
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
Subroutine next_aln redefined at Bio\AlignIO\mase.pm line 82.
Subroutine write_aln redefined at Bio\AlignIO\mase.pm line 158.
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
Subroutine next_aln redefined at Bio\AlignIO\mega.pm line 115.
Subroutine write_aln redefined at Bio\AlignIO\mega.pm line 188.
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
Subroutine next_aln redefined at Bio\AlignIO\meme.pm line 103.
Subroutine write_aln redefined at Bio\AlignIO\meme.pm line 218.
Subroutine _initialize redefined at Bio\AlignIO\meme.pm line 227.
t/AlignIO/meme.t ....................... 
1..20
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 15 - The object isa Bio::AlignIO
ok 16 - The object isa Bio::Align::AlignI
ok 17
ok 18
ok 19
ok 20
ok
Subroutine _initialize redefined at Bio\AlignIO\metafasta.pm line 89.
Subroutine next_aln redefined at Bio\AlignIO\metafasta.pm line 107.
Subroutine write_aln redefined at Bio\AlignIO\metafasta.pm line 181.
Subroutine width redefined at Bio\AlignIO\metafasta.pm line 225.
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
Subroutine next_aln redefined at Bio\AlignIO\msf.pm line 90.
Subroutine write_aln redefined at Bio\AlignIO\msf.pm line 173.
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
# WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support
t/AlignIO/nexml.t ...................... 
1..125
ok 1 - use Bio::AlignIO::nexml;
ok 2 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 3 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 4 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 5 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 6 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 7 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 8 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 9 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 10 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 11 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 12 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 13 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 14 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 15 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 16 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 17 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 18 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 19 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 20 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 21 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 22 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 23 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 24 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 25 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 26 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 27 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 28 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 29 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 30 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 31 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 32 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 33 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 34 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 35 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 36 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 37 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 38 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 39 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 40 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 41 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 42 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 43 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 44 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 45 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 46 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 47 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 48 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 49 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 50 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 51 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 52 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 53 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 54 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 55 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 56 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 57 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 58 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 59 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 60 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 61 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 62 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 63 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 64 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 65 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 66 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 67 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 68 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 69 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 70 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 71 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 72 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 73 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 74 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 75 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 76 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 77 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 78 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 79 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 80 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 81 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 82 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 83 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 84 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 85 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 86 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 87 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 88 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 89 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 90 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 91 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 92 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 93 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 94 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 95 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 96 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 97 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 98 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 99 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 100 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 101 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 102 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 103 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 104 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 105 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 106 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 107 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 108 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 109 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 110 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 111 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 112 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 113 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 114 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 115 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 116 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 117 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 118 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 119 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 120 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 121 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 122 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 123 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 124 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 125 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok
Subroutine _initialize redefined at Bio\AlignIO\nexus.pm line 103.
Subroutine next_aln redefined at Bio\AlignIO\nexus.pm line 142.
Subroutine _read_taxlabels redefined at Bio\AlignIO\nexus.pm line 339.
Subroutine write_aln redefined at Bio\AlignIO\nexus.pm line 367.
Subroutine flag redefined at Bio\AlignIO\nexus.pm line 463.
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
Subroutine next_aln redefined at Bio\AlignIO\pfam.pm line 81.
Subroutine write_aln redefined at Bio\AlignIO\pfam.pm line 140.
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
Subroutine _initialize redefined at Bio\AlignIO\phylip.pm line 134.
Subroutine next_aln redefined at Bio\AlignIO\phylip.pm line 171.
Subroutine write_aln redefined at Bio\AlignIO\phylip.pm line 298.
Subroutine interleaved redefined at Bio\AlignIO\phylip.pm line 418.
Subroutine flag_SI redefined at Bio\AlignIO\phylip.pm line 441.
Subroutine idlength redefined at Bio\AlignIO\phylip.pm line 461.
Subroutine line_length redefined at Bio\AlignIO\phylip.pm line 480.
Subroutine tag_length redefined at Bio\AlignIO\phylip.pm line 501.
Subroutine id_linebreak redefined at Bio\AlignIO\phylip.pm line 521.
Subroutine wrap_sequential redefined at Bio\AlignIO\phylip.pm line 541.
Subroutine longid redefined at Bio\AlignIO\phylip.pm line 560.
t/AlignIO/phylip.t ..................... 
1..17
ok 1 - use Bio::AlignIO::phylip;
ok 2 - The object isa Bio::Align::AlignI
ok 3
ok 4 - The object isa Bio::Align::AlignI
ok 5
ok 6
ok 7 - The object isa Bio::Align::AlignI
ok 8
ok 9 - The object isa Bio::Align::AlignI
ok 10
ok 11 - phylip output test
ok 12
ok 13
ok 14
not ok 15 # TODO problems with default strand, length?

#   Failed (TODO) test at t/AlignIO/phylip.t line 81.
#          got: undef
#     expected: '0'
not ok 16 # TODO problems with default strand, length?

#   Failed (TODO) test at t/AlignIO/phylip.t line 82.
#          got: '50'
#     expected: '47'
ok 17 - newline between header and sequences is parsed correctly
ok
Subroutine next_aln redefined at Bio\AlignIO\po.pm line 83.
Subroutine write_aln redefined at Bio\AlignIO\po.pm line 228.
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
Subroutine next_aln redefined at Bio\AlignIO\prodom.pm line 81.
Subroutine write_aln redefined at Bio\AlignIO\prodom.pm line 134.
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
Subroutine next_aln redefined at Bio\AlignIO\psi.pm line 107.
Subroutine write_aln redefined at Bio\AlignIO\psi.pm line 147.
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
Subroutine next_aln redefined at Bio\AlignIO\selex.pm line 95.
Subroutine write_aln redefined at Bio\AlignIO\selex.pm line 162.
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
Subroutine _initialize redefined at Bio\AlignIO\stockholm.pm line 354.
Subroutine next_aln redefined at Bio\AlignIO\stockholm.pm line 379.
Subroutine write_aln redefined at Bio\AlignIO\stockholm.pm line 514.
Subroutine line_length redefined at Bio\AlignIO\stockholm.pm line 660.
Subroutine spaces redefined at Bio\AlignIO\stockholm.pm line 679.
Subroutine alignhandler redefined at Bio\AlignIO\stockholm.pm line 695.
Subroutine _print_seqs redefined at Bio\AlignIO\stockholm.pm line 707.
Subroutine new redefined at Bio\Seq\Meta.pm line 225, <GEN0> line 64.
Subroutine meta redefined at Bio\Seq\Meta.pm line 269, <GEN0> line 64.
Subroutine meta_text redefined at Bio\Seq\Meta.pm line 284, <GEN0> line 64.
Subroutine named_meta redefined at Bio\Seq\Meta.pm line 300, <GEN0> line 64.
Subroutine _test_gap_positions redefined at Bio\Seq\Meta.pm line 347, <GEN0> line 64.
Subroutine named_meta_text redefined at Bio\Seq\Meta.pm line 377, <GEN0> line 64.
Subroutine submeta redefined at Bio\Seq\Meta.pm line 409, <GEN0> line 64.
Subroutine submeta_text redefined at Bio\Seq\Meta.pm line 425, <GEN0> line 64.
Subroutine named_submeta redefined at Bio\Seq\Meta.pm line 444, <GEN0> line 64.
Subroutine named_submeta_text redefined at Bio\Seq\Meta.pm line 503, <GEN0> line 64.
Subroutine meta_names redefined at Bio\Seq\Meta.pm line 518, <GEN0> line 64.
Subroutine meta_length redefined at Bio\Seq\Meta.pm line 540, <GEN0> line 64.
Subroutine named_meta_length redefined at Bio\Seq\Meta.pm line 556, <GEN0> line 64.
Subroutine force_flush redefined at Bio\Seq\Meta.pm line 577, <GEN0> line 64.
Subroutine _do_flush redefined at Bio\Seq\Meta.pm line 605, <GEN0> line 64.
Subroutine is_flush redefined at Bio\Seq\Meta.pm line 637, <GEN0> line 64.
Subroutine revcom redefined at Bio\Seq\Meta.pm line 679, <GEN0> line 64.
Subroutine trunc redefined at Bio\Seq\Meta.pm line 702, <GEN0> line 64.
Subroutine to_string redefined at Bio\Seq\Meta.pm line 726, <GEN0> line 64.
t/AlignIO/stockholm.t .................. 
1..87
ok 1 - use Bio::AlignIO::stockholm;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9 - The object isa Bio::Annotation::Comment
ok 10 - Stockholm annotation
ok 11 - Stockholm annotation
ok 12 - stockholm output test
ok 13 - The object isa Bio::Align::AlignI
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20 - Stockholm annotation isa Bio::Annotation::Reference
ok 21 - Stockholm annotation
ok 22 - Stockholm annotation
ok 23 - Stockholm annotation
ok 24 - Stockholm annotation
ok 25 - The object isa Bio::Seq::MetaI
ok 26 - Rfam meta data
ok 27 - Rfam meta data
ok 28
ok 29 - The object isa Bio::Align::AlignI
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35 - The object isa Bio::Seq::MetaI
ok 36 - Rfam meta data
ok 37 - Rfam meta data
ok 38 - The object isa Bio::AlignIO
ok 39
ok 40 - The object isa Bio::Align::AlignI
ok 41
ok 42
ok 43
ok 44
ok 45 - The object isa Bio::Annotation::SimpleValue
ok 46 - Pfam annotation
ok 47
ok 48 - The object isa Bio::Align::AlignI
ok 49
ok 50
ok 51
ok 52
ok 53 - The object isa Bio::Align::AlignI
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59 - The object isa Bio::Seq::MetaI
ok 60 - Pfam aln meta data
ok 61 - Pfam aln meta data
ok 62 - Pfam aln meta data
ok 63 - Pfam aln meta data
ok 64 - Pfam aln meta data
ok 65 - Pfam aln meta data
ok 66 - Pfam seq meta data
ok 67 - Pfam seq meta data
ok 68 - Pfam seq meta data
ok 69 - Pfam seq meta data
ok 70
ok 71 - The object isa Bio::SeqFeatureI
ok 72 - The object isa Bio::Seq::Meta
ok 73 - The object isa Bio::AnnotationI
ok 74 - The object isa Bio::Annotation::DBLink
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok
Subroutine next_aln redefined at Bio\AlignIO\xmfa.pm line 87.
Subroutine write_aln redefined at Bio\AlignIO\xmfa.pm line 141.
Subroutine _get_len redefined at Bio\AlignIO\xmfa.pm line 194.
Subroutine width redefined at Bio\AlignIO\xmfa.pm line 212.
Subroutine _process_seq redefined at Bio\AlignIO\xmfa.pm line 221.
t/AlignIO/xmfa.t ....................... 
1..30
ok 1 - use Bio::AlignIO::xmfa;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - xmfa input test 
ok 4 - xmfa input test for start
ok 5 - xmfa input test for end
ok 6 - xmfa strand test
ok 7 - xmfa input test for id
ok 8 - xmfa input test for id
ok 9 - xmfa input test 
ok 10 - xmfa input test for start
ok 11 - xmfa input test for end
ok 12 - xmfa strand test
ok 13 - xmfa input test for id
ok 14 - xmfa input test for id
ok 15 - xmfa input test 
ok 16 - xmfa input test for start
ok 17 - xmfa input test for end
ok 18 - xmfa strand test
ok 19 - xmfa input test for id
ok 20 - xmfa input test for id
ok 21 - xmfa alignment score
ok 22 - The object isa Bio::Align::AlignI
ok 23 - xmfa input test 
ok 24 - xmfa strand
ok 25 - xmfa input test for description
ok 26 - xmfa input test for id
ok 27 - xmfa input test for end
ok 28 - xmfa input test for end
ok 29 - xmfa alignment score
ok 30 - xmfa output test
ok
t/Alphabet.t ........................... 
1..100
ok 1 - use Bio::Symbol::Alphabet;
ok 2 - use Bio::Symbol::Symbol;
ok 3 - use Bio::Symbol::DNAAlphabet;
ok 4 - use Bio::Symbol::ProteinAlphabet;
ok 5 - The object isa Bio::Symbol::Alphabet
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11 - The object isa Bio::Symbol::AlphabetI
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46 - The object isa Bio::Symbol::AlphabetI
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok
Subroutine new redefined at Bio\Annotation\SimpleValue.pm line 96.
Subroutine as_text redefined at Bio\Annotation\SimpleValue.pm line 128.
Subroutine display_text redefined at Bio\Annotation\SimpleValue.pm line 153.
Subroutine hash_tree redefined at Bio\Annotation\SimpleValue.pm line 174.
Subroutine tagname redefined at Bio\Annotation\SimpleValue.pm line 199.
Subroutine value redefined at Bio\Annotation\SimpleValue.pm line 229.
Subroutine tag_term redefined at Bio\Annotation\SimpleValue.pm line 265.
Subroutine new redefined at Bio\Annotation\OntologyTerm.pm line 128.
Subroutine as_text redefined at Bio\Annotation\OntologyTerm.pm line 172.
Subroutine display_text redefined at Bio\Annotation\OntologyTerm.pm line 197.
Subroutine hash_tree redefined at Bio\Annotation\OntologyTerm.pm line 218.
Subroutine tagname redefined at Bio\Annotation\OntologyTerm.pm line 246.
Subroutine term redefined at Bio\Annotation\OntologyTerm.pm line 274.
Subroutine identifier redefined at Bio\Annotation\OntologyTerm.pm line 297.
Subroutine name redefined at Bio\Annotation\OntologyTerm.pm line 313.
Subroutine definition redefined at Bio\Annotation\OntologyTerm.pm line 330.
Subroutine ontology redefined at Bio\Annotation\OntologyTerm.pm line 348.
Subroutine is_obsolete redefined at Bio\Annotation\OntologyTerm.pm line 364.
Subroutine comment redefined at Bio\Annotation\OntologyTerm.pm line 380.
Subroutine get_synonyms redefined at Bio\Annotation\OntologyTerm.pm line 394.
Subroutine add_synonym redefined at Bio\Annotation\OntologyTerm.pm line 410.
Subroutine remove_synonyms redefined at Bio\Annotation\OntologyTerm.pm line 425.
Subroutine get_dblinks redefined at Bio\Annotation\OntologyTerm.pm line 441.
Subroutine get_dbxrefs redefined at Bio\Annotation\OntologyTerm.pm line 457.
Subroutine add_dblink redefined at Bio\Annotation\OntologyTerm.pm line 477.
Subroutine add_dbxref redefined at Bio\Annotation\OntologyTerm.pm line 496.
Subroutine remove_dblinks redefined at Bio\Annotation\OntologyTerm.pm line 512.
Subroutine remove_dbxrefs redefined at Bio\Annotation\OntologyTerm.pm line 528.
Subroutine get_secondary_ids redefined at Bio\Annotation\OntologyTerm.pm line 546.
Subroutine add_secondary_id redefined at Bio\Annotation\OntologyTerm.pm line 563.
Subroutine remove_secondary_ids redefined at Bio\Annotation\OntologyTerm.pm line 578.
Subroutine new redefined at Bio\Annotation\Comment.pm line 64.
Subroutine as_text redefined at Bio\Annotation\Comment.pm line 92.
Subroutine display_text redefined at Bio\Annotation\Comment.pm line 117.
Subroutine hash_tree redefined at Bio\Annotation\Comment.pm line 138.
Subroutine tagname redefined at Bio\Annotation\Comment.pm line 166.
Subroutine text redefined at Bio\Annotation\Comment.pm line 193.
Subroutine type redefined at Bio\Annotation\Comment.pm line 231.
Subroutine Bio::Annotation::Comment::value redefined at Bio\Annotation\Comment.pm line 215.
Subroutine new redefined at Bio\Annotation\Target.pm line 67.
Subroutine as_text redefined at Bio\Annotation\Target.pm line 104.
Subroutine display_text redefined at Bio\Annotation\Target.pm line 134.
Subroutine tagname redefined at Bio\Annotation\Target.pm line 163.
Subroutine target_id redefined at Bio\Annotation\Target.pm line 198.
Subroutine new redefined at Bio\Tree\Tree.pm line 132.
Subroutine nodelete redefined at Bio\Tree\Tree.pm line 180.
Subroutine get_nodes redefined at Bio\Tree\Tree.pm line 200.
Subroutine get_root_node redefined at Bio\Tree\Tree.pm line 241.
Subroutine set_root_node redefined at Bio\Tree\Tree.pm line 257.
Subroutine total_branch_length redefined at Bio\Tree\Tree.pm line 281.
Subroutine subtree_length redefined at Bio\Tree\Tree.pm line 296.
Subroutine id redefined at Bio\Tree\Tree.pm line 318.
Subroutine score redefined at Bio\Tree\Tree.pm line 339.
Subroutine as_text redefined at Bio\Tree\Tree.pm line 383.
Subroutine set_tag_value redefined at Bio\Tree\Tree.pm line 420.
Subroutine add_tag_value redefined at Bio\Tree\Tree.pm line 442.
Subroutine remove_tag redefined at Bio\Tree\Tree.pm line 462.
Subroutine remove_all_tags redefined at Bio\Tree\Tree.pm line 483.
Subroutine get_all_tags redefined at Bio\Tree\Tree.pm line 500.
Subroutine get_tag_values redefined at Bio\Tree\Tree.pm line 517.
Subroutine has_tag redefined at Bio\Tree\Tree.pm line 534.
Subroutine clone redefined at Bio\Tree\Tree.pm line 554.
Subroutine cleanup_tree redefined at Bio\Tree\Tree.pm line 573.
Subroutine new redefined at Bio\Tree\Node.pm line 110.
Subroutine create_node_on_branch redefined at Bio\Tree\Node.pm line 163.
Subroutine add_Descendent redefined at Bio\Tree\Node.pm line 221.
Subroutine each_Descendent redefined at Bio\Tree\Node.pm line 259.
Subroutine remove_Descendent redefined at Bio\Tree\Node.pm line 322.
Subroutine remove_all_Descendents redefined at Bio\Tree\Node.pm line 357.
Subroutine ancestor redefined at Bio\Tree\Node.pm line 396.
Subroutine branch_length redefined at Bio\Tree\Node.pm line 437.
Subroutine bootstrap redefined at Bio\Tree\Node.pm line 461.
Subroutine description redefined at Bio\Tree\Node.pm line 482.
Subroutine id redefined at Bio\Tree\Node.pm line 511.
Subroutine internal_id redefined at Bio\Tree\Node.pm line 553.
Subroutine _creation_id redefined at Bio\Tree\Node.pm line 567.
Subroutine is_Leaf redefined at Bio\Tree\Node.pm line 588.
Subroutine height redefined at Bio\Tree\Node.pm line 606.
Subroutine invalidate_height redefined at Bio\Tree\Node.pm line 631.
Subroutine set_tag_value redefined at Bio\Tree\Node.pm line 652.
Subroutine add_tag_value redefined at Bio\Tree\Node.pm line 674.
Subroutine remove_tag redefined at Bio\Tree\Node.pm line 695.
Subroutine remove_all_tags redefined at Bio\Tree\Node.pm line 715.
Subroutine get_all_tags redefined at Bio\Tree\Node.pm line 731.
Subroutine get_tag_values redefined at Bio\Tree\Node.pm line 749.
Subroutine has_tag redefined at Bio\Tree\Node.pm line 765.
Subroutine node_cleanup redefined at Bio\Tree\Node.pm line 770.
Subroutine reverse_edge redefined at Bio\Tree\Node.pm line 800.
Subroutine new redefined at Bio\Annotation\Tree.pm line 73.
Subroutine as_text redefined at Bio\Annotation\Tree.pm line 114.
Subroutine display_text redefined at Bio\Annotation\Tree.pm line 141.
Subroutine hash_tree redefined at Bio\Annotation\Tree.pm line 161.
Subroutine tagname redefined at Bio\Annotation\Tree.pm line 185.
Subroutine tree_id redefined at Bio\Annotation\Tree.pm line 206.
Subroutine tree redefined at Bio\Annotation\Tree.pm line 223.
Subroutine new redefined at Bio\Annotation\TagTree.pm line 139.
Subroutine as_text redefined at Bio\Annotation\TagTree.pm line 178.
Subroutine display_text redefined at Bio\Annotation\TagTree.pm line 202.
Subroutine hash_tree redefined at Bio\Annotation\TagTree.pm line 223.
Subroutine tagname redefined at Bio\Annotation\TagTree.pm line 243.
Subroutine value redefined at Bio\Annotation\TagTree.pm line 265.
Subroutine tagformat redefined at Bio\Annotation\TagTree.pm line 313.
Subroutine node redefined at Bio\Annotation\TagTree.pm line 336.
Subroutine element redefined at Bio\Annotation\TagTree.pm line 378.
Subroutine data redefined at Bio\Annotation\TagTree.pm line 394.
Subroutine children redefined at Bio\Annotation\TagTree.pm line 418.
Subroutine subnodes redefined at Bio\Annotation\TagTree.pm line 436.
Subroutine get redefined at Bio\Annotation\TagTree.pm line 453.
Subroutine find redefined at Bio\Annotation\TagTree.pm line 470.
Subroutine findnode redefined at Bio\Annotation\TagTree.pm line 487.
Subroutine findval redefined at Bio\Annotation\TagTree.pm line 503.
Subroutine addchild redefined at Bio\Annotation\TagTree.pm line 526.
Subroutine add redefined at Bio\Annotation\TagTree.pm line 561.
Subroutine set redefined at Bio\Annotation\TagTree.pm line 583.
Subroutine unset redefined at Bio\Annotation\TagTree.pm line 604.
Subroutine free redefined at Bio\Annotation\TagTree.pm line 619.
Subroutine hash redefined at Bio\Annotation\TagTree.pm line 635.
Subroutine pairs redefined at Bio\Annotation\TagTree.pm line 652.
Subroutine qmatch redefined at Bio\Annotation\TagTree.pm line 668.
Subroutine tnodes redefined at Bio\Annotation\TagTree.pm line 683.
Subroutine ntnodes redefined at Bio\Annotation\TagTree.pm line 698.
Subroutine get_all_values redefined at Bio\Annotation\TagTree.pm line 721.
t/Annotation/Annotation.t .............. 
1..152
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 - The object isa Bio::AnnotationI
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18 - The object isa Bio::AnnotationI
ok 19
ok 20
ok 21
ok 22 - The object isa Bio::AnnotationCollectionI
ok 23
ok 24
ok 25 - The object isa Bio::AnnotationI
ok 26
ok 27 - The object isa Bio::AnnotationI
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 - The object isa Bio::AnnotationI
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 - The object isa Bio::AnnotationCollectionI
ok 66
ok 67
ok 68
ok 69
ok 70 - The object isa Bio::Annotation::StructuredValue
ok 71
ok 72
ok 73
ok 74
ok 75 - use Bio::Annotation::OntologyTerm;
ok 76 - The object isa Bio::Ontology::Term
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82 # skip The optional module Bio::SeqFeature::Annotated (or dependencies thereof) was not installed
ok 83 # skip The optional module Bio::SeqFeature::Annotated (or dependencies thereof) was not installed
ok 84 # skip The optional module Bio::SeqFeature::Annotated (or dependencies thereof) was not installed
ok 85 # skip The optional module Bio::SeqFeature::Annotated (or dependencies thereof) was not installed
ok 86 - The object isa Bio::Factory::ObjectFactoryI
ok 87 - The object isa Bio::Annotation::SimpleValue
ok 88
ok 89 - The object isa Bio::Annotation::OntologyTerm
ok 90 - Bio::Annotation::Comment
ok 91 - The object isa Bio::Annotation::Comment
ok 92
ok 93 - Bio::Annotation::Comment
ok 94 - The object isa Bio::Annotation::Comment
ok 95 - Bio::Annotation::Comment
ok 96 - The object isa Bio::Annotation::Comment
ok 97
ok 98 - The object isa Bio::Annotation::Target
ok 99
ok 100
ok 101 - The object isa Bio::AnnotationI
ok 102 - tree_id()
ok 103 - tagname()
ok 104
ok 105 - add tree to AlignI
ok 106 - get seq from node id
ok 107
ok 108 - The object isa Bio::Annotation::Tree
ok 109 - The object isa Bio::AnnotationI
ok 110 - default itext
ok 111 - roundtrip
ok 112 - itext
ok 113 - spxr
ok 114 - indent
ok 115 - xml
ok 116 - The object isa Data::Stag::StagI
ok 117
ok 118 - child changes
ok 119 - The object isa Data::Stag::StagI
ok 120
ok 121 - child changes
ok 122 - The object isa Data::Stag::StagI
ok 123
ok 124 - child changes
ok 125 - child changes in parent node
ok 126 - no tags
ok 127 - before Stag node
ok 128 - after Stag node
ok 129 - both stag nodes
ok 130 - different instances
ok 131 - before TagTree
ok 132 - after TagTree
ok 133 - both stag nodes
ok 134 - different instances
ok 135 - before TagTree
ok 136 - after TagTree
ok 137 - stag nodes
ok 138 - same instance
ok 139 - before TagTree
ok 140 - after TagTree
ok 141 - stag nodes
ok 142 - different instance
ok 143 - The object isa Bio::AnnotationI
ok 144 - The object isa Data::Stag::StagI
ok 145 - child changes
ok 146 - The object isa Data::Stag::StagI
ok 147 - child changes
ok 148 - The object isa Data::Stag::StagI
ok 149 - child changes
ok 150
ok 151
ok 152 - The object isa Bio::Annotation::TagTree
ok
t/Annotation/AnnotationAdaptor.t ....... 
1..23
ok 1 - use Bio::SeqFeature::Generic;
ok 2 - use Bio::SeqFeature::AnnotationAdaptor;
ok 3 - use Bio::Annotation::DBLink;
ok 4 - use Bio::Annotation::Comment;
ok 5 - use Bio::Annotation::SimpleValue;
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok
Bio::Assembly::IO: could not load tigr - for more details on supported formats please see the Assembly::IO docs
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::Assembly::IO::tigr. Can't locate DB_File.pm in @INC (@INC contains: . C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv\blib\lib C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv\blib\arch C:/cpanfly-5.16/var/cpan/build/BioPerl-1.6.920-c7McWv C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv C:\cpanfly-5.16\var\megalib C:/cpanfly-5.16/var/megalib C:/Perl-5.16/site/lib C:/Perl-5.16/lib) at Bio/SeqFeature/Collection.pm line 146.
BEGIN failed--compilation aborted at Bio/SeqFeature/Collection.pm line 146.
Compilation failed in require at Bio/Assembly/Singlet.pm line 91.
BEGIN failed--compilation aborted at Bio/Assembly/Singlet.pm line 91.
Compilation failed in require at Bio\Assembly\IO\tigr.pm line 237.
BEGIN failed--compilation aborted at Bio\Assembly\IO\tigr.pm line 237.
Compilation failed in require at Bio/Root/Root.pm line 558.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:560
STACK: Bio::Assembly::IO::_load_format_module Bio/Assembly/IO.pm:309
STACK: Bio::Assembly::IO::new Bio/Assembly/IO.pm:138
STACK: t/Assembly/ContigSpectrum.t:13
-----------------------------------------------------------


#   Failed test 'The thing isa Bio::Assembly::IO'
#   at t/Assembly/ContigSpectrum.t line 17.
#     The thing isn't defined
Can't call method "next_assembly" on an undefined value at t/Assembly/ContigSpectrum.t line 18.
# Looks like you planned 239 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..239
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 237/239 subtests 
t/Assembly/IO/bowtie.t ................. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Assembly/IO/sam.t .................... skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Assembly/core.t ...................... skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Cluster/UniGene.t .................... 
1..2
ok 1 - use Bio::Cluster::UniGene;
ok 2 - The object isa Bio::AnnotatableI
ok
t/ClusterIO/ClusterIO.t ................ 
1..12
ok 1 - use Bio::ClusterIO;
ok 2 - use Bio::Cluster::ClusterFactory;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11 - The object isa Bio::Cluster::UniGeneI
ok 12 - The object isa Bio::Cluster::UniGeneI
ok
t/ClusterIO/SequenceFamily.t ........... 
1..17
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
Subroutine new redefined at Bio\Cluster\UniGene.pm line 258.
Subroutine unigene_id redefined at Bio\Cluster\UniGene.pm line 320.
Subroutine title redefined at Bio\Cluster\UniGene.pm line 342.
Subroutine gene redefined at Bio\Cluster\UniGene.pm line 363.
Subroutine cytoband redefined at Bio\Cluster\UniGene.pm line 381.
Subroutine mgi redefined at Bio\Cluster\UniGene.pm line 398.
Subroutine locuslink redefined at Bio\Cluster\UniGene.pm line 426.
Subroutine homol redefined at Bio\Cluster\UniGene.pm line 455.
Subroutine restr_expr redefined at Bio\Cluster\UniGene.pm line 472.
Subroutine gnm_terminus redefined at Bio\Cluster\UniGene.pm line 490.
Subroutine scount redefined at Bio\Cluster\UniGene.pm line 506.
Subroutine express redefined at Bio\Cluster\UniGene.pm line 528.
Subroutine chromosome redefined at Bio\Cluster\UniGene.pm line 546.
Subroutine sts redefined at Bio\Cluster\UniGene.pm line 564.
Subroutine txmap redefined at Bio\Cluster\UniGene.pm line 582.
Subroutine protsim redefined at Bio\Cluster\UniGene.pm line 600.
Subroutine sequences redefined at Bio\Cluster\UniGene.pm line 623.
Subroutine species redefined at Bio\Cluster\UniGene.pm line 643.
Subroutine display_id redefined at Bio\Cluster\UniGene.pm line 675.
Subroutine description redefined at Bio\Cluster\UniGene.pm line 692.
Subroutine size redefined at Bio\Cluster\UniGene.pm line 710.
Subroutine cluster_score redefined at Bio\Cluster\UniGene.pm line 742.
Subroutine get_members redefined at Bio\Cluster\UniGene.pm line 765.
Subroutine annotation redefined at Bio\Cluster\UniGene.pm line 814.
Subroutine add_member redefined at Bio\Cluster\UniGene.pm line 846.
Subroutine remove_members redefined at Bio\Cluster\UniGene.pm line 876.
Subroutine next_locuslink redefined at Bio\Cluster\UniGene.pm line 905.
Subroutine next_express redefined at Bio\Cluster\UniGene.pm line 931.
Subroutine next_chromosome redefined at Bio\Cluster\UniGene.pm line 958.
Subroutine next_protsim redefined at Bio\Cluster\UniGene.pm line 985.
Subroutine next_sts redefined at Bio\Cluster\UniGene.pm line 1012.
Subroutine next_txmap redefined at Bio\Cluster\UniGene.pm line 1039.
Subroutine _next_element redefined at Bio\Cluster\UniGene.pm line 1052.
Subroutine object_id redefined at Bio\Cluster\UniGene.pm line 1089.
Subroutine version redefined at Bio\Cluster\UniGene.pm line 1111.
Subroutine authority redefined at Bio\Cluster\UniGene.pm line 1133.
Subroutine namespace redefined at Bio\Cluster\UniGene.pm line 1155.
Subroutine display_name redefined at Bio\Cluster\UniGene.pm line 1183.
Subroutine next_seq redefined at Bio\Cluster\UniGene.pm line 1234.
Subroutine sequence_factory redefined at Bio\Cluster\UniGene.pm line 1292.
Subroutine _annotation_value redefined at Bio\Cluster\UniGene.pm line 1320.
Subroutine _annotation_value_ary redefined at Bio\Cluster\UniGene.pm line 1361.
Subroutine _annotation_dblink redefined at Bio\Cluster\UniGene.pm line 1397.
Subroutine _remove_dblink redefined at Bio\Cluster\UniGene.pm line 1432.
Subroutine Bio::Cluster::UniGene::sequence redefined at Bio\Cluster\UniGene.pm line 1456.
t/ClusterIO/unigene.t .................. 
1..73
ok 1 - use Bio::ClusterIO;
ok 2 - new Bio::ClusterIO object defined
ok 3
ok 4 - The object isa Bio::Cluster::UniGeneI
ok 5 - The object isa Bio::ClusterI
ok 6 - The object isa Bio::IdentifiableI
ok 7 - The object isa Bio::DescribableI
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48 - The object isa Bio::PrimarySeqI
ok 49
ok 50
ok 51 - annotation object defined
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66 - The object isa Bio::PrimarySeqI
ok 67
ok 68 - next cluster
ok 69
ok 70
ok 71
ok 72
ok 73
ok
t/Coordinate/CoordinateBoundaryTest.t .. 
1..174
ok 1 - use Bio::Location::Simple;
ok 2 - use Bio::Coordinate::Pair;
ok 3
ok 4 - The object isa Bio::Location::Simple
ok 5
ok 6 - The object isa Bio::Location::Simple
ok 7
ok 8 - The object isa Bio::Location::Simple
ok 9
ok 10 - The object isa Bio::Coordinate::Pair
ok 11
ok 12 - The object isa Bio::Coordinate::Pair
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32 - The object isa Bio::LocationI
ok 33
ok 34 - The object isa Bio::Coordinate::Result
ok 35
ok 36 - The object isa Bio::Coordinate::Result
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50 - The object isa Bio::LocationI
ok 51
ok 52 - The object isa Bio::Coordinate::Result
ok 53
ok 54 - The object isa Bio::Coordinate::Result
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68 - The object isa Bio::LocationI
ok 69
ok 70 - The object isa Bio::Coordinate::Result
ok 71
ok 72 - The object isa Bio::Coordinate::Result
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88 - The object isa Bio::LocationI
ok 89
ok 90 - The object isa Bio::Coordinate::Result
ok 91
ok 92 - The object isa Bio::Coordinate::Result
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108 - The object isa Bio::Location::Simple
ok 109
ok 110 - The object isa Bio::Location::Simple
ok 111
ok 112 - The object isa Bio::Location::Simple
ok 113
ok 114 - The object isa Bio::Coordinate::Pair
ok 115
ok 116 - The object isa Bio::Coordinate::Pair
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132 - The object isa Bio::Coordinate::Result
ok 133
ok 134 - The object isa Bio::Coordinate::Result
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142 - The object isa Bio::Coordinate::Result
ok 143
ok 144 - The object isa Bio::Coordinate::Result
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152 - The object isa Bio::Coordinate::Result
ok 153
ok 154 - The object isa Bio::Coordinate::Result
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164 - The object isa Bio::Coordinate::Result
ok 165
ok 166 - The object isa Bio::Coordinate::Result
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok
t/Coordinate/CoordinateGraph.t ......... 
1..7
ok 1 - use Bio::Coordinate::Graph;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok
t/Coordinate/CoordinateMapper.t ........ 
1..175
ok 1 - use Bio::Location::Simple;
ok 2 - use Bio::Coordinate::Pair;
ok 3 - use Bio::Coordinate::Result::Match;
ok 4 - use Bio::Coordinate::Result::Gap;
ok 5 - use Bio::Coordinate::Chain;
ok 6 - use Bio::Coordinate::Collection;
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14 - The object isa Bio::Coordinate::Result
ok 15 - The object isa Bio::Location::SplitLocationI
ok 16
ok 17
ok 18
ok 19 - The object isa Bio::LocationI
ok 20 - The object isa Bio::Coordinate::Result::Match
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - The object isa Bio::Coordinate::Result::Gap
ok 38 - The object isa Bio::LocationI
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106 - The object isa Bio::Coordinate::Result::Match
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138 - Match: |314696| Test: 314696|
ok 139
ok 140
ok 141
ok 142 - Match: |341| Test: 341|
ok 143
ok 144
ok 145
ok 146 - Match: |315843| Test: 315843|
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152 - Match: |627011| Test: 627011|
ok 153
ok 154
ok 155
ok 156 - Match: |chr1| Test: chr1|
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok
t/Coordinate/GeneCoordinateMapper.t .... 
1..116
ok 1 - use Bio::Location::Simple;
ok 2 - use Bio::Coordinate::Pair;
ok 3 - use Bio::Coordinate::ExtrapolatingPair;
ok 4 - use Bio::Coordinate::GeneMapper;
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14 - The object isa Bio::Location::Simple
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75 - The object isa Bio::Location::Simple
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok
t/Draw/Pictogram.t ..................... 
1..6
ok 1 - use Bio::Draw::Pictogram;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::Matrix::PSM::IO;
ok 4 - The object isa Bio::Draw::Pictogram
ok 5
ok 6
ok
t/LiveSeq/Chain.t ...................... 
1..45
ok 1 - use Bio::LiveSeq::Chain;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok
t/LiveSeq/LiveSeq.t .................... 
1..48
ok 1 - use Bio::LiveSeq::IO::BioPerl;
ok 2
ok 3
ok 4 - Bio::LiveSeq::Gene
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok
t/LiveSeq/Mutation.t ................... 
1..19
ok 1 - use Bio::LiveSeq::Mutation;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok
t/LiveSeq/Mutator.t .................... 
1..24
ok 1 - use Bio::LiveSeq::Mutator;
ok 2 - use Bio::LiveSeq::IO::BioPerl;
ok 3 - use Bio::Variation::IO;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok
t/LocalDB/BioDBGFF.t ................... skipped: Not compatible with your Operating System
Subroutine new redefined at Bio/DB/IndexedBase.pm line 1075.
Subroutine next_seq redefined at Bio/DB/IndexedBase.pm line 1084.
Subroutine TIEHANDLE redefined at Bio/DB/IndexedBase.pm line 1093.
Subroutine READLINE redefined at Bio/DB/IndexedBase.pm line 1098.
Subroutine new redefined at Bio/DB/Fasta.pm line 359.
Subroutine fetch_sequence redefined at Bio/DB/Fasta.pm line 372.
Subroutine seq redefined at Bio/DB/Fasta.pm line 376.
Subroutine subseq redefined at Bio/DB/Fasta.pm line 381.
Subroutine trunc redefined at Bio/DB/Fasta.pm line 386.
Subroutine is_circular redefined at Bio/DB/Fasta.pm line 401.
Subroutine display_id redefined at Bio/DB/Fasta.pm line 406.
Subroutine accession_number redefined at Bio/DB/Fasta.pm line 411.
Subroutine primary_id redefined at Bio/DB/Fasta.pm line 416.
Subroutine can_call_new redefined at Bio/DB/Fasta.pm line 423.
Subroutine alphabet redefined at Bio/DB/Fasta.pm line 427.
Subroutine revcom redefined at Bio/DB/Fasta.pm line 432.
Subroutine length redefined at Bio/DB/Fasta.pm line 438.
Subroutine description redefined at Bio/DB/Fasta.pm line 446.
Subroutine Bio::PrimarySeq::Fasta::desc redefined at Bio/DB/Fasta.pm line 452.

#   Failed test at t/LocalDB/Fasta.t line 185.

#   Failed test at t/LocalDB/Fasta.t line 197.
#     Structures begin differing at:
#          $got->[1] = '123'
#     $expected->[1] = '194473622'

#   Failed test at t/LocalDB/Fasta.t line 198.
#          got: 'gi|352962148|ref|NM_001251825.1|'
#     expected: undef

#   Failed test at t/LocalDB/Fasta.t line 208.
#     Structures begin differing at:
#          $got->[1] = '123'
#     $expected->[1] = '194473622'

#   Failed test at t/LocalDB/Fasta.t line 209.
#          got: 'gi|352962148|ref|NM_001251825.1|'
#     expected: undef
# Looks like you failed 5 tests of 107.
t/LocalDB/Fasta.t ...................... 
1..107
ok 1 - Index a directory
ok 2
ok 3 - The object isa Bio::DB::Fasta
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 - The object isa Bio::PrimarySeq::Fasta
ok 29 - The object isa Bio::PrimarySeqI
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - bug 3126
ok 38
ok 39
ok 40 - The object isa Bio::PrimarySeq::Fasta
ok 41 - The object isa Bio::PrimarySeqI
ok 42
ok 43
ok 44
ok 45 - The object isa Bio::PrimarySeq::Fasta
ok 46 - The object isa Bio::PrimarySeqI
ok 47
ok 48
ok 49 - use Class::Unload;
ok 50 - Re-open an existing index
ok 51
ok 52 - Tied hash access
ok 53
ok 54
ok 55
ok 56
ok 57 - Writing with SeqIO
ok 58
ok 59
ok 60 - Index a single file
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::DB::Indexed::Stream
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
not ok 86
ok 87
ok 88 - Make single ID
not ok 89
not ok 90
ok 91 - The object isa Bio::PrimarySeqI
ok 92 - Make multiple IDs, bug \#3389
not ok 93
not ok 94
ok 95 - The object isa Bio::PrimarySeqI
ok 96 - Index a set of files
ok 97
ok 98
ok 99
ok 100
ok 101 - threw Regexp ((?^:FASTA header doesn't match))
ok 102 - threw Regexp ((?^:Blank lines can only precede header lines))
ok 103
ok 104 - length is correct in sequences past spaces
ok 105
ok 106 - subseq is correct
ok 107 - subseq is correct
Dubious, test returned 5 (wstat 1280, 0x500)
Failed 5/107 subtests 
t/LocalDB/Flat.t ....................... skipped: The optional module DB_File (or dependencies thereof) was not installed
Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175.
Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264.
Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284.
Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311.
Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337.
Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357.
Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378.
Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399.
Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420.
Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442.
Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465.
Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487.
Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508.
Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523.
Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540.
Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555.
Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574.
Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599.
Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616.
Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629.
Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646.
Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663.
Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680.
Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700.
Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728.
Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747.
Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763.
Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777.
Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794.
Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815.
Subroutine new redefined at Bio/Search/Hit/GenericHit.pm line 127.
Subroutine add_hsp redefined at Bio/Search/Hit/GenericHit.pm line 204.
Subroutine hsp_factory redefined at Bio/Search/Hit/GenericHit.pm line 228.
Subroutine name redefined at Bio/Search/Hit/GenericHit.pm line 248.
Subroutine accession redefined at Bio/Search/Hit/GenericHit.pm line 268.
Subroutine description redefined at Bio/Search/Hit/GenericHit.pm line 288.
Subroutine length redefined at Bio/Search/Hit/GenericHit.pm line 308.
Subroutine algorithm redefined at Bio/Search/Hit/GenericHit.pm line 333.
Subroutine raw_score redefined at Bio/Search/Hit/GenericHit.pm line 355.
Subroutine score redefined at Bio/Search/Hit/GenericHit.pm line 385.
Subroutine significance redefined at Bio/Search/Hit/GenericHit.pm line 400.
Subroutine bits redefined at Bio/Search/Hit/GenericHit.pm line 430.
Subroutine next_hsp redefined at Bio/Search/Hit/GenericHit.pm line 458.
Subroutine hsps redefined at Bio/Search/Hit/GenericHit.pm line 494.
Subroutine num_hsps redefined at Bio/Search/Hit/GenericHit.pm line 517.
Subroutine rewind redefined at Bio/Search/Hit/GenericHit.pm line 538.
Subroutine ambiguous_aln redefined at Bio/Search/Hit/GenericHit.pm line 564.
Subroutine overlap redefined at Bio/Search/Hit/GenericHit.pm line 576.
Subroutine n redefined at Bio/Search/Hit/GenericHit.pm line 605.
Subroutine p redefined at Bio/Search/Hit/GenericHit.pm line 652.
Subroutine hsp redefined at Bio/Search/Hit/GenericHit.pm line 694.
Subroutine logical_length redefined at Bio/Search/Hit/GenericHit.pm line 740.
Subroutine length_aln redefined at Bio/Search/Hit/GenericHit.pm line 786.
Subroutine gaps redefined at Bio/Search/Hit/GenericHit.pm line 849.
Subroutine matches redefined at Bio/Search/Hit/GenericHit.pm line 887.
Subroutine start redefined at Bio/Search/Hit/GenericHit.pm line 948.
Subroutine end redefined at Bio/Search/Hit/GenericHit.pm line 1025.
Subroutine range redefined at Bio/Search/Hit/GenericHit.pm line 1093.
Subroutine frac_identical redefined at Bio/Search/Hit/GenericHit.pm line 1150.
Subroutine frac_conserved redefined at Bio/Search/Hit/GenericHit.pm line 1226.
Subroutine frac_aligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1274.
Subroutine frac_aligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1310.
Subroutine num_unaligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1364.
Subroutine num_unaligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1400.
Subroutine seq_inds redefined at Bio/Search/Hit/GenericHit.pm line 1442.
Subroutine strand redefined at Bio/Search/Hit/GenericHit.pm line 1473.
Subroutine frame redefined at Bio/Search/Hit/GenericHit.pm line 1535.
Subroutine rank redefined at Bio/Search/Hit/GenericHit.pm line 1574.
Subroutine locus redefined at Bio/Search/Hit/GenericHit.pm line 1590.
Subroutine each_accession_number redefined at Bio/Search/Hit/GenericHit.pm line 1618.
Subroutine tiled_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1666.
Subroutine query_length redefined at Bio/Search/Hit/GenericHit.pm line 1683.
Subroutine ncbi_gi redefined at Bio/Search/Hit/GenericHit.pm line 1701.
Subroutine sort_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1732.
Subroutine iteration redefined at Bio/Search/Hit/GenericHit.pm line 1772.
Subroutine found_again redefined at Bio/Search/Hit/GenericHit.pm line 1807.
Subroutine Bio::Search::Hit::GenericHit::frac_aligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1333.
Subroutine Bio::Search::Hit::GenericHit::num_unaligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1341.
t/LocalDB/Index/Blast.t ................ 
1..26
ok 1 - use Cwd;
ok 2 - use Bio::SearchIO;
ok 3 - use Bio::Index::Blast;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok

--------------------- WARNING ---------------------
MSG: overwriting a current value stored for SP130_MOUSE

---------------------------------------------------

--------------------- WARNING ---------------------
MSG: overwriting a current value stored for SDS3_MOUSE

---------------------------------------------------

--------------------- WARNING ---------------------
MSG: overwriting a current value stored for IKZF1_MOUSE

---------------------------------------------------
t/LocalDB/Index/BlastTable.t ........... 
1..27
ok 1 - use Cwd;
ok 2 - use Bio::SearchIO;
ok 3 - use Bio::Index::BlastTable;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok
t/LocalDB/Index/Index.t ................ skipped: The optional module DB_File (or dependencies thereof) was not installed
t/LocalDB/Qual.t ....................... 
1..56
ok 1 - use Bio::Root::IO;
ok 2 - use File::Copy;
ok 3
ok 4
ok 5 - The object isa Bio::DB::Qual
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 - The object isa Bio::Seq::PrimaryQual::Qual
ok 23 - The object isa Bio::Seq::QualI
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::Seq::PrimaryQual::Qual
ok 38 - The object isa Bio::Seq::QualI
ok 39
ok 40
ok 41
ok 42 - The object isa Bio::Seq::PrimaryQual::Qual
ok 43 - The object isa Bio::Seq::PrimaryQual
ok 44
ok 45
ok 46
ok 47
ok 48 - The object isa Bio::DB::Indexed::Stream
ok 49
ok 50 - The object isa Bio::Seq::PrimaryQual
ok 51
ok 52 - The object isa Bio::Seq::PrimaryQual
ok 53
ok 54
ok 55
ok 56
ok
t/LocalDB/Registry.t ................... 
1..14
ok 1 - use Bio::DB::Registry;
ok 2 - use Bio::DB::Flat;
ok 3
ok 4 # skip The optional module DB_File (or dependencies thereof) was not installed
ok 5 # skip The optional module DB_File (or dependencies thereof) was not installed
ok 6 # skip Network tests have not been requested
ok 7 # skip Network tests have not been requested
ok 8 # skip Network tests have not been requested
ok 9 # skip Network tests have not been requested
ok 10 # skip Network tests have not been requested
ok 11 # skip Network tests have not been requested
ok 12 # skip Network tests have not been requested
ok 13 # skip Network tests have not been requested
ok 14 # skip Network tests have not been requested
ok

#   Failed test 'use Bio::DB::SeqFeature::Store::GFF3Loader;'
#   at t/LocalDB/SeqFeature.t line 16.
#     Tried to use 'Bio::DB::SeqFeature::Store::GFF3Loader'.
#     Error:  Can't locate DB_File.pm in @INC (@INC contains: . .. ./t/lib C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv\blib\lib C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv\blib\arch C:/cpanfly-5.16/var/cpan/build/BioPerl-1.6.920-c7McWv C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv C:\cpanfly-5.16\var\megalib C:/cpanfly-5.16/var/megalib C:/Perl-5.16/site/lib C:/Perl-5.16/lib) at Bio/DB/SeqFeature/Store/LoadHelper.pm line 37.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/LoadHelper.pm line 37.
# 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 124) line 2.
# BEGIN failed--compilation aborted at (eval 124) line 2.
# Looks like you failed 1 test of 116.
t/LocalDB/SeqFeature.t ................. 
1..116
ok 1 - use Bio::SeqFeature::Generic;
ok 2 - use Bio::DB::SeqFeature::Store;
not ok 3 - use Bio::DB::SeqFeature::Store::GFF3Loader;
ok 4 - use Bio::Root::IO;
ok 5 - use Bio::DB::Fasta;
ok 6 - use File::Copy;
ok 7 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 60 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 61 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 62 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 63 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 64 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 65 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 66 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 67 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 68 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 69 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 70 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 71 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 72 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 73 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 74 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 75 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 76 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 77 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 78 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 79 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 80 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 81 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 82 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 83 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 84 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 85 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 86 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 87 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 88 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 89 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 90 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 91 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 92 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 93 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 94 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 95 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 96 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 97 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 98 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 99 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 100 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 101 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 102 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 103 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 104 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 105 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 106 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 107 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 108 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 109 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 110 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 111 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 112 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 113 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 114 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 115 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 116 # 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 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 139) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/116 subtests 
	(less 110 skipped subtests: 5 okay)
t/LocalDB/Taxonomy/greengenes.t ........ 
1..38
ok 1 - use Bio::DB::Taxonomy;
ok 2 - use Bio::Tree::Tree;
ok 3
ok 4 - The object isa Bio::DB::Taxonomy::greengenes
ok 5 - The object isa Bio::DB::Taxonomy::list
ok 6 - The object isa Bio::DB::Taxonomy
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/LocalDB/Taxonomy/silva.t ............. 
1..42
ok 1 - use Bio::DB::Taxonomy;
ok 2 - use Bio::Tree::Tree;
ok 3
ok 4 - The object isa Bio::DB::Taxonomy::silva
ok 5 - The object isa Bio::DB::Taxonomy::list
ok 6 - The object isa Bio::DB::Taxonomy
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

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't locate DB_File.pm in @INC (@INC contains: . C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv\blib\lib C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv\blib\arch C:/cpanfly-5.16/var/cpan/build/BioPerl-1.6.920-c7McWv C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv C:\cpanfly-5.16\var\megalib C:/cpanfly-5.16/var/megalib C:/Perl-5.16/site/lib C:/Perl-5.16/lib) at Bio\DB\Taxonomy\flatfile.pm line 88.
BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 88.
Compilation failed in require at Bio/Root/Root.pm line 558.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:560
STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:294
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:118
STACK: t/LocalDB/transfac_pro.t:18
-----------------------------------------------------------
Bio::DB::Taxonomy: flatfile cannot be found
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't locate DB_File.pm in @INC (@INC contains: . C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv\blib\lib C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv\blib\arch C:/cpanfly-5.16/var/cpan/build/BioPerl-1.6.920-c7McWv C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv C:\cpanfly-5.16\var\megalib C:/cpanfly-5.16/var/megalib C:/Perl-5.16/site/lib C:/Perl-5.16/lib) at Bio\DB\Taxonomy\flatfile.pm line 88.
BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 88.
Compilation failed in require at Bio/Root/Root.pm line 558.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:560
STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:294
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:118
STACK: t/LocalDB/transfac_pro.t:18
-----------------------------------------------------------

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

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::TFBS::transfac_pro. Can't locate DB_File.pm in @INC (@INC contains: . C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv\blib\lib C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv\blib\arch C:/cpanfly-5.16/var/cpan/build/BioPerl-1.6.920-c7McWv C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv C:\cpanfly-5.16\var\megalib C:/cpanfly-5.16/var/megalib C:/Perl-5.16/site/lib C:/Perl-5.16/lib) at Bio\DB\TFBS\transfac_pro.pm line 118.
BEGIN failed--compilation aborted at Bio\DB\TFBS\transfac_pro.pm line 118.
Compilation failed in require at Bio/Root/Root.pm line 558.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:560
STACK: Bio::DB::TFBS::_load_tax_module Bio/DB/TFBS.pm:151
STACK: Bio::DB::TFBS::new Bio/DB/TFBS.pm:130
STACK: t/LocalDB/transfac_pro.t:25
-----------------------------------------------------------
Bio::DB::TFBS: transfac_pro cannot be found
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::TFBS::transfac_pro. Can't locate DB_File.pm in @INC (@INC contains: . C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv\blib\lib C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv\blib\arch C:/cpanfly-5.16/var/cpan/build/BioPerl-1.6.920-c7McWv C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv C:\cpanfly-5.16\var\megalib C:/cpanfly-5.16/var/megalib C:/Perl-5.16/site/lib C:/Perl-5.16/lib) at Bio\DB\TFBS\transfac_pro.pm line 118.
BEGIN failed--compilation aborted at Bio\DB\TFBS\transfac_pro.pm line 118.
Compilation failed in require at Bio/Root/Root.pm line 558.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:560
STACK: Bio::DB::TFBS::_load_tax_module Bio/DB/TFBS.pm:151
STACK: Bio::DB::TFBS::new Bio/DB/TFBS.pm:130
STACK: t/LocalDB/transfac_pro.t:25
-----------------------------------------------------------

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

#   Failed test at t/LocalDB/transfac_pro.t line 25.
Can't call method "get_reference_ids" on an undefined value at t/LocalDB/transfac_pro.t line 33.
# Looks like you planned 115 tests but ran 4.
# Looks like you failed 1 test of 4 run.
# Looks like your test exited with 2 just after 4.
t/LocalDB/transfac_pro.t ............... 
1..115
ok 1 - use Bio::Matrix::PSM::IO;
ok 2 - use Bio::DB::TFBS;
ok 3 - use Bio::DB::Taxonomy;
not ok 4
Dubious, test returned 2 (wstat 512, 0x200)
Failed 112/115 subtests 
t/Map/Cyto.t ........................... 
1..110
ok 1 - use Bio::Map::CytoMap;
ok 2 - use Bio::Map::CytoPosition;
ok 3 - use Bio::Map::CytoMarker;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14 - The object isa Bio::Map::CytoPosition
ok 15
ok 16
ok 17
ok 18 - The object isa Bio::Range
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok
t/Map/Linkage.t ........................ 
1..18
ok 1 - use Bio::Map::LinkagePosition;
ok 2 - use Bio::Map::Microsatellite;
ok 3 - use Bio::Map::LinkageMap;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok
t/Map/Map.t ............................ 
1..267
ok 1 - use Bio::Map::SimpleMap;
ok 2 - use Bio::Map::Marker;
ok 3 - use Bio::Map::Position;
ok 4 - use Bio::Map::Relative;
ok 5 - use Bio::Map::Mappable;
ok 6
ok 7
ok 8
ok 9
ok 10 - Length is 0
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151 - use Bio::Map::Gene;
ok 152 - use Bio::Map::GeneMap;
ok 153 - use Bio::Map::TranscriptionFactor;
ok 154 - use Bio::Map::GeneRelative;
ok 155 - use Bio::Map::GenePosition;
ok 156 - use Bio::Map::Prediction;
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok 176
ok 177
ok 178
ok 179
ok 180
ok 181
ok 182
ok 183
ok 184
ok 185
ok 186
ok 187
ok 188
ok 189
ok 190
ok 191
ok 192
ok 193
ok 194
ok 195
ok 196
ok 197
ok 198
ok 199
ok 200
ok 201
ok 202
ok 203
ok 204
ok 205
ok 206
ok 207
ok 208
ok 209
ok 210
ok 211
ok 212
ok 213
ok 214
ok 215
ok 216
ok 217
ok 218
ok 219
ok 220
ok 221
ok 222
ok 223
ok 224
ok 225
ok 226
ok 227
ok 228
ok 229
ok 230
ok 231
ok 232
ok 233
ok 234
ok 235
ok 236
ok 237
ok 238
ok 239
ok 240
ok 241
ok 242
ok 243
ok 244
ok 245
ok 246
ok 247
ok 248
ok 249 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 250 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 251 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 252 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 253 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 254 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 255 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 256 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 257 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 258 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 259 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 260 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 261 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 262 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 263 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 264 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 265 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 266 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 267 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok
t/Map/MapIO.t .......................... 
1..51
ok 1 - use Bio::MapIO;
ok 2
ok 3 - The object isa Bio::Map::MapI
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok
t/Map/MicrosatelliteMarker.t ........... 
1..8
ok 1 - use Bio::Map::SimpleMap;
ok 2 - use Bio::Map::Position;
ok 3 - use Bio::Map::Microsatellite;
ok 4
ok 5
ok 6
ok 7
ok 8
ok
t/Map/Physical.t ....................... 
1..40
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 40 # TODO Possible hash randomization-related bug, sum of contig pos values sometimes fails with off-by-one
ok
t/Matrix/IO/masta.t .................... 
1..16
ok 1 - use Bio::Matrix::PSM::IO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok
t/Matrix/IO/psm.t ...................... 
1..63
ok 1 - use Bio::Matrix::PSM::IO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok
t/Matrix/InstanceSite.t ................ 
1..6
ok 1 - use Bio::Matrix::PSM::InstanceSite;
ok 2
ok 3
ok 4
ok 5
ok 6
ok
t/Matrix/Matrix.t ...................... 
1..77
ok 1 - use Bio::Matrix::Generic;
ok 2 - use Bio::Matrix::IO;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30 - The object isa Bio::Matrix::Scoring
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42 - The object isa Bio::Matrix::Scoring
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok
t/Matrix/ProtMatrix.t .................. 
1..14
ok 1 - use Bio::Matrix::PSM::ProtMatrix;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok
t/Matrix/ProtPsm.t ..................... 
1..14
ok 1 - use Bio::Matrix::PSM::IO;
ok 2
ok 3
ok 4
ok 5 # skip TODO: Module incomplete
ok 6 # skip TODO: Module incomplete
ok 7 # skip TODO: Module incomplete
ok 8 # skip TODO: Module incomplete
ok 9 # skip TODO: Module incomplete
ok 10 # skip TODO: Module incomplete
ok 11 # skip TODO: Module incomplete
ok 12 # skip TODO: Module incomplete
ok 13 # skip TODO: Module incomplete
ok 14 # skip TODO: Module incomplete
ok
t/Matrix/SiteMatrix.t .................. 
1..14
ok 1 - use Bio::Matrix::PSM::SiteMatrix;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok
t/Ontology/GOterm.t .................... 
1..62
ok 1 - use Bio::Ontology::GOterm;
ok 2 - use Bio::Ontology::Ontology;
ok 3 - use Bio::Annotation::DBLink;
ok 4 - The object isa Bio::Ontology::GOterm
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok
t/Ontology/GraphAdaptor.t .............. 
1..28
ok 1 - use Bio::Ontology::SimpleGOEngine::GraphAdaptor;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok
t/Ontology/IO/go.t ..................... 
1..102
ok 1 - use Bio::OntologyIO;
ok 2
ok 3 - The object isa Bio::Ontology::OntologyI
ok 4
ok 5 - The object isa Bio::Ontology::OntologyEngineI
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok
t/Ontology/IO/interpro.t ............... 
1..69
ok 1 - use Bio::OntologyIO;
ok 2 - The object isa Bio::OntologyIO::InterProParser
ok 3
ok 4 - get_dbxrefs on leaf terms is non-empty
ok 5 - get_dbxrefs(member_list) on leaf terms is non-empty
ok 6 - get_dbxrefs(sec_list) on leaf terms is non-empty
ok 7 - get_dbxrefs(class_list) on leaf terms is non-empty
ok 8 - get_dbxrefs(pub_list) on leaf terms is non-empty
ok 9 - get_dbxrefs(example_list) on leaf terms is non-empty
ok 10 - get_dbxrefs(external_doc_list) on leaf terms is non-empty
ok 11 - get_members on leaf terms is non-empty
ok 12 - class_list on leaf terms is non-empty
ok 13 - get_examples on leaf terms is non-empty
ok 14 - get_external_documents on leaf terms is non-empty
ok 15 - get_references on leaf terms is non-empty
ok 16 - protein_count on leaf terms is non-empty
ok 17 - to_string looks reasonable
ok 18 - There are 8 root InterPro terms
ok 19 - The object isa Bio::Ontology::Ontology
ok 20 - term Integrins alpha chain in ontology InterPro
ok 21 - The object isa Bio::Ontology::Ontology
ok 22 - term post-translational modification in ontology InterPro
ok 23 - The object isa Bio::Ontology::Ontology
ok 24 - term Repeat in ontology InterPro
ok 25 - The object isa Bio::Ontology::Ontology
ok 26 - term Binding Site in ontology InterPro
ok 27 - The object isa Bio::Ontology::Ontology
ok 28 - term Cdc20/Fizzy in ontology InterPro
ok 29 - The object isa Bio::Ontology::Ontology
ok 30 - term Conserved Site in ontology InterPro
ok 31 - The object isa Bio::Ontology::Ontology
ok 32 - term Region in ontology InterPro
ok 33 - The object isa Bio::Ontology::Ontology
ok 34 - term Kringle in ontology InterPro
ok 35 - The object isa Bio::Ontology::Ontology
ok 36 - term Helix-turn-helix, AraC type  in ontology InterPro
ok 37 - The object isa Bio::Ontology::Ontology
ok 38 - term Active Site in ontology InterPro
ok 39 - The object isa Bio::Ontology::Ontology
ok 40 - term Active Site in ontology InterPro
ok 41 - The object isa Bio::Ontology::Ontology
ok 42 - term Binding Site in ontology InterPro
ok 43 - The object isa Bio::Ontology::Ontology
ok 44 - term Conserved Site in ontology InterPro
ok 45 - The object isa Bio::Ontology::Ontology
ok 46 - term Domain in ontology InterPro
ok 47 - The object isa Bio::Ontology::Ontology
ok 48 - term Family in ontology InterPro
ok 49 - The object isa Bio::Ontology::Ontology
ok 50 - term Region in ontology InterPro
ok 51 - The object isa Bio::Ontology::Ontology
ok 52 - term Repeat in ontology InterPro
ok 53 - The object isa Bio::Ontology::Ontology
ok 54 - term post-translational modification in ontology InterPro
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61 - Integrins alpha chain term has one parent
ok 62 - Integrins alpha chain term has one ancestor
ok 63 - Cdc20/Fizzy term has one parent
ok 64 - Cdc20/Fizzy term has one ancestor
ok 65 - Kringle term has one parent
ok 66 - Kringle term has one ancestor
ok 67 - Helix-turn-helix, AraC type  term has one parent
ok 68 - Helix-turn-helix, AraC type  term has one ancestor
ok 69 - secondary accession map has 2 keys
ok
t/Ontology/IO/obo.t .................... 
1..92
ok 1 - use Bio::OntologyIO;
ok 2 - use Bio::Ontology::RelationshipType;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46 - got a ontology IO handler isa Bio::OntologyIO
ok 47 - got ontology parser2 isa Bio::Ontology::Ontology
ok 48 - got OBO engine object isa Bio::Ontology::OBOEngine
ok 49 - got ontology parser2 isa Bio::Ontology::Ontology
ok 50 - got OBO engine object isa Bio::Ontology::OBOEngine
ok 51 - got ontology parser2 isa Bio::Ontology::Ontology
ok 52 - got OBO engine object isa Bio::Ontology::OBOEngine
ok 53 - Gene ontology
ok 54 - biological process
ok 55 - molecular function
ok 56 - Got root
ok 57 - Got root
ok 58 - Got regulates
# 	 from gene_ontology
ok 59 - Got
# 	 positively regulates from gene_ontology
ok 60 - Got
# 	  regulates from biological_process
ok 61 - Got
# 	 positively regulates from biological_process
ok 62 - Got predicates for gene_ontology
ok 63 - Got predicates for biological_process
ok 64 - Got regulates predicate
ok 65 - Got positively regulates predicate
ok 66 - Got relationships for biological_process
ok 67 - Got relationships for molecular_function
ok 68 - Got is a relationship from
# 	 molecular_function
ok 69 - Got term object isa Bio::Ontology::Term
ok 70 - Got term id
ok 71 - Got term name
ok 72 - Got regulated object isa Bio::Ontology::Term
ok 73 - Got regulated term1 id
ok 74 - Got term1 object isa Bio::Ontology::Term
ok 75 - Got back the child
ok 76 - Got term object isa Bio::Ontology::Term
ok 77 - Got term id
ok 78 - Got term name
ok 79 - Got regulated object isa Bio::Ontology::Term
ok 80 - Got regulated term1 id
ok 81 - Got identical regulation
ok 82 - Got term1 object isa Bio::Ontology::Term
ok 83 - Got back the child
ok 84 - got a ontology IO handler isa Bio::OntologyIO
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok
t/Ontology/Ontology.t .................. 
1..55
ok 1 - use Bio::OntologyIO;
ok 2 - use Bio::Ontology::RelationshipType;
ok 3 - The object isa Bio::Ontology::Ontology
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53 - Interpro XML file interpro.xml can be parsed
ok 54 - Interpro XML file interpro_sample.xml can be parsed
ok 55 - Interpro XML file interpro_relationship.xml can be parsed
ok
Subroutine new redefined at Bio\Ontology\Relationship.pm line 139.
Subroutine init redefined at Bio\Ontology\Relationship.pm line 190.
Subroutine identifier redefined at Bio\Ontology\Relationship.pm line 215.
Subroutine subject_term redefined at Bio\Ontology\Relationship.pm line 245.
Subroutine object_term redefined at Bio\Ontology\Relationship.pm line 276.
Subroutine predicate_term redefined at Bio\Ontology\Relationship.pm line 307.
Subroutine ontology redefined at Bio\Ontology\Relationship.pm line 333.
Subroutine to_string redefined at Bio\Ontology\Relationship.pm line 361.
Subroutine _check_class redefined at Bio\Ontology\Relationship.pm line 383.
Subroutine Bio::Ontology::Relationship::child_term redefined at Bio\Ontology\Relationship.pm line 409.
Subroutine Bio::Ontology::Relationship::parent_term redefined at Bio\Ontology\Relationship.pm line 410.
Subroutine Bio::Ontology::Relationship::relationship_type redefined at Bio\Ontology\Relationship.pm line 411.
t/Ontology/OntologyEngine.t ............ 
1..31
ok 1 - use Bio::Ontology::Term;
ok 2 - use Bio::Ontology::Relationship;
ok 3 - use Bio::Ontology::RelationshipType;
ok 4 - use Bio::Ontology::SimpleOntologyEngine;
ok 5 - use Bio::Ontology::Ontology;
ok 6 - The object isa Bio::Ontology::OntologyEngineI
ok 7
ok 8 - adding a relationship with an undef object term fails
ok 9 - adding a relationship with an undef object term fails
ok 10 - adding a relationship with an undef subject term fails
ok 11 - adding a relationship with an undef subject term fails
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok
t/Ontology/OntologyStore.t ............. skipped: Network tests have not been requested
t/Ontology/Relationship.t .............. 
1..12
ok 1 - use Bio::Ontology::Relationship;
ok 2 - use Bio::Ontology::GOterm;
ok 3 - use Bio::Ontology::RelationshipType;
ok 4 - The object isa Bio::Ontology::RelationshipType
ok 5 - The object isa Bio::Ontology::GOterm
ok 6 - The object isa Bio::Ontology::GOterm
ok 7 - The object isa Bio::Ontology::Relationship
ok 8
ok 9
ok 10
ok 11
ok 12
ok
t/Ontology/RelationshipType.t .......... 
1..23
ok 1 - use Bio::Ontology::RelationshipType;
ok 2 - use Bio::Ontology::Ontology;
ok 3 - The object isa Bio::Ontology::RelationshipType
ok 4 - The object isa Bio::Ontology::TermI
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok
Constant subroutine Bio::Ontology::Term::TRUE redefined at C:\cpanfly-5.16\var\megalib/constant.pm line 140.
Constant subroutine Bio::Ontology::Term::FALSE redefined at C:\cpanfly-5.16\var\megalib/constant.pm line 140.
Subroutine new redefined at Bio\Ontology\Term.pm line 145.
Subroutine init redefined at Bio\Ontology\Term.pm line 176.
Subroutine identifier redefined at Bio\Ontology\Term.pm line 207.
Subroutine name redefined at Bio\Ontology\Term.pm line 227.
Subroutine definition redefined at Bio\Ontology\Term.pm line 247.
Subroutine ontology redefined at Bio\Ontology\Term.pm line 275.
Subroutine version redefined at Bio\Ontology\Term.pm line 305.
Subroutine is_obsolete redefined at Bio\Ontology\Term.pm line 324.
Subroutine comment redefined at Bio\Ontology\Term.pm line 344.
Subroutine get_synonyms redefined at Bio\Ontology\Term.pm line 361.
Subroutine add_synonym redefined at Bio\Ontology\Term.pm line 381.
Subroutine remove_synonyms redefined at Bio\Ontology\Term.pm line 405.
Subroutine get_dblinks redefined at Bio\Ontology\Term.pm line 428.
Subroutine get_dbxrefs redefined at Bio\Ontology\Term.pm line 454.
Subroutine get_dblink_context redefined at Bio\Ontology\Term.pm line 479.
Subroutine get_dbxref_context redefined at Bio\Ontology\Term.pm line 495.
Subroutine add_dblink redefined at Bio\Ontology\Term.pm line 515.
Subroutine add_dbxref redefined at Bio\Ontology\Term.pm line 542.
Subroutine has_dblink redefined at Bio\Ontology\Term.pm line 581.
Subroutine has_dbxref redefined at Bio\Ontology\Term.pm line 599.
Subroutine add_dblink_context redefined at Bio\Ontology\Term.pm line 630.
Subroutine remove_dblinks redefined at Bio\Ontology\Term.pm line 651.
Subroutine remove_dbxrefs redefined at Bio\Ontology\Term.pm line 668.
Subroutine get_references redefined at Bio\Ontology\Term.pm line 690.
Subroutine add_reference redefined at Bio\Ontology\Term.pm line 706.
Subroutine remove_references redefined at Bio\Ontology\Term.pm line 729.
Subroutine get_secondary_ids redefined at Bio\Ontology\Term.pm line 750.
Subroutine add_secondary_id redefined at Bio\Ontology\Term.pm line 770.
Subroutine remove_secondary_ids redefined at Bio\Ontology\Term.pm line 794.
Subroutine _is_true_or_false redefined at Bio\Ontology\Term.pm line 808.
Subroutine object_id redefined at Bio\Ontology\Term.pm line 833.
Subroutine authority redefined at Bio\Ontology\Term.pm line 854.
Subroutine namespace redefined at Bio\Ontology\Term.pm line 883.
Subroutine display_name redefined at Bio\Ontology\Term.pm line 907.
Subroutine description redefined at Bio\Ontology\Term.pm line 931.
Subroutine each_dblink redefined at Bio\Ontology\Term.pm line 945.
Subroutine add_dblinks redefined at Bio\Ontology\Term.pm line 946.
Subroutine Bio::Ontology::Term::add_dbxrefs redefined at Bio\Ontology\Term.pm line 566.
Subroutine Bio::Ontology::Term::each_synonym redefined at Bio\Ontology\Term.pm line 947.
Subroutine Bio::Ontology::Term::add_synonyms redefined at Bio\Ontology\Term.pm line 948.
t/Ontology/Term.t ...................... 
1..54
ok 1 - use Bio::Ontology::Term;
ok 2 - use Bio::Ontology::TermFactory;
ok 3 - use Bio::Annotation::DBLink;
ok 4 - The object isa Bio::Ontology::TermI
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44 - The object isa Bio::Ontology::TermI
ok 45
ok 46 - The object isa Bio::Ontology::TermI
ok 47 - The object isa Bio::Ontology::GOterm
ok 48
ok 49
ok 50 - The object isa Bio::Ontology::TermI
ok 51 - The object isa Bio::AnnotationI
ok 52
ok 53
ok 54
ok
t/Perl.t ............................... 
1..31
ok 1 - use Bio::Perl;
ok 2
ok 3 - The object isa Bio::SeqI
ok 4
ok 5 - The object isa Bio::SeqI
ok 6
ok 7 - The object isa Bio::SeqI
ok 8 - The object isa Bio::SeqI
ok 9
ok 10
ok 11 - The object isa Bio::SeqI
ok 12
ok 13 - The object isa Bio::SeqI
ok 14
ok 15 - The object isa Bio::PrimarySeqI
ok 16
ok 17
ok 18
ok 19
ok 20 # skip Network tests have not been requested
ok 21 # skip Network tests have not been requested
ok 22 # skip Network tests have not been requested
ok 23 # skip Network tests have not been requested
ok 24 # skip Network tests have not been requested
ok 25 # skip Network tests have not been requested
ok 26 # skip Network tests have not been requested
ok 27 # skip Network tests have not been requested
ok 28 # skip Network tests have not been requested
ok 29 # skip Network tests have not been requested
ok 30 # skip Network tests have not been requested
ok 31 # skip Network tests have not been requested
ok
t/Phenotype/Correlate.t ................ 
1..17
ok 1 - use Bio::Phenotype::Correlate;
ok 2 - use Bio::Species;
ok 3 - The object isa Bio::Phenotype::Correlate
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok
t/Phenotype/MeSH.t ..................... 
1..24
ok 1 - use Bio::Phenotype::MeSH::Term;
ok 2 - use Bio::Phenotype::MeSH::Twig;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok
t/Phenotype/Measure.t .................. 
1..21
ok 1 - use Bio::Phenotype::Measure;
ok 2 - The object isa Bio::Phenotype::Measure
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok
t/Phenotype/MiniMIMentry.t ............. 
1..15
ok 1 - use Bio::Phenotype::OMIM::MiniMIMentry;
ok 2 - The object isa Bio::Phenotype::OMIM::MiniMIMentry
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok
t/Phenotype/OMIMentry.t ................ 
1..153
ok 1 - use Bio::Phenotype::OMIM::OMIMentry;
ok 2 - use Bio::Phenotype::OMIM::MiniMIMentry;
ok 3 - use Bio::Species;
ok 4 - use Bio::Annotation::Reference;
ok 5 - use Bio::Map::CytoPosition;
ok 6 - use Bio::Phenotype::Correlate;
ok 7 - use Bio::Phenotype::Measure;
ok 8 - use Bio::Annotation::DBLink;
ok 9 - The object isa Bio::Phenotype::OMIM::OMIMentry
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79 - operator overloading in AnnotationI is deprecated
ok 80 - operator overloading in AnnotationI is deprecated
ok 81
ok 82
ok 83 - operator overloading in AnnotationI is deprecated
ok 84 - operator overloading in AnnotationI is deprecated
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136 - operator overloading in AnnotationI is deprecated
ok 137 - operator overloading in AnnotationI is deprecated
ok 138
ok 139
ok 140 - operator overloading in AnnotationI is deprecated
ok 141 - operator overloading in AnnotationI is deprecated
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok
t/Phenotype/OMIMentryAllelicVariant.t .. 
1..27
ok 1 - use Bio::Phenotype::OMIM::OMIMentryAllelicVariant;
ok 2 - The object isa Bio::Phenotype::OMIM::OMIMentryAllelicVariant
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok
t/Phenotype/OMIMparser.t ............... 
1..175
ok 1 - use Bio::Phenotype::OMIM::OMIMparser;
ok 2 - The object isa Bio::Phenotype::OMIM::OMIMparser
ok 3 - The object isa Bio::Phenotype::OMIM::OMIMentry
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19 - The object isa Bio::Phenotype::OMIM::MiniMIMentry
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
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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
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ok 42 - operator overloading in AnnotationI is deprecated
ok 43 - operator overloading in AnnotationI is deprecated
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ok 46 - operator overloading in AnnotationI is deprecated
ok 47 - operator overloading in AnnotationI is deprecated
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ok 99 - operator overloading in AnnotationI is deprecated
ok 100 - operator overloading in AnnotationI is deprecated
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ok 103 - operator overloading in AnnotationI is deprecated
ok 104 - operator overloading in AnnotationI is deprecated
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t/PodSyntax.t .......................... 
1..953
ok 1 - POD test for Bio/AlignIO.pm
ok 2 - POD test for Bio/AnalysisI.pm
ok 3 - POD test for Bio/AnalysisParserI.pm
ok 4 - POD test for Bio/AnalysisResultI.pm
ok 5 - POD test for Bio/AnnotatableI.pm
ok 6 - POD test for Bio/AnnotationCollectionI.pm
ok 7 - POD test for Bio/AnnotationI.pm
ok 8 - POD test for Bio/ClusterI.pm
ok 9 - POD test for Bio/ClusterIO.pm
ok 10 - POD test for Bio/DasI.pm
ok 11 - POD test for Bio/DBLinkContainerI.pm
ok 12 - POD test for Bio/DescribableI.pm
ok 13 - POD test for Bio/FeatureHolderI.pm
ok 14 - POD test for Bio/HandlerBaseI.pm
ok 15 - POD test for Bio/IdCollectionI.pm
ok 16 - POD test for Bio/IdentifiableI.pm
ok 17 - POD test for Bio/LocatableSeq.pm
ok 18 - POD test for Bio/LocationI.pm
ok 19 - POD test for Bio/MapIO.pm
ok 20 - POD test for Bio/NexmlIO.pm
ok 21 - POD test for Bio/OntologyIO.pm
ok 22 - POD test for Bio/ParameterBaseI.pm
ok 23 - POD test for Bio/Perl.pm
ok 24 - POD test for Bio/PhyloNetwork.pm
ok 25 - POD test for Bio/PrimarySeq.pm
ok 26 - POD test for Bio/PrimarySeqI.pm
ok 27 - POD test for Bio/PullParserI.pm
ok 28 - POD test for Bio/Range.pm
ok 29 - POD test for Bio/RangeI.pm
ok 30 - POD test for Bio/SearchDist.pm
ok 31 - POD test for Bio/SearchIO.pm
ok 32 - POD test for Bio/Seq.pm
ok 33 - POD test for Bio/SeqAnalysisParserI.pm
ok 34 - POD test for Bio/SeqFeatureI.pm
ok 35 - POD test for Bio/SeqI.pm
ok 36 - POD test for Bio/SeqIO.pm
ok 37 - POD test for Bio/SeqUtils.pm
ok 38 - POD test for Bio/SimpleAlign.pm
ok 39 - POD test for Bio/SimpleAnalysisI.pm
ok 40 - POD test for Bio/Species.pm
ok 41 - POD test for Bio/Taxon.pm
ok 42 - POD test for Bio/Taxonomy.pm
ok 43 - POD test for Bio/TreeIO.pm
ok 44 - POD test for Bio/UpdateableSeqI.pm
ok 45 - POD test for Bio/WebAgent.pm
ok 46 - POD test for Bio/Align/AlignI.pm
ok 47 - POD test for Bio/Align/DNAStatistics.pm
ok 48 - POD test for Bio/Align/Graphics.pm
ok 49 - POD test for Bio/Align/PairwiseStatistics.pm
ok 50 - POD test for Bio/Align/ProteinStatistics.pm
ok 51 - POD test for Bio/Align/StatisticsI.pm
ok 52 - POD test for Bio/Align/Utilities.pm
ok 53 - POD test for Bio/AlignIO/arp.pm
ok 54 - POD test for Bio/AlignIO/bl2seq.pm
ok 55 - POD test for Bio/AlignIO/clustalw.pm
ok 56 - POD test for Bio/AlignIO/emboss.pm
ok 57 - POD test for Bio/AlignIO/fasta.pm
ok 58 - POD test for Bio/AlignIO/largemultifasta.pm
ok 59 - POD test for Bio/AlignIO/maf.pm
ok 60 - POD test for Bio/AlignIO/mase.pm
ok 61 - POD test for Bio/AlignIO/mega.pm
ok 62 - POD test for Bio/AlignIO/meme.pm
ok 63 - POD test for Bio/AlignIO/metafasta.pm
ok 64 - POD test for Bio/AlignIO/msf.pm
ok 65 - POD test for Bio/AlignIO/nexml.pm
ok 66 - POD test for Bio/AlignIO/nexus.pm
ok 67 - POD test for Bio/AlignIO/pfam.pm
ok 68 - POD test for Bio/AlignIO/phylip.pm
ok 69 - POD test for Bio/AlignIO/po.pm
ok 70 - POD test for Bio/AlignIO/proda.pm
ok 71 - POD test for Bio/AlignIO/prodom.pm
ok 72 - POD test for Bio/AlignIO/psi.pm
ok 73 - POD test for Bio/AlignIO/selex.pm
ok 74 - POD test for Bio/AlignIO/stockholm.pm
ok 75 - POD test for Bio/AlignIO/xmfa.pm
ok 76 - POD test for Bio/AlignIO/Handler/GenericAlignHandler.pm
ok 77 - POD test for Bio/Annotation/AnnotationFactory.pm
ok 78 - POD test for Bio/Annotation/Collection.pm
ok 79 - POD test for Bio/Annotation/Comment.pm
ok 80 - POD test for Bio/Annotation/DBLink.pm
ok 81 - POD test for Bio/Annotation/OntologyTerm.pm
ok 82 - POD test for Bio/Annotation/Reference.pm
ok 83 - POD test for Bio/Annotation/Relation.pm
ok 84 - POD test for Bio/Annotation/SimpleValue.pm
ok 85 - POD test for Bio/Annotation/StructuredValue.pm
ok 86 - POD test for Bio/Annotation/TagTree.pm
ok 87 - POD test for Bio/Annotation/Target.pm
ok 88 - POD test for Bio/Annotation/Tree.pm
ok 89 - POD test for Bio/Annotation/TypeManager.pm
ok 90 - POD test for Bio/Assembly/Contig.pm
ok 91 - POD test for Bio/Assembly/ContigAnalysis.pm
ok 92 - POD test for Bio/Assembly/IO.pm
ok 93 - POD test for Bio/Assembly/Scaffold.pm
ok 94 - POD test for Bio/Assembly/ScaffoldI.pm
ok 95 - POD test for Bio/Assembly/Singlet.pm
ok 96 - POD test for Bio/Assembly/IO/ace.pm
ok 97 - POD test for Bio/Assembly/IO/bowtie.pm
ok 98 - POD test for Bio/Assembly/IO/maq.pm
ok 99 - POD test for Bio/Assembly/IO/phrap.pm
ok 100 - POD test for Bio/Assembly/IO/sam.pm
ok 101 - POD test for Bio/Assembly/IO/tigr.pm
ok 102 - POD test for Bio/Assembly/Tools/ContigSpectrum.pm
ok 103 - POD test for Bio/Cluster/ClusterFactory.pm
ok 104 - POD test for Bio/Cluster/FamilyI.pm
ok 105 - POD test for Bio/Cluster/SequenceFamily.pm
ok 106 - POD test for Bio/Cluster/UniGene.pm
ok 107 - POD test for Bio/Cluster/UniGeneI.pm
ok 108 - POD test for Bio/ClusterIO/dbsnp.pm
ok 109 - POD test for Bio/ClusterIO/unigene.pm
ok 110 - POD test for Bio/CodonUsage/IO.pm
ok 111 - POD test for Bio/CodonUsage/Table.pm
ok 112 - POD test for Bio/Coordinate/Chain.pm
ok 113 - POD test for Bio/Coordinate/Collection.pm
ok 114 - POD test for Bio/Coordinate/ExtrapolatingPair.pm
ok 115 - POD test for Bio/Coordinate/GeneMapper.pm
ok 116 - POD test for Bio/Coordinate/Graph.pm
ok 117 - POD test for Bio/Coordinate/MapperI.pm
ok 118 - POD test for Bio/Coordinate/Pair.pm
ok 119 - POD test for Bio/Coordinate/Result.pm
ok 120 - POD test for Bio/Coordinate/ResultI.pm
ok 121 - POD test for Bio/Coordinate/Utils.pm
ok 122 - POD test for Bio/Coordinate/Result/Gap.pm
ok 123 - POD test for Bio/Coordinate/Result/Match.pm
ok 124 - POD test for Bio/Das/FeatureTypeI.pm
ok 125 - POD test for Bio/Das/SegmentI.pm
ok 126 - POD test for Bio/DB/Ace.pm
ok 127 - POD test for Bio/DB/BioFetch.pm
ok 128 - POD test for Bio/DB/CUTG.pm
ok 129 - POD test for Bio/DB/DBFetch.pm
ok 130 - POD test for Bio/DB/EMBL.pm
ok 131 - POD test for Bio/DB/EntrezGene.pm
ok 132 - POD test for Bio/DB/Expression.pm
ok 133 - POD test for Bio/DB/Failover.pm
ok 134 - POD test for Bio/DB/Fasta.pm
ok 135 - POD test for Bio/DB/FileCache.pm
ok 136 - POD test for Bio/DB/Flat.pm
ok 137 - POD test for Bio/DB/GenBank.pm
ok 138 - POD test for Bio/DB/GenericWebAgent.pm
ok 139 - POD test for Bio/DB/GenPept.pm
ok 140 - POD test for Bio/DB/GFF.pm
ok 141 - POD test for Bio/DB/HIV.pm
ok 142 - POD test for Bio/DB/IndexedBase.pm
ok 143 - POD test for Bio/DB/InMemoryCache.pm
ok 144 - POD test for Bio/DB/LocationI.pm
ok 145 - POD test for Bio/DB/MeSH.pm
ok 146 - POD test for Bio/DB/NCBIHelper.pm
ok 147 - POD test for Bio/DB/Qual.pm
ok 148 - POD test for Bio/DB/QueryI.pm
ok 149 - POD test for Bio/DB/RandomAccessI.pm
ok 150 - POD test for Bio/DB/ReferenceI.pm
ok 151 - POD test for Bio/DB/RefSeq.pm
ok 152 - POD test for Bio/DB/Registry.pm
ok 153 - POD test for Bio/DB/SeqFeature.pm
ok 154 - POD test for Bio/DB/SeqHound.pm
ok 155 - POD test for Bio/DB/SeqI.pm
ok 156 - POD test for Bio/DB/SeqVersion.pm
ok 157 - POD test for Bio/DB/SwissProt.pm
ok 158 - POD test for Bio/DB/Taxonomy.pm
ok 159 - POD test for Bio/DB/TFBS.pm
ok 160 - POD test for Bio/DB/Universal.pm
ok 161 - POD test for Bio/DB/UpdateableSeqI.pm
ok 162 - POD test for Bio/DB/WebDBSeqI.pm
ok 163 - POD test for Bio/DB/Expression/geo.pm
ok 164 - POD test for Bio/DB/Flat/BDB.pm
ok 165 - POD test for Bio/DB/Flat/BinarySearch.pm
ok 166 - POD test for Bio/DB/Flat/BDB/embl.pm
ok 167 - POD test for Bio/DB/Flat/BDB/fasta.pm
ok 168 - POD test for Bio/DB/Flat/BDB/genbank.pm
ok 169 - POD test for Bio/DB/Flat/BDB/swiss.pm
ok 170 - POD test for Bio/DB/GFF/Aggregator.pm
ok 171 - POD test for Bio/DB/GFF/Featname.pm
ok 172 - POD test for Bio/DB/GFF/Feature.pm
ok 173 - POD test for Bio/DB/GFF/Homol.pm
ok 174 - POD test for Bio/DB/GFF/RelSegment.pm
ok 175 - POD test for Bio/DB/GFF/Segment.pm
ok 176 - POD test for Bio/DB/GFF/Typename.pm
ok 177 - POD test for Bio/DB/GFF/Adaptor/ace.pm
ok 178 - POD test for Bio/DB/GFF/Adaptor/berkeleydb.pm
ok 179 - POD test for Bio/DB/GFF/Adaptor/biofetch.pm
ok 180 - POD test for Bio/DB/GFF/Adaptor/biofetch_oracle.pm
ok 181 - POD test for Bio/DB/GFF/Adaptor/dbi.pm
ok 182 - POD test for Bio/DB/GFF/Adaptor/memory.pm
ok 183 - POD test for Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
ok 184 - POD test for Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
ok 185 - POD test for Bio/DB/GFF/Adaptor/dbi/iterator.pm
ok 186 - POD test for Bio/DB/GFF/Adaptor/dbi/mysql.pm
ok 187 - POD test for Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
ok 188 - POD test for Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm
ok 189 - POD test for Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm
ok 190 - POD test for Bio/DB/GFF/Adaptor/dbi/oracle.pm
ok 191 - POD test for Bio/DB/GFF/Adaptor/dbi/oracleace.pm
ok 192 - POD test for Bio/DB/GFF/Adaptor/dbi/pg.pm
ok 193 - POD test for Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
ok 194 - POD test for Bio/DB/GFF/Adaptor/memory/feature_serializer.pm
ok 195 - POD test for Bio/DB/GFF/Adaptor/memory/iterator.pm
ok 196 - POD test for Bio/DB/GFF/Aggregator/alignment.pm
ok 197 - POD test for Bio/DB/GFF/Aggregator/clone.pm
ok 198 - POD test for Bio/DB/GFF/Aggregator/coding.pm
ok 199 - POD test for Bio/DB/GFF/Aggregator/gene.pm
ok 200 - POD test for Bio/DB/GFF/Aggregator/match.pm
ok 201 - POD test for Bio/DB/GFF/Aggregator/none.pm
ok 202 - POD test for Bio/DB/GFF/Aggregator/orf.pm
ok 203 - POD test for Bio/DB/GFF/Aggregator/processed_transcript.pm
ok 204 - POD test for Bio/DB/GFF/Aggregator/so_transcript.pm
ok 205 - POD test for Bio/DB/GFF/Aggregator/transcript.pm
ok 206 - POD test for Bio/DB/GFF/Aggregator/ucsc_acembly.pm
ok 207 - POD test for Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
ok 208 - POD test for Bio/DB/GFF/Aggregator/ucsc_genscan.pm
ok 209 - POD test for Bio/DB/GFF/Aggregator/ucsc_refgene.pm
ok 210 - POD test for Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
ok 211 - POD test for Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm
ok 212 - POD test for Bio/DB/GFF/Aggregator/ucsc_softberry.pm
ok 213 - POD test for Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
ok 214 - POD test for Bio/DB/GFF/Aggregator/ucsc_unigene.pm
ok 215 - POD test for Bio/DB/GFF/Util/Binning.pm
ok 216 - POD test for Bio/DB/GFF/Util/Rearrange.pm
ok 217 - POD test for Bio/DB/HIV/HIVAnnotProcessor.pm
ok 218 - POD test for Bio/DB/HIV/HIVQueryHelper.pm
ok 219 - POD test for Bio/DB/Query/GenBank.pm
ok 220 - POD test for Bio/DB/Query/HIVQuery.pm
ok 221 - POD test for Bio/DB/Query/WebQuery.pm
ok 222 - POD test for Bio/DB/SeqFeature/NormalizedFeature.pm
ok 223 - POD test for Bio/DB/SeqFeature/NormalizedFeatureI.pm
ok 224 - POD test for Bio/DB/SeqFeature/NormalizedTableFeatureI.pm
ok 225 - POD test for Bio/DB/SeqFeature/Segment.pm
ok 226 - POD test for Bio/DB/SeqFeature/Store.pm
ok 227 - POD test for Bio/DB/SeqFeature/Store/bdb.pm
ok 228 - POD test for Bio/DB/SeqFeature/Store/berkeleydb.pm
ok 229 - POD test for Bio/DB/SeqFeature/Store/berkeleydb3.pm
ok 230 - POD test for Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
ok 231 - POD test for Bio/DB/SeqFeature/Store/GFF2Loader.pm
ok 232 - POD test for Bio/DB/SeqFeature/Store/GFF3Loader.pm
ok 233 - POD test for Bio/DB/SeqFeature/Store/Loader.pm
ok 234 - POD test for Bio/DB/SeqFeature/Store/LoadHelper.pm
ok 235 - POD test for Bio/DB/SeqFeature/Store/memory.pm
ok 236 - POD test for Bio/DB/SeqFeature/Store/DBI/Iterator.pm
ok 237 - POD test for Bio/DB/SeqFeature/Store/DBI/mysql.pm
ok 238 - POD test for Bio/DB/SeqFeature/Store/DBI/Pg.pm
ok 239 - POD test for Bio/DB/SeqFeature/Store/DBI/SQLite.pm
ok 240 - POD test for Bio/DB/SeqVersion/gi.pm
ok 241 - POD test for Bio/DB/Taxonomy/entrez.pm
ok 242 - POD test for Bio/DB/Taxonomy/flatfile.pm
ok 243 - POD test for Bio/DB/Taxonomy/greengenes.pm
ok 244 - POD test for Bio/DB/Taxonomy/list.pm
ok 245 - POD test for Bio/DB/Taxonomy/silva.pm
ok 246 - POD test for Bio/DB/TFBS/transfac_pro.pm
ok 247 - POD test for Bio/Draw/Pictogram.pm
ok 248 - POD test for Bio/Event/EventGeneratorI.pm
ok 249 - POD test for Bio/Event/EventHandlerI.pm
ok 250 - POD test for Bio/Factory/AnalysisI.pm
ok 251 - POD test for Bio/Factory/ApplicationFactoryI.pm
ok 252 - POD test for Bio/Factory/DriverFactory.pm
ok 253 - POD test for Bio/Factory/FTLocationFactory.pm
ok 254 - POD test for Bio/Factory/LocationFactoryI.pm
ok 255 - POD test for Bio/Factory/MapFactoryI.pm
ok 256 - POD test for Bio/Factory/ObjectBuilderI.pm
ok 257 - POD test for Bio/Factory/ObjectFactory.pm
ok 258 - POD test for Bio/Factory/ObjectFactoryI.pm
ok 259 - POD test for Bio/Factory/SeqAnalysisParserFactory.pm
ok 260 - POD test for Bio/Factory/SeqAnalysisParserFactoryI.pm
ok 261 - POD test for Bio/Factory/SequenceFactoryI.pm
ok 262 - POD test for Bio/Factory/SequenceProcessorI.pm
ok 263 - POD test for Bio/Factory/SequenceStreamI.pm
ok 264 - POD test for Bio/Factory/TreeFactoryI.pm
ok 265 - POD test for Bio/Index/Abstract.pm
ok 266 - POD test for Bio/Index/AbstractSeq.pm
ok 267 - POD test for Bio/Index/Blast.pm
ok 268 - POD test for Bio/Index/BlastTable.pm
ok 269 - POD test for Bio/Index/EMBL.pm
ok 270 - POD test for Bio/Index/Fasta.pm
ok 271 - POD test for Bio/Index/Fastq.pm
ok 272 - POD test for Bio/Index/GenBank.pm
ok 273 - POD test for Bio/Index/Hmmer.pm
ok 274 - POD test for Bio/Index/Qual.pm
ok 275 - POD test for Bio/Index/Stockholm.pm
ok 276 - POD test for Bio/Index/SwissPfam.pm
ok 277 - POD test for Bio/Index/Swissprot.pm
ok 278 - POD test for Bio/LiveSeq/AARange.pm
ok 279 - POD test for Bio/LiveSeq/Chain.pm
ok 280 - POD test for Bio/LiveSeq/ChainI.pm
ok 281 - POD test for Bio/LiveSeq/DNA.pm
ok 282 - POD test for Bio/LiveSeq/Exon.pm
ok 283 - POD test for Bio/LiveSeq/Gene.pm
ok 284 - POD test for Bio/LiveSeq/Intron.pm
ok 285 - POD test for Bio/LiveSeq/Mutation.pm
ok 286 - POD test for Bio/LiveSeq/Mutator.pm
ok 287 - POD test for Bio/LiveSeq/Prim_Transcript.pm
ok 288 - POD test for Bio/LiveSeq/Range.pm
ok 289 - POD test for Bio/LiveSeq/Repeat_Region.pm
ok 290 - POD test for Bio/LiveSeq/Repeat_Unit.pm
ok 291 - POD test for Bio/LiveSeq/SeqI.pm
ok 292 - POD test for Bio/LiveSeq/Transcript.pm
ok 293 - POD test for Bio/LiveSeq/Translation.pm
ok 294 - POD test for Bio/LiveSeq/IO/BioPerl.pm
ok 295 - POD test for Bio/LiveSeq/IO/Loader.pm
ok 296 - POD test for Bio/Location/Atomic.pm
ok 297 - POD test for Bio/Location/AvWithinCoordPolicy.pm
ok 298 - POD test for Bio/Location/CoordinatePolicyI.pm
ok 299 - POD test for Bio/Location/Fuzzy.pm
ok 300 - POD test for Bio/Location/FuzzyLocationI.pm
ok 301 - POD test for Bio/Location/NarrowestCoordPolicy.pm
ok 302 - POD test for Bio/Location/Simple.pm
ok 303 - POD test for Bio/Location/Split.pm
ok 304 - POD test for Bio/Location/SplitLocationI.pm
ok 305 - POD test for Bio/Location/WidestCoordPolicy.pm
ok 306 - POD test for Bio/Map/Clone.pm
ok 307 - POD test for Bio/Map/Contig.pm
ok 308 - POD test for Bio/Map/CytoMap.pm
ok 309 - POD test for Bio/Map/CytoMarker.pm
ok 310 - POD test for Bio/Map/CytoPosition.pm
ok 311 - POD test for Bio/Map/EntityI.pm
ok 312 - POD test for Bio/Map/FPCMarker.pm
ok 313 - POD test for Bio/Map/Gene.pm
ok 314 - POD test for Bio/Map/GeneMap.pm
ok 315 - POD test for Bio/Map/GenePosition.pm
ok 316 - POD test for Bio/Map/GeneRelative.pm
ok 317 - POD test for Bio/Map/LinkageMap.pm
ok 318 - POD test for Bio/Map/LinkagePosition.pm
ok 319 - POD test for Bio/Map/MapI.pm
ok 320 - POD test for Bio/Map/Mappable.pm
ok 321 - POD test for Bio/Map/MappableI.pm
ok 322 - POD test for Bio/Map/Marker.pm
ok 323 - POD test for Bio/Map/MarkerI.pm
ok 324 - POD test for Bio/Map/Microsatellite.pm
ok 325 - POD test for Bio/Map/OrderedPosition.pm
ok 326 - POD test for Bio/Map/OrderedPositionWithDistance.pm
ok 327 - POD test for Bio/Map/Physical.pm
ok 328 - POD test for Bio/Map/Position.pm
ok 329 - POD test for Bio/Map/PositionHandler.pm
ok 330 - POD test for Bio/Map/PositionHandlerI.pm
ok 331 - POD test for Bio/Map/PositionI.pm
ok 332 - POD test for Bio/Map/PositionWithSequence.pm
ok 333 - POD test for Bio/Map/Prediction.pm
ok 334 - POD test for Bio/Map/Relative.pm
ok 335 - POD test for Bio/Map/RelativeI.pm
ok 336 - POD test for Bio/Map/SimpleMap.pm
ok 337 - POD test for Bio/Map/TranscriptionFactor.pm
ok 338 - POD test for Bio/MapIO/fpc.pm
ok 339 - POD test for Bio/MapIO/mapmaker.pm
ok 340 - POD test for Bio/Matrix/Generic.pm
ok 341 - POD test for Bio/Matrix/IO.pm
ok 342 - POD test for Bio/Matrix/MatrixI.pm
ok 343 - POD test for Bio/Matrix/Mlagan.pm
ok 344 - POD test for Bio/Matrix/PhylipDist.pm
ok 345 - POD test for Bio/Matrix/Scoring.pm
ok 346 - POD test for Bio/Matrix/IO/mlagan.pm
ok 347 - POD test for Bio/Matrix/IO/phylip.pm
ok 348 - POD test for Bio/Matrix/IO/scoring.pm
ok 349 - POD test for Bio/Matrix/PSM/InstanceSite.pm
ok 350 - POD test for Bio/Matrix/PSM/InstanceSiteI.pm
ok 351 - POD test for Bio/Matrix/PSM/IO.pm
ok 352 - POD test for Bio/Matrix/PSM/ProtMatrix.pm
ok 353 - POD test for Bio/Matrix/PSM/ProtPsm.pm
ok 354 - POD test for Bio/Matrix/PSM/Psm.pm
ok 355 - POD test for Bio/Matrix/PSM/PsmHeader.pm
ok 356 - POD test for Bio/Matrix/PSM/PsmHeaderI.pm
ok 357 - POD test for Bio/Matrix/PSM/PsmI.pm
ok 358 - POD test for Bio/Matrix/PSM/SiteMatrix.pm
ok 359 - POD test for Bio/Matrix/PSM/SiteMatrixI.pm
ok 360 - POD test for Bio/Matrix/PSM/IO/mast.pm
ok 361 - POD test for Bio/Matrix/PSM/IO/masta.pm
ok 362 - POD test for Bio/Matrix/PSM/IO/meme.pm
ok 363 - POD test for Bio/Matrix/PSM/IO/psiblast.pm
ok 364 - POD test for Bio/Matrix/PSM/IO/transfac.pm
ok 365 - POD test for Bio/MolEvol/CodonModel.pm
ok 366 - POD test for Bio/Nexml/Factory.pm
ok 367 - POD test for Bio/Ontology/DocumentRegistry.pm
ok 368 - POD test for Bio/Ontology/GOterm.pm
ok 369 - POD test for Bio/Ontology/InterProTerm.pm
ok 370 - POD test for Bio/Ontology/OBOEngine.pm
ok 371 - POD test for Bio/Ontology/OBOterm.pm
ok 372 - POD test for Bio/Ontology/Ontology.pm
ok 373 - POD test for Bio/Ontology/OntologyEngineI.pm
ok 374 - POD test for Bio/Ontology/OntologyI.pm
ok 375 - POD test for Bio/Ontology/OntologyStore.pm
ok 376 - POD test for Bio/Ontology/Path.pm
ok 377 - POD test for Bio/Ontology/PathI.pm
ok 378 - POD test for Bio/Ontology/Relationship.pm
ok 379 - POD test for Bio/Ontology/RelationshipFactory.pm
ok 380 - POD test for Bio/Ontology/RelationshipI.pm
ok 381 - POD test for Bio/Ontology/RelationshipType.pm
ok 382 - POD test for Bio/Ontology/SimpleOntologyEngine.pm
ok 383 - POD test for Bio/Ontology/Term.pm
ok 384 - POD test for Bio/Ontology/TermFactory.pm
ok 385 - POD test for Bio/Ontology/TermI.pm
ok 386 - POD test for Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm
ok 387 - POD test for Bio/OntologyIO/dagflat.pm
ok 388 - POD test for Bio/OntologyIO/goflat.pm
ok 389 - POD test for Bio/OntologyIO/InterProParser.pm
ok 390 - POD test for Bio/OntologyIO/obo.pm
ok 391 - POD test for Bio/OntologyIO/simplehierarchy.pm
ok 392 - POD test for Bio/OntologyIO/soflat.pm
ok 393 - POD test for Bio/OntologyIO/Handlers/BaseSAXHandler.pm
ok 394 - POD test for Bio/OntologyIO/Handlers/InterProHandler.pm
ok 395 - POD test for Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
ok 396 - POD test for Bio/Phenotype/Correlate.pm
ok 397 - POD test for Bio/Phenotype/Measure.pm
ok 398 - POD test for Bio/Phenotype/Phenotype.pm
ok 399 - POD test for Bio/Phenotype/PhenotypeI.pm
ok 400 - POD test for Bio/Phenotype/MeSH/Term.pm
ok 401 - POD test for Bio/Phenotype/MeSH/Twig.pm
ok 402 - POD test for Bio/Phenotype/OMIM/MiniMIMentry.pm
ok 403 - POD test for Bio/Phenotype/OMIM/OMIMentry.pm
ok 404 - POD test for Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm
ok 405 - POD test for Bio/Phenotype/OMIM/OMIMparser.pm
ok 406 - POD test for Bio/PhyloNetwork/Factory.pm
ok 407 - POD test for Bio/PhyloNetwork/FactoryX.pm
ok 408 - POD test for Bio/PhyloNetwork/GraphViz.pm
ok 409 - POD test for Bio/PhyloNetwork/muVector.pm
ok 410 - POD test for Bio/PhyloNetwork/RandomFactory.pm
ok 411 - POD test for Bio/PhyloNetwork/TreeFactory.pm
ok 412 - POD test for Bio/PhyloNetwork/TreeFactoryMulti.pm
ok 413 - POD test for Bio/PhyloNetwork/TreeFactoryX.pm
ok 414 - POD test for Bio/PopGen/Genotype.pm
ok 415 - POD test for Bio/PopGen/GenotypeI.pm
ok 416 - POD test for Bio/PopGen/HtSNP.pm
ok 417 - POD test for Bio/PopGen/Individual.pm
ok 418 - POD test for Bio/PopGen/IndividualI.pm
ok 419 - POD test for Bio/PopGen/IO.pm
ok 420 - POD test for Bio/PopGen/Marker.pm
ok 421 - POD test for Bio/PopGen/MarkerI.pm
ok 422 - POD test for Bio/PopGen/PopStats.pm
ok 423 - POD test for Bio/PopGen/Population.pm
ok 424 - POD test for Bio/PopGen/PopulationI.pm
ok 425 - POD test for Bio/PopGen/Statistics.pm
ok 426 - POD test for Bio/PopGen/TagHaplotype.pm
ok 427 - POD test for Bio/PopGen/Utilities.pm
ok 428 - POD test for Bio/PopGen/IO/csv.pm
ok 429 - POD test for Bio/PopGen/IO/hapmap.pm
ok 430 - POD test for Bio/PopGen/IO/phase.pm
ok 431 - POD test for Bio/PopGen/IO/prettybase.pm
ok 432 - POD test for Bio/PopGen/Simulation/Coalescent.pm
ok 433 - POD test for Bio/PopGen/Simulation/GeneticDrift.pm
ok 434 - POD test for Bio/Restriction/Analysis.pm
ok 435 - POD test for Bio/Restriction/Enzyme.pm
ok 436 - POD test for Bio/Restriction/EnzymeCollection.pm
ok 437 - POD test for Bio/Restriction/EnzymeI.pm
ok 438 - POD test for Bio/Restriction/IO.pm
ok 439 - POD test for Bio/Restriction/Enzyme/MultiCut.pm
ok 440 - POD test for Bio/Restriction/Enzyme/MultiSite.pm
ok 441 - POD test for Bio/Restriction/IO/bairoch.pm
ok 442 - POD test for Bio/Restriction/IO/base.pm
ok 443 - POD test for Bio/Restriction/IO/itype2.pm
ok 444 - POD test for Bio/Restriction/IO/prototype.pm
ok 445 - POD test for Bio/Restriction/IO/withrefm.pm
ok 446 - POD test for Bio/Root/Build.pm
ok 447 - POD test for Bio/Root/Exception.pm
ok 448 - POD test for Bio/Root/HTTPget.pm
ok 449 - POD test for Bio/Root/IO.pm
ok 450 - POD test for Bio/Root/Root.pm
ok 451 - POD test for Bio/Root/RootI.pm
ok 452 - POD test for Bio/Root/Storable.pm
ok 453 - POD test for Bio/Root/Test.pm
ok 454 - POD test for Bio/Root/Utilities.pm
ok 455 - POD test for Bio/Root/Version.pm
ok 456 - POD test for Bio/Search/BlastStatistics.pm
ok 457 - POD test for Bio/Search/BlastUtils.pm
ok 458 - POD test for Bio/Search/DatabaseI.pm
ok 459 - POD test for Bio/Search/GenericDatabase.pm
ok 460 - POD test for Bio/Search/GenericStatistics.pm
ok 461 - POD test for Bio/Search/Processor.pm
ok 462 - POD test for Bio/Search/SearchUtils.pm
ok 463 - POD test for Bio/Search/StatisticsI.pm
ok 464 - POD test for Bio/Search/Hit/BlastHit.pm
ok 465 - POD test for Bio/Search/Hit/BlastPullHit.pm
ok 466 - POD test for Bio/Search/Hit/Fasta.pm
ok 467 - POD test for Bio/Search/Hit/GenericHit.pm
ok 468 - POD test for Bio/Search/Hit/HitFactory.pm
ok 469 - POD test for Bio/Search/Hit/HitI.pm
ok 470 - POD test for Bio/Search/Hit/hmmer3Hit.pm
ok 471 - POD test for Bio/Search/Hit/HMMERHit.pm
ok 472 - POD test for Bio/Search/Hit/HmmpfamHit.pm
ok 473 - POD test for Bio/Search/Hit/ModelHit.pm
ok 474 - POD test for Bio/Search/Hit/PsiBlastHit.pm
ok 475 - POD test for Bio/Search/Hit/PullHitI.pm
ok 476 - POD test for Bio/Search/HSP/BlastHSP.pm
ok 477 - POD test for Bio/Search/HSP/BlastPullHSP.pm
ok 478 - POD test for Bio/Search/HSP/FastaHSP.pm
ok 479 - POD test for Bio/Search/HSP/GenericHSP.pm
ok 480 - POD test for Bio/Search/HSP/HMMERHSP.pm
ok 481 - POD test for Bio/Search/HSP/HmmpfamHSP.pm
ok 482 - POD test for Bio/Search/HSP/HSPFactory.pm
ok 483 - POD test for Bio/Search/HSP/HSPI.pm
ok 484 - POD test for Bio/Search/HSP/ModelHSP.pm
ok 485 - POD test for Bio/Search/HSP/PsiBlastHSP.pm
ok 486 - POD test for Bio/Search/HSP/PSLHSP.pm
ok 487 - POD test for Bio/Search/HSP/PullHSPI.pm
ok 488 - POD test for Bio/Search/HSP/WABAHSP.pm
ok 489 - POD test for Bio/Search/Iteration/GenericIteration.pm
ok 490 - POD test for Bio/Search/Iteration/IterationI.pm
ok 491 - POD test for Bio/Search/Result/BlastPullResult.pm
ok 492 - POD test for Bio/Search/Result/BlastResult.pm
ok 493 - POD test for Bio/Search/Result/CrossMatchResult.pm
ok 494 - POD test for Bio/Search/Result/GenericResult.pm
ok 495 - POD test for Bio/Search/Result/hmmer3Result.pm
ok 496 - POD test for Bio/Search/Result/HMMERResult.pm
ok 497 - POD test for Bio/Search/Result/HmmpfamResult.pm
ok 498 - POD test for Bio/Search/Result/PullResultI.pm
ok 499 - POD test for Bio/Search/Result/ResultFactory.pm
ok 500 - POD test for Bio/Search/Result/ResultI.pm
ok 501 - POD test for Bio/Search/Result/WABAResult.pm
ok 502 - POD test for Bio/Search/Tiling/MapTileUtils.pm
ok 503 - POD test for Bio/Search/Tiling/MapTiling.pm
ok 504 - POD test for Bio/Search/Tiling/TilingI.pm
ok 505 - POD test for Bio/SearchIO/axt.pm
ok 506 - POD test for Bio/SearchIO/blast.pm
ok 507 - POD test for Bio/SearchIO/blasttable.pm
ok 508 - POD test for Bio/SearchIO/blastxml.pm
ok 509 - POD test for Bio/SearchIO/blast_pull.pm
ok 510 - POD test for Bio/SearchIO/cross_match.pm
ok 511 - POD test for Bio/SearchIO/erpin.pm
ok 512 - POD test for Bio/SearchIO/EventHandlerI.pm
ok 513 - POD test for Bio/SearchIO/exonerate.pm
ok 514 - POD test for Bio/SearchIO/fasta.pm
ok 515 - POD test for Bio/SearchIO/FastHitEventBuilder.pm
ok 516 - POD test for Bio/SearchIO/gmap_f9.pm
ok 517 - POD test for Bio/SearchIO/hmmer.pm
ok 518 - POD test for Bio/SearchIO/hmmer2.pm
ok 519 - POD test for Bio/SearchIO/hmmer3.pm
ok 520 - POD test for Bio/SearchIO/hmmer_pull.pm
ok 521 - POD test for Bio/SearchIO/infernal.pm
ok 522 - POD test for Bio/SearchIO/IteratedSearchResultEventBuilder.pm
ok 523 - POD test for Bio/SearchIO/megablast.pm
ok 524 - POD test for Bio/SearchIO/psl.pm
ok 525 - POD test for Bio/SearchIO/rnamotif.pm
ok 526 - POD test for Bio/SearchIO/SearchResultEventBuilder.pm
ok 527 - POD test for Bio/SearchIO/SearchWriterI.pm
ok 528 - POD test for Bio/SearchIO/sim4.pm
ok 529 - POD test for Bio/SearchIO/waba.pm
ok 530 - POD test for Bio/SearchIO/wise.pm
ok 531 - POD test for Bio/SearchIO/Writer/BSMLResultWriter.pm
ok 532 - POD test for Bio/SearchIO/Writer/GbrowseGFF.pm
ok 533 - POD test for Bio/SearchIO/Writer/HitTableWriter.pm
ok 534 - POD test for Bio/SearchIO/Writer/HSPTableWriter.pm
ok 535 - POD test for Bio/SearchIO/Writer/HTMLResultWriter.pm
ok 536 - POD test for Bio/SearchIO/Writer/ResultTableWriter.pm
ok 537 - POD test for Bio/SearchIO/Writer/TextResultWriter.pm
ok 538 - POD test for Bio/SearchIO/XML/BlastHandler.pm
ok 539 - POD test for Bio/SearchIO/XML/PsiBlastHandler.pm
ok 540 - POD test for Bio/Seq/BaseSeqProcessor.pm
ok 541 - POD test for Bio/Seq/EncodedSeq.pm
ok 542 - POD test for Bio/Seq/LargeLocatableSeq.pm
ok 543 - POD test for Bio/Seq/LargePrimarySeq.pm
ok 544 - POD test for Bio/Seq/LargeSeq.pm
ok 545 - POD test for Bio/Seq/LargeSeqI.pm
ok 546 - POD test for Bio/Seq/Meta.pm
ok 547 - POD test for Bio/Seq/MetaI.pm
ok 548 - POD test for Bio/Seq/PrimaryQual.pm
ok 549 - POD test for Bio/Seq/PrimedSeq.pm
ok 550 - POD test for Bio/Seq/QualI.pm
ok 551 - POD test for Bio/Seq/Quality.pm
ok 552 - POD test for Bio/Seq/RichSeq.pm
ok 553 - POD test for Bio/Seq/RichSeqI.pm
ok 554 - POD test for Bio/Seq/SeqBuilder.pm
ok 555 - POD test for Bio/Seq/SeqFactory.pm
ok 556 - POD test for Bio/Seq/SeqFastaSpeedFactory.pm
ok 557 - POD test for Bio/Seq/SequenceTrace.pm
ok 558 - POD test for Bio/Seq/SeqWithQuality.pm
ok 559 - POD test for Bio/Seq/SimulatedRead.pm
ok 560 - POD test for Bio/Seq/TraceI.pm
ok 561 - POD test for Bio/Seq/Meta/Array.pm
ok 562 - POD test for Bio/SeqEvolution/DNAPoint.pm
ok 563 - POD test for Bio/SeqEvolution/EvolutionI.pm
ok 564 - POD test for Bio/SeqEvolution/Factory.pm
ok 565 - POD test for Bio/SeqFeature/Amplicon.pm
ok 566 - POD test for Bio/SeqFeature/AnnotationAdaptor.pm
ok 567 - POD test for Bio/SeqFeature/Collection.pm
ok 568 - POD test for Bio/SeqFeature/CollectionI.pm
ok 569 - POD test for Bio/SeqFeature/Computation.pm
ok 570 - POD test for Bio/SeqFeature/FeaturePair.pm
ok 571 - POD test for Bio/SeqFeature/Generic.pm
ok 572 - POD test for Bio/SeqFeature/Lite.pm
ok 573 - POD test for Bio/SeqFeature/PositionProxy.pm
ok 574 - POD test for Bio/SeqFeature/Primer.pm
ok 575 - POD test for Bio/SeqFeature/Similarity.pm
ok 576 - POD test for Bio/SeqFeature/SimilarityPair.pm
ok 577 - POD test for Bio/SeqFeature/SubSeq.pm
ok 578 - POD test for Bio/SeqFeature/TypedSeqFeatureI.pm
ok 579 - POD test for Bio/SeqFeature/Gene/Exon.pm
ok 580 - POD test for Bio/SeqFeature/Gene/ExonI.pm
ok 581 - POD test for Bio/SeqFeature/Gene/GeneStructure.pm
ok 582 - POD test for Bio/SeqFeature/Gene/GeneStructureI.pm
ok 583 - POD test for Bio/SeqFeature/Gene/Intron.pm
ok 584 - POD test for Bio/SeqFeature/Gene/NC_Feature.pm
ok 585 - POD test for Bio/SeqFeature/Gene/Poly_A_site.pm
ok 586 - POD test for Bio/SeqFeature/Gene/Promoter.pm
ok 587 - POD test for Bio/SeqFeature/Gene/Transcript.pm
ok 588 - POD test for Bio/SeqFeature/Gene/TranscriptI.pm
ok 589 - POD test for Bio/SeqFeature/Gene/UTR.pm
ok 590 - POD test for Bio/SeqFeature/SiRNA/Oligo.pm
ok 591 - POD test for Bio/SeqFeature/SiRNA/Pair.pm
ok 592 - POD test for Bio/SeqFeature/Tools/FeatureNamer.pm
ok 593 - POD test for Bio/SeqFeature/Tools/IDHandler.pm
ok 594 - POD test for Bio/SeqFeature/Tools/TypeMapper.pm
ok 595 - POD test for Bio/SeqFeature/Tools/Unflattener.pm
ok 596 - POD test for Bio/SeqIO/abi.pm
ok 597 - POD test for Bio/SeqIO/ace.pm
ok 598 - POD test for Bio/SeqIO/agave.pm
ok 599 - POD test for Bio/SeqIO/alf.pm
ok 600 - POD test for Bio/SeqIO/asciitree.pm
ok 601 - POD test for Bio/SeqIO/bsml.pm
ok 602 - POD test for Bio/SeqIO/bsml_sax.pm
ok 603 - POD test for Bio/SeqIO/chadoxml.pm
ok 604 - POD test for Bio/SeqIO/chaos.pm
ok 605 - POD test for Bio/SeqIO/chaosxml.pm
ok 606 - POD test for Bio/SeqIO/ctf.pm
ok 607 - POD test for Bio/SeqIO/embl.pm
ok 608 - POD test for Bio/SeqIO/embldriver.pm
ok 609 - POD test for Bio/SeqIO/entrezgene.pm
ok 610 - POD test for Bio/SeqIO/excel.pm
ok 611 - POD test for Bio/SeqIO/exp.pm
ok 612 - POD test for Bio/SeqIO/fasta.pm
ok 613 - POD test for Bio/SeqIO/fastq.pm
ok 614 - POD test for Bio/SeqIO/flybase_chadoxml.pm
ok 615 - POD test for Bio/SeqIO/FTHelper.pm
ok 616 - POD test for Bio/SeqIO/game.pm
ok 617 - POD test for Bio/SeqIO/gbdriver.pm
ok 618 - POD test for Bio/SeqIO/gbxml.pm
ok 619 - POD test for Bio/SeqIO/gcg.pm
ok 620 - POD test for Bio/SeqIO/genbank.pm
ok 621 - POD test for Bio/SeqIO/interpro.pm
ok 622 - POD test for Bio/SeqIO/kegg.pm
ok 623 - POD test for Bio/SeqIO/largefasta.pm
ok 624 - POD test for Bio/SeqIO/lasergene.pm
ok 625 - POD test for Bio/SeqIO/locuslink.pm
ok 626 - POD test for Bio/SeqIO/mbsout.pm
ok 627 - POD test for Bio/SeqIO/metafasta.pm
ok 628 - POD test for Bio/SeqIO/msout.pm
ok 629 - POD test for Bio/SeqIO/MultiFile.pm
ok 630 - POD test for Bio/SeqIO/nexml.pm
ok 631 - POD test for Bio/SeqIO/phd.pm
ok 632 - POD test for Bio/SeqIO/pir.pm
ok 633 - POD test for Bio/SeqIO/pln.pm
ok 634 - POD test for Bio/SeqIO/qual.pm
ok 635 - POD test for Bio/SeqIO/raw.pm
ok 636 - POD test for Bio/SeqIO/scf.pm
ok 637 - POD test for Bio/SeqIO/seqxml.pm
ok 638 - POD test for Bio/SeqIO/strider.pm
ok 639 - POD test for Bio/SeqIO/swiss.pm
ok 640 - POD test for Bio/SeqIO/swissdriver.pm
ok 641 - POD test for Bio/SeqIO/tab.pm
ok 642 - POD test for Bio/SeqIO/table.pm
ok 643 - POD test for Bio/SeqIO/tigr.pm
ok 644 - POD test for Bio/SeqIO/tigrxml.pm
ok 645 - POD test for Bio/SeqIO/tinyseq.pm
ok 646 - POD test for Bio/SeqIO/ztr.pm
ok 647 - POD test for Bio/SeqIO/game/featHandler.pm
ok 648 - POD test for Bio/SeqIO/game/gameHandler.pm
ok 649 - POD test for Bio/SeqIO/game/gameSubs.pm
ok 650 - POD test for Bio/SeqIO/game/gameWriter.pm
ok 651 - POD test for Bio/SeqIO/game/seqHandler.pm
ok 652 - POD test for Bio/SeqIO/Handler/GenericRichSeqHandler.pm
ok 653 - POD test for Bio/SeqIO/tinyseq/tinyseqHandler.pm
ok 654 - POD test for Bio/Structure/Atom.pm
ok 655 - POD test for Bio/Structure/Chain.pm
ok 656 - POD test for Bio/Structure/Entry.pm
ok 657 - POD test for Bio/Structure/IO.pm
ok 658 - POD test for Bio/Structure/Model.pm
ok 659 - POD test for Bio/Structure/Residue.pm
ok 660 - POD test for Bio/Structure/StructureI.pm
ok 661 - POD test for Bio/Structure/IO/pdb.pm
ok 662 - POD test for Bio/Structure/SecStr/DSSP/Res.pm
ok 663 - POD test for Bio/Structure/SecStr/STRIDE/Res.pm
ok 664 - POD test for Bio/Symbol/Alphabet.pm
ok 665 - POD test for Bio/Symbol/AlphabetI.pm
ok 666 - POD test for Bio/Symbol/DNAAlphabet.pm
ok 667 - POD test for Bio/Symbol/ProteinAlphabet.pm
ok 668 - POD test for Bio/Symbol/Symbol.pm
ok 669 - POD test for Bio/Symbol/SymbolI.pm
ok 670 - POD test for Bio/Taxonomy/FactoryI.pm
ok 671 - POD test for Bio/Taxonomy/Node.pm
ok 672 - POD test for Bio/Taxonomy/Taxon.pm
ok 673 - POD test for Bio/Taxonomy/Tree.pm
ok 674 - POD test for Bio/Tools/AlignFactory.pm
ok 675 - POD test for Bio/Tools/AmpliconSearch.pm
ok 676 - POD test for Bio/Tools/AnalysisResult.pm
ok 677 - POD test for Bio/Tools/Blat.pm
ok 678 - POD test for Bio/Tools/CodonTable.pm
ok 679 - POD test for Bio/Tools/Coil.pm
ok 680 - POD test for Bio/Tools/dpAlign.pm
ok 681 - POD test for Bio/Tools/ECnumber.pm
ok 682 - POD test for Bio/Tools/EPCR.pm
ok 683 - POD test for Bio/Tools/Eponine.pm
ok 684 - POD test for Bio/Tools/ERPIN.pm
ok 685 - POD test for Bio/Tools/Est2Genome.pm
ok 686 - POD test for Bio/Tools/ESTScan.pm
ok 687 - POD test for Bio/Tools/Fgenesh.pm
ok 688 - POD test for Bio/Tools/FootPrinter.pm
ok 689 - POD test for Bio/Tools/Gel.pm
ok 690 - POD test for Bio/Tools/Geneid.pm
ok 691 - POD test for Bio/Tools/Genemark.pm
ok 692 - POD test for Bio/Tools/Genewise.pm
ok 693 - POD test for Bio/Tools/Genomewise.pm
ok 694 - POD test for Bio/Tools/Genscan.pm
ok 695 - POD test for Bio/Tools/GFF.pm
ok 696 - POD test for Bio/Tools/Glimmer.pm
ok 697 - POD test for Bio/Tools/Grail.pm
ok 698 - POD test for Bio/Tools/GuessSeqFormat.pm
ok 699 - POD test for Bio/Tools/Hmmpfam.pm
ok 700 - POD test for Bio/Tools/Infernal.pm
ok 701 - POD test for Bio/Tools/ipcress.pm
ok 702 - POD test for Bio/Tools/isPcr.pm
ok 703 - POD test for Bio/Tools/IUPAC.pm
ok 704 - POD test for Bio/Tools/Lucy.pm
ok 705 - POD test for Bio/Tools/Match.pm
ok 706 - POD test for Bio/Tools/MZEF.pm
ok 707 - POD test for Bio/Tools/OddCodes.pm
ok 708 - POD test for Bio/Tools/pICalculator.pm
ok 709 - POD test for Bio/Tools/Primer3.pm
ok 710 - POD test for Bio/Tools/Prints.pm
ok 711 - POD test for Bio/Tools/Profile.pm
ok 712 - POD test for Bio/Tools/Promoterwise.pm
ok 713 - POD test for Bio/Tools/PrositeScan.pm
ok 714 - POD test for Bio/Tools/Protparam.pm
ok 715 - POD test for Bio/Tools/Pseudowise.pm
ok 716 - POD test for Bio/Tools/pSW.pm
ok 717 - POD test for Bio/Tools/QRNA.pm
ok 718 - POD test for Bio/Tools/RandomDistFunctions.pm
ok 719 - POD test for Bio/Tools/RepeatMasker.pm
ok 720 - POD test for Bio/Tools/RNAMotif.pm
ok 721 - POD test for Bio/Tools/Seg.pm
ok 722 - POD test for Bio/Tools/SeqPattern.pm
ok 723 - POD test for Bio/Tools/SeqStats.pm
ok 724 - POD test for Bio/Tools/SeqWords.pm
ok 725 - POD test for Bio/Tools/Sigcleave.pm
ok 726 - POD test for Bio/Tools/Signalp.pm
ok 727 - POD test for Bio/Tools/SiRNA.pm
ok 728 - POD test for Bio/Tools/TandemRepeatsFinder.pm
ok 729 - POD test for Bio/Tools/TargetP.pm
ok 730 - POD test for Bio/Tools/Tmhmm.pm
ok 731 - POD test for Bio/Tools/tRNAscanSE.pm
ok 732 - POD test for Bio/Tools/Alignment/Consed.pm
ok 733 - POD test for Bio/Tools/Alignment/Trim.pm
ok 734 - POD test for Bio/Tools/Analysis/SimpleAnalysisBase.pm
ok 735 - POD test for Bio/Tools/Analysis/DNA/ESEfinder.pm
ok 736 - POD test for Bio/Tools/Analysis/Protein/Domcut.pm
ok 737 - POD test for Bio/Tools/Analysis/Protein/ELM.pm
ok 738 - POD test for Bio/Tools/Analysis/Protein/GOR4.pm
ok 739 - POD test for Bio/Tools/Analysis/Protein/HNN.pm
ok 740 - POD test for Bio/Tools/Analysis/Protein/Mitoprot.pm
ok 741 - POD test for Bio/Tools/Analysis/Protein/NetPhos.pm
ok 742 - POD test for Bio/Tools/Analysis/Protein/Scansite.pm
ok 743 - POD test for Bio/Tools/Analysis/Protein/Sopma.pm
ok 744 - POD test for Bio/Tools/EMBOSS/Palindrome.pm
ok 745 - POD test for Bio/Tools/HMMER/Domain.pm
ok 746 - POD test for Bio/Tools/HMMER/Results.pm
ok 747 - POD test for Bio/Tools/HMMER/Set.pm
ok 748 - POD test for Bio/Tools/Phylo/Gerp.pm
ok 749 - POD test for Bio/Tools/Phylo/Gumby.pm
ok 750 - POD test for Bio/Tools/Phylo/Molphy.pm
ok 751 - POD test for Bio/Tools/Phylo/PAML.pm
ok 752 - POD test for Bio/Tools/Phylo/Molphy/Result.pm
ok 753 - POD test for Bio/Tools/Phylo/PAML/Codeml.pm
ok 754 - POD test for Bio/Tools/Phylo/PAML/ModelResult.pm
ok 755 - POD test for Bio/Tools/Phylo/PAML/Result.pm
ok 756 - POD test for Bio/Tools/Phylo/Phylip/ProtDist.pm
ok 757 - POD test for Bio/Tools/Prediction/Exon.pm
ok 758 - POD test for Bio/Tools/Prediction/Gene.pm
ok 759 - POD test for Bio/Tools/Primer/AssessorI.pm
ok 760 - POD test for Bio/Tools/Primer/Feature.pm
ok 761 - POD test for Bio/Tools/Primer/Pair.pm
ok 762 - POD test for Bio/Tools/Primer/Assessor/Base.pm
ok 763 - POD test for Bio/Tools/Run/GenericParameters.pm
ok 764 - POD test for Bio/Tools/Run/hmmer3.pm (no pod)
ok 765 - POD test for Bio/Tools/Run/ParametersI.pm
ok 766 - POD test for Bio/Tools/Run/RemoteBlast.pm
ok 767 - POD test for Bio/Tools/Run/StandAloneBlast.pm
ok 768 - POD test for Bio/Tools/Run/StandAloneNCBIBlast.pm
ok 769 - POD test for Bio/Tools/Run/StandAloneWUBlast.pm
ok 770 - POD test for Bio/Tools/Run/WrapperBase.pm
ok 771 - POD test for Bio/Tools/Run/WrapperBase/CommandExts.pm
ok 772 - POD test for Bio/Tools/SeqPattern/Backtranslate.pm
ok 773 - POD test for Bio/Tools/Signalp/ExtendedSignalp.pm
ok 774 - POD test for Bio/Tools/Sim4/Exon.pm
ok 775 - POD test for Bio/Tools/Sim4/Results.pm
ok 776 - POD test for Bio/Tools/SiRNA/Ruleset/saigo.pm
ok 777 - POD test for Bio/Tools/SiRNA/Ruleset/tuschl.pm
ok 778 - POD test for Bio/Tools/Spidey/Exon.pm
ok 779 - POD test for Bio/Tools/Spidey/Results.pm
ok 780 - POD test for Bio/Tree/AlleleNode.pm
ok 781 - POD test for Bio/Tree/AnnotatableNode.pm
ok 782 - POD test for Bio/Tree/Compatible.pm
ok 783 - POD test for Bio/Tree/DistanceFactory.pm
ok 784 - POD test for Bio/Tree/Node.pm
ok 785 - POD test for Bio/Tree/NodeI.pm
ok 786 - POD test for Bio/Tree/NodeNHX.pm
ok 787 - POD test for Bio/Tree/RandomFactory.pm
ok 788 - POD test for Bio/Tree/Statistics.pm
ok 789 - POD test for Bio/Tree/Tree.pm
ok 790 - POD test for Bio/Tree/TreeFunctionsI.pm
ok 791 - POD test for Bio/Tree/TreeI.pm
ok 792 - POD test for Bio/Tree/Draw/Cladogram.pm
ok 793 - POD test for Bio/TreeIO/cluster.pm
ok 794 - POD test for Bio/TreeIO/lintree.pm
ok 795 - POD test for Bio/TreeIO/newick.pm
ok 796 - POD test for Bio/TreeIO/NewickParser.pm
ok 797 - POD test for Bio/TreeIO/nexml.pm
ok 798 - POD test for Bio/TreeIO/nexus.pm
ok 799 - POD test for Bio/TreeIO/nhx.pm
ok 800 - POD test for Bio/TreeIO/pag.pm
ok 801 - POD test for Bio/TreeIO/phyloxml.pm
ok 802 - POD test for Bio/TreeIO/svggraph.pm
ok 803 - POD test for Bio/TreeIO/tabtree.pm
ok 804 - POD test for Bio/TreeIO/TreeEventBuilder.pm
ok 805 - POD test for Bio/Variation/AAChange.pm
ok 806 - POD test for Bio/Variation/AAReverseMutate.pm
ok 807 - POD test for Bio/Variation/Allele.pm
ok 808 - POD test for Bio/Variation/DNAMutation.pm
ok 809 - POD test for Bio/Variation/IO.pm
ok 810 - POD test for Bio/Variation/RNAChange.pm
ok 811 - POD test for Bio/Variation/SeqDiff.pm
ok 812 - POD test for Bio/Variation/SNP.pm
ok 813 - POD test for Bio/Variation/VariantI.pm
ok 814 - POD test for Bio/Variation/IO/flat.pm
ok 815 - POD test for Bio/Variation/IO/xml.pm
ok 816 - POD test for scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
ok 817 - POD test for scripts/Bio-DB-GFF/bp_fast_load_gff.pl
ok 818 - POD test for scripts/Bio-DB-GFF/bp_genbank2gff.pl
ok 819 - POD test for scripts/Bio-DB-GFF/bp_genbank2gff3.pl
ok 820 - POD test for scripts/Bio-DB-GFF/bp_generate_histogram.pl
ok 821 - POD test for scripts/Bio-DB-GFF/bp_load_gff.pl
ok 822 - POD test for scripts/Bio-DB-GFF/bp_meta_gff.pl
ok 823 - POD test for scripts/Bio-DB-GFF/bp_process_gadfly.pl
ok 824 - POD test for scripts/Bio-DB-GFF/bp_process_sgd.pl
ok 825 - POD test for scripts/Bio-DB-GFF/bp_process_wormbase.pl
ok 826 - POD test for scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl (no pod)
ok 827 - POD test for scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl (no pod)
ok 828 - POD test for scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
ok 829 - POD test for scripts/das/bp_das_server.pl (no pod)
ok 830 - POD test for scripts/DB/bp_biofetch_genbank_proxy.pl
ok 831 - POD test for scripts/DB/bp_bioflat_index.pl
ok 832 - POD test for scripts/DB/bp_biogetseq.pl
ok 833 - POD test for scripts/DB/bp_flanks.pl
ok 834 - POD test for scripts/DB-HIV/bp_hivq.pl
ok 835 - POD test for scripts/index/bp_fetch.pl
ok 836 - POD test for scripts/index/bp_index.pl
ok 837 - POD test for scripts/index/bp_seqret.pl
ok 838 - POD test for scripts/popgen/bp_composite_LD.pl
ok 839 - POD test for scripts/popgen/bp_heterogeneity_test.pl
ok 840 - POD test for scripts/searchio/bp_fastam9_to_table.pl
ok 841 - POD test for scripts/searchio/bp_filter_search.pl
ok 842 - POD test for scripts/searchio/bp_hmmer_to_table.pl
ok 843 - POD test for scripts/searchio/bp_parse_hmmsearch.pl
ok 844 - POD test for scripts/searchio/bp_search2table.pl
ok 845 - POD test for scripts/seq/bp_extract_feature_seq.pl
ok 846 - POD test for scripts/seq/bp_make_mrna_protein.pl
ok 847 - POD test for scripts/seq/bp_seqconvert.pl
ok 848 - POD test for scripts/seq/bp_seqcut.pl
ok 849 - POD test for scripts/seq/bp_seqpart.pl
ok 850 - POD test for scripts/seq/bp_seqretsplit.pl
ok 851 - POD test for scripts/seq/bp_split_seq.pl
ok 852 - POD test for scripts/seq/bp_translate_seq.pl
ok 853 - POD test for scripts/seq/bp_unflatten_seq.pl
ok 854 - POD test for scripts/seqstats/bp_aacomp.pl
ok 855 - POD test for scripts/seqstats/bp_chaos_plot.pl
ok 856 - POD test for scripts/seqstats/bp_gccalc.pl
ok 857 - POD test for scripts/seqstats/bp_oligo_count.pl
ok 858 - POD test for scripts/taxa/bp_classify_hits_kingdom.pl
ok 859 - POD test for scripts/taxa/bp_local_taxonomydb_query.pl
ok 860 - POD test for scripts/taxa/bp_query_entrez_taxa.pl
ok 861 - POD test for scripts/taxa/bp_taxid4species.pl
ok 862 - POD test for scripts/taxa/bp_taxonomy2tree.pl
ok 863 - POD test for scripts/tree/bp_blast2tree.pl
ok 864 - POD test for scripts/tree/bp_nexus2nh.pl
ok 865 - POD test for scripts/tree/bp_tree2pag.pl
ok 866 - POD test for scripts/utilities/bp_dbsplit.pl
ok 867 - POD test for scripts/utilities/bp_download_query_genbank.pl
ok 868 - POD test for scripts/utilities/bp_mask_by_search.pl
ok 869 - POD test for scripts/utilities/bp_mrtrans.pl
ok 870 - POD test for scripts/utilities/bp_mutate.pl
ok 871 - POD test for scripts/utilities/bp_netinstall.pl
ok 872 - POD test for scripts/utilities/bp_nrdb.pl
ok 873 - POD test for scripts/utilities/bp_pairwise_kaks.pl
ok 874 - POD test for scripts/utilities/bp_remote_blast.pl
ok 875 - POD test for scripts/utilities/bp_revtrans-motif.pl
ok 876 - POD test for scripts/utilities/bp_search2alnblocks.pl
ok 877 - POD test for scripts/utilities/bp_search2BSML.pl
ok 878 - POD test for scripts/utilities/bp_search2gff.pl
ok 879 - POD test for scripts/utilities/bp_search2tribe.pl
ok 880 - POD test for scripts/utilities/bp_seq_length.pl
ok 881 - POD test for scripts/utilities/bp_sreformat.pl
ok 882 - POD test for examples/bioperl.pl (no pod)
ok 883 - POD test for examples/generate_random_seq.pl (no pod)
ok 884 - POD test for examples/longorf.pl
ok 885 - POD test for examples/make_primers.pl (no pod)
ok 886 - POD test for examples/revcom_dir.pl (no pod)
ok 887 - POD test for examples/rev_and_trans.pl (no pod)
ok 888 - POD test for examples/subsequence.cgi (no pod)
ok 889 - POD test for examples/align/aligntutorial.pl (no pod)
ok 890 - POD test for examples/align/align_on_codons.pl (no pod)
ok 891 - POD test for examples/align/clustalw.pl (no pod)
ok 892 - POD test for examples/align/FastAlign.pl
ok 893 - POD test for examples/align/simplealign.pl (no pod)
ok 894 - POD test for examples/Bio-DB-GFF/load_ucsc.pl (no pod)
ok 895 - POD test for examples/cluster/dbsnp.pl (no pod)
ok 896 - POD test for examples/contributed/nmrpdb_parse.pl (no pod)
ok 897 - POD test for examples/contributed/prosite2perl.pl (no pod)
ok 898 - POD test for examples/contributed/rebase2list.pl (no pod)
ok 899 - POD test for examples/db/dbfetch
ok 900 - POD test for examples/db/est_tissue_query.pl (no pod)
ok 901 - POD test for examples/db/gb2features.pl (no pod)
ok 902 - POD test for examples/db/getGenBank.pl (no pod)
ok 903 - POD test for examples/db/get_seqs.pl (no pod)
ok 904 - POD test for examples/db/rfetch.pl (no pod)
ok 905 - POD test for examples/db/use_registry.pl (no pod)
ok 906 - POD test for examples/liveseq/change_gene.pl (no pod)
ok 907 - POD test for examples/popgen/parse_calc_stats.pl (no pod)
ok 908 - POD test for examples/quality/svgtrace.pl (no pod)
ok 909 - POD test for examples/root/exceptions1.pl (no pod)
ok 910 - POD test for examples/root/exceptions2.pl (no pod)
ok 911 - POD test for examples/root/exceptions3.pl (no pod)
ok 912 - POD test for examples/root/exceptions4.pl (no pod)
ok 913 - POD test for examples/root/lib/TestInterface.pm
ok 914 - POD test for examples/root/lib/TestObject.pm
ok 915 - POD test for examples/searchio/blast_example.pl (no pod)
ok 916 - POD test for examples/searchio/custom_writer.pl (no pod)
ok 917 - POD test for examples/searchio/hitwriter.pl (no pod)
ok 918 - POD test for examples/searchio/hspwriter.pl (no pod)
ok 919 - POD test for examples/searchio/htmlwriter.pl (no pod)
ok 920 - POD test for examples/searchio/psiblast_features.pl (no pod)
ok 921 - POD test for examples/searchio/psiblast_iterations.pl (no pod)
ok 922 - POD test for examples/searchio/rawwriter.pl (no pod)
ok 923 - POD test for examples/searchio/resultwriter.pl (no pod)
ok 924 - POD test for examples/searchio/waba2gff.pl (no pod)
ok 925 - POD test for examples/searchio/waba2gff3.pl
ok 926 - POD test for examples/sirna/rnai_finder.cgi
ok 927 - POD test for examples/structure/structure-io.pl (no pod)
ok 928 - POD test for examples/tk/gsequence.pl (no pod)
ok 929 - POD test for examples/tk/hitdisplay.pl (no pod)
ok 930 - POD test for examples/tools/extract_genes.pl
ok 931 - POD test for examples/tools/gb_to_gff.pl (no pod)
ok 932 - POD test for examples/tools/gff2ps.pl
ok 933 - POD test for examples/tools/parse_codeml.pl (no pod)
ok 934 - POD test for examples/tools/psw.pl (no pod)
ok 935 - POD test for examples/tools/reverse-translate.pl
ok 936 - POD test for examples/tools/run_genscan.pl (no pod)
ok 937 - POD test for examples/tools/run_primer3.pl
ok 938 - POD test for examples/tools/seq_pattern.pl (no pod)
ok 939 - POD test for examples/tools/standaloneblast.pl (no pod)
ok 940 - POD test for examples/tree/paup2phylip.pl (no pod)
ok 941 - POD test for maintenance/authors.pl
ok 942 - POD test for maintenance/check_NAME.pl
ok 943 - POD test for maintenance/check_URLs.pl
ok 944 - POD test for maintenance/cvs2cl_by_file.pl
ok 945 - POD test for maintenance/dependencies.pl
ok 946 - POD test for maintenance/deprecated.pl
ok 947 - POD test for maintenance/find_mod_deps.pl
ok 948 - POD test for maintenance/modules.pl
ok 949 - POD test for maintenance/module_usage.pl (no pod)
ok 950 - POD test for maintenance/ncbi_blast_switches.pl (no pod)
ok 951 - POD test for maintenance/pod.pl
ok 952 - POD test for maintenance/symlink_script.pl
ok 953 - POD test for maintenance/version.pl
ok
Subroutine new redefined at Bio\Tree\Tree.pm line 132.
Subroutine nodelete redefined at Bio\Tree\Tree.pm line 180.
Subroutine get_nodes redefined at Bio\Tree\Tree.pm line 200.
Subroutine get_root_node redefined at Bio\Tree\Tree.pm line 241.
Subroutine set_root_node redefined at Bio\Tree\Tree.pm line 257.
Subroutine total_branch_length redefined at Bio\Tree\Tree.pm line 281.
Subroutine subtree_length redefined at Bio\Tree\Tree.pm line 296.
Subroutine id redefined at Bio\Tree\Tree.pm line 318.
Subroutine score redefined at Bio\Tree\Tree.pm line 339.
Subroutine as_text redefined at Bio\Tree\Tree.pm line 383.
Subroutine set_tag_value redefined at Bio\Tree\Tree.pm line 420.
Subroutine add_tag_value redefined at Bio\Tree\Tree.pm line 442.
Subroutine remove_tag redefined at Bio\Tree\Tree.pm line 462.
Subroutine remove_all_tags redefined at Bio\Tree\Tree.pm line 483.
Subroutine get_all_tags redefined at Bio\Tree\Tree.pm line 500.
Subroutine get_tag_values redefined at Bio\Tree\Tree.pm line 517.
Subroutine has_tag redefined at Bio\Tree\Tree.pm line 534.
Subroutine clone redefined at Bio\Tree\Tree.pm line 554.
Subroutine cleanup_tree redefined at Bio\Tree\Tree.pm line 573.
Subroutine new redefined at Bio\Tree\Node.pm line 110.
Subroutine create_node_on_branch redefined at Bio\Tree\Node.pm line 163.
Subroutine add_Descendent redefined at Bio\Tree\Node.pm line 221.
Subroutine each_Descendent redefined at Bio\Tree\Node.pm line 259.
Subroutine remove_Descendent redefined at Bio\Tree\Node.pm line 322.
Subroutine remove_all_Descendents redefined at Bio\Tree\Node.pm line 357.
Subroutine ancestor redefined at Bio\Tree\Node.pm line 396.
Subroutine branch_length redefined at Bio\Tree\Node.pm line 437.
Subroutine bootstrap redefined at Bio\Tree\Node.pm line 461.
Subroutine description redefined at Bio\Tree\Node.pm line 482.
Subroutine id redefined at Bio\Tree\Node.pm line 511.
Subroutine internal_id redefined at Bio\Tree\Node.pm line 553.
Subroutine _creation_id redefined at Bio\Tree\Node.pm line 567.
Subroutine is_Leaf redefined at Bio\Tree\Node.pm line 588.
Subroutine height redefined at Bio\Tree\Node.pm line 606.
Subroutine invalidate_height redefined at Bio\Tree\Node.pm line 631.
Subroutine set_tag_value redefined at Bio\Tree\Node.pm line 652.
Subroutine add_tag_value redefined at Bio\Tree\Node.pm line 674.
Subroutine remove_tag redefined at Bio\Tree\Node.pm line 695.
Subroutine remove_all_tags redefined at Bio\Tree\Node.pm line 715.
Subroutine get_all_tags redefined at Bio\Tree\Node.pm line 731.
Subroutine get_tag_values redefined at Bio\Tree\Node.pm line 749.
Subroutine has_tag redefined at Bio\Tree\Node.pm line 765.
Subroutine node_cleanup redefined at Bio\Tree\Node.pm line 770.
Subroutine reverse_edge redefined at Bio\Tree\Node.pm line 800.
t/PopGen/Coalescent.t .................. 
1..13
ok 1 - use Bio::PopGen::Simulation::Coalescent;
ok 2 - use Bio::PopGen::Statistics;
ok 3 - use Bio::TreeIO;
ok 4
ok 5
ok 6 - pi
ok 7 - theta
ok 8 - tajimaD
ok 9 - all the mutations should be polymorphic (by definition)
ok 10 - fu and li D
ok 11 - fu and li D*
ok 12 - fu and li F
ok 13 - fu and li F
ok
t/PopGen/HtSNP.t ....................... 
1..8
ok 1 - use Bio::PopGen::HtSNP;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok
t/PopGen/MK.t .......................... 
1..46
ok 1 - use Bio::AlignIO;
ok 2 - use Bio::PopGen::Statistics;
ok 3 - use Bio::PopGen::Utilities;
ok 4 - The object isa Bio::PopGen::Statistics
ok 5 - The object isa Bio::SimpleAlign
ok 6 - The object isa Bio::PopGen::Population
ok 7 - Marker Names
ok 8 - Number of Inds
ok 9 - number of ingroup sequences
ok 10 - number of outgroup1 sequences
ok 11 - number of outgroup2 sequences
ok 12 - NSpoly
ok 13 - NSfixed
ok 14 - Spoly
ok 15 - Sfixed
ok 16 - McDonald Kreitman
ok 17 - NSpoly
ok 18 - NSfixed
ok 19 - Spoly
ok 20 - Sfixed
ok 21 - McDonald Kreitman
ok 22 - NSpoly
ok 23 - NSfixed
ok 24 - Spoly
ok 25 - Sfixed
ok 26 - The object isa Bio::SimpleAlign
ok 27 - The object isa Bio::PopGen::Population
ok 28 - Marker Names
ok 29 - Number of Inds
ok 30 - number of ingroup sequences
ok 31 - number of outgroup1 sequences
ok 32 - number of outgroup2 sequences
ok 33 - NSpoly
ok 34 - NSfixed
ok 35 - Spoly
ok 36 - Sfixed
ok 37 - McDonald Kreitman
ok 38 - NSpoly
ok 39 - NSfixed
ok 40 - Spoly
ok 41 - Sfixed
ok 42 - McDonald Kreitman
ok 43 - NSpoly
ok 44 - NSfixed
ok 45 - Spoly
ok 46 - Sfixed
ok
t/PopGen/PopGen.t ...................... 
1..105
ok 1 - use IO::String;
ok 2 - use Bio::PopGen::Individual;
ok 3 - use Bio::PopGen::Genotype;
ok 4 - use Bio::PopGen::Population;
ok 5 - use Bio::PopGen::IO;
ok 6 - use Bio::PopGen::PopStats;
ok 7 - use Bio::AlignIO;
ok 8 - use Bio::PopGen::Statistics;
ok 9 - use Bio::PopGen::Utilities;
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 - mrsa,mssa aflp1
ok 41 - all pops, aflp1
ok 42 - mrsa,envpop aflp1,aflp2
ok 43
ok 44
ok 45
ok 46 - mssa,mrsa all_bands
ok 47 - env,mssa mkr1
ok 48 - env,mssa,mrsa all bands
ok 49 - env,mssa,mrsa mkr2
ok 50 - mrsa,nc all_bands
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 - Pi on 3-allele data
ok 105 - Theta on 3-allele data
ok
t/PopGen/PopGenSims.t .................. 
1..23
ok 1 - use Bio::PopGen::Simulation::GeneticDrift;
ok 2 - Allele freqs should sum to 1
ok 3 - Allele freqs should sum to 1
ok 4 - Allele freqs should sum to 1
ok 5 - Allele freqs should sum to 1
ok 6 - Allele freqs should sum to 1
ok 7 - Allele freqs should sum to 1
ok 8 - Allele freqs should sum to 1
ok 9 - Allele freqs should sum to 1
ok 10 - Allele freqs should sum to 1
ok 11 - Allele freqs should sum to 1
ok 12
ok 13 - All frequencies should be <= 1
ok 14 - Allele freqs should sum to 1
ok 15 - Allele freqs should sum to 1
ok 16 - Allele freqs should sum to 1
ok 17 - Allele freqs should sum to 1
ok 18 - Allele freqs should sum to 1
ok 19 - Allele freqs should sum to 1
ok 20 - Allele freqs should sum to 1
ok 21 - Allele freqs should sum to 1
ok 22 - Allele freqs should sum to 1
ok 23 - Allele freqs should sum to 1
ok
t/PopGen/TagHaplotype.t ................ 
1..3
ok 1 - use Bio::PopGen::TagHaplotype;
ok 2
ok 3
ok
t/RemoteDB/BioFetch.t .................. skipped: Network tests have not been requested
t/RemoteDB/CUTG.t ...................... 
1..37
ok 1 - use Bio::DB::CUTG;
ok 2 - use Bio::CodonUsage::Table;
ok 3 - use Bio::CodonUsage::IO;
ok 4 - use Bio::SeqIO;
ok 5 - use Bio::Tools::SeqStats;
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24 # skip Network tests have not been requested
ok 25 # skip Network tests have not been requested
ok 26 # skip Network tests have not been requested
ok 27 # skip Network tests have not been requested
ok 28 # skip Network tests have not been requested
ok 29 # skip Network tests have not been requested
ok 30 # skip Network tests have not been requested
ok 31 # skip Network tests have not been requested
ok 32 # skip Network tests have not been requested
ok 33 # skip Network tests have not been requested
ok 34 # skip Network tests have not been requested
ok 35 # skip Network tests have not been requested
ok 36 # skip Network tests have not been requested
ok 37 # skip Network tests have not been requested
ok
t/RemoteDB/EMBL.t ...................... skipped: Network tests have not been requested
t/RemoteDB/EntrezGene.t ................ skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed
t/RemoteDB/GenBank.t ................... skipped: Network tests have not been requested
t/RemoteDB/GenPept.t ................... skipped: Network tests have not been requested
t/RemoteDB/HIV/HIV.t ................... 
1..30
ok 1 - use Bio::DB::HIV;
ok 2 - use Bio::DB::WebDBSeqI;
ok 3 - use Bio::DB::HIV::HIVAnnotProcessor;
ok 4 - The object isa Bio::DB::HIV
ok 5 - The object isa Bio::Root::Root
ok 6 - Bio::DB::HIV->can(...)
ok 7 - Bio::DB::HIV->can(...)
ok 8 - Bio::DB::HIV->can(...)
ok 9 - lanl_base set in default object
ok 10 - map_db set in default object
ok 11 - make_search_if set in default object
ok 12 - search_ set in default object
ok 13 - url_base_address set in default object
ok 14 - default sequence request format (fasta)
ok 15 - sorry till implemented
ok 16 - sorry till implemented
ok 17 - HIVQuery type exception check
ok 18 # skip Network tests have not been requested
ok 19 # skip Network tests have not been requested
ok 20 # skip Network tests have not been requested
ok 21 # skip Network tests have not been requested
ok 22 # skip Network tests have not been requested
ok 23 # skip Network tests have not been requested
ok 24 # skip Network tests have not been requested
ok 25 # skip Network tests have not been requested
ok 26 # skip Network tests have not been requested
ok 27 # skip Network tests have not been requested
ok 28 # skip Network tests have not been requested
ok 29 # skip Network tests have not been requested
ok 30 # skip Network tests have not been requested
ok
t/RemoteDB/HIV/HIVAnnotProcessor.t ..... 
1..11
ok 1 - use Bio::Seq;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::DB::HIV::HIVAnnotProcessor;
ok 4 - The object isa Bio::DB::HIV::HIVAnnotProcessor
ok 5 - The object isa Bio::Root::Root
ok 6 - Bio::DB::HIV::HIVAnnotProcessor->can(...)
ok 7 - Bio::DB::HIV::HIVAnnotProcessor->can('hiv_query')
ok 8 - bad type set exception
ok 9 - attach stream
ok 10 - write exception
ok 11 - access stream
ok
t/RemoteDB/HIV/HIVQuery.t .............. 
1..41
ok 1 - use Bio::DB::Query::HIVQuery;
ok 2 - use Bio::DB::HIV;
ok 3 - use Bio::Annotation::Collection;
ok 4 - use Bio::Annotation::Comment;
ok 5 - use Bio::Annotation::Reference;
ok 6 - use Bio::DB::HIV::HIVQueryHelper;
ok 7 - The object isa Bio::DB::Query::HIVQuery
ok 8 - The object isa Bio::Root::Root
ok 9 - Bio::DB::Query::HIVQuery->can(...)
ok 10 - Bio::DB::Query::HIVQuery->can(...)
ok 11 - Bio::DB::Query::HIVQuery->can(...)
ok 12 - _map_db_uri set in default object
ok 13 - _make_search_if_uri set in default object
ok 14 - _search_uri set in default object
ok 15 - _schema_file set in default object
ok 16 - _run_option set in default object
ok 17 - annotations container available
ok 18 - query syntax check 1
ok 19 - query syntax check 2
ok 20 - query syntax check 3
ok 21 - query parser check
ok 22 - multiquery parse check
ok 23 # skip The optional module HTML::Parser generated the following error: 
# HTML::Parser object version 3.69 does not match bootstrap parameter 3.71 at C:\cpanfly-5.16\var\megalib/XSLoader.pm line 92.
# Compilation failed in require at (eval 114) line 1.
# 
ok 24 # skip The optional module HTML::Parser generated the following error: 
# HTML::Parser object version 3.69 does not match bootstrap parameter 3.71 at C:\cpanfly-5.16\var\megalib/XSLoader.pm line 92.
# Compilation failed in require at (eval 114) line 1.
# 
ok 25 # skip The optional module HTML::Parser generated the following error: 
# HTML::Parser object version 3.69 does not match bootstrap parameter 3.71 at C:\cpanfly-5.16\var\megalib/XSLoader.pm line 92.
# Compilation failed in require at (eval 114) line 1.
# 
ok 26 - bad field exception check
ok 27 - bad match data exception check
ok 28 - empty field not ok exception check
ok 29 - uninitialized schema exception check
ok 30 - query not run (level 1) warning check
ok 31 - query not run (level 2) warning check
ok 32 # skip Network tests have not been requested
ok 33 # skip Network tests have not been requested
ok 34 # skip Network tests have not been requested
ok 35 # skip Network tests have not been requested
ok 36 # skip Network tests have not been requested
ok 37 # skip Network tests have not been requested
ok 38 # skip Network tests have not been requested
ok 39 # skip Network tests have not been requested
ok 40 # skip Network tests have not been requested
ok 41 # skip Network tests have not been requested
ok
t/RemoteDB/HIV/HIVQueryHelper.t ........ 
1..40
ok 1 - use Bio::DB::HIV::HIVQueryHelper;
ok 2 - The object isa HIVSchema
ok 3 - The object isa QRY
ok 4 - The object isa R
ok 5 - The object isa Q
ok 6 - schema load
ok 7 - HIVSchema->can(...)
ok 8 - fields complete
ok 9 - tables complete
ok 10 - aliases complete
ok 11
ok 12 - test field syntax ok
ok 13 - test field syntax ok
ok 14 - test alias by field name
ok 15 - correct primary key for SequenceEntry
ok 16 - correct number of foreign keys for AUthor
ok 17 - correct foreign table for au_pub_id
ok 18 - correct annotation key hash
ok 19 - QRY->can(...)
ok 20 - R->can(...)
ok 21 - Q->can(...)
ok 22 - null QRY
ok 23 - null R (request object)
ok 24 - null Q (atomic query object)
ok 25 - R obj create and init (1)
ok 26 - R obj create and init (2)
ok 27 - R::In
ok 28 - !R::In
ok 29 - R::Eq
ok 30 - QRY obj create and init (1)
ok 31 - QRY obj create and init (2)
ok 32 - QRY obj create and init (3)
ok 33 - QRY overload |
ok 34 - QRY overload &
ok 35 - QRY nontrivial &
ok 36 - parse: ('odds bodkins', a)[X] m[Y] u[Z] OR 'b'[X] {A B [C] [D]} 
ok 37 - make: 2 queries returned
ok 38 - {annotation fields} parsed correctly
ok 39 - parse: ('odds bodkins', a)[X] m[Y] u[Z] AND b[X] {A B [C] [D]} 
ok 40 - above query is null
ok
t/RemoteDB/MeSH.t ...................... skipped: Network tests have not been requested
t/RemoteDB/Query/GenBank.t ............. skipped: Network tests have not been requested
t/RemoteDB/RefSeq.t .................... 
1..16
ok 1 - use Bio::DB::RefSeq;
ok 2 - use Bio::DB::GenBank;
ok 3 - use Bio::DB::EMBL;
ok 4
ok 5
ok 6
ok 7 # skip Network tests have not been requested
ok 8 # skip Network tests have not been requested
ok 9 # skip Network tests have not been requested
ok 10 # skip Network tests have not been requested
ok 11 # skip Network tests have not been requested
ok 12 # skip Network tests have not been requested
ok 13 # skip Network tests have not been requested
ok 14 # skip Network tests have not been requested
ok 15 # skip Network tests have not been requested
ok 16 # skip Network tests have not been requested
ok
t/RemoteDB/SeqHound.t .................. skipped: Network tests have not been requested
t/RemoteDB/SeqRead_fail.t .............. skipped: Network tests have not been requested
t/RemoteDB/SeqVersion.t ................ skipped: The optional module HTML::TableExtract generated the following error:
t/RemoteDB/SwissProt.t ................. skipped: Network tests have not been requested

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't locate DB_File.pm in @INC (@INC contains: . C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv\blib\lib C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv\blib\arch C:/cpanfly-5.16/var/cpan/build/BioPerl-1.6.920-c7McWv C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv C:\cpanfly-5.16\var\megalib C:/cpanfly-5.16/var/megalib C:/Perl-5.16/site/lib C:/Perl-5.16/lib) at Bio\DB\Taxonomy\flatfile.pm line 88.
BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 88.
Compilation failed in require at Bio/Root/Root.pm line 558.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:560
STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:294
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:118
STACK: t/RemoteDB/Taxonomy.t:28
-----------------------------------------------------------
Bio::DB::Taxonomy: flatfile cannot be found
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't locate DB_File.pm in @INC (@INC contains: . C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv\blib\lib C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv\blib\arch C:/cpanfly-5.16/var/cpan/build/BioPerl-1.6.920-c7McWv C:\cpanfly-5.16\var\cpan\build\BioPerl-1.6.920-c7McWv C:\cpanfly-5.16\var\megalib C:/cpanfly-5.16/var/megalib C:/Perl-5.16/site/lib C:/Perl-5.16/lib) at Bio\DB\Taxonomy\flatfile.pm line 88.
BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 88.
Compilation failed in require at Bio/Root/Root.pm line 558.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:560
STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:294
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:118
STACK: t/RemoteDB/Taxonomy.t:28
-----------------------------------------------------------

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 28.

#   Failed test 'The thing isa Bio::DB::Taxonomy::flatfile'
#   at t/RemoteDB/Taxonomy.t line 33.
#     The thing isn't defined

#   Failed test 'The thing isa Bio::DB::Taxonomy'
#   at t/RemoteDB/Taxonomy.t line 34.
#     The thing isn't defined

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Attempt to reload Bio\DB\Taxonomy\flatfile.pm aborted.
Compilation failed in require at Bio/Root/Root.pm line 558.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:560
STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:294
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:118
STACK: t/RemoteDB/Taxonomy.t:36
-----------------------------------------------------------
Bio::DB::Taxonomy: flatfile cannot be found
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Attempt to reload Bio\DB\Taxonomy\flatfile.pm aborted.
Compilation failed in require at Bio/Root/Root.pm line 558.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:486
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:560
STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:294
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:118
STACK: t/RemoteDB/Taxonomy.t:36
-----------------------------------------------------------

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 36.
Use of uninitialized value $db in string eq at t/RemoteDB/Taxonomy.t line 46.
Use of uninitialized value $db in string eq at t/RemoteDB/Taxonomy.t line 50.
Can't call method "get_num_taxa" on an undefined value at t/RemoteDB/Taxonomy.t line 53.
# Looks like you planned 191 tests but ran 55.
# Looks like you failed 4 tests of 55 run.
# Looks like your test exited with 2 just after 55.
t/RemoteDB/Taxonomy.t .................. 
1..191
ok 1 - use Bio::DB::Taxonomy;
ok 2 - use Bio::Tree::Tree;
ok 3
ok 4 - The object isa Bio::DB::Taxonomy::entrez
ok 5 - The object isa Bio::DB::Taxonomy
not ok 6
not ok 7 - The thing isa Bio::DB::Taxonomy::flatfile
not ok 8 - The thing isa Bio::DB::Taxonomy
not ok 9
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 Network tests have not been requested
ok 44 # skip Network tests have not been requested
ok 45 # skip Network tests have not been requested
ok 46 # skip Network tests have not been requested
ok 47 # skip Network tests have not been requested
ok 48 # skip Network tests have not been requested
ok 49 # skip Network tests have not been requested
ok 50 # skip Network tests have not been requested
ok 51 # skip Network tests have not been requested
ok 52 # skip Network tests have not been requested
ok 53 # skip Network tests have not been requested
ok 54 # skip Network tests have not been requested
ok 55 # skip Network tests have not been requested
Dubious, test returned 2 (wstat 512, 0x200)
Failed 140/191 subtests 
	(less 46 skipped subtests: 5 okay)
t/Restriction/Analysis-refac.t ......... 
1..91
ok 1 - use Bio::Restriction::IO;
ok 2 - use Bio::Restriction::Analysis;
ok 3 - use Bio::Restriction::EnzymeCollection;
ok 4 - use Bio::Restriction::Enzyme;
ok 5 - read withrefm file
ok 6 - parse withrefm file
ok 7 - HindIII: nonambiguous intrasite cutter
ok 8 - AarI: nonambiguous extrasite cutter
ok 9 - AasI: ambiguous intrasite cutter
ok 10 - BceSI: ambiguous extrasite cutter
ok 11 - AjuI: cutter with central recog site
ok 12 - TaqII: multi-extrasite cutter
ok 13
ok 14 - HindIII plus
ok 15 - HindIII minus
ok 16 - AasI plus
ok 17 - AasI  minus
ok 18 - AarI plus
ok 19 - AarI  minus
ok 20 - BceSI plus
ok 21 - BceSI  minus
ok 22 - AjuI plus
ok 23 - AjuI minus
ok 24 - TaqII plus
ok 25 - TaqII minus
ok 26 - build real B:R::Analysis object
ok 27 - 13 fragments
ok 28 - circularize
ok 29 - recut
ok 30 - circ: AasI
# site at origin
ok 31 - circ: still 13 fragments (cut site at origin)
ok 32 - use Bio::Restriction::IO;
ok 33 - use Bio::Restriction::Analysis;
ok 34 - read withrefm file
ok 35 - parse withrefm file
ok 36 - Collection initiated
ok 37 - AbeI: found ok into collection
ok 38 - AccBSI: found ok into collection
ok 39 - AciI: found ok into collection
ok 40 - Asp26HI: found ok into collection
ok 41 - BmgBI: found ok into collection
ok 42 - AbeI plus
ok 43 - AbeI minus
ok 44 - AbeI fragment
ok 45 - AbeI positions
ok 46 - AbeI Overhang
ok 47 - AbeI name
ok 48 - AbeI site
ok 49 - AbeI revcom_site
ok 50 - AbeI cut
ok 51 - AbeI complementary_cut
ok 52 - AccBSI plus
ok 53 - AccBSI minus
ok 54 - AccBSI fragment
ok 55 - AccBSI positions
ok 56 - AccBSI Overhang
ok 57 - AccBSI name
ok 58 - AccBSI site
ok 59 - AccBSI revcom_site
ok 60 - AccBSI cut
ok 61 - AccBSI complementary_cut
ok 62 - AciI plus
ok 63 - AciI minus
ok 64 - AciI fragment
ok 65 - AciI positions
ok 66 - AciI Overhang
ok 67 - AciI name
ok 68 - AciI site
ok 69 - AciI revcom_site
ok 70 - AciI cut
ok 71 - AciI complementary_cut
ok 72 - Asp26HI plus
ok 73 - Asp26HI minus
ok 74 - Asp26HI fragment
ok 75 - Asp26HI positions
ok 76 - Asp26HI Overhang
ok 77 - Asp26HI name
ok 78 - Asp26HI site
ok 79 - Asp26HI revcom_site
ok 80 - Asp26HI cut
ok 81 - Asp26HI complementary_cut
ok 82 - BmgBI plus
ok 83 - BmgBI minus
ok 84 - BmgBI fragment
ok 85 - BmgBI positions
ok 86 - BmgBI Overhang
ok 87 - BmgBI name
ok 88 - BmgBI site
ok 89 - BmgBI revcom_site
ok 90 - BmgBI cut
ok 91 - BmgBI complementary_cut
ok
t/Restriction/Analysis.t ............... 
1..182
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 - expected 2 sizes for PspEI
ok 132
ok 133 - not circular expected 1 fragments for MwoI as it doesnt cut
ok 134
ok 135
ok 136 - number of RsaI fragments
ok 137 - 3 circular MseI fragments
ok 138 - 3 circular MseI cut sites
ok 139 - number for AciI a non-palindromic enzyme
ok 140 - 1 fragment for MwoI as it cuts across the circ point
ok 141
ok 142
ok 143
ok 144
ok 145 - 7 fragments in the multiple digest
ok 146 - 7 positions in the multiple digest
ok 147 - 7 sizes in the multiple digest
ok 148
ok 149 -  expected 9 cuts for HindI
ok 150 - expect 9 fragment maps for HindI
ok 151 - sequence for GT
ok 152 - start at 40
ok 153 - end at 41
ok 154 - sequence for GGATTAAAAAAAGAGT
ok 155 - start at 42
ok 156 - end at 57
ok 157 - sequence for GTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGT
ok 158 - start at 58
ok 159 - end at 92
ok 160 - sequence for GAGTAAATTAAAATTTTATTGACTTAGGTCA
ok 161 - start at 93
ok 162 - end at 123
ok 163 - sequence for CTAAATACTTTAACCAATATAGGCATAGCGCA
ok 164 - start at 124
ok 165 - end at 155
ok 166 - sequence for CAGACAGATAAAAATTACAGAGTACA
ok 167 - start at 156
ok 168 - end at 181
ok 169 - sequence for CAACATCCATGAAACGCATTAGCA
ok 170 - start at 182
ok 171 - end at 205
ok 172 - sequence for CCA
ok 173 - start at 206
ok 174 - end at 208
ok 175 - sequence for CCAGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGT
ok 176 - start at 209
ok 177 - end at 39
ok 178
ok 179 - bug 2139
ok 180 - number of HindIII fragments
ok 181 - number of EcoRI fragments
ok 182 - number of RsaI fragments
ok
t/Restriction/Gel.t .................... 
1..9
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::Restriction::Analysis;
ok 3 - use Bio::Tools::Gel;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok
Subroutine new redefined at Bio/Restriction/IO/base.pm line 90, <DATA> line 532.
Subroutine _initialize redefined at Bio/Restriction/IO/base.pm line 114, <DATA> line 532.
Subroutine read redefined at Bio/Restriction/IO/base.pm line 144, <DATA> line 532.
Subroutine _xln_sub redefined at Bio/Restriction/IO/base.pm line 172, <DATA> line 532.
Subroutine write redefined at Bio/Restriction/IO/base.pm line 189, <DATA> line 532.
Subroutine verify_prototype redefined at Bio/Restriction/IO/base.pm line 221, <DATA> line 532.
Subroutine _cuts_from_site redefined at Bio/Restriction/IO/base.pm line 258, <DATA> line 532.
Subroutine _meth redefined at Bio/Restriction/IO/base.pm line 279, <DATA> line 532.
Subroutine _coordinate_shift_to_cut redefined at Bio/Restriction/IO/base.pm line 305, <DATA> line 532.
Subroutine _make_multisites redefined at Bio/Restriction/IO/base.pm line 327, <DATA> line 532.
Subroutine _make_multicuts redefined at Bio/Restriction/IO/base.pm line 412, <DATA> line 532.
Subroutine _companies redefined at Bio/Restriction/IO/base.pm line 441, <DATA> line 532.
t/Restriction/IO.t ..................... 
1..18
ok 1 - use Bio::Restriction::IO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
not ok 8 # TODO writing to a file doesn't seem to work? prints to STDOUT!

#   Failed (TODO) test at t/Restriction/IO.t line 31.
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16 # skip Network tests have not been requested
ok 17 # skip Network tests have not been requested
ok 18 # skip Network tests have not been requested
ok
t/Root/Exception.t ..................... 
1..8
ok 1 - use TestObject;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok
t/Root/HTTPget.t ....................... skipped: Network tests have not been requested
t/Root/RootI.t ......................... 
1..63
ok 1 - use Bio::Root::Root;
ok 2 - use Bio::Seq;
ok 3
ok 4 - The object isa Bio::Root::RootI
ok 5 - threw Regexp ((?^:Testing throw))
ok 6 - threw Regexp ((?^:EXCEPTION: Bio::Root::NotImplemented))
ok 7 - threw Regexp ((?^:EXCEPTION ))
ok 8 - threw Regexp ((?^:Testing throw))
ok 9
ok 10 - threw Regexp ((?^:Testing throw))
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16 - simple
ok 17 - simple
ok 18 - warns for versions below current version 1.00692
ok 19 - warns for versions below current version 1.00692
ok 20 - throws for versions above 1.00692
ok 21 - throws for versions above 1.00692
ok 22 - throws for versions equal to 1.00692
ok 23 - simple
ok 24 - simple
ok 25 - warns for versions below current version 1.00692
ok 26 - warns for versions below current version 1.00692
ok 27 - throws for versions above 1.00692
ok 28 - throws for versions above 1.00692
ok 29 - arg callable since method was created
ok 30 - mal-formed arg callable since method was created with good name
ok 31 - Bio::Foo2->can('t3')
ok 32 - Methods don't pollute original Bio::Root::Root namespace
ok 33 - Bio::Foo2->can('test_4')
ok 34 - Methods don't pollute original Bio::Root::Root namespace
ok 35 - Bio::Foo3->can('t5')
ok 36 - arg not in method list not created
ok 37 - Bio::Foo3->can('t5')
ok 38 - Methods don't pollute original Bio::Root::Root namespace
ok 39 - verbose was set correctly
ok 40 - synonym was set correctly
ok 41 - real method of synonym was set correctly
ok 42 - mal-formed arg correctly resolved to created method
ok 43 - synonym of set method was set correctly
ok 44 - Bio::Foo4->can('t7')
ok 45 - Methods don't pollute original Bio::Root::Root namespace
ok 46 - Bio::Foo4->can('test7')
ok 47 - Methods don't pollute original Bio::Root::Root namespace
ok 48 - Bio::Foo4->can('test_8')
ok 49 - Methods don't pollute original Bio::Root::Root namespace
ok 50 - Bio::Foo4->can('t8')
ok 51 - Methods don't pollute original Bio::Root::Root namespace
ok 52 - clone
ok 53 - clone
ok 54 - clone
ok 55 - clone changed, original didn't
ok 56 - parameters passed to clone() modify object
ok 57 - original is not modified
ok 58 - must use proper versioning scheme
ok 59 - warns for versions >= 1.00692
ok 60 - warns for versions >= 1.00692
ok 61 - throws for versions >= 1.00692
ok 62 - throws for versions >= 1.00692
ok 63 - No warnings/exceptions below 1.00692
ok

#   Failed test 'executable file'
#   at t/Root/RootIO.t line 59.
Can't do inplace edit without backup at Bio/Root/IO.pm line 570.
Error removing C:\cpanfly-5.16\var\tmp\3EMjCxvjk_ at C:\cpanfly-5.16\var\megalib/File/Temp.pm line 890.
# Looks like you planned 77 tests but ran 45.
# Looks like you failed 1 test of 45 run.
# Looks like your test exited with 25 just after 45.
t/Root/RootIO.t ........................ 
1..77
ok 1 - use Bio::Root::IO;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::Assembly::IO;
ok 4
ok 5 - throw()
ok 6 - throw() verbose(-1)
ok 7 - warn()
ok 8 - throw() verbose(1)
ok 9 - stack_trace()
ok 10 - set verbosity to 1
ok 11
ok 12
not ok 13 - executable file
ok 14 - non-executable file
ok 15 - executable dir
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21 - filename, read
ok 22
ok 23
ok 24 - filename, write
ok 25
ok 26
ok 27
ok 28
ok 29 - handle, read
ok 30
ok 31
ok 32 - handle, write
ok 33 - The object isa Bio::Root::IO
ok 34 - is a write handle
ok 35 - no warnings in ->close call
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44 - _print
ok 45
Dubious, test returned 25 (wstat 6400, 0x1900)
Failed 33/77 subtests 
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
t/Root/Utilities.t ..................... 
1..56
ok 1 - use Bio::Root::Utilities;
ok 2 - The object isa Bio::Root::Utilities
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - file_date()
ok 38 - unix (\n or 012 or ^J)
ok 39 - date format
ok 40 - date format
ok 41 - date format
ok 42 - date format
ok 43 - date format
ok 44
ok 45 # skip gzip not found, skipping gzip tests
ok 46 # skip gzip not found, skipping gzip tests
ok 47 # skip gzip not found, skipping gzip tests
ok 48 # skip gzip not found, skipping gzip tests
ok 49 # skip gzip not found, skipping gzip tests
ok 50 # skip gzip not found, skipping gzip tests
ok 51 # skip gzip not found, skipping gzip tests
ok 52 # skip gzip not found, skipping gzip tests
ok 53 # skip gzip not found, skipping gzip tests
ok 54 # skip gzip not found, skipping gzip tests
ok 55 # skip gzip not found, skipping gzip tests
ok 56 # skip gzip not found, skipping gzip tests
ok
t/SearchDist.t ......................... skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed
Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175.
Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264.
Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284.
Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311.
Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337.
Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357.
Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378.
Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399.
Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420.
Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442.
Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465.
Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487.
Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508.
Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523.
Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540.
Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555.
Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574.
Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599.
Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616.
Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629.
Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646.
Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663.
Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680.
Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700.
Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728.
Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747.
Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763.
Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777.
Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794.
Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815.
Subroutine new redefined at Bio/Search/Hit/GenericHit.pm line 127.
Subroutine add_hsp redefined at Bio/Search/Hit/GenericHit.pm line 204.
Subroutine hsp_factory redefined at Bio/Search/Hit/GenericHit.pm line 228.
Subroutine name redefined at Bio/Search/Hit/GenericHit.pm line 248.
Subroutine accession redefined at Bio/Search/Hit/GenericHit.pm line 268.
Subroutine description redefined at Bio/Search/Hit/GenericHit.pm line 288.
Subroutine length redefined at Bio/Search/Hit/GenericHit.pm line 308.
Subroutine algorithm redefined at Bio/Search/Hit/GenericHit.pm line 333.
Subroutine raw_score redefined at Bio/Search/Hit/GenericHit.pm line 355.
Subroutine score redefined at Bio/Search/Hit/GenericHit.pm line 385.
Subroutine significance redefined at Bio/Search/Hit/GenericHit.pm line 400.
Subroutine bits redefined at Bio/Search/Hit/GenericHit.pm line 430.
Subroutine next_hsp redefined at Bio/Search/Hit/GenericHit.pm line 458.
Subroutine hsps redefined at Bio/Search/Hit/GenericHit.pm line 494.
Subroutine num_hsps redefined at Bio/Search/Hit/GenericHit.pm line 517.
Subroutine rewind redefined at Bio/Search/Hit/GenericHit.pm line 538.
Subroutine ambiguous_aln redefined at Bio/Search/Hit/GenericHit.pm line 564.
Subroutine overlap redefined at Bio/Search/Hit/GenericHit.pm line 576.
Subroutine n redefined at Bio/Search/Hit/GenericHit.pm line 605.
Subroutine p redefined at Bio/Search/Hit/GenericHit.pm line 652.
Subroutine hsp redefined at Bio/Search/Hit/GenericHit.pm line 694.
Subroutine logical_length redefined at Bio/Search/Hit/GenericHit.pm line 740.
Subroutine length_aln redefined at Bio/Search/Hit/GenericHit.pm line 786.
Subroutine gaps redefined at Bio/Search/Hit/GenericHit.pm line 849.
Subroutine matches redefined at Bio/Search/Hit/GenericHit.pm line 887.
Subroutine start redefined at Bio/Search/Hit/GenericHit.pm line 948.
Subroutine end redefined at Bio/Search/Hit/GenericHit.pm line 1025.
Subroutine range redefined at Bio/Search/Hit/GenericHit.pm line 1093.
Subroutine frac_identical redefined at Bio/Search/Hit/GenericHit.pm line 1150.
Subroutine frac_conserved redefined at Bio/Search/Hit/GenericHit.pm line 1226.
Subroutine frac_aligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1274.
Subroutine frac_aligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1310.
Subroutine num_unaligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1364.
Subroutine num_unaligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1400.
Subroutine seq_inds redefined at Bio/Search/Hit/GenericHit.pm line 1442.
Subroutine strand redefined at Bio/Search/Hit/GenericHit.pm line 1473.
Subroutine frame redefined at Bio/Search/Hit/GenericHit.pm line 1535.
Subroutine rank redefined at Bio/Search/Hit/GenericHit.pm line 1574.
Subroutine locus redefined at Bio/Search/Hit/GenericHit.pm line 1590.
Subroutine each_accession_number redefined at Bio/Search/Hit/GenericHit.pm line 1618.
Subroutine tiled_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1666.
Subroutine query_length redefined at Bio/Search/Hit/GenericHit.pm line 1683.
Subroutine ncbi_gi redefined at Bio/Search/Hit/GenericHit.pm line 1701.
Subroutine sort_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1732.
Subroutine iteration redefined at Bio/Search/Hit/GenericHit.pm line 1772.
Subroutine found_again redefined at Bio/Search/Hit/GenericHit.pm line 1807.
Subroutine Bio::Search::Hit::GenericHit::frac_aligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1333.
Subroutine Bio::Search::Hit::GenericHit::num_unaligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1341.
Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, <GEN1> line 434.
Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, <GEN1> line 434.
Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, <GEN1> line 434.
Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, <GEN1> line 434.
Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, <GEN1> line 434.
Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, <GEN1> line 434.
t/SearchIO/CigarString.t ............... 
1..4
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok 4
ok
t/SearchIO/SearchIO.t .................. 
1..19
ok 1 - use Bio::SearchIO;
ok 2 - blastxml for f.blastxml
ok 3 - fasta for f.fy
ok 4 - exonerate for f.exonerate
ok 5 - blast for f.tblx
ok 6 - fasta for f.fx
ok 7 - fasta for f.osearch
ok 8 - blast for filename.bls
ok 9 - exonerate for f.exon
ok 10 - fasta for f.SSEARCH.m9
ok 11 - blast for filename.blast
ok 12 - fasta for f.m9
ok 13 - blast for f.blx
ok 14 - blastxml for f.xml
ok 15 - fasta for f.fasta
ok 16 - fasta for f.fa
ok 17 - blast for fast.bls
ok 18 - fasta for f.ssearch
ok 19 - fasta for f.psearch
ok
Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175.
Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264.
Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284.
Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311.
Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337.
Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357.
Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378.
Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399.
Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420.
Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442.
Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465.
Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487.
Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508.
Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523.
Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540.
Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555.
Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574.
Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599.
Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616.
Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629.
Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646.
Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663.
Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680.
Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700.
Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728.
Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747.
Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763.
Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777.
Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794.
Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815.
Subroutine new redefined at Bio/Search/Hit/GenericHit.pm line 127.
Subroutine add_hsp redefined at Bio/Search/Hit/GenericHit.pm line 204.
Subroutine hsp_factory redefined at Bio/Search/Hit/GenericHit.pm line 228.
Subroutine name redefined at Bio/Search/Hit/GenericHit.pm line 248.
Subroutine accession redefined at Bio/Search/Hit/GenericHit.pm line 268.
Subroutine description redefined at Bio/Search/Hit/GenericHit.pm line 288.
Subroutine length redefined at Bio/Search/Hit/GenericHit.pm line 308.
Subroutine algorithm redefined at Bio/Search/Hit/GenericHit.pm line 333.
Subroutine raw_score redefined at Bio/Search/Hit/GenericHit.pm line 355.
Subroutine score redefined at Bio/Search/Hit/GenericHit.pm line 385.
Subroutine significance redefined at Bio/Search/Hit/GenericHit.pm line 400.
Subroutine bits redefined at Bio/Search/Hit/GenericHit.pm line 430.
Subroutine next_hsp redefined at Bio/Search/Hit/GenericHit.pm line 458.
Subroutine hsps redefined at Bio/Search/Hit/GenericHit.pm line 494.
Subroutine num_hsps redefined at Bio/Search/Hit/GenericHit.pm line 517.
Subroutine rewind redefined at Bio/Search/Hit/GenericHit.pm line 538.
Subroutine ambiguous_aln redefined at Bio/Search/Hit/GenericHit.pm line 564.
Subroutine overlap redefined at Bio/Search/Hit/GenericHit.pm line 576.
Subroutine n redefined at Bio/Search/Hit/GenericHit.pm line 605.
Subroutine p redefined at Bio/Search/Hit/GenericHit.pm line 652.
Subroutine hsp redefined at Bio/Search/Hit/GenericHit.pm line 694.
Subroutine logical_length redefined at Bio/Search/Hit/GenericHit.pm line 740.
Subroutine length_aln redefined at Bio/Search/Hit/GenericHit.pm line 786.
Subroutine gaps redefined at Bio/Search/Hit/GenericHit.pm line 849.
Subroutine matches redefined at Bio/Search/Hit/GenericHit.pm line 887.
Subroutine start redefined at Bio/Search/Hit/GenericHit.pm line 948.
Subroutine end redefined at Bio/Search/Hit/GenericHit.pm line 1025.
Subroutine range redefined at Bio/Search/Hit/GenericHit.pm line 1093.
Subroutine frac_identical redefined at Bio/Search/Hit/GenericHit.pm line 1150.
Subroutine frac_conserved redefined at Bio/Search/Hit/GenericHit.pm line 1226.
Subroutine frac_aligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1274.
Subroutine frac_aligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1310.
Subroutine num_unaligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1364.
Subroutine num_unaligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1400.
Subroutine seq_inds redefined at Bio/Search/Hit/GenericHit.pm line 1442.
Subroutine strand redefined at Bio/Search/Hit/GenericHit.pm line 1473.
Subroutine frame redefined at Bio/Search/Hit/GenericHit.pm line 1535.
Subroutine rank redefined at Bio/Search/Hit/GenericHit.pm line 1574.
Subroutine locus redefined at Bio/Search/Hit/GenericHit.pm line 1590.
Subroutine each_accession_number redefined at Bio/Search/Hit/GenericHit.pm line 1618.
Subroutine tiled_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1666.
Subroutine query_length redefined at Bio/Search/Hit/GenericHit.pm line 1683.
Subroutine ncbi_gi redefined at Bio/Search/Hit/GenericHit.pm line 1701.
Subroutine sort_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1732.
Subroutine iteration redefined at Bio/Search/Hit/GenericHit.pm line 1772.
Subroutine found_again redefined at Bio/Search/Hit/GenericHit.pm line 1807.
Subroutine Bio::Search::Hit::GenericHit::frac_aligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1333.
Subroutine Bio::Search::Hit::GenericHit::num_unaligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1341.
Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, <GEN2> line 434.
Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, <GEN2> line 434.
Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, <GEN2> line 434.
Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, <GEN2> line 434.
Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, <GEN2> line 434.
Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, <GEN2> line 434.
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
Subroutine new redefined at Bio\Search\Hit\GenericHit.pm line 127.
Subroutine add_hsp redefined at Bio\Search\Hit\GenericHit.pm line 204.
Subroutine hsp_factory redefined at Bio\Search\Hit\GenericHit.pm line 228.
Subroutine name redefined at Bio\Search\Hit\GenericHit.pm line 248.
Subroutine accession redefined at Bio\Search\Hit\GenericHit.pm line 268.
Subroutine description redefined at Bio\Search\Hit\GenericHit.pm line 288.
Subroutine length redefined at Bio\Search\Hit\GenericHit.pm line 308.
Subroutine algorithm redefined at Bio\Search\Hit\GenericHit.pm line 333.
Subroutine raw_score redefined at Bio\Search\Hit\GenericHit.pm line 355.
Subroutine score redefined at Bio\Search\Hit\GenericHit.pm line 385.
Subroutine significance redefined at Bio\Search\Hit\GenericHit.pm line 400.
Subroutine bits redefined at Bio\Search\Hit\GenericHit.pm line 430.
Subroutine next_hsp redefined at Bio\Search\Hit\GenericHit.pm line 458.
Subroutine hsps redefined at Bio\Search\Hit\GenericHit.pm line 494.
Subroutine num_hsps redefined at Bio\Search\Hit\GenericHit.pm line 517.
Subroutine rewind redefined at Bio\Search\Hit\GenericHit.pm line 538.
Subroutine ambiguous_aln redefined at Bio\Search\Hit\GenericHit.pm line 564.
Subroutine overlap redefined at Bio\Search\Hit\GenericHit.pm line 576.
Subroutine n redefined at Bio\Search\Hit\GenericHit.pm line 605.
Subroutine p redefined at Bio\Search\Hit\GenericHit.pm line 652.
Subroutine hsp redefined at Bio\Search\Hit\GenericHit.pm line 694.
Subroutine logical_length redefined at Bio\Search\Hit\GenericHit.pm line 740.
Subroutine length_aln redefined at Bio\Search\Hit\GenericHit.pm line 786.
Subroutine gaps redefined at Bio\Search\Hit\GenericHit.pm line 849.
Subroutine matches redefined at Bio\Search\Hit\GenericHit.pm line 887.
Subroutine start redefined at Bio\Search\Hit\GenericHit.pm line 948.
Subroutine end redefined at Bio\Search\Hit\GenericHit.pm line 1025.
Subroutine range redefined at Bio\Search\Hit\GenericHit.pm line 1093.
Subroutine frac_identical redefined at Bio\Search\Hit\GenericHit.pm line 1150.
Subroutine frac_conserved redefined at Bio\Search\Hit\GenericHit.pm line 1226.
Subroutine frac_aligned_query redefined at Bio\Search\Hit\GenericHit.pm line 1274.
Subroutine frac_aligned_hit redefined at Bio\Search\Hit\GenericHit.pm line 1310.
Subroutine num_unaligned_hit redefined at Bio\Search\Hit\GenericHit.pm line 1364.
Subroutine num_unaligned_query redefined at Bio\Search\Hit\GenericHit.pm line 1400.
Subroutine seq_inds redefined at Bio\Search\Hit\GenericHit.pm line 1442.
Subroutine strand redefined at Bio\Search\Hit\GenericHit.pm line 1473.
Subroutine frame redefined at Bio\Search\Hit\GenericHit.pm line 1535.
Subroutine rank redefined at Bio\Search\Hit\GenericHit.pm line 1574.
Subroutine locus redefined at Bio\Search\Hit\GenericHit.pm line 1590.
Subroutine each_accession_number redefined at Bio\Search\Hit\GenericHit.pm line 1618.
Subroutine tiled_hsps redefined at Bio\Search\Hit\GenericHit.pm line 1666.
Subroutine query_length redefined at Bio\Search\Hit\GenericHit.pm line 1683.
Subroutine ncbi_gi redefined at Bio\Search\Hit\GenericHit.pm line 1701.
Subroutine sort_hsps redefined at Bio\Search\Hit\GenericHit.pm line 1732.
Subroutine iteration redefined at Bio\Search\Hit\GenericHit.pm line 1772.
Subroutine found_again redefined at Bio\Search\Hit\GenericHit.pm line 1807.
Subroutine Bio::Search::Hit::GenericHit::frac_aligned_sbjct redefined at Bio\Search\Hit\GenericHit.pm line 1333.
Subroutine Bio::Search::Hit::GenericHit::num_unaligned_sbjct redefined at Bio\Search\Hit\GenericHit.pm line 1341.
Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175.
Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264.
Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284.
Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311.
Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337.
Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357.
Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378.
Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399.
Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420.
Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442.
Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465.
Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487.
Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508.
Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523.
Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540.
Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555.
Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574.
Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599.
Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616.
Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629.
Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646.
Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663.
Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680.
Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700.
Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728.
Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747.
Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763.
Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777.
Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794.
Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815.
Subroutine new redefined at Bio\Search\Hit\BlastHit.pm line 105.
Subroutine iteration redefined at Bio\Search\Hit\BlastHit.pm line 134.
Subroutine found_again redefined at Bio\Search\Hit\BlastHit.pm line 169.
Subroutine expect redefined at Bio\Search\Hit\BlastHit.pm line 176.
Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, <GEN1> line 2564.
Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, <GEN1> line 2564.
Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, <GEN1> line 2564.
Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, <GEN1> line 2564.
Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, <GEN1> line 2564.
Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, <GEN1> line 2564.
t/SearchIO/Tiling.t .................... 
1..1141
ok 1 - use Bio::Search::Tiling::MapTiling;
ok 2 - use Bio::Search::Tiling::MapTileUtils;
ok 3 - use Bio::SearchIO;
ok 4 - use Bio::Search::Hit::BlastHit;
ok 5 - use File::Spec;
ok 6 - parse data file
ok 7 - got test hit
ok 8 - create tiling
ok 9 - The object isa Bio::Search::Tiling::TilingI
ok 10 - implements 'next_tiling'
ok 11 - implements 'rewind_tilings'
ok 12 - implements 'identities'
ok 13 - implements 'conserved'
ok 14 - implements 'length'
ok 15 - identities regression test
ok 16 - conserved regression test
ok 17 - tiling iterator regression test(1)
ok 18 - tiling iterator regression test(2)
ok 19 - tiling iterator regression test(3, rewind)
ok 20 - ecolitst.wublastp
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29 - dnaEbsub_ecoli.wublastx
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36 - tricky.wublast
ok 37 - tricky.wublast(1)
ok 38 - tricky.wublast(2)
ok 39 - tricky.wublast(3)
ok 40 - tricky.wublast(4)
ok 41 - ecolitst.bls
ok 42 - tile ecolitst.bls hit 1 \#hsps 1
ok 43 - q id: est (0.98293) = fast (0.98293)
ok 44 - q cn: est (0.98293) = fast (0.98293)
ok 45 - h id: est (0.98293) = fast (0.98293)
ok 46 - h cn: est (0.98293) = fast (0.98293)
ok 47 - tile ecolitst.bls hit 2 \#hsps 1
ok 48 - q id: est (0.30074) = fast (0.30074)
ok 49 - q cn: est (0.49876) = fast (0.49876)
ok 50 - h id: est (0.30759) = fast (0.30759)
ok 51 - h cn: est (0.51013) = fast (0.51013)
ok 52 - tile ecolitst.bls hit 3 \#hsps 1
ok 53 - q id: est (0.31004) = fast (0.31004)
ok 54 - q cn: est (0.49782) = fast (0.49782)
ok 55 - h id: est (0.32054) = fast (0.32054)
ok 56 - h cn: est (0.51467) = fast (0.51467)
ok 57 - tile ecolitst.bls hit 4 \#hsps 1
ok 58 - q id: est (0.30435) = fast (0.30435)
ok 59 - q cn: est (0.47826) = fast (0.47826)
ok 60 - h id: est (0.29787) = fast (0.29787)
ok 61 - h cn: est (0.46809) = fast (0.46809)
ok 62 - tricky.wublast
ok 63 - tile tricky.wublast hit 1 \#hsps 7
ok 64 - q id: exact (0.22153) ~ est (0.22153)
ok 65 - q id: exact (0.22153) <= max (0.22153)
ok 66 - q cn: exact (0.42760) ~ est (0.42760)
ok 67 - q cn: exact (0.42760) <= max (0.42760)
ok 68 - h id: exact (0.22704) ~ est (0.22704)
ok 69 - h id: exact (0.22704) <= max (0.22704)
ok 70 - h cn: exact (0.43335) ~ est (0.43335)
ok 71 - h cn: exact (0.43335) <= max (0.43335)
ok 72 - a_thaliana.blastn
ok 73 - tile a_thaliana.blastn hit 1 \#hsps 1
ok 74 - q id: est (0.96667) = fast (0.96667)
ok 75 - q cn: est (0.96667) = fast (0.96667)
ok 76 - h id: est (0.98305) = fast (0.98305)
ok 77 - h cn: est (0.98305) = fast (0.98305)
ok 78 - tile a_thaliana.blastn hit 2 \#hsps 1
ok 79 - q id: est (0.96667) = fast (0.96667)
ok 80 - q cn: est (0.96667) = fast (0.96667)
ok 81 - h id: est (0.98305) = fast (0.98305)
ok 82 - h cn: est (0.98305) = fast (0.98305)
ok 83 - tile a_thaliana.blastn hit 3 \#hsps 1
ok 84 - q id: est (1.00000) = fast (1.00000)
ok 85 - q cn: est (1.00000) = fast (1.00000)
ok 86 - h id: est (1.00000) = fast (1.00000)
ok 87 - h cn: est (1.00000) = fast (1.00000)
ok 88 - tile a_thaliana.blastn hit 4 \#hsps 1
ok 89 - q id: est (1.00000) = fast (1.00000)
ok 90 - q cn: est (1.00000) = fast (1.00000)
ok 91 - h id: est (1.00000) = fast (1.00000)
ok 92 - h cn: est (1.00000) = fast (1.00000)
ok 93 - tile a_thaliana.blastn hit 5 \#hsps 1
ok 94 - q id: est (0.92308) = fast (0.92308)
ok 95 - q cn: est (0.92308) = fast (0.92308)
ok 96 - h id: est (0.92308) = fast (0.92308)
ok 97 - h cn: est (0.92308) = fast (0.92308)
ok 98 - tile a_thaliana.blastn hit 6 \#hsps 1
ok 99 - q id: est (1.00000) = fast (1.00000)
ok 100 - q cn: est (1.00000) = fast (1.00000)
ok 101 - h id: est (1.00000) = fast (1.00000)
ok 102 - h cn: est (1.00000) = fast (1.00000)
ok 103 - tile a_thaliana.blastn hit 7 \#hsps 1
ok 104 - q id: est (1.00000) = fast (1.00000)
ok 105 - q cn: est (1.00000) = fast (1.00000)
ok 106 - h id: est (1.00000) = fast (1.00000)
ok 107 - h cn: est (1.00000) = fast (1.00000)
ok 108 - tile a_thaliana.blastn hit 8 \#hsps 1
ok 109 - q id: est (1.00000) = fast (1.00000)
ok 110 - q cn: est (1.00000) = fast (1.00000)
ok 111 - h id: est (1.00000) = fast (1.00000)
ok 112 - h cn: est (1.00000) = fast (1.00000)
ok 113 - tile a_thaliana.blastn hit 9 \#hsps 1
ok 114 - q id: est (1.00000) = fast (1.00000)
ok 115 - q cn: est (1.00000) = fast (1.00000)
ok 116 - h id: est (1.00000) = fast (1.00000)
ok 117 - h cn: est (1.00000) = fast (1.00000)
ok 118 - tile a_thaliana.blastn hit 10 \#hsps 1
ok 119 - q id: est (1.00000) = fast (1.00000)
ok 120 - q cn: est (1.00000) = fast (1.00000)
ok 121 - h id: est (1.00000) = fast (1.00000)
ok 122 - h cn: est (1.00000) = fast (1.00000)
ok 123 - tile a_thaliana.blastn hit 11 \#hsps 1
ok 124 - q id: est (1.00000) = fast (1.00000)
ok 125 - q cn: est (1.00000) = fast (1.00000)
ok 126 - h id: est (1.00000) = fast (1.00000)
ok 127 - h cn: est (1.00000) = fast (1.00000)
ok 128 - tile a_thaliana.blastn hit 12 \#hsps 1
ok 129 - q id: est (1.00000) = fast (1.00000)
ok 130 - q cn: est (1.00000) = fast (1.00000)
ok 131 - h id: est (1.00000) = fast (1.00000)
ok 132 - h cn: est (1.00000) = fast (1.00000)
ok 133 - tile a_thaliana.blastn hit 13 \#hsps 1
ok 134 - q id: est (1.00000) = fast (1.00000)
ok 135 - q cn: est (1.00000) = fast (1.00000)
ok 136 - h id: est (1.00000) = fast (1.00000)
ok 137 - h cn: est (1.00000) = fast (1.00000)
ok 138 - tile a_thaliana.blastn hit 14 \#hsps 1
ok 139 - q id: est (1.00000) = fast (1.00000)
ok 140 - q cn: est (1.00000) = fast (1.00000)
ok 141 - h id: est (1.00000) = fast (1.00000)
ok 142 - h cn: est (1.00000) = fast (1.00000)
ok 143 - tile a_thaliana.blastn hit 15 \#hsps 1
ok 144 - q id: est (1.00000) = fast (1.00000)
ok 145 - q cn: est (1.00000) = fast (1.00000)
ok 146 - h id: est (1.00000) = fast (1.00000)
ok 147 - h cn: est (1.00000) = fast (1.00000)
ok 148 - tile a_thaliana.blastn hit 16 \#hsps 1
ok 149 - q id: est (1.00000) = fast (1.00000)
ok 150 - q cn: est (1.00000) = fast (1.00000)
ok 151 - h id: est (1.00000) = fast (1.00000)
ok 152 - h cn: est (1.00000) = fast (1.00000)
ok 153 - tile a_thaliana.blastn hit 17 \#hsps 1
ok 154 - q id: est (1.00000) = fast (1.00000)
ok 155 - q cn: est (1.00000) = fast (1.00000)
ok 156 - h id: est (1.00000) = fast (1.00000)
ok 157 - h cn: est (1.00000) = fast (1.00000)
ok 158 - tile a_thaliana.blastn hit 18 \#hsps 1
ok 159 - q id: est (1.00000) = fast (1.00000)
ok 160 - q cn: est (1.00000) = fast (1.00000)
ok 161 - h id: est (1.00000) = fast (1.00000)
ok 162 - h cn: est (1.00000) = fast (1.00000)
ok 163 - tile a_thaliana.blastn hit 19 \#hsps 1
ok 164 - q id: est (1.00000) = fast (1.00000)
ok 165 - q cn: est (1.00000) = fast (1.00000)
ok 166 - h id: est (1.00000) = fast (1.00000)
ok 167 - h cn: est (1.00000) = fast (1.00000)
ok 168 - tile a_thaliana.blastn hit 20 \#hsps 1
ok 169 - q id: est (0.95238) = fast (0.95238)
ok 170 - q cn: est (0.95238) = fast (0.95238)
ok 171 - h id: est (0.95238) = fast (0.95238)
ok 172 - h cn: est (0.95238) = fast (0.95238)
ok 173 - tile a_thaliana.blastn hit 21 \#hsps 1
ok 174 - q id: est (1.00000) = fast (1.00000)
ok 175 - q cn: est (1.00000) = fast (1.00000)
ok 176 - h id: est (1.00000) = fast (1.00000)
ok 177 - h cn: est (1.00000) = fast (1.00000)
ok 178 - tile a_thaliana.blastn hit 22 \#hsps 1
ok 179 - q id: est (0.95238) = fast (0.95238)
ok 180 - q cn: est (0.95238) = fast (0.95238)
ok 181 - h id: est (0.95238) = fast (0.95238)
ok 182 - h cn: est (0.95238) = fast (0.95238)
ok 183 - tile a_thaliana.blastn hit 23 \#hsps 1
ok 184 - q id: est (1.00000) = fast (1.00000)
ok 185 - q cn: est (1.00000) = fast (1.00000)
ok 186 - h id: est (1.00000) = fast (1.00000)
ok 187 - h cn: est (1.00000) = fast (1.00000)
ok 188 - tile a_thaliana.blastn hit 24 \#hsps 1
ok 189 - q id: est (0.95238) = fast (0.95238)
ok 190 - q cn: est (0.95238) = fast (0.95238)
ok 191 - h id: est (0.95238) = fast (0.95238)
ok 192 - h cn: est (0.95238) = fast (0.95238)
ok 193 - tile a_thaliana.blastn hit 25 \#hsps 1
ok 194 - q id: est (1.00000) = fast (1.00000)
ok 195 - q cn: est (1.00000) = fast (1.00000)
ok 196 - h id: est (1.00000) = fast (1.00000)
ok 197 - h cn: est (1.00000) = fast (1.00000)
ok 198 - tile a_thaliana.blastn hit 26 \#hsps 1
ok 199 - q id: est (1.00000) = fast (1.00000)
ok 200 - q cn: est (1.00000) = fast (1.00000)
ok 201 - h id: est (1.00000) = fast (1.00000)
ok 202 - h cn: est (1.00000) = fast (1.00000)
ok 203 - tile a_thaliana.blastn hit 27 \#hsps 1
ok 204 - q id: est (1.00000) = fast (1.00000)
ok 205 - q cn: est (1.00000) = fast (1.00000)
ok 206 - h id: est (1.00000) = fast (1.00000)
ok 207 - h cn: est (1.00000) = fast (1.00000)
ok 208 - tile a_thaliana.blastn hit 28 \#hsps 1
ok 209 - q id: est (1.00000) = fast (1.00000)
ok 210 - q cn: est (1.00000) = fast (1.00000)
ok 211 - h id: est (1.00000) = fast (1.00000)
ok 212 - h cn: est (1.00000) = fast (1.00000)
ok 213 - tile a_thaliana.blastn hit 29 \#hsps 1
ok 214 - q id: est (1.00000) = fast (1.00000)
ok 215 - q cn: est (1.00000) = fast (1.00000)
ok 216 - h id: est (1.00000) = fast (1.00000)
ok 217 - h cn: est (1.00000) = fast (1.00000)
ok 218 - tile a_thaliana.blastn hit 30 \#hsps 1
ok 219 - q id: est (1.00000) = fast (1.00000)
ok 220 - q cn: est (1.00000) = fast (1.00000)
ok 221 - h id: est (1.00000) = fast (1.00000)
ok 222 - h cn: est (1.00000) = fast (1.00000)
ok 223 - tile a_thaliana.blastn hit 31 \#hsps 1
ok 224 - q id: est (1.00000) = fast (1.00000)
ok 225 - q cn: est (1.00000) = fast (1.00000)
ok 226 - h id: est (1.00000) = fast (1.00000)
ok 227 - h cn: est (1.00000) = fast (1.00000)
ok 228 - brassica_ATH.WUBLASTN
ok 229 - tile brassica_ATH.WUBLASTN hit 1 \#hsps 3
ok 230 - q id: exact (0.82465) ~ est (0.82343)
ok 231 - q id: exact (0.82465) <= max (0.83333)
ok 232 - q cn: exact (0.85590) ~ est (0.85312)
ok 233 - q cn: exact (0.85590) <= max (0.86458)
ok 234 - h id: exact (0.83920) ~ est (0.83920)
ok 235 - h id: exact (0.83920) <= max (0.83920)
ok 236 - h cn: exact (0.86935) ~ est (0.86935)
ok 237 - h cn: exact (0.86935) <= max (0.86935)
ok 238 - tile brassica_ATH.WUBLASTN hit 2 \#hsps 2
ok 239 - q id: exact (0.82486) ~ est (0.82486)
ok 240 - q id: exact (0.82486) <= max (0.82486)
ok 241 - q cn: exact (0.85122) ~ est (0.85122)
ok 242 - q cn: exact (0.85122) <= max (0.85122)
ok 243 - h id: exact (0.82955) ~ est (0.82955)
ok 244 - h id: exact (0.82955) <= max (0.82955)
ok 245 - h cn: exact (0.85606) ~ est (0.85606)
ok 246 - h cn: exact (0.85606) <= max (0.85606)
ok 247 - no_hsps.blastp
ok 248 - tile no_hsps.blastp hit 1 \#hsps 0
ok 249 - tile no_hsps.blastp hit 2 \#hsps 0
ok 250 - tile no_hsps.blastp hit 3 \#hsps 0
ok 251 - tile no_hsps.blastp hit 4 \#hsps 0
ok 252 - tile no_hsps.blastp hit 5 \#hsps 0
ok 253 - tile no_hsps.blastp hit 6 \#hsps 0
ok 254 - tile no_hsps.blastp hit 7 \#hsps 0
ok 255 - tile no_hsps.blastp hit 8 \#hsps 0
ok 256 - tile no_hsps.blastp hit 9 \#hsps 0
ok 257 - tile no_hsps.blastp hit 10 \#hsps 0
ok 258 - tile no_hsps.blastp hit 11 \#hsps 0
ok 259 - tile no_hsps.blastp hit 12 \#hsps 0
ok 260 - tile no_hsps.blastp hit 13 \#hsps 0
ok 261 - tile no_hsps.blastp hit 14 \#hsps 0
ok 262 - tile no_hsps.blastp hit 15 \#hsps 0
ok 263 - tile no_hsps.blastp hit 16 \#hsps 0
ok 264 - tile no_hsps.blastp hit 17 \#hsps 0
ok 265 - tile no_hsps.blastp hit 18 \#hsps 0
ok 266 - tile no_hsps.blastp hit 19 \#hsps 0
ok 267 - tile no_hsps.blastp hit 20 \#hsps 0
ok 268 - tile no_hsps.blastp hit 21 \#hsps 0
ok 269 - tile no_hsps.blastp hit 22 \#hsps 0
ok 270 - tile no_hsps.blastp hit 23 \#hsps 0
ok 271 - tile no_hsps.blastp hit 24 \#hsps 0
ok 272 - tile no_hsps.blastp hit 25 \#hsps 0
ok 273 - tile no_hsps.blastp hit 26 \#hsps 0
ok 274 - tile no_hsps.blastp hit 27 \#hsps 0
ok 275 - tile no_hsps.blastp hit 28 \#hsps 0
ok 276 - tile no_hsps.blastp hit 29 \#hsps 0
ok 277 - tile no_hsps.blastp hit 30 \#hsps 0
ok 278 - tile no_hsps.blastp hit 31 \#hsps 0
ok 279 - tile no_hsps.blastp hit 32 \#hsps 0
ok 280 - tile no_hsps.blastp hit 33 \#hsps 0
ok 281 - tile no_hsps.blastp hit 34 \#hsps 0
ok 282 - tile no_hsps.blastp hit 35 \#hsps 0
ok 283 - tile no_hsps.blastp hit 36 \#hsps 0
ok 284 - tile no_hsps.blastp hit 37 \#hsps 0
ok 285 - tile no_hsps.blastp hit 38 \#hsps 0
ok 286 - tile no_hsps.blastp hit 39 \#hsps 0
ok 287 - tile no_hsps.blastp hit 40 \#hsps 0
ok 288 - tile no_hsps.blastp hit 41 \#hsps 0
ok 289 - tile no_hsps.blastp hit 42 \#hsps 0
ok 290 - tile no_hsps.blastp hit 43 \#hsps 0
ok 291 - tile no_hsps.blastp hit 44 \#hsps 0
ok 292 - tile no_hsps.blastp hit 45 \#hsps 0
ok 293 - tile no_hsps.blastp hit 46 \#hsps 0
ok 294 - tile no_hsps.blastp hit 47 \#hsps 0
ok 295 - tile no_hsps.blastp hit 48 \#hsps 0
ok 296 - tile no_hsps.blastp hit 49 \#hsps 0
ok 297 - tile no_hsps.blastp hit 50 \#hsps 0
ok 298 - tile no_hsps.blastp hit 51 \#hsps 0
ok 299 - tile no_hsps.blastp hit 52 \#hsps 0
ok 300 - tile no_hsps.blastp hit 53 \#hsps 0
ok 301 - tile no_hsps.blastp hit 54 \#hsps 0
ok 302 - tile no_hsps.blastp hit 55 \#hsps 0
ok 303 - tile no_hsps.blastp hit 56 \#hsps 0
ok 304 - tile no_hsps.blastp hit 57 \#hsps 0
ok 305 - tile no_hsps.blastp hit 58 \#hsps 0
ok 306 - tile no_hsps.blastp hit 59 \#hsps 0
ok 307 - tile no_hsps.blastp hit 60 \#hsps 0
ok 308 - tile no_hsps.blastp hit 61 \#hsps 0
ok 309 - tile no_hsps.blastp hit 62 \#hsps 0
ok 310 - tile no_hsps.blastp hit 63 \#hsps 0
ok 311 - tile no_hsps.blastp hit 64 \#hsps 0
ok 312 - tile no_hsps.blastp hit 65 \#hsps 0
ok 313 - tile no_hsps.blastp hit 66 \#hsps 0
ok 314 - tile no_hsps.blastp hit 67 \#hsps 0
ok 315 - tile no_hsps.blastp hit 68 \#hsps 0
ok 316 - tile no_hsps.blastp hit 69 \#hsps 0
ok 317 - tile no_hsps.blastp hit 70 \#hsps 0
ok 318 - tile no_hsps.blastp hit 71 \#hsps 0
ok 319 - tile no_hsps.blastp hit 72 \#hsps 0
ok 320 - tile no_hsps.blastp hit 73 \#hsps 0
ok 321 - tile no_hsps.blastp hit 74 \#hsps 0
ok 322 - tile no_hsps.blastp hit 75 \#hsps 0
ok 323 - tile no_hsps.blastp hit 76 \#hsps 0
ok 324 - tile no_hsps.blastp hit 77 \#hsps 0
ok 325 - tile no_hsps.blastp hit 78 \#hsps 0
ok 326 - tile no_hsps.blastp hit 79 \#hsps 0
ok 327 - tile no_hsps.blastp hit 80 \#hsps 0
ok 328 - tile no_hsps.blastp hit 81 \#hsps 0
ok 329 - tile no_hsps.blastp hit 82 \#hsps 0
ok 330 - tile no_hsps.blastp hit 83 \#hsps 0
ok 331 - tile no_hsps.blastp hit 84 \#hsps 0
ok 332 - tile no_hsps.blastp hit 85 \#hsps 0
ok 333 - tile no_hsps.blastp hit 86 \#hsps 0
ok 334 - tile no_hsps.blastp hit 87 \#hsps 0
ok 335 - tile no_hsps.blastp hit 88 \#hsps 0
ok 336 - tile no_hsps.blastp hit 89 \#hsps 0
ok 337 - tile no_hsps.blastp hit 90 \#hsps 0
ok 338 - tile no_hsps.blastp hit 91 \#hsps 0
ok 339 - tile no_hsps.blastp hit 92 \#hsps 0
ok 340 - tile no_hsps.blastp hit 93 \#hsps 0
ok 341 - tile no_hsps.blastp hit 94 \#hsps 0
ok 342 - tile no_hsps.blastp hit 95 \#hsps 0
ok 343 - tile no_hsps.blastp hit 96 \#hsps 0
ok 344 - tile no_hsps.blastp hit 97 \#hsps 0
ok 345 - tile no_hsps.blastp hit 98 \#hsps 0
ok 346 - tile no_hsps.blastp hit 99 \#hsps 0
ok 347 - tile no_hsps.blastp hit 100 \#hsps 0
ok 348 - tile no_hsps.blastp hit 101 \#hsps 0
ok 349 - tile no_hsps.blastp hit 102 \#hsps 0
ok 350 - tile no_hsps.blastp hit 103 \#hsps 0
ok 351 - tile no_hsps.blastp hit 104 \#hsps 0
ok 352 - tile no_hsps.blastp hit 105 \#hsps 0
ok 353 - tile no_hsps.blastp hit 106 \#hsps 0
ok 354 - tile no_hsps.blastp hit 107 \#hsps 0
ok 355 - tile no_hsps.blastp hit 108 \#hsps 0
ok 356 - tile no_hsps.blastp hit 109 \#hsps 0
ok 357 - tile no_hsps.blastp hit 110 \#hsps 0
ok 358 - tile no_hsps.blastp hit 111 \#hsps 0
ok 359 - tile no_hsps.blastp hit 112 \#hsps 0
ok 360 - tile no_hsps.blastp hit 113 \#hsps 0
ok 361 - tile no_hsps.blastp hit 114 \#hsps 0
ok 362 - tile no_hsps.blastp hit 115 \#hsps 0
ok 363 - tile no_hsps.blastp hit 116 \#hsps 0
ok 364 - tile no_hsps.blastp hit 117 \#hsps 0
ok 365 - tile no_hsps.blastp hit 118 \#hsps 0
ok 366 - tile no_hsps.blastp hit 119 \#hsps 0
ok 367 - tile no_hsps.blastp hit 120 \#hsps 0
ok 368 - tile no_hsps.blastp hit 121 \#hsps 0
ok 369 - tile no_hsps.blastp hit 122 \#hsps 0
ok 370 - tile no_hsps.blastp hit 123 \#hsps 0
ok 371 - tile no_hsps.blastp hit 124 \#hsps 0
ok 372 - tile no_hsps.blastp hit 125 \#hsps 0
ok 373 - tile no_hsps.blastp hit 126 \#hsps 0
ok 374 - tile no_hsps.blastp hit 127 \#hsps 0
ok 375 - tile no_hsps.blastp hit 128 \#hsps 0
ok 376 - tile no_hsps.blastp hit 129 \#hsps 0
ok 377 - tile no_hsps.blastp hit 130 \#hsps 0
ok 378 - tile no_hsps.blastp hit 131 \#hsps 0
ok 379 - tile no_hsps.blastp hit 132 \#hsps 0
ok 380 - tile no_hsps.blastp hit 133 \#hsps 0
ok 381 - tile no_hsps.blastp hit 134 \#hsps 0
ok 382 - tile no_hsps.blastp hit 135 \#hsps 0
ok 383 - tile no_hsps.blastp hit 136 \#hsps 0
ok 384 - tile no_hsps.blastp hit 137 \#hsps 0
ok 385 - tile no_hsps.blastp hit 138 \#hsps 0
ok 386 - tile no_hsps.blastp hit 139 \#hsps 0
ok 387 - tile no_hsps.blastp hit 140 \#hsps 0
ok 388 - tile no_hsps.blastp hit 141 \#hsps 0
ok 389 - tile no_hsps.blastp hit 142 \#hsps 0
ok 390 - tile no_hsps.blastp hit 143 \#hsps 0
ok 391 - tile no_hsps.blastp hit 144 \#hsps 0
ok 392 - tile no_hsps.blastp hit 145 \#hsps 0
ok 393 - tile no_hsps.blastp hit 146 \#hsps 0
ok 394 - tile no_hsps.blastp hit 147 \#hsps 0
ok 395 - tile no_hsps.blastp hit 148 \#hsps 0
ok 396 - tile no_hsps.blastp hit 149 \#hsps 0
ok 397 - tile no_hsps.blastp hit 150 \#hsps 0
ok 398 - tile no_hsps.blastp hit 151 \#hsps 0
ok 399 - tile no_hsps.blastp hit 152 \#hsps 0
ok 400 - tile no_hsps.blastp hit 153 \#hsps 0
ok 401 - tile no_hsps.blastp hit 154 \#hsps 0
ok 402 - tile no_hsps.blastp hit 155 \#hsps 0
ok 403 - tile no_hsps.blastp hit 156 \#hsps 0
ok 404 - tile no_hsps.blastp hit 157 \#hsps 0
ok 405 - tile no_hsps.blastp hit 158 \#hsps 0
ok 406 - tile no_hsps.blastp hit 159 \#hsps 0
ok 407 - tile no_hsps.blastp hit 160 \#hsps 0
ok 408 - tile no_hsps.blastp hit 161 \#hsps 0
ok 409 - tile no_hsps.blastp hit 162 \#hsps 0
ok 410 - tile no_hsps.blastp hit 163 \#hsps 0
ok 411 - tile no_hsps.blastp hit 164 \#hsps 0
ok 412 - tile no_hsps.blastp hit 165 \#hsps 0
ok 413 - tile no_hsps.blastp hit 166 \#hsps 0
ok 414 - tile no_hsps.blastp hit 167 \#hsps 0
ok 415 - tile no_hsps.blastp hit 168 \#hsps 0
ok 416 - tile no_hsps.blastp hit 169 \#hsps 0
ok 417 - tile no_hsps.blastp hit 170 \#hsps 0
ok 418 - tile no_hsps.blastp hit 171 \#hsps 0
ok 419 - tile no_hsps.blastp hit 172 \#hsps 0
ok 420 - tile no_hsps.blastp hit 173 \#hsps 0
ok 421 - tile no_hsps.blastp hit 174 \#hsps 0
ok 422 - tile no_hsps.blastp hit 175 \#hsps 0
ok 423 - tile no_hsps.blastp hit 176 \#hsps 0
ok 424 - tile no_hsps.blastp hit 177 \#hsps 0
ok 425 - tile no_hsps.blastp hit 178 \#hsps 0
ok 426 - tile no_hsps.blastp hit 179 \#hsps 0
ok 427 - tile no_hsps.blastp hit 180 \#hsps 0
ok 428 - tile no_hsps.blastp hit 181 \#hsps 0
ok 429 - tile no_hsps.blastp hit 182 \#hsps 0
ok 430 - tile no_hsps.blastp hit 183 \#hsps 0
ok 431 - tile no_hsps.blastp hit 184 \#hsps 0
ok 432 - tile no_hsps.blastp hit 185 \#hsps 0
ok 433 - tile no_hsps.blastp hit 186 \#hsps 0
ok 434 - tile no_hsps.blastp hit 187 \#hsps 0
ok 435 - tile no_hsps.blastp hit 188 \#hsps 0
ok 436 - tile no_hsps.blastp hit 189 \#hsps 0
ok 437 - tile no_hsps.blastp hit 190 \#hsps 0
ok 438 - tile no_hsps.blastp hit 191 \#hsps 0
ok 439 - tile no_hsps.blastp hit 192 \#hsps 0
ok 440 - tile no_hsps.blastp hit 193 \#hsps 0
ok 441 - tile no_hsps.blastp hit 194 \#hsps 0
ok 442 - tile no_hsps.blastp hit 195 \#hsps 0
ok 443 - tile no_hsps.blastp hit 196 \#hsps 0
ok 444 - tile no_hsps.blastp hit 197 \#hsps 0
ok 445 - tile no_hsps.blastp hit 198 \#hsps 0
ok 446 - tile no_hsps.blastp hit 199 \#hsps 0
ok 447 - tile no_hsps.blastp hit 200 \#hsps 0
ok 448 - tile no_hsps.blastp hit 201 \#hsps 0
ok 449 - tile no_hsps.blastp hit 202 \#hsps 0
ok 450 - tile no_hsps.blastp hit 203 \#hsps 0
ok 451 - tile no_hsps.blastp hit 204 \#hsps 0
ok 452 - tile no_hsps.blastp hit 205 \#hsps 0
ok 453 - tile no_hsps.blastp hit 206 \#hsps 0
ok 454 - tile no_hsps.blastp hit 207 \#hsps 0
ok 455 - tile no_hsps.blastp hit 208 \#hsps 0
ok 456 - tile no_hsps.blastp hit 209 \#hsps 0
ok 457 - tile no_hsps.blastp hit 210 \#hsps 0
ok 458 - tile no_hsps.blastp hit 211 \#hsps 0
ok 459 - tile no_hsps.blastp hit 212 \#hsps 0
ok 460 - tile no_hsps.blastp hit 213 \#hsps 0
ok 461 - tile no_hsps.blastp hit 214 \#hsps 0
ok 462 - tile no_hsps.blastp hit 215 \#hsps 0
ok 463 - tile no_hsps.blastp hit 216 \#hsps 0
ok 464 - tile no_hsps.blastp hit 217 \#hsps 0
ok 465 - tile no_hsps.blastp hit 218 \#hsps 0
ok 466 - tile no_hsps.blastp hit 219 \#hsps 0
ok 467 - tile no_hsps.blastp hit 220 \#hsps 0
ok 468 - tile no_hsps.blastp hit 221 \#hsps 0
ok 469 - tile no_hsps.blastp hit 222 \#hsps 0
ok 470 - tile no_hsps.blastp hit 223 \#hsps 0
ok 471 - tile no_hsps.blastp hit 224 \#hsps 0
ok 472 - tile no_hsps.blastp hit 225 \#hsps 0
ok 473 - tile no_hsps.blastp hit 226 \#hsps 0
ok 474 - tile no_hsps.blastp hit 227 \#hsps 0
ok 475 - tile no_hsps.blastp hit 228 \#hsps 0
ok 476 - tile no_hsps.blastp hit 229 \#hsps 0
ok 477 - tile no_hsps.blastp hit 230 \#hsps 0
ok 478 - tile no_hsps.blastp hit 231 \#hsps 0
ok 479 - tile no_hsps.blastp hit 232 \#hsps 0
ok 480 - tile no_hsps.blastp hit 233 \#hsps 0
ok 481 - tile no_hsps.blastp hit 234 \#hsps 0
ok 482 - tile no_hsps.blastp hit 235 \#hsps 0
ok 483 - tile no_hsps.blastp hit 236 \#hsps 0
ok 484 - tile no_hsps.blastp hit 237 \#hsps 0
ok 485 - tile no_hsps.blastp hit 238 \#hsps 0
ok 486 - tile no_hsps.blastp hit 239 \#hsps 0
ok 487 - tile no_hsps.blastp hit 240 \#hsps 0
ok 488 - tile no_hsps.blastp hit 241 \#hsps 0
ok 489 - tile no_hsps.blastp hit 242 \#hsps 0
ok 490 - tile no_hsps.blastp hit 243 \#hsps 0
ok 491 - tile no_hsps.blastp hit 244 \#hsps 0
ok 492 - tile no_hsps.blastp hit 245 \#hsps 0
ok 493 - tile no_hsps.blastp hit 246 \#hsps 0
ok 494 - tile no_hsps.blastp hit 247 \#hsps 0
ok 495 - tile no_hsps.blastp hit 248 \#hsps 0
ok 496 - tile no_hsps.blastp hit 249 \#hsps 0
ok 497 - tile no_hsps.blastp hit 250 \#hsps 0
ok 498 - tile no_hsps.blastp hit 251 \#hsps 0
ok 499 - tile no_hsps.blastp hit 252 \#hsps 0
ok 500 - tile no_hsps.blastp hit 253 \#hsps 0
ok 501 - tile no_hsps.blastp hit 254 \#hsps 0
ok 502 - tile no_hsps.blastp hit 255 \#hsps 0
ok 503 - tile no_hsps.blastp hit 256 \#hsps 0
ok 504 - tile no_hsps.blastp hit 257 \#hsps 0
ok 505 - tile no_hsps.blastp hit 258 \#hsps 0
ok 506 - tile no_hsps.blastp hit 259 \#hsps 0
ok 507 - tile no_hsps.blastp hit 260 \#hsps 0
ok 508 - tile no_hsps.blastp hit 261 \#hsps 0
ok 509 - tile no_hsps.blastp hit 262 \#hsps 0
ok 510 - tile no_hsps.blastp hit 263 \#hsps 0
ok 511 - tile no_hsps.blastp hit 264 \#hsps 0
ok 512 - tile no_hsps.blastp hit 265 \#hsps 0
ok 513 - tile no_hsps.blastp hit 266 \#hsps 0
ok 514 - tile no_hsps.blastp hit 267 \#hsps 0
ok 515 - tile no_hsps.blastp hit 268 \#hsps 0
ok 516 - tile no_hsps.blastp hit 269 \#hsps 0
ok 517 - tile no_hsps.blastp hit 270 \#hsps 0
ok 518 - tile no_hsps.blastp hit 271 \#hsps 0
ok 519 - tile no_hsps.blastp hit 272 \#hsps 0
ok 520 - tile no_hsps.blastp hit 273 \#hsps 0
ok 521 - tile no_hsps.blastp hit 274 \#hsps 0
ok 522 - tile no_hsps.blastp hit 275 \#hsps 0
ok 523 - tile no_hsps.blastp hit 276 \#hsps 0
ok 524 - tile no_hsps.blastp hit 277 \#hsps 0
ok 525 - tile no_hsps.blastp hit 278 \#hsps 0
ok 526 - tile no_hsps.blastp hit 279 \#hsps 0
ok 527 - tile no_hsps.blastp hit 280 \#hsps 0
ok 528 - tile no_hsps.blastp hit 281 \#hsps 0
ok 529 - tile no_hsps.blastp hit 282 \#hsps 0
ok 530 - tile no_hsps.blastp hit 283 \#hsps 0
ok 531 - tile no_hsps.blastp hit 284 \#hsps 0
ok 532 - tile no_hsps.blastp hit 285 \#hsps 0
ok 533 - tile no_hsps.blastp hit 286 \#hsps 0
ok 534 - tile no_hsps.blastp hit 287 \#hsps 0
ok 535 - tile no_hsps.blastp hit 288 \#hsps 0
ok 536 - tile no_hsps.blastp hit 289 \#hsps 0
ok 537 - tile no_hsps.blastp hit 290 \#hsps 0
ok 538 - tile no_hsps.blastp hit 291 \#hsps 0
ok 539 - tile no_hsps.blastp hit 292 \#hsps 0
ok 540 - tile no_hsps.blastp hit 293 \#hsps 0
ok 541 - tile no_hsps.blastp hit 294 \#hsps 0
ok 542 - tile no_hsps.blastp hit 295 \#hsps 0
ok 543 - tile no_hsps.blastp hit 296 \#hsps 0
ok 544 - tile no_hsps.blastp hit 297 \#hsps 0
ok 545 - tile no_hsps.blastp hit 298 \#hsps 0
ok 546 - tile no_hsps.blastp hit 299 \#hsps 0
ok 547 - tile no_hsps.blastp hit 300 \#hsps 0
ok 548 - tile no_hsps.blastp hit 301 \#hsps 0
ok 549 - tile no_hsps.blastp hit 302 \#hsps 0
ok 550 - tile no_hsps.blastp hit 303 \#hsps 0
ok 551 - tile no_hsps.blastp hit 304 \#hsps 0
ok 552 - tile no_hsps.blastp hit 305 \#hsps 0
ok 553 - tile no_hsps.blastp hit 306 \#hsps 0
ok 554 - tile no_hsps.blastp hit 307 \#hsps 0
ok 555 - tile no_hsps.blastp hit 308 \#hsps 0
ok 556 - tile no_hsps.blastp hit 309 \#hsps 0
ok 557 - tile no_hsps.blastp hit 310 \#hsps 0
ok 558 - tile no_hsps.blastp hit 311 \#hsps 0
ok 559 - tile no_hsps.blastp hit 312 \#hsps 0
ok 560 - tile no_hsps.blastp hit 313 \#hsps 0
ok 561 - tile no_hsps.blastp hit 314 \#hsps 0
ok 562 - tile no_hsps.blastp hit 315 \#hsps 0
ok 563 - tile no_hsps.blastp hit 316 \#hsps 0
ok 564 - tile no_hsps.blastp hit 317 \#hsps 0
ok 565 - tile no_hsps.blastp hit 318 \#hsps 0
ok 566 - tile no_hsps.blastp hit 319 \#hsps 0
ok 567 - tile no_hsps.blastp hit 320 \#hsps 0
ok 568 - tile no_hsps.blastp hit 321 \#hsps 0
ok 569 - tile no_hsps.blastp hit 322 \#hsps 0
ok 570 - tile no_hsps.blastp hit 323 \#hsps 0
ok 571 - tile no_hsps.blastp hit 324 \#hsps 0
ok 572 - tile no_hsps.blastp hit 325 \#hsps 0
ok 573 - tile no_hsps.blastp hit 326 \#hsps 0
ok 574 - tile no_hsps.blastp hit 327 \#hsps 0
ok 575 - tile no_hsps.blastp hit 328 \#hsps 0
ok 576 - tile no_hsps.blastp hit 329 \#hsps 0
ok 577 - tile no_hsps.blastp hit 330 \#hsps 0
ok 578 - tile no_hsps.blastp hit 331 \#hsps 0
ok 579 - tile no_hsps.blastp hit 332 \#hsps 0
ok 580 - tile no_hsps.blastp hit 333 \#hsps 0
ok 581 - tile no_hsps.blastp hit 334 \#hsps 0
ok 582 - tile no_hsps.blastp hit 335 \#hsps 0
ok 583 - tile no_hsps.blastp hit 336 \#hsps 0
ok 584 - tile no_hsps.blastp hit 337 \#hsps 0
ok 585 - tile no_hsps.blastp hit 338 \#hsps 0
ok 586 - tile no_hsps.blastp hit 339 \#hsps 0
ok 587 - tile no_hsps.blastp hit 340 \#hsps 0
ok 588 - tile no_hsps.blastp hit 341 \#hsps 0
ok 589 - tile no_hsps.blastp hit 342 \#hsps 0
ok 590 - tile no_hsps.blastp hit 343 \#hsps 0
ok 591 - tile no_hsps.blastp hit 344 \#hsps 0
ok 592 - tile no_hsps.blastp hit 345 \#hsps 0
ok 593 - tile no_hsps.blastp hit 346 \#hsps 0
ok 594 - tile no_hsps.blastp hit 347 \#hsps 0
ok 595 - tile no_hsps.blastp hit 348 \#hsps 0
ok 596 - tile no_hsps.blastp hit 349 \#hsps 0
ok 597 - tile no_hsps.blastp hit 350 \#hsps 0
ok 598 - tile no_hsps.blastp hit 351 \#hsps 0
ok 599 - tile no_hsps.blastp hit 352 \#hsps 0
ok 600 - tile no_hsps.blastp hit 353 \#hsps 0
ok 601 - tile no_hsps.blastp hit 354 \#hsps 0
ok 602 - tile no_hsps.blastp hit 355 \#hsps 0
ok 603 - tile no_hsps.blastp hit 356 \#hsps 0
ok 604 - tile no_hsps.blastp hit 357 \#hsps 0
ok 605 - tile no_hsps.blastp hit 358 \#hsps 0
ok 606 - tile no_hsps.blastp hit 359 \#hsps 0
ok 607 - tile no_hsps.blastp hit 360 \#hsps 0
ok 608 - tile no_hsps.blastp hit 361 \#hsps 0
ok 609 - tile no_hsps.blastp hit 362 \#hsps 0
ok 610 - tile no_hsps.blastp hit 363 \#hsps 0
ok 611 - tile no_hsps.blastp hit 364 \#hsps 0
ok 612 - tile no_hsps.blastp hit 365 \#hsps 0
ok 613 - tile no_hsps.blastp hit 366 \#hsps 0
ok 614 - tile no_hsps.blastp hit 367 \#hsps 0
ok 615 - tile no_hsps.blastp hit 368 \#hsps 0
ok 616 - tile no_hsps.blastp hit 369 \#hsps 0
ok 617 - tile no_hsps.blastp hit 370 \#hsps 0
ok 618 - tile no_hsps.blastp hit 371 \#hsps 0
ok 619 - tile no_hsps.blastp hit 372 \#hsps 0
ok 620 - tile no_hsps.blastp hit 373 \#hsps 0
ok 621 - tile no_hsps.blastp hit 374 \#hsps 0
ok 622 - tile no_hsps.blastp hit 375 \#hsps 0
ok 623 - tile no_hsps.blastp hit 376 \#hsps 0
ok 624 - tile no_hsps.blastp hit 377 \#hsps 0
ok 625 - tile no_hsps.blastp hit 378 \#hsps 0
ok 626 - tile no_hsps.blastp hit 379 \#hsps 0
ok 627 - tile no_hsps.blastp hit 380 \#hsps 0
ok 628 - tile no_hsps.blastp hit 381 \#hsps 0
ok 629 - tile no_hsps.blastp hit 382 \#hsps 0
ok 630 - tile no_hsps.blastp hit 383 \#hsps 0
ok 631 - tile no_hsps.blastp hit 384 \#hsps 0
ok 632 - tile no_hsps.blastp hit 385 \#hsps 0
ok 633 - tile no_hsps.blastp hit 386 \#hsps 0
ok 634 - tile no_hsps.blastp hit 387 \#hsps 0
ok 635 - tile no_hsps.blastp hit 388 \#hsps 0
ok 636 - tile no_hsps.blastp hit 389 \#hsps 0
ok 637 - tile no_hsps.blastp hit 390 \#hsps 0
ok 638 - tile no_hsps.blastp hit 391 \#hsps 0
ok 639 - tile no_hsps.blastp hit 392 \#hsps 0
ok 640 - tile no_hsps.blastp hit 393 \#hsps 0
ok 641 - tile no_hsps.blastp hit 394 \#hsps 0
ok 642 - tile no_hsps.blastp hit 395 \#hsps 0
ok 643 - tile no_hsps.blastp hit 396 \#hsps 0
ok 644 - tile no_hsps.blastp hit 397 \#hsps 0
ok 645 - tile no_hsps.blastp hit 398 \#hsps 0
ok 646 - tile no_hsps.blastp hit 399 \#hsps 0
ok 647 - tile no_hsps.blastp hit 400 \#hsps 0
ok 648 - tile no_hsps.blastp hit 401 \#hsps 0
ok 649 - tile no_hsps.blastp hit 402 \#hsps 0
ok 650 - tile no_hsps.blastp hit 403 \#hsps 0
ok 651 - tile no_hsps.blastp hit 404 \#hsps 0
ok 652 - tile no_hsps.blastp hit 405 \#hsps 0
ok 653 - tile no_hsps.blastp hit 406 \#hsps 0
ok 654 - tile no_hsps.blastp hit 407 \#hsps 0
ok 655 - tile no_hsps.blastp hit 408 \#hsps 0
ok 656 - tile no_hsps.blastp hit 409 \#hsps 0
ok 657 - tile no_hsps.blastp hit 410 \#hsps 0
ok 658 - tile no_hsps.blastp hit 411 \#hsps 0
ok 659 - tile no_hsps.blastp hit 412 \#hsps 0
ok 660 - tile no_hsps.blastp hit 413 \#hsps 0
ok 661 - tile no_hsps.blastp hit 414 \#hsps 0
ok 662 - tile no_hsps.blastp hit 415 \#hsps 0
ok 663 - catalase-webblast.BLASTP
ok 664 - tile catalase-webblast.BLASTP hit 1 \#hsps 1
ok 665 - q id: est (1.00000) = fast (1.00000)
ok 666 - q cn: est (1.00000) = fast (1.00000)
ok 667 - h id: est (1.00000) = fast (1.00000)
ok 668 - h cn: est (1.00000) = fast (1.00000)
ok 669 - tile catalase-webblast.BLASTP hit 2 \#hsps 1
ok 670 - q id: est (0.80973) = fast (0.80973)
ok 671 - q cn: est (0.89006) = fast (0.89006)
ok 672 - h id: est (0.82543) = fast (0.82543)
ok 673 - h cn: est (0.90733) = fast (0.90733)
ok 674 - tile catalase-webblast.BLASTP hit 3 \#hsps 1
ok 675 - q id: est (0.71670) = fast (0.71670)
ok 676 - q cn: est (0.84144) = fast (0.84144)
ok 677 - h id: est (0.72747) = fast (0.72747)
ok 678 - h cn: est (0.85408) = fast (0.85408)
ok 679 - tile catalase-webblast.BLASTP hit 4 \#hsps 1
ok 680 - q id: est (0.58910) = fast (0.58910)
ok 681 - q cn: est (0.70860) = fast (0.70860)
ok 682 - h id: est (0.65654) = fast (0.65654)
ok 683 - h cn: est (0.78972) = fast (0.78972)
ok 684 - tile catalase-webblast.BLASTP hit 5 \#hsps 1
ok 685 - q id: est (0.49245) = fast (0.49245)
ok 686 - q cn: est (0.65257) = fast (0.65257)
ok 687 - h id: est (0.49544) = fast (0.49544)
ok 688 - h cn: est (0.65653) = fast (0.65653)
ok 689 - tile catalase-webblast.BLASTP hit 6 \#hsps 1
ok 690 - q id: est (0.44366) = fast (0.44366)
ok 691 - q cn: est (0.58920) = fast (0.58920)
ok 692 - h id: est (0.44787) = fast (0.44787)
ok 693 - h cn: est (0.59479) = fast (0.59479)
ok 694 - tile catalase-webblast.BLASTP hit 7 \#hsps 1
ok 695 - q id: est (0.42564) = fast (0.42564)
ok 696 - q cn: est (0.61282) = fast (0.61282)
ok 697 - h id: est (0.43229) = fast (0.43229)
ok 698 - h cn: est (0.62240) = fast (0.62240)
ok 699 - tile catalase-webblast.BLASTP hit 8 \#hsps 1
ok 700 - q id: est (0.48358) = fast (0.48358)
ok 701 - q cn: est (0.63881) = fast (0.63881)
ok 702 - h id: est (0.48943) = fast (0.48943)
ok 703 - h cn: est (0.64653) = fast (0.64653)
ok 704 - tile catalase-webblast.BLASTP hit 9 \#hsps 1
ok 705 - q id: est (0.42308) = fast (0.42308)
ok 706 - q cn: est (0.61282) = fast (0.61282)
ok 707 - h id: est (0.42969) = fast (0.42969)
ok 708 - h cn: est (0.62240) = fast (0.62240)
ok 709 - tile catalase-webblast.BLASTP hit 10 \#hsps 1
ok 710 - q id: est (0.39675) = fast (0.39675)
ok 711 - q cn: est (0.58933) = fast (0.58933)
ok 712 - h id: est (0.39767) = fast (0.39767)
ok 713 - h cn: est (0.59070) = fast (0.59070)
ok 714 - dcr1_sp.WUBLASTP
ok 715 - tile dcr1_sp.WUBLASTP hit 1 \#hsps 1
ok 716 - q id: est (1.00000) = fast (1.00000)
ok 717 - q cn: est (1.00000) = fast (1.00000)
ok 718 - h id: est (1.00000) = fast (1.00000)
ok 719 - h cn: est (1.00000) = fast (1.00000)
ok 720 - tile dcr1_sp.WUBLASTP hit 2 \#hsps 4
ok 721 - q id: exact (0.36876) ~ est (0.36973)
ok 722 - q id: exact (0.36876) <= max (0.37070)
ok 723 - q cn: exact (0.55022) ~ est (0.55041)
ok 724 - q cn: exact (0.55022) <= max (0.55105)
ok 725 - h id: exact (0.35111) ~ est (0.35111)
ok 726 - h id: exact (0.35111) <= max (0.35111)
ok 727 - h cn: exact (0.52305) ~ est (0.52305)
ok 728 - h cn: exact (0.52305) <= max (0.52305)
ok 729 - tile dcr1_sp.WUBLASTP hit 3 \#hsps 1
ok 730 - q id: est (0.38685) = fast (0.38685)
ok 731 - q cn: est (0.55397) = fast (0.55397)
ok 732 - h id: est (0.37613) = fast (0.37613)
ok 733 - h cn: est (0.53863) = fast (0.53863)
ok 734 - tile dcr1_sp.WUBLASTP hit 4 \#hsps 1
ok 735 - q id: est (0.38247) = fast (0.38247)
ok 736 - q cn: est (0.55068) = fast (0.55068)
ok 737 - h id: est (0.37306) = fast (0.37306)
ok 738 - h cn: est (0.53715) = fast (0.53715)
ok 739 - tile dcr1_sp.WUBLASTP hit 5 \#hsps 5
ok 740 - q id: exact (0.35010) ~ est (0.35010)
ok 741 - q id: exact (0.35010) <= max (0.35010)
ok 742 - q cn: exact (0.53183) ~ est (0.53183)
ok 743 - q cn: exact (0.53183) <= max (0.53183)
ok 744 - h id: exact (0.35082) ~ est (0.35082)
ok 745 - h id: exact (0.35082) <= max (0.35082)
ok 746 - h cn: exact (0.53292) ~ est (0.53292)
ok 747 - h cn: exact (0.53292) <= max (0.53292)
ok 748 - tile dcr1_sp.WUBLASTP hit 6 \#hsps 8
ok 749 - q id: exact (0.30547) ~ est (0.30659)
ok 750 - q id: exact (0.30547) <= max (0.30623)
ok 751 - q cn: exact (0.50076) ~ est (0.50205)
ok 752 - q cn: exact (0.50076) <= max (0.50076)
ok 753 - h id: exact (0.31390) ~ est (0.31179)
ok 754 - h id: exact (0.31390) <= max (0.31795)
ok 755 - h cn: exact (0.50531) ~ est (0.50557)
ok 756 - h cn: exact (0.50531) <= max (0.51091)
ok 757 - tile dcr1_sp.WUBLASTP hit 7 \#hsps 7
ok 758 - q id: exact (0.30136) ~ est (0.30184)
ok 759 - q id: exact (0.30136) <= max (0.30498)
ok 760 - q cn: exact (0.48688) ~ est (0.48742)
ok 761 - q cn: exact (0.48688) <= max (0.49140)
ok 762 - h id: exact (0.30944) ~ est (0.31034)
ok 763 - h id: exact (0.30944) <= max (0.30988)
ok 764 - h cn: exact (0.50178) ~ est (0.50277)
ok 765 - h cn: exact (0.50178) <= max (0.50223)
ok 766 - tile dcr1_sp.WUBLASTP hit 8 \#hsps 10
ok 767 - q id: exact (0.28918) ~ est (0.28961)
ok 768 - q id: exact (0.28918) <= max (0.28955)
ok 769 - q cn: exact (0.46418) ~ est (0.46247)
ok 770 - q cn: exact (0.46418) <= max (0.46866)
ok 771 - h id: exact (0.30166) ~ est (0.30299)
ok 772 - h id: exact (0.30166) <= max (0.30800)
ok 773 - h cn: exact (0.48179) ~ est (0.48439)
ok 774 - h cn: exact (0.48179) <= max (0.48535)
ok 775 - tile dcr1_sp.WUBLASTP hit 9 \#hsps 8
ok 776 - q id: exact (0.30289) ~ est (0.30238)
ok 777 - q id: exact (0.30289) <= max (0.30651)
ok 778 - q cn: exact (0.49955) ~ est (0.49787)
ok 779 - q cn: exact (0.49955) <= max (0.50362)
ok 780 - h id: exact (0.31395) ~ est (0.31347)
ok 781 - h id: exact (0.31395) <= max (0.31721)
ok 782 - h cn: exact (0.51535) ~ est (0.51578)
ok 783 - h cn: exact (0.51535) <= max (0.51814)
ok 784 - tile dcr1_sp.WUBLASTP hit 10 \#hsps 5
ok 785 - q id: exact (0.29334) ~ est (0.29534)
ok 786 - q id: exact (0.29334) <= max (0.29810)
ok 787 - q cn: exact (0.46617) ~ est (0.46719)
ok 788 - q cn: exact (0.46617) <= max (0.47040)
ok 789 - h id: exact (0.31176) ~ est (0.31176)
ok 790 - h id: exact (0.31176) <= max (0.31176)
ok 791 - h cn: exact (0.49299) ~ est (0.49299)
ok 792 - h cn: exact (0.49299) <= max (0.49299)
ok 793 - tile dcr1_sp.WUBLASTP hit 11 \#hsps 7
ok 794 - q id: exact (0.30456) ~ est (0.30514)
ok 795 - q id: exact (0.30456) <= max (0.30650)
ok 796 - q cn: exact (0.48739) ~ est (0.48879)
ok 797 - q cn: exact (0.48739) <= max (0.49370)
ok 798 - h id: exact (0.32062) ~ est (0.31987)
ok 799 - h id: exact (0.32062) <= max (0.32932)
ok 800 - h cn: exact (0.51071) ~ est (0.51306)
ok 801 - h cn: exact (0.51071) <= max (0.52410)
ok 802 - tile dcr1_sp.WUBLASTP hit 12 \#hsps 8
ok 803 - q id: exact (0.29615) ~ est (0.29879)
ok 804 - q id: exact (0.29615) <= max (0.30009)
ok 805 - q cn: exact (0.47419) ~ est (0.47394)
ok 806 - q cn: exact (0.47419) <= max (0.48119)
ok 807 - h id: exact (0.31611) ~ est (0.31482)
ok 808 - h id: exact (0.31611) <= max (0.32227)
ok 809 - h cn: exact (0.49779) ~ est (0.49788)
ok 810 - h cn: exact (0.49779) <= max (0.50616)
ok 811 - tile dcr1_sp.WUBLASTP hit 13 \#hsps 8
ok 812 - q id: exact (0.30390) ~ est (0.30440)
ok 813 - q id: exact (0.30390) <= max (0.30701)
ok 814 - q cn: exact (0.45874) ~ est (0.45993)
ok 815 - q cn: exact (0.45874) <= max (0.45963)
ok 816 - h id: exact (0.32282) ~ est (0.32324)
ok 817 - h id: exact (0.32282) <= max (0.32560)
ok 818 - h cn: exact (0.48052) ~ est (0.48136)
ok 819 - h cn: exact (0.48052) <= max (0.48330)
ok 820 - tile dcr1_sp.WUBLASTP hit 14 \#hsps 6
ok 821 - q id: exact (0.29769) ~ est (0.29851)
ok 822 - q id: exact (0.29769) <= max (0.29769)
ok 823 - q cn: exact (0.48480) ~ est (0.48628)
ok 824 - q cn: exact (0.48480) <= max (0.48637)
ok 825 - h id: exact (0.30704) ~ est (0.30810)
ok 826 - h id: exact (0.30704) <= max (0.30917)
ok 827 - h cn: exact (0.50107) ~ est (0.50292)
ok 828 - h cn: exact (0.50107) <= max (0.50320)
ok 829 - tile dcr1_sp.WUBLASTP hit 15 \#hsps 6
ok 830 - q id: exact (0.27854) ~ est (0.27854)
ok 831 - q id: exact (0.27854) <= max (0.27854)
ok 832 - q cn: exact (0.48174) ~ est (0.48174)
ok 833 - q cn: exact (0.48174) <= max (0.48174)
ok 834 - h id: exact (0.28514) ~ est (0.28623)
ok 835 - h id: exact (0.28514) <= max (0.28594)
ok 836 - h cn: exact (0.49197) ~ est (0.49154)
ok 837 - h cn: exact (0.49197) <= max (0.49237)
ok 838 - tile dcr1_sp.WUBLASTP hit 16 \#hsps 8
ok 839 - q id: exact (0.30362) ~ est (0.30824)
ok 840 - q id: exact (0.30362) <= max (0.30852)
ok 841 - q cn: exact (0.47111) ~ est (0.47587)
ok 842 - q cn: exact (0.47111) <= max (0.47405)
ok 843 - h id: exact (0.32347) ~ est (0.32392)
ok 844 - h id: exact (0.32347) <= max (0.32643)
ok 845 - h cn: exact (0.49310) ~ est (0.49360)
ok 846 - h cn: exact (0.49310) <= max (0.49606)
ok 847 - tile dcr1_sp.WUBLASTP hit 17 \#hsps 4
ok 848 - q id: exact (0.29174) ~ est (0.29174)
ok 849 - q id: exact (0.29174) <= max (0.29174)
ok 850 - q cn: exact (0.46230) ~ est (0.46230)
ok 851 - q cn: exact (0.46230) <= max (0.46230)
ok 852 - h id: exact (0.30204) ~ est (0.30204)
ok 853 - h id: exact (0.30204) <= max (0.30204)
ok 854 - h cn: exact (0.47862) ~ est (0.47862)
ok 855 - h cn: exact (0.47862) <= max (0.47862)
ok 856 - tile dcr1_sp.WUBLASTP hit 18 \#hsps 6
ok 857 - q id: exact (0.29064) ~ est (0.29089)
ok 858 - q id: exact (0.29064) <= max (0.29115)
ok 859 - q cn: exact (0.48765) ~ est (0.48670)
ok 860 - q cn: exact (0.48765) <= max (0.48868)
ok 861 - h id: exact (0.29848) ~ est (0.29887)
ok 862 - h id: exact (0.29848) <= max (0.29902)
ok 863 - h cn: exact (0.50108) ~ est (0.50116)
ok 864 - h cn: exact (0.50108) <= max (0.50163)
ok 865 - tile dcr1_sp.WUBLASTP hit 19 \#hsps 5
ok 866 - q id: exact (0.29510) ~ est (0.29505)
ok 867 - q id: exact (0.29510) <= max (0.29510)
ok 868 - q cn: exact (0.48982) ~ est (0.49039)
ok 869 - q cn: exact (0.48982) <= max (0.49029)
ok 870 - h id: exact (0.30019) ~ est (0.30019)
ok 871 - h id: exact (0.30019) <= max (0.30019)
ok 872 - h cn: exact (0.49906) ~ est (0.49906)
ok 873 - h cn: exact (0.49906) <= max (0.49906)
ok 874 - 503384.MEGABLAST.2
ok 875 - tile 503384.MEGABLAST.2 hit 1 \#hsps 5
ok 876 - q id: exact (0.91435) ~ est (0.91435)
ok 877 - q id: exact (0.91435) <= max (0.91435)
ok 878 - q cn: exact (0.91435) ~ est (0.91435)
ok 879 - q cn: exact (0.91435) <= max (0.91435)
ok 880 - h id: exact (0.91157) ~ est (0.91157)
ok 881 - h id: exact (0.91157) <= max (0.91157)
ok 882 - h cn: exact (0.91157) ~ est (0.91157)
ok 883 - h cn: exact (0.91157) <= max (0.91157)
ok 884 - tile 503384.MEGABLAST.2 hit 2 \#hsps 9
ok 885 - q id: exact (0.92895) ~ est (0.92895)
ok 886 - q id: exact (0.92895) <= max (0.92895)
ok 887 - q cn: exact (0.92895) ~ est (0.92895)
ok 888 - q cn: exact (0.92895) <= max (0.92895)
ok 889 - h id: exact (0.92854) ~ est (0.92854)
ok 890 - h id: exact (0.92854) <= max (0.92854)
ok 891 - h cn: exact (0.92854) ~ est (0.92854)
ok 892 - h cn: exact (0.92854) <= max (0.92854)
ok 893 - tile 503384.MEGABLAST.2 hit 3 \#hsps 3
ok 894 - q id: exact (0.93516) ~ est (0.93516)
ok 895 - q id: exact (0.93516) <= max (0.93516)
ok 896 - q cn: exact (0.93516) ~ est (0.93516)
ok 897 - q cn: exact (0.93516) <= max (0.93516)
ok 898 - h id: exact (0.93651) ~ est (0.93651)
ok 899 - h id: exact (0.93651) <= max (0.93651)
ok 900 - h cn: exact (0.93651) ~ est (0.93651)
ok 901 - h cn: exact (0.93651) <= max (0.93651)
ok 902 - tile 503384.MEGABLAST.2 hit 4 \#hsps 3
ok 903 - q id: exact (0.93064) ~ est (0.93064)
ok 904 - q id: exact (0.93064) <= max (0.93064)
ok 905 - q cn: exact (0.93064) ~ est (0.93064)
ok 906 - q cn: exact (0.93064) <= max (0.93064)
ok 907 - h id: exact (0.92885) ~ est (0.92885)
ok 908 - h id: exact (0.92885) <= max (0.92885)
ok 909 - h cn: exact (0.92885) ~ est (0.92885)
ok 910 - h cn: exact (0.92885) <= max (0.92885)
ok 911 - bl2seq.blastx.out
ok 912 - tile bl2seq.blastx.out hit 1 \#hsps 6
ok 913 - q id: est (0.71429) = fast (0.71429)
ok 914 - q cn: est (1.00000) = fast (1.00000)
ok 915 - q id: exact (0.70536) ~ est (0.70495)
ok 916 - q id: exact (0.70536) <= max (0.94286)
ok 917 - q cn: exact (0.78810) ~ est (0.78803)
ok 918 - q cn: exact (0.78810) <= max (0.96429)
ok 919 - q id: est (0.35714) = fast (0.35714)
ok 920 - q cn: est (0.57143) = fast (0.57143)
ok 921 - h id: exact (0.61923) ~ est (0.61955)
ok 922 - h id: exact (0.61923) <= max (0.64231)
ok 923 - h cn: exact (0.73077) ~ est (0.73077)
ok 924 - h cn: exact (0.73077) <= max (0.75000)
ok 925 - dnaEbsub_ecoli.wublastx
ok 926 - tile dnaEbsub_ecoli.wublastx hit 1 \#hsps 1
ok 927 - q id: est (0.36386) = fast (0.36386)
ok 928 - q cn: est (0.53735) = fast (0.53735)
ok 929 - h id: est (0.36562) = fast (0.36562)
ok 930 - h cn: est (0.53995) = fast (0.53995)
ok 931 - tblastn.out
ok 932 - tile tblastn.out hit 1 \#hsps 2
ok 933 - q id: exact (0.31250) ~ est (0.33325)
ok 934 - q id: exact (0.31250) <= max (0.33333)
ok 935 - q cn: exact (0.44792) ~ est (0.47055)
ok 936 - q cn: exact (0.44792) <= max (0.45833)
ok 937 - h id: exact (0.33333) ~ est (0.33333)
ok 938 - h id: exact (0.33333) <= max (0.33333)
ok 939 - h cn: exact (0.47059) ~ est (0.47059)
ok 940 - h cn: exact (0.47059) <= max (0.47059)
ok 941 - tile tblastn.out hit 2 \#hsps 2
ok 942 - q id: exact (0.68750) ~ est (0.68750)
ok 943 - q id: exact (0.68750) <= max (0.68750)
ok 944 - q cn: exact (0.81250) ~ est (0.81250)
ok 945 - q cn: exact (0.81250) <= max (0.81250)
ok 946 - h id: est (0.66667) = fast (0.66667)
ok 947 - h cn: est (0.77778) = fast (0.77778)
ok 948 - h id: est (0.71429) = fast (0.71429)
ok 949 - h cn: est (0.85714) = fast (0.85714)
ok 950 - dnaEbsub_ecoli.wutblastn
ok 951 - tile dnaEbsub_ecoli.wutblastn hit 1 \#hsps 1
ok 952 - q id: est (0.36386) = fast (0.36386)
ok 953 - q cn: est (0.53735) = fast (0.53735)
ok 954 - h id: est (0.36562) = fast (0.36562)
ok 955 - h cn: est (0.53995) = fast (0.53995)
ok 956 - HUMBETGLOA.tblastx
ok 957 - tile HUMBETGLOA.tblastx hit 1 \#hsps 1
ok 958 - q id: est (0.42308) = fast (0.42308)
ok 959 - q cn: est (0.61538) = fast (0.61538)
ok 960 - h id: est (0.42308) = fast (0.42308)
ok 961 - h cn: est (0.61538) = fast (0.61538)
ok 962 - tile HUMBETGLOA.tblastx hit 2 \#hsps 1
ok 963 - q id: est (0.47059) = fast (0.47059)
ok 964 - q cn: est (0.76471) = fast (0.76471)
ok 965 - h id: est (0.47059) = fast (0.47059)
ok 966 - h cn: est (0.76471) = fast (0.76471)
ok 967 - tile HUMBETGLOA.tblastx hit 3 \#hsps 1
ok 968 - q id: est (0.36000) = fast (0.36000)
ok 969 - q cn: est (0.56000) = fast (0.56000)
ok 970 - h id: est (0.36000) = fast (0.36000)
ok 971 - h cn: est (0.56000) = fast (0.56000)
ok 972 - tile HUMBETGLOA.tblastx hit 4 \#hsps 1
ok 973 - q id: est (0.29268) = fast (0.29268)
ok 974 - q cn: est (0.58537) = fast (0.58537)
ok 975 - h id: est (0.29268) = fast (0.29268)
ok 976 - h cn: est (0.58537) = fast (0.58537)
ok 977 - tile HUMBETGLOA.tblastx hit 5 \#hsps 1
ok 978 - q id: est (0.38889) = fast (0.38889)
ok 979 - q cn: est (0.55556) = fast (0.55556)
ok 980 - h id: est (0.38889) = fast (0.38889)
ok 981 - h cn: est (0.55556) = fast (0.55556)
ok 982 - tile HUMBETGLOA.tblastx hit 6 \#hsps 1
ok 983 - q id: est (0.43590) = fast (0.43590)
ok 984 - q cn: est (0.51282) = fast (0.51282)
ok 985 - h id: est (0.43590) = fast (0.43590)
ok 986 - h cn: est (0.51282) = fast (0.51282)
ok 987 - tile HUMBETGLOA.tblastx hit 7 \#hsps 1
ok 988 - q id: est (0.35714) = fast (0.35714)
ok 989 - q cn: est (0.42857) = fast (0.42857)
ok 990 - h id: est (0.35714) = fast (0.35714)
ok 991 - h cn: est (0.42857) = fast (0.42857)
ok 992 - tile HUMBETGLOA.tblastx hit 8 \#hsps 1
ok 993 - q id: est (0.33333) = fast (0.33333)
ok 994 - q cn: est (0.66667) = fast (0.66667)
ok 995 - h id: est (0.33333) = fast (0.33333)
ok 996 - h cn: est (0.66667) = fast (0.66667)
ok 997 - tile HUMBETGLOA.tblastx hit 9 \#hsps 2
ok 998 - q id: exact (0.40541) ~ est (0.40541)
ok 999 - q id: exact (0.40541) <= max (0.40541)
ok 1000 - q cn: exact (0.56757) ~ est (0.56757)
ok 1001 - q cn: exact (0.56757) <= max (0.56757)
ok 1002 - h id: est (0.36364) = fast (0.36364)
ok 1003 - h cn: est (0.63636) = fast (0.63636)
ok 1004 - h id: est (0.42308) = fast (0.42308)
ok 1005 - h cn: est (0.53846) = fast (0.53846)
ok 1006 - tile HUMBETGLOA.tblastx hit 10 \#hsps 1
ok 1007 - q id: est (0.29167) = fast (0.29167)
ok 1008 - q cn: est (0.39583) = fast (0.39583)
ok 1009 - h id: est (0.29167) = fast (0.29167)
ok 1010 - h cn: est (0.39583) = fast (0.39583)
ok 1011 - tile HUMBETGLOA.tblastx hit 11 \#hsps 1
ok 1012 - q id: est (0.60000) = fast (0.60000)
ok 1013 - q cn: est (0.65000) = fast (0.65000)
ok 1014 - h id: est (0.60000) = fast (0.60000)
ok 1015 - h cn: est (0.65000) = fast (0.65000)
ok 1016 - tile HUMBETGLOA.tblastx hit 12 \#hsps 1
ok 1017 - q id: est (0.50000) = fast (0.50000)
ok 1018 - q cn: est (0.68182) = fast (0.68182)
ok 1019 - h id: est (0.50000) = fast (0.50000)
ok 1020 - h cn: est (0.68182) = fast (0.68182)
ok 1021 - tile HUMBETGLOA.tblastx hit 13 \#hsps 1
ok 1022 - q id: est (0.29630) = fast (0.29630)
ok 1023 - q cn: est (0.48148) = fast (0.48148)
ok 1024 - h id: est (0.29630) = fast (0.29630)
ok 1025 - h cn: est (0.48148) = fast (0.48148)
ok 1026 - tile HUMBETGLOA.tblastx hit 14 \#hsps 1
ok 1027 - q id: est (0.47826) = fast (0.47826)
ok 1028 - q cn: est (0.52174) = fast (0.52174)
ok 1029 - h id: est (0.47826) = fast (0.47826)
ok 1030 - h cn: est (0.52174) = fast (0.52174)
ok 1031 - tile HUMBETGLOA.tblastx hit 15 \#hsps 1
ok 1032 - q id: est (0.47368) = fast (0.47368)
ok 1033 - q cn: est (0.63158) = fast (0.63158)
ok 1034 - h id: est (0.47368) = fast (0.47368)
ok 1035 - h cn: est (0.63158) = fast (0.63158)
ok 1036 - tile HUMBETGLOA.tblastx hit 16 \#hsps 1
ok 1037 - q id: est (0.44444) = fast (0.44444)
ok 1038 - q cn: est (0.55556) = fast (0.55556)
ok 1039 - h id: est (0.44444) = fast (0.44444)
ok 1040 - h cn: est (0.55556) = fast (0.55556)
ok 1041 - tile HUMBETGLOA.tblastx hit 17 \#hsps 1
ok 1042 - q id: est (0.47059) = fast (0.47059)
ok 1043 - q cn: est (0.70588) = fast (0.70588)
ok 1044 - h id: est (0.47059) = fast (0.47059)
ok 1045 - h cn: est (0.70588) = fast (0.70588)
ok 1046 - tile HUMBETGLOA.tblastx hit 18 \#hsps 1
ok 1047 - q id: est (0.38889) = fast (0.38889)
ok 1048 - q cn: est (0.66667) = fast (0.66667)
ok 1049 - h id: est (0.38889) = fast (0.38889)
ok 1050 - h cn: est (0.66667) = fast (0.66667)
ok 1051 - tile HUMBETGLOA.tblastx hit 19 \#hsps 1
ok 1052 - q id: est (0.27660) = fast (0.27660)
ok 1053 - q cn: est (0.48936) = fast (0.48936)
ok 1054 - h id: est (0.27660) = fast (0.27660)
ok 1055 - h cn: est (0.48936) = fast (0.48936)
ok 1056 - tile HUMBETGLOA.tblastx hit 20 \#hsps 1
ok 1057 - q id: est (0.40000) = fast (0.40000)
ok 1058 - q cn: est (0.60000) = fast (0.60000)
ok 1059 - h id: est (0.40000) = fast (0.40000)
ok 1060 - h cn: est (0.60000) = fast (0.60000)
ok 1061 - dnaEbsub_ecoli.wutblastx
ok 1062 - tile dnaEbsub_ecoli.wutblastx hit 1 \#hsps 12
ok 1063 - q id: exact (0.40224) ~ est (0.40912)
ok 1064 - q id: exact (0.40224) <= max (0.42628)
ok 1065 - q cn: exact (0.58494) ~ est (0.58968)
ok 1066 - q cn: exact (0.58494) <= max (0.62179)
ok 1067 - q id: est (0.25352) = fast (0.25352)
ok 1068 - q cn: est (0.47887) = fast (0.47887)
ok 1069 - q id: est (0.37500) = fast (0.37500)
ok 1070 - q cn: est (0.62500) = fast (0.62500)
ok 1071 - q id: exact (0.44118) ~ est (0.44118)
ok 1072 - q id: exact (0.44118) <= max (0.44118)
ok 1073 - q cn: exact (0.54412) ~ est (0.54412)
ok 1074 - q cn: exact (0.54412) <= max (0.54412)
ok 1075 - h id: est (0.25352) = fast (0.25352)
ok 1076 - h cn: est (0.47887) = fast (0.47887)
ok 1077 - h id: exact (0.39848) ~ est (0.40304)
ok 1078 - h id: exact (0.39848) <= max (0.40355)
ok 1079 - h cn: exact (0.58376) ~ est (0.58889)
ok 1080 - h cn: exact (0.58376) <= max (0.58883)
ok 1081 - h id: exact (0.44118) ~ est (0.44118)
ok 1082 - h id: exact (0.44118) <= max (0.44118)
ok 1083 - h cn: exact (0.54412) ~ est (0.54412)
ok 1084 - h cn: exact (0.54412) <= max (0.54412)
ok 1085 - tile dnaEbsub_ecoli.wutblastx hit 2 \#hsps 2
ok 1086 - q id: exact (0.41818) ~ est (0.41818)
ok 1087 - q id: exact (0.41818) <= max (0.41818)
ok 1088 - q cn: exact (0.52727) ~ est (0.52727)
ok 1089 - q cn: exact (0.52727) <= max (0.52727)
ok 1090 - h id: est (0.53333) = fast (0.53333)
ok 1091 - h cn: est (0.66667) = fast (0.66667)
ok 1092 - h id: est (0.37500) = fast (0.37500)
ok 1093 - h cn: est (0.47500) = fast (0.47500)
ok 1094 - bug2942: query m0: range correct
ok 1095 - bug2942: query m1: range correct
ok 1096 - bug2942: query m2: range correct
ok 1097 - bug2942: subject all : range correct
ok 1098 - get_tiled_alns
ok 1099 - got all alns
ok 1100
ok 1101 - aln and qfeat lengths correspond
ok 1102 - q length correct
ok 1103
ok 1104 - features on q and s correspond
ok 1105 - aln and hfeat lengths correspond
ok 1106 - s length correct
ok 1107
ok 1108 - aln and qfeat lengths correspond
ok 1109 - q length correct
ok 1110
ok 1111 - features on q and s correspond
ok 1112 - aln and hfeat lengths correspond
ok 1113 - s length correct
ok 1114
ok 1115 - aln and qfeat lengths correspond
ok 1116 - q length correct
ok 1117
ok 1118 - features on q and s correspond
ok 1119 - aln and hfeat lengths correspond
ok 1120 - s length correct
ok 1121
ok 1122 - aln and qfeat lengths correspond
ok 1123 - q length correct
ok 1124
ok 1125 - features on q and s correspond
ok 1126 - aln and hfeat lengths correspond
ok 1127 - s length correct
ok 1128
ok 1129 - aln and qfeat lengths correspond
ok 1130 - q length correct
ok 1131
ok 1132 - features on q and s correspond
ok 1133 - aln and hfeat lengths correspond
ok 1134 - s length correct
ok 1135
ok 1136 - aln and qfeat lengths correspond
ok 1137 - q length correct
ok 1138
ok 1139 - features on q and s correspond
ok 1140 - aln and hfeat lengths correspond
ok 1141 - s length correct
ok
Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175.
Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264.
Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284.
Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311.
Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337.
Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357.
Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378.
Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399.
Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420.
Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442.
Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465.
Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487.
Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508.
Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523.
Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540.
Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555.
Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574.
Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599.
Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616.
Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629.
Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646.
Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663.
Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680.
Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700.
Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728.
Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747.
Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763.
Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777.
Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794.
Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815.
Subroutine new redefined at Bio/Search/Hit/GenericHit.pm line 127.
Subroutine add_hsp redefined at Bio/Search/Hit/GenericHit.pm line 204.
Subroutine hsp_factory redefined at Bio/Search/Hit/GenericHit.pm line 228.
Subroutine name redefined at Bio/Search/Hit/GenericHit.pm line 248.
Subroutine accession redefined at Bio/Search/Hit/GenericHit.pm line 268.
Subroutine description redefined at Bio/Search/Hit/GenericHit.pm line 288.
Subroutine length redefined at Bio/Search/Hit/GenericHit.pm line 308.
Subroutine algorithm redefined at Bio/Search/Hit/GenericHit.pm line 333.
Subroutine raw_score redefined at Bio/Search/Hit/GenericHit.pm line 355.
Subroutine score redefined at Bio/Search/Hit/GenericHit.pm line 385.
Subroutine significance redefined at Bio/Search/Hit/GenericHit.pm line 400.
Subroutine bits redefined at Bio/Search/Hit/GenericHit.pm line 430.
Subroutine next_hsp redefined at Bio/Search/Hit/GenericHit.pm line 458.
Subroutine hsps redefined at Bio/Search/Hit/GenericHit.pm line 494.
Subroutine num_hsps redefined at Bio/Search/Hit/GenericHit.pm line 517.
Subroutine rewind redefined at Bio/Search/Hit/GenericHit.pm line 538.
Subroutine ambiguous_aln redefined at Bio/Search/Hit/GenericHit.pm line 564.
Subroutine overlap redefined at Bio/Search/Hit/GenericHit.pm line 576.
Subroutine n redefined at Bio/Search/Hit/GenericHit.pm line 605.
Subroutine p redefined at Bio/Search/Hit/GenericHit.pm line 652.
Subroutine hsp redefined at Bio/Search/Hit/GenericHit.pm line 694.
Subroutine logical_length redefined at Bio/Search/Hit/GenericHit.pm line 740.
Subroutine length_aln redefined at Bio/Search/Hit/GenericHit.pm line 786.
Subroutine gaps redefined at Bio/Search/Hit/GenericHit.pm line 849.
Subroutine matches redefined at Bio/Search/Hit/GenericHit.pm line 887.
Subroutine start redefined at Bio/Search/Hit/GenericHit.pm line 948.
Subroutine end redefined at Bio/Search/Hit/GenericHit.pm line 1025.
Subroutine range redefined at Bio/Search/Hit/GenericHit.pm line 1093.
Subroutine frac_identical redefined at Bio/Search/Hit/GenericHit.pm line 1150.
Subroutine frac_conserved redefined at Bio/Search/Hit/GenericHit.pm line 1226.
Subroutine frac_aligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1274.
Subroutine frac_aligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1310.
Subroutine num_unaligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1364.
Subroutine num_unaligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1400.
Subroutine seq_inds redefined at Bio/Search/Hit/GenericHit.pm line 1442.
Subroutine strand redefined at Bio/Search/Hit/GenericHit.pm line 1473.
Subroutine frame redefined at Bio/Search/Hit/GenericHit.pm line 1535.
Subroutine rank redefined at Bio/Search/Hit/GenericHit.pm line 1574.
Subroutine locus redefined at Bio/Search/Hit/GenericHit.pm line 1590.
Subroutine each_accession_number redefined at Bio/Search/Hit/GenericHit.pm line 1618.
Subroutine tiled_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1666.
Subroutine query_length redefined at Bio/Search/Hit/GenericHit.pm line 1683.
Subroutine ncbi_gi redefined at Bio/Search/Hit/GenericHit.pm line 1701.
Subroutine sort_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1732.
Subroutine iteration redefined at Bio/Search/Hit/GenericHit.pm line 1772.
Subroutine found_again redefined at Bio/Search/Hit/GenericHit.pm line 1807.
Subroutine Bio::Search::Hit::GenericHit::frac_aligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1333.
Subroutine Bio::Search::Hit::GenericHit::num_unaligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1341.
Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, <GEN1> line 193.
Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, <GEN1> line 193.
Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, <GEN1> line 193.
Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, <GEN1> line 193.
Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, <GEN1> line 193.
Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, <GEN1> line 193.
t/SearchIO/Writer/GbrowseGFF.t ......... 
1..4
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok 4
ok
Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175.
Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264.
Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284.
Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311.
Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337.
Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357.
Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378.
Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399.
Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420.
Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442.
Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465.
Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487.
Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508.
Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523.
Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540.
Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555.
Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574.
Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599.
Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616.
Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629.
Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646.
Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663.
Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680.
Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700.
Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728.
Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747.
Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763.
Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777.
Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794.
Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815.
Subroutine new redefined at Bio/Search/Hit/GenericHit.pm line 127.
Subroutine add_hsp redefined at Bio/Search/Hit/GenericHit.pm line 204.
Subroutine hsp_factory redefined at Bio/Search/Hit/GenericHit.pm line 228.
Subroutine name redefined at Bio/Search/Hit/GenericHit.pm line 248.
Subroutine accession redefined at Bio/Search/Hit/GenericHit.pm line 268.
Subroutine description redefined at Bio/Search/Hit/GenericHit.pm line 288.
Subroutine length redefined at Bio/Search/Hit/GenericHit.pm line 308.
Subroutine algorithm redefined at Bio/Search/Hit/GenericHit.pm line 333.
Subroutine raw_score redefined at Bio/Search/Hit/GenericHit.pm line 355.
Subroutine score redefined at Bio/Search/Hit/GenericHit.pm line 385.
Subroutine significance redefined at Bio/Search/Hit/GenericHit.pm line 400.
Subroutine bits redefined at Bio/Search/Hit/GenericHit.pm line 430.
Subroutine next_hsp redefined at Bio/Search/Hit/GenericHit.pm line 458.
Subroutine hsps redefined at Bio/Search/Hit/GenericHit.pm line 494.
Subroutine num_hsps redefined at Bio/Search/Hit/GenericHit.pm line 517.
Subroutine rewind redefined at Bio/Search/Hit/GenericHit.pm line 538.
Subroutine ambiguous_aln redefined at Bio/Search/Hit/GenericHit.pm line 564.
Subroutine overlap redefined at Bio/Search/Hit/GenericHit.pm line 576.
Subroutine n redefined at Bio/Search/Hit/GenericHit.pm line 605.
Subroutine p redefined at Bio/Search/Hit/GenericHit.pm line 652.
Subroutine hsp redefined at Bio/Search/Hit/GenericHit.pm line 694.
Subroutine logical_length redefined at Bio/Search/Hit/GenericHit.pm line 740.
Subroutine length_aln redefined at Bio/Search/Hit/GenericHit.pm line 786.
Subroutine gaps redefined at Bio/Search/Hit/GenericHit.pm line 849.
Subroutine matches redefined at Bio/Search/Hit/GenericHit.pm line 887.
Subroutine start redefined at Bio/Search/Hit/GenericHit.pm line 948.
Subroutine end redefined at Bio/Search/Hit/GenericHit.pm line 1025.
Subroutine range redefined at Bio/Search/Hit/GenericHit.pm line 1093.
Subroutine frac_identical redefined at Bio/Search/Hit/GenericHit.pm line 1150.
Subroutine frac_conserved redefined at Bio/Search/Hit/GenericHit.pm line 1226.
Subroutine frac_aligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1274.
Subroutine frac_aligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1310.
Subroutine num_unaligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1364.
Subroutine num_unaligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1400.
Subroutine seq_inds redefined at Bio/Search/Hit/GenericHit.pm line 1442.
Subroutine strand redefined at Bio/Search/Hit/GenericHit.pm line 1473.
Subroutine frame redefined at Bio/Search/Hit/GenericHit.pm line 1535.
Subroutine rank redefined at Bio/Search/Hit/GenericHit.pm line 1574.
Subroutine locus redefined at Bio/Search/Hit/GenericHit.pm line 1590.
Subroutine each_accession_number redefined at Bio/Search/Hit/GenericHit.pm line 1618.
Subroutine tiled_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1666.
Subroutine query_length redefined at Bio/Search/Hit/GenericHit.pm line 1683.
Subroutine ncbi_gi redefined at Bio/Search/Hit/GenericHit.pm line 1701.
Subroutine sort_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1732.
Subroutine iteration redefined at Bio/Search/Hit/GenericHit.pm line 1772.
Subroutine found_again redefined at Bio/Search/Hit/GenericHit.pm line 1807.
Subroutine Bio::Search::Hit::GenericHit::frac_aligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1333.
Subroutine Bio::Search::Hit::GenericHit::num_unaligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1341.
Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, <GEN1> line 353.
Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, <GEN1> line 353.
Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, <GEN1> line 353.
Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, <GEN1> line 353.
Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, <GEN1> line 353.
Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, <GEN1> line 353.
t/SearchIO/Writer/HSPTableWriter.t ..... 
1..8
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::SearchIO::Writer::HSPTableWriter;
ok 3 - The object isa Bio::Search::Result::ResultI
ok 4
ok 5
ok 6
ok 7 - The object isa Bio::Align::AlignI
ok 8
ok
Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175.
Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264.
Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284.
Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311.
Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337.
Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357.
Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378.
Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399.
Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420.
Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442.
Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465.
Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487.
Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508.
Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523.
Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540.
Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555.
Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574.
Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599.
Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616.
Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629.
Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646.
Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663.
Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680.
Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700.
Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728.
Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747.
Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763.
Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777.
Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794.
Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815.
Subroutine new redefined at Bio/Search/Hit/GenericHit.pm line 127.
Subroutine add_hsp redefined at Bio/Search/Hit/GenericHit.pm line 204.
Subroutine hsp_factory redefined at Bio/Search/Hit/GenericHit.pm line 228.
Subroutine name redefined at Bio/Search/Hit/GenericHit.pm line 248.
Subroutine accession redefined at Bio/Search/Hit/GenericHit.pm line 268.
Subroutine description redefined at Bio/Search/Hit/GenericHit.pm line 288.
Subroutine length redefined at Bio/Search/Hit/GenericHit.pm line 308.
Subroutine algorithm redefined at Bio/Search/Hit/GenericHit.pm line 333.
Subroutine raw_score redefined at Bio/Search/Hit/GenericHit.pm line 355.
Subroutine score redefined at Bio/Search/Hit/GenericHit.pm line 385.
Subroutine significance redefined at Bio/Search/Hit/GenericHit.pm line 400.
Subroutine bits redefined at Bio/Search/Hit/GenericHit.pm line 430.
Subroutine next_hsp redefined at Bio/Search/Hit/GenericHit.pm line 458.
Subroutine hsps redefined at Bio/Search/Hit/GenericHit.pm line 494.
Subroutine num_hsps redefined at Bio/Search/Hit/GenericHit.pm line 517.
Subroutine rewind redefined at Bio/Search/Hit/GenericHit.pm line 538.
Subroutine ambiguous_aln redefined at Bio/Search/Hit/GenericHit.pm line 564.
Subroutine overlap redefined at Bio/Search/Hit/GenericHit.pm line 576.
Subroutine n redefined at Bio/Search/Hit/GenericHit.pm line 605.
Subroutine p redefined at Bio/Search/Hit/GenericHit.pm line 652.
Subroutine hsp redefined at Bio/Search/Hit/GenericHit.pm line 694.
Subroutine logical_length redefined at Bio/Search/Hit/GenericHit.pm line 740.
Subroutine length_aln redefined at Bio/Search/Hit/GenericHit.pm line 786.
Subroutine gaps redefined at Bio/Search/Hit/GenericHit.pm line 849.
Subroutine matches redefined at Bio/Search/Hit/GenericHit.pm line 887.
Subroutine start redefined at Bio/Search/Hit/GenericHit.pm line 948.
Subroutine end redefined at Bio/Search/Hit/GenericHit.pm line 1025.
Subroutine range redefined at Bio/Search/Hit/GenericHit.pm line 1093.
Subroutine frac_identical redefined at Bio/Search/Hit/GenericHit.pm line 1150.
Subroutine frac_conserved redefined at Bio/Search/Hit/GenericHit.pm line 1226.
Subroutine frac_aligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1274.
Subroutine frac_aligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1310.
Subroutine num_unaligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1364.
Subroutine num_unaligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1400.
Subroutine seq_inds redefined at Bio/Search/Hit/GenericHit.pm line 1442.
Subroutine strand redefined at Bio/Search/Hit/GenericHit.pm line 1473.
Subroutine frame redefined at Bio/Search/Hit/GenericHit.pm line 1535.
Subroutine rank redefined at Bio/Search/Hit/GenericHit.pm line 1574.
Subroutine locus redefined at Bio/Search/Hit/GenericHit.pm line 1590.
Subroutine each_accession_number redefined at Bio/Search/Hit/GenericHit.pm line 1618.
Subroutine tiled_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1666.
Subroutine query_length redefined at Bio/Search/Hit/GenericHit.pm line 1683.
Subroutine ncbi_gi redefined at Bio/Search/Hit/GenericHit.pm line 1701.
Subroutine sort_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1732.
Subroutine iteration redefined at Bio/Search/Hit/GenericHit.pm line 1772.
Subroutine found_again redefined at Bio/Search/Hit/GenericHit.pm line 1807.
Subroutine Bio::Search::Hit::GenericHit::frac_aligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1333.
Subroutine Bio::Search::Hit::GenericHit::num_unaligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1341.
Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, <GEN1> line 353.
Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, <GEN1> line 353.
Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, <GEN1> line 353.
Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, <GEN1> line 353.
Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, <GEN1> line 353.
Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, <GEN1> line 353.
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
Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175.
Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264.
Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284.
Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311.
Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337.
Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357.
Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378.
Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399.
Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420.
Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442.
Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465.
Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487.
Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508.
Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523.
Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540.
Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555.
Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574.
Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599.
Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616.
Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629.
Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646.
Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663.
Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680.
Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700.
Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728.
Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747.
Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763.
Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777.
Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794.
Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815.
Subroutine new redefined at Bio/Search/Hit/GenericHit.pm line 127.
Subroutine add_hsp redefined at Bio/Search/Hit/GenericHit.pm line 204.
Subroutine hsp_factory redefined at Bio/Search/Hit/GenericHit.pm line 228.
Subroutine name redefined at Bio/Search/Hit/GenericHit.pm line 248.
Subroutine accession redefined at Bio/Search/Hit/GenericHit.pm line 268.
Subroutine description redefined at Bio/Search/Hit/GenericHit.pm line 288.
Subroutine length redefined at Bio/Search/Hit/GenericHit.pm line 308.
Subroutine algorithm redefined at Bio/Search/Hit/GenericHit.pm line 333.
Subroutine raw_score redefined at Bio/Search/Hit/GenericHit.pm line 355.
Subroutine score redefined at Bio/Search/Hit/GenericHit.pm line 385.
Subroutine significance redefined at Bio/Search/Hit/GenericHit.pm line 400.
Subroutine bits redefined at Bio/Search/Hit/GenericHit.pm line 430.
Subroutine next_hsp redefined at Bio/Search/Hit/GenericHit.pm line 458.
Subroutine hsps redefined at Bio/Search/Hit/GenericHit.pm line 494.
Subroutine num_hsps redefined at Bio/Search/Hit/GenericHit.pm line 517.
Subroutine rewind redefined at Bio/Search/Hit/GenericHit.pm line 538.
Subroutine ambiguous_aln redefined at Bio/Search/Hit/GenericHit.pm line 564.
Subroutine overlap redefined at Bio/Search/Hit/GenericHit.pm line 576.
Subroutine n redefined at Bio/Search/Hit/GenericHit.pm line 605.
Subroutine p redefined at Bio/Search/Hit/GenericHit.pm line 652.
Subroutine hsp redefined at Bio/Search/Hit/GenericHit.pm line 694.
Subroutine logical_length redefined at Bio/Search/Hit/GenericHit.pm line 740.
Subroutine length_aln redefined at Bio/Search/Hit/GenericHit.pm line 786.
Subroutine gaps redefined at Bio/Search/Hit/GenericHit.pm line 849.
Subroutine matches redefined at Bio/Search/Hit/GenericHit.pm line 887.
Subroutine start redefined at Bio/Search/Hit/GenericHit.pm line 948.
Subroutine end redefined at Bio/Search/Hit/GenericHit.pm line 1025.
Subroutine range redefined at Bio/Search/Hit/GenericHit.pm line 1093.
Subroutine frac_identical redefined at Bio/Search/Hit/GenericHit.pm line 1150.
Subroutine frac_conserved redefined at Bio/Search/Hit/GenericHit.pm line 1226.
Subroutine frac_aligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1274.
Subroutine frac_aligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1310.
Subroutine num_unaligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1364.
Subroutine num_unaligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1400.
Subroutine seq_inds redefined at Bio/Search/Hit/GenericHit.pm line 1442.
Subroutine strand redefined at Bio/Search/Hit/GenericHit.pm line 1473.
Subroutine frame redefined at Bio/Search/Hit/GenericHit.pm line 1535.
Subroutine rank redefined at Bio/Search/Hit/GenericHit.pm line 1574.
Subroutine locus redefined at Bio/Search/Hit/GenericHit.pm line 1590.
Subroutine each_accession_number redefined at Bio/Search/Hit/GenericHit.pm line 1618.
Subroutine tiled_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1666.
Subroutine query_length redefined at Bio/Search/Hit/GenericHit.pm line 1683.
Subroutine ncbi_gi redefined at Bio/Search/Hit/GenericHit.pm line 1701.
Subroutine sort_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1732.
Subroutine iteration redefined at Bio/Search/Hit/GenericHit.pm line 1772.
Subroutine found_again redefined at Bio/Search/Hit/GenericHit.pm line 1807.
Subroutine Bio::Search::Hit::GenericHit::frac_aligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1333.
Subroutine Bio::Search::Hit::GenericHit::num_unaligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1341.
Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, <GEN1> line 353.
Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, <GEN1> line 353.
Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, <GEN1> line 353.
Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, <GEN1> line 353.
Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, <GEN1> line 353.
Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, <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
Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175.
Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264.
Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284.
Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311.
Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337.
Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357.
Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378.
Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399.
Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420.
Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442.
Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465.
Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487.
Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508.
Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523.
Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540.
Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555.
Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574.
Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599.
Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616.
Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629.
Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646.
Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663.
Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680.
Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700.
Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728.
Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747.
Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763.
Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777.
Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794.
Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815.
Subroutine new redefined at Bio/Search/Hit/GenericHit.pm line 127.
Subroutine add_hsp redefined at Bio/Search/Hit/GenericHit.pm line 204.
Subroutine hsp_factory redefined at Bio/Search/Hit/GenericHit.pm line 228.
Subroutine name redefined at Bio/Search/Hit/GenericHit.pm line 248.
Subroutine accession redefined at Bio/Search/Hit/GenericHit.pm line 268.
Subroutine description redefined at Bio/Search/Hit/GenericHit.pm line 288.
Subroutine length redefined at Bio/Search/Hit/GenericHit.pm line 308.
Subroutine algorithm redefined at Bio/Search/Hit/GenericHit.pm line 333.
Subroutine raw_score redefined at Bio/Search/Hit/GenericHit.pm line 355.
Subroutine score redefined at Bio/Search/Hit/GenericHit.pm line 385.
Subroutine significance redefined at Bio/Search/Hit/GenericHit.pm line 400.
Subroutine bits redefined at Bio/Search/Hit/GenericHit.pm line 430.
Subroutine next_hsp redefined at Bio/Search/Hit/GenericHit.pm line 458.
Subroutine hsps redefined at Bio/Search/Hit/GenericHit.pm line 494.
Subroutine num_hsps redefined at Bio/Search/Hit/GenericHit.pm line 517.
Subroutine rewind redefined at Bio/Search/Hit/GenericHit.pm line 538.
Subroutine ambiguous_aln redefined at Bio/Search/Hit/GenericHit.pm line 564.
Subroutine overlap redefined at Bio/Search/Hit/GenericHit.pm line 576.
Subroutine n redefined at Bio/Search/Hit/GenericHit.pm line 605.
Subroutine p redefined at Bio/Search/Hit/GenericHit.pm line 652.
Subroutine hsp redefined at Bio/Search/Hit/GenericHit.pm line 694.
Subroutine logical_length redefined at Bio/Search/Hit/GenericHit.pm line 740.
Subroutine length_aln redefined at Bio/Search/Hit/GenericHit.pm line 786.
Subroutine gaps redefined at Bio/Search/Hit/GenericHit.pm line 849.
Subroutine matches redefined at Bio/Search/Hit/GenericHit.pm line 887.
Subroutine start redefined at Bio/Search/Hit/GenericHit.pm line 948.
Subroutine end redefined at Bio/Search/Hit/GenericHit.pm line 1025.
Subroutine range redefined at Bio/Search/Hit/GenericHit.pm line 1093.
Subroutine frac_identical redefined at Bio/Search/Hit/GenericHit.pm line 1150.
Subroutine frac_conserved redefined at Bio/Search/Hit/GenericHit.pm line 1226.
Subroutine frac_aligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1274.
Subroutine frac_aligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1310.
Subroutine num_unaligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1364.
Subroutine num_unaligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1400.
Subroutine seq_inds redefined at Bio/Search/Hit/GenericHit.pm line 1442.
Subroutine strand redefined at Bio/Search/Hit/GenericHit.pm line 1473.
Subroutine frame redefined at Bio/Search/Hit/GenericHit.pm line 1535.
Subroutine rank redefined at Bio/Search/Hit/GenericHit.pm line 1574.
Subroutine locus redefined at Bio/Search/Hit/GenericHit.pm line 1590.
Subroutine each_accession_number redefined at Bio/Search/Hit/GenericHit.pm line 1618.
Subroutine tiled_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1666.
Subroutine query_length redefined at Bio/Search/Hit/GenericHit.pm line 1683.
Subroutine ncbi_gi redefined at Bio/Search/Hit/GenericHit.pm line 1701.
Subroutine sort_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1732.
Subroutine iteration redefined at Bio/Search/Hit/GenericHit.pm line 1772.
Subroutine found_again redefined at Bio/Search/Hit/GenericHit.pm line 1807.
Subroutine Bio::Search::Hit::GenericHit::frac_aligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1333.
Subroutine Bio::Search::Hit::GenericHit::num_unaligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1341.
Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, <GEN1> line 353.
Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, <GEN1> line 353.
Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, <GEN1> line 353.
Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, <GEN1> line 353.
Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, <GEN1> line 353.
Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, <GEN1> line 353.
t/SearchIO/Writer/TextWriter.t ......... 
1..8
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::SearchIO::Writer::TextResultWriter;
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
Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, <GEN1> line 7.
Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, <GEN1> line 7.
Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, <GEN1> line 7.
Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, <GEN1> line 7.
Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, <GEN1> line 7.
Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, <GEN1> line 7.
t/SearchIO/axt.t ....................... 
1..19
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
Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175.
Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 264.
Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 284.
Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 311.
Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 337.
Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 357.
Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 378.
Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 399.
Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 420.
Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 442.
Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 465.
Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 487.
Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 508.
Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 523.
Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 540.
Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 555.
Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 574.
Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 599.
Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 616.
Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 629.
Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 646.
Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 663.
Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 680.
Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 700.
Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 728.
Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 747.
Subroutine rid redefined at Bio/Search/Result/GenericResult.pm line 763.
Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 777.
Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 794.
Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 815.
Subroutine new redefined at Bio/Search/Hit/GenericHit.pm line 127.
Subroutine add_hsp redefined at Bio/Search/Hit/GenericHit.pm line 204.
Subroutine hsp_factory redefined at Bio/Search/Hit/GenericHit.pm line 228.
Subroutine name redefined at Bio/Search/Hit/GenericHit.pm line 248.
Subroutine accession redefined at Bio/Search/Hit/GenericHit.pm line 268.
Subroutine description redefined at Bio/Search/Hit/GenericHit.pm line 288.
Subroutine length redefined at Bio/Search/Hit/GenericHit.pm line 308.
Subroutine algorithm redefined at Bio/Search/Hit/GenericHit.pm line 333.
Subroutine raw_score redefined at Bio/Search/Hit/GenericHit.pm line 355.
Subroutine score redefined at Bio/Search/Hit/GenericHit.pm line 385.
Subroutine significance redefined at Bio/Search/Hit/GenericHit.pm line 400.
Subroutine bits redefined at Bio/Search/Hit/GenericHit.pm line 430.
Subroutine next_hsp redefined at Bio/Search/Hit/GenericHit.pm line 458.
Subroutine hsps redefined at Bio/Search/Hit/GenericHit.pm line 494.
Subroutine num_hsps redefined at Bio/Search/Hit/GenericHit.pm line 517.
Subroutine rewind redefined at Bio/Search/Hit/GenericHit.pm line 538.
Subroutine ambiguous_aln redefined at Bio/Search/Hit/GenericHit.pm line 564.
Subroutine overlap redefined at Bio/Search/Hit/GenericHit.pm line 576.
Subroutine n redefined at Bio/Search/Hit/GenericHit.pm line 605.
Subroutine p redefined at Bio/Search/Hit/GenericHit.pm line 652.
Subroutine hsp redefined at Bio/Search/Hit/GenericHit.pm line 694.
Subroutine logical_length redefined at Bio/Search/Hit/GenericHit.pm line 740.
Subroutine length_aln redefined at Bio/Search/Hit/GenericHit.pm line 786.
Subroutine gaps redefined at Bio/Search/Hit/GenericHit.pm line 849.
Subroutine matches redefined at Bio/Search/Hit/GenericHit.pm line 887.
Subroutine start redefined at Bio/Search/Hit/GenericHit.pm line 948.
Subroutine end redefined at Bio/Search/Hit/GenericHit.pm line 1025.
Subroutine range redefined at Bio/Search/Hit/GenericHit.pm line 1093.
Subroutine frac_identical redefined at Bio/Search/Hit/GenericHit.pm line 1150.
Subroutine frac_conserved redefined at Bio/Search/Hit/GenericHit.pm line 1226.
Subroutine frac_aligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1274.
Subroutine frac_aligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1310.
Subroutine num_unaligned_hit redefined at Bio/Search/Hit/GenericHit.pm line 1364.
Subroutine num_unaligned_query redefined at Bio/Search/Hit/GenericHit.pm line 1400.
Subroutine seq_inds redefined at Bio/Search/Hit/GenericHit.pm line 1442.
Subroutine strand redefined at Bio/Search/Hit/GenericHit.pm line 1473.
Subroutine frame redefined at Bio/Search/Hit/GenericHit.pm line 1535.
Subroutine rank redefined at Bio/Search/Hit/GenericHit.pm line 1574.
Subroutine locus redefined at Bio/Search/Hit/GenericHit.pm line 1590.
Subroutine each_accession_number redefined at Bio/Search/Hit/GenericHit.pm line 1618.
Subroutine tiled_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1666.
Subroutine query_length redefined at Bio/Search/Hit/GenericHit.pm line 1683.
Subroutine ncbi_gi redefined at Bio/Search/Hit/GenericHit.pm line 1701.
Subroutine sort_hsps redefined at Bio/Search/Hit/GenericHit.pm line 1732.
Subroutine iteration redefined at Bio/Search/Hit/GenericHit.pm line 1772.
Subroutine found_again redefined at Bio/Search/Hit/GenericHit.pm line 1807.
Subroutine Bio::Search::Hit::GenericHit::frac_aligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1333.
Subroutine Bio::Search::Hit::GenericHit::num_unaligned_sbjct redefined at Bio/Search/Hit/GenericHit.pm line 1341.
Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 85, <GEN9> line 245.
Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 122, <GEN9> line 245.
Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 138, <GEN9> line 245.
Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 154, <GEN9> line 245.
Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 170, <GEN9> line 245.
Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 190, <GEN9> line 245.

Timeout (max run time is 420s)
C:\Perl-5.16\bin\perl.exe exits with 37.