Start 2010-04-19T21:52:22
ActivePerl-1200 CPAN-1.9402
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~1.12/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:\Perl-5.12\site\bin;C:\Perl-5.12\bin;C:\cygwin\bin;C:\PROGRA~1\Perforce;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WINDOW~2\v1.0
Going to read 'C:\cpanfly-5.12\var\cpan\Metadata'
  Database was generated on Sun, 18 Apr 2010 06:26:59 GMT
Running make for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
Checksum for C:\cpanfly-5.12\var\cpan\sources\authors\id\C\CJ\CJFIELDS\BioPerl-1.6.1.tar.gz ok
BioPerl-1.6.1
BioPerl-1.6.1/AUTHORS
BioPerl-1.6.1/BioPerl.pm
BioPerl-1.6.1/BUGS
BioPerl-1.6.1/Build.PL
BioPerl-1.6.1/Changes
BioPerl-1.6.1/DEPENDENCIES
BioPerl-1.6.1/DEPRECATED
BioPerl-1.6.1/INSTALL
BioPerl-1.6.1/INSTALL.SKIP
BioPerl-1.6.1/INSTALL.WIN
BioPerl-1.6.1/LICENSE
BioPerl-1.6.1/Makefile.PL
BioPerl-1.6.1/MANIFEST
BioPerl-1.6.1/MANIFEST.SKIP
BioPerl-1.6.1/META.yml
BioPerl-1.6.1/README
BioPerl-1.6.1/Bio
BioPerl-1.6.1/Bio/AlignIO.pm
BioPerl-1.6.1/Bio/AnalysisI.pm
BioPerl-1.6.1/Bio/AnalysisParserI.pm
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BioPerl-1.6.1/Bio/AnnotatableI.pm
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BioPerl-1.6.1/Bio/HandlerBaseI.pm
BioPerl-1.6.1/Bio/IdCollectionI.pm
BioPerl-1.6.1/Bio/IdentifiableI.pm
BioPerl-1.6.1/Bio/LocatableSeq.pm
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BioPerl-1.6.1/Bio/OntologyIO.pm
BioPerl-1.6.1/Bio/ParameterBaseI.pm
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BioPerl-1.6.1/Bio/Align/ProteinStatistics.pm
BioPerl-1.6.1/Bio/Align/StatisticsI.pm
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BioPerl-1.6.1/Bio/AlignIO
BioPerl-1.6.1/Bio/AlignIO/arp.pm
BioPerl-1.6.1/Bio/AlignIO/bl2seq.pm
BioPerl-1.6.1/Bio/AlignIO/clustalw.pm
BioPerl-1.6.1/Bio/AlignIO/emboss.pm
BioPerl-1.6.1/Bio/AlignIO/fasta.pm
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BioPerl-1.6.1/Bio/Annotation/StructuredValue.pm
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BioPerl-1.6.1/Bio/Annotation/Target.pm
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BioPerl-1.6.1/Bio/Assembly/IO
BioPerl-1.6.1/Bio/Assembly/IO/ace.pm
BioPerl-1.6.1/Bio/Assembly/IO/phrap.pm
BioPerl-1.6.1/Bio/Assembly/IO/tigr.pm
BioPerl-1.6.1/Bio/Assembly/Tools
BioPerl-1.6.1/Bio/Assembly/Tools/ContigSpectrum.pm
BioPerl-1.6.1/Bio/Biblio
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BioPerl-1.6.1/Bio/Biblio/Journal.pm
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BioPerl-1.6.1/Bio/Biblio/PubmedBookArticle.pm
BioPerl-1.6.1/Bio/Biblio/PubmedJournalArticle.pm
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BioPerl-1.6.1/Bio/Biblio/Thesis.pm
BioPerl-1.6.1/Bio/Biblio/WebResource.pm
BioPerl-1.6.1/Bio/Biblio/IO
BioPerl-1.6.1/Bio/Biblio/IO/medline2ref.pm
BioPerl-1.6.1/Bio/Biblio/IO/medlinexml.pm
BioPerl-1.6.1/Bio/Biblio/IO/pubmed2ref.pm
BioPerl-1.6.1/Bio/Biblio/IO/pubmedxml.pm
BioPerl-1.6.1/Bio/Cluster
BioPerl-1.6.1/Bio/Cluster/ClusterFactory.pm
BioPerl-1.6.1/Bio/Cluster/FamilyI.pm
BioPerl-1.6.1/Bio/Cluster/SequenceFamily.pm
BioPerl-1.6.1/Bio/Cluster/UniGene.pm
BioPerl-1.6.1/Bio/Cluster/UniGeneI.pm
BioPerl-1.6.1/Bio/ClusterIO
BioPerl-1.6.1/Bio/ClusterIO/dbsnp.pm
BioPerl-1.6.1/Bio/ClusterIO/unigene.pm
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BioPerl-1.6.1/Bio/DB/EMBL.pm
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BioPerl-1.6.1/Bio/DB/Expression.pm
BioPerl-1.6.1/Bio/DB/Failover.pm
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BioPerl-1.6.1/Bio/DB/MeSH.pm
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BioPerl-1.6.1/Bio/DB/RefSeq.pm
BioPerl-1.6.1/Bio/DB/Registry.pm
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BioPerl-1.6.1/Bio/DB/SwissProt.pm
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BioPerl-1.6.1/Bio/DB/TFBS.pm
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BioPerl-1.6.1/Bio/DB/Expression
BioPerl-1.6.1/Bio/DB/Expression/geo.pm
BioPerl-1.6.1/Bio/DB/Flat
BioPerl-1.6.1/Bio/DB/Flat/BDB.pm
BioPerl-1.6.1/Bio/DB/Flat/BinarySearch.pm
BioPerl-1.6.1/Bio/DB/Flat/BDB
BioPerl-1.6.1/Bio/DB/Flat/BDB/embl.pm
BioPerl-1.6.1/Bio/DB/Flat/BDB/fasta.pm
BioPerl-1.6.1/Bio/DB/Flat/BDB/genbank.pm
BioPerl-1.6.1/Bio/DB/Flat/BDB/swiss.pm
BioPerl-1.6.1/Bio/DB/GFF
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BioPerl-1.6.1/Bio/DB/GFF/Featname.pm
BioPerl-1.6.1/Bio/DB/GFF/Feature.pm
BioPerl-1.6.1/Bio/DB/GFF/Homol.pm
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BioPerl-1.6.1/Bio/DB/GFF/Util/Rearrange.pm
BioPerl-1.6.1/Bio/DB/HIV
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BioPerl-1.6.1/examples
BioPerl-1.6.1/examples/bioperl.pl
BioPerl-1.6.1/examples/generate_random_seq.pl
BioPerl-1.6.1/examples/longorf.pl
BioPerl-1.6.1/examples/make_primers.pl
BioPerl-1.6.1/examples/rev_and_trans.pl
BioPerl-1.6.1/examples/revcom_dir.pl
BioPerl-1.6.1/examples/subsequence.cgi
BioPerl-1.6.1/examples/align
BioPerl-1.6.1/examples/align/align_on_codons.pl
BioPerl-1.6.1/examples/align/aligntutorial.pl
BioPerl-1.6.1/examples/align/clustalw.pl
BioPerl-1.6.1/examples/align/simplealign.pl
BioPerl-1.6.1/examples/biblio
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BioPerl-1.6.1/examples/biblio/biblio-soap-example.pl
BioPerl-1.6.1/examples/biblio/biblio_soap.pl
BioPerl-1.6.1/examples/Bio-DB-GFF
BioPerl-1.6.1/examples/Bio-DB-GFF/load_ucsc.pl
BioPerl-1.6.1/examples/cluster
BioPerl-1.6.1/examples/cluster/dbsnp.pl
BioPerl-1.6.1/examples/contributed
BioPerl-1.6.1/examples/contributed/nmrpdb_parse.pl
BioPerl-1.6.1/examples/contributed/prosite2perl.pl
BioPerl-1.6.1/examples/contributed/rebase2list.pl
BioPerl-1.6.1/examples/db
BioPerl-1.6.1/examples/db/dbfetch
BioPerl-1.6.1/examples/db/est_tissue_query.pl
BioPerl-1.6.1/examples/db/gb2features.pl
BioPerl-1.6.1/examples/db/get_seqs.pl
BioPerl-1.6.1/examples/db/getGenBank.pl
BioPerl-1.6.1/examples/db/rfetch.pl
BioPerl-1.6.1/examples/db/use_registry.pl
BioPerl-1.6.1/examples/liveseq
BioPerl-1.6.1/examples/liveseq/change_gene.pl
BioPerl-1.6.1/examples/popgen
BioPerl-1.6.1/examples/popgen/parse_calc_stats.pl
BioPerl-1.6.1/examples/quality
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BioPerl-1.6.1/examples/root
BioPerl-1.6.1/examples/root/exceptions1.pl
BioPerl-1.6.1/examples/root/exceptions2.pl
BioPerl-1.6.1/examples/root/exceptions3.pl
BioPerl-1.6.1/examples/root/exceptions4.pl
BioPerl-1.6.1/examples/root/README
BioPerl-1.6.1/examples/root/lib
BioPerl-1.6.1/examples/root/lib/TestInterface.pm
BioPerl-1.6.1/examples/root/lib/TestObject.pm
BioPerl-1.6.1/examples/root/lib/Bio
BioPerl-1.6.1/examples/root/lib/Bio/PrimarySeq.pm
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BioPerl-1.6.1/examples/root/lib/Bio/Seq.pm
BioPerl-1.6.1/examples/root/lib/Bio/SeqI.pm
BioPerl-1.6.1/examples/searchio
BioPerl-1.6.1/examples/searchio/blast_example.pl
BioPerl-1.6.1/examples/searchio/custom_writer.pl
BioPerl-1.6.1/examples/searchio/hitwriter.pl
BioPerl-1.6.1/examples/searchio/hspwriter.pl
BioPerl-1.6.1/examples/searchio/htmlwriter.pl
BioPerl-1.6.1/examples/searchio/psiblast_features.pl
BioPerl-1.6.1/examples/searchio/psiblast_iterations.pl
BioPerl-1.6.1/examples/searchio/rawwriter.pl
BioPerl-1.6.1/examples/searchio/resultwriter.pl
BioPerl-1.6.1/examples/searchio/waba2gff.pl
BioPerl-1.6.1/examples/searchio/waba2gff3.pl
BioPerl-1.6.1/examples/sirna
BioPerl-1.6.1/examples/sirna/rnai_finder.cgi
BioPerl-1.6.1/examples/sirna/TAG
BioPerl-1.6.1/examples/structure
BioPerl-1.6.1/examples/structure/structure-io.pl
BioPerl-1.6.1/examples/tk
BioPerl-1.6.1/examples/tk/gsequence.pl
BioPerl-1.6.1/examples/tk/hitdisplay.pl
BioPerl-1.6.1/examples/tools
BioPerl-1.6.1/examples/tools/extract_genes.pl
BioPerl-1.6.1/examples/tools/gb_to_gff.pl
BioPerl-1.6.1/examples/tools/gff2ps.pl
BioPerl-1.6.1/examples/tools/parse_codeml.pl
BioPerl-1.6.1/examples/tools/psw.pl
BioPerl-1.6.1/examples/tools/reverse-translate.pl
BioPerl-1.6.1/examples/tools/run_genscan.pl
BioPerl-1.6.1/examples/tools/run_primer3.pl
BioPerl-1.6.1/examples/tools/seq_pattern.pl
BioPerl-1.6.1/examples/tools/standaloneblast.pl
BioPerl-1.6.1/examples/tree
BioPerl-1.6.1/examples/tree/paup2phylip.pl
BioPerl-1.6.1/ide
BioPerl-1.6.1/ide/bioperl.komodo
BioPerl-1.6.1/ide/bioperl-mode
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BioPerl-1.6.1/ide/bioperl-mode/dist
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BioPerl-1.6.1/ide/bioperl-mode/dist/package-me
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BioPerl-1.6.1/ide/bioperl-mode/etc
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BioPerl-1.6.1/models/maps_and_markers.dia
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BioPerl-1.6.1/models/population_proposal.txt
BioPerl-1.6.1/models/README
BioPerl-1.6.1/scripts
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BioPerl-1.6.1/scripts/Bio-DB-GFF
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BioPerl-1.6.1/scripts/Bio-DB-GFF/meta_gff.PLS
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BioPerl-1.6.1/scripts/Bio-DB-GFF/process_wormbase.PLS
BioPerl-1.6.1/scripts/Bio-DB-GFF/README
BioPerl-1.6.1/scripts/Bio-SeqFeature-Store
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BioPerl-1.6.1/scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
BioPerl-1.6.1/scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
BioPerl-1.6.1/scripts/das
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BioPerl-1.6.1/scripts/DB
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BioPerl-1.6.1/scripts/DB/bioflat_index.PLS
BioPerl-1.6.1/scripts/DB/biogetseq.PLS
BioPerl-1.6.1/scripts/DB/flanks.PLS
BioPerl-1.6.1/scripts/DB/TAG
BioPerl-1.6.1/scripts/DB-HIV
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BioPerl-1.6.1/scripts/index
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BioPerl-1.6.1/scripts/index/bp_index.PLS
BioPerl-1.6.1/scripts/index/bp_seqret.PLS
BioPerl-1.6.1/scripts/index/TAG
BioPerl-1.6.1/scripts/popgen
BioPerl-1.6.1/scripts/popgen/composite_LD.PLS
BioPerl-1.6.1/scripts/popgen/heterogeneity_test.PLS
BioPerl-1.6.1/scripts/searchio
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BioPerl-1.6.1/scripts/searchio/filter_search.PLS
BioPerl-1.6.1/scripts/searchio/hmmer_to_table.PLS
BioPerl-1.6.1/scripts/searchio/parse_hmmsearch.PLS
BioPerl-1.6.1/scripts/searchio/README
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BioPerl-1.6.1/scripts/searchio/TAG
BioPerl-1.6.1/scripts/seq
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BioPerl-1.6.1/scripts/seq/make_mrna_protein.PLS
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BioPerl-1.6.1/scripts/seq/seqretsplit.PLS
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BioPerl-1.6.1/scripts/seqstats
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BioPerl-1.6.1/scripts/taxa/query_entrez_taxa.PLS
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BioPerl-1.6.1/scripts/tree/tree2pag.PLS
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BioPerl-1.6.1/scripts/utilities/bp_nrdb.PLS
BioPerl-1.6.1/scripts/utilities/bp_sreformat.PLS
BioPerl-1.6.1/scripts/utilities/dbsplit.PLS
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BioPerl-1.6.1/scripts/utilities/mask_by_search.PLS
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BioPerl-1.6.1/scripts/utilities/search2tribe.PLS
BioPerl-1.6.1/scripts/utilities/seq_length.PLS
BioPerl-1.6.1/scripts/utilities/TAG
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BioPerl-1.6.1/t/SeqFeature/SeqFeature.t
BioPerl-1.6.1/t/SeqFeature/SeqFeaturePrimer.t
BioPerl-1.6.1/t/SeqFeature/Unflattener.t
BioPerl-1.6.1/t/SeqFeature/Unflattener2.t
BioPerl-1.6.1/t/SeqIO
BioPerl-1.6.1/t/SeqIO/abi.t
BioPerl-1.6.1/t/SeqIO/ace.t
BioPerl-1.6.1/t/SeqIO/agave.t
BioPerl-1.6.1/t/SeqIO/alf.t
BioPerl-1.6.1/t/SeqIO/asciitree.t
BioPerl-1.6.1/t/SeqIO/bsml.t
BioPerl-1.6.1/t/SeqIO/bsml_sax.t
BioPerl-1.6.1/t/SeqIO/chadoxml.t
BioPerl-1.6.1/t/SeqIO/chaos.t
BioPerl-1.6.1/t/SeqIO/chaosxml.t
BioPerl-1.6.1/t/SeqIO/ctf.t
BioPerl-1.6.1/t/SeqIO/embl.t
BioPerl-1.6.1/t/SeqIO/entrezgene.t
BioPerl-1.6.1/t/SeqIO/excel.t
BioPerl-1.6.1/t/SeqIO/exp.t
BioPerl-1.6.1/t/SeqIO/fasta.t
BioPerl-1.6.1/t/SeqIO/fastq.t
BioPerl-1.6.1/t/SeqIO/flybase_chadoxml.t
BioPerl-1.6.1/t/SeqIO/game.t
BioPerl-1.6.1/t/SeqIO/gcg.t
BioPerl-1.6.1/t/SeqIO/genbank.t
BioPerl-1.6.1/t/SeqIO/Handler.t
BioPerl-1.6.1/t/SeqIO/interpro.t
BioPerl-1.6.1/t/SeqIO/kegg.t
BioPerl-1.6.1/t/SeqIO/largefasta.t
BioPerl-1.6.1/t/SeqIO/lasergene.t
BioPerl-1.6.1/t/SeqIO/locuslink.t
BioPerl-1.6.1/t/SeqIO/metafasta.t
BioPerl-1.6.1/t/SeqIO/MultiFile.t
BioPerl-1.6.1/t/SeqIO/Multiple_fasta.t
BioPerl-1.6.1/t/SeqIO/phd.t
BioPerl-1.6.1/t/SeqIO/pir.t
BioPerl-1.6.1/t/SeqIO/pln.t
BioPerl-1.6.1/t/SeqIO/qual.t
BioPerl-1.6.1/t/SeqIO/raw.t
BioPerl-1.6.1/t/SeqIO/scf.t
BioPerl-1.6.1/t/SeqIO/SeqBuilder.t
BioPerl-1.6.1/t/SeqIO/Splicedseq.t
BioPerl-1.6.1/t/SeqIO/strider.t
BioPerl-1.6.1/t/SeqIO/swiss.t
BioPerl-1.6.1/t/SeqIO/tab.t
BioPerl-1.6.1/t/SeqIO/table.t
BioPerl-1.6.1/t/SeqIO/tigr.t
BioPerl-1.6.1/t/SeqIO/tigrxml.t
BioPerl-1.6.1/t/SeqIO/tinyseq.t
BioPerl-1.6.1/t/SeqIO/ztr.t
BioPerl-1.6.1/t/SeqTools
BioPerl-1.6.1/t/SeqTools/Backtranslate.t
BioPerl-1.6.1/t/SeqTools/CodonTable.t
BioPerl-1.6.1/t/SeqTools/ECnumber.t
BioPerl-1.6.1/t/SeqTools/GuessSeqFormat.t
BioPerl-1.6.1/t/SeqTools/OddCodes.t
BioPerl-1.6.1/t/SeqTools/SeqPattern.t
BioPerl-1.6.1/t/SeqTools/SeqStats.t
BioPerl-1.6.1/t/SeqTools/SeqUtils.t
BioPerl-1.6.1/t/SeqTools/SeqWords.t
BioPerl-1.6.1/t/Structure
BioPerl-1.6.1/t/Structure/IO.t
BioPerl-1.6.1/t/Structure/Structure.t
BioPerl-1.6.1/t/Tools
BioPerl-1.6.1/t/Tools/ePCR.t
BioPerl-1.6.1/t/Tools/Est2Genome.t
BioPerl-1.6.1/t/Tools/FootPrinter.t
BioPerl-1.6.1/t/Tools/Geneid.t
BioPerl-1.6.1/t/Tools/Genewise.t
BioPerl-1.6.1/t/Tools/Genomewise.t
BioPerl-1.6.1/t/Tools/Genpred.t
BioPerl-1.6.1/t/Tools/GFF.t
BioPerl-1.6.1/t/Tools/Hmmer.t
BioPerl-1.6.1/t/Tools/IUPAC.t
BioPerl-1.6.1/t/Tools/Lucy.t
BioPerl-1.6.1/t/Tools/Match.t
BioPerl-1.6.1/t/Tools/pICalculator.t
BioPerl-1.6.1/t/Tools/Primer3.t
BioPerl-1.6.1/t/Tools/Promoterwise.t
BioPerl-1.6.1/t/Tools/Pseudowise.t
BioPerl-1.6.1/t/Tools/QRNA.t
BioPerl-1.6.1/t/Tools/RandDistFunctions.t
BioPerl-1.6.1/t/Tools/RepeatMasker.t
BioPerl-1.6.1/t/Tools/rnamotif.t
BioPerl-1.6.1/t/Tools/Seg.t
BioPerl-1.6.1/t/Tools/Sigcleave.t
BioPerl-1.6.1/t/Tools/Signalp.t
BioPerl-1.6.1/t/Tools/Sim4.t
BioPerl-1.6.1/t/Tools/SiRNA.t
BioPerl-1.6.1/t/Tools/TandemRepeatsFinder.t
BioPerl-1.6.1/t/Tools/TargetP.t
BioPerl-1.6.1/t/Tools/Tmhmm.t
BioPerl-1.6.1/t/Tools/tRNAscanSE.t
BioPerl-1.6.1/t/Tools/Alignment
BioPerl-1.6.1/t/Tools/Alignment/Consed.t
BioPerl-1.6.1/t/Tools/Analysis
BioPerl-1.6.1/t/Tools/Analysis/DNA
BioPerl-1.6.1/t/Tools/Analysis/DNA/ESEfinder.t
BioPerl-1.6.1/t/Tools/Analysis/Protein
BioPerl-1.6.1/t/Tools/Analysis/Protein/Domcut.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/ELM.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/GOR4.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/HNN.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/Mitoprot.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/NetPhos.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/Scansite.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/Sopma.t
BioPerl-1.6.1/t/Tools/EMBOSS
BioPerl-1.6.1/t/Tools/EMBOSS/Palindrome.t
BioPerl-1.6.1/t/Tools/EUtilities
BioPerl-1.6.1/t/Tools/EUtilities/egquery.t
BioPerl-1.6.1/t/Tools/EUtilities/einfo.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_acheck.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_lcheck.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_llinks.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_ncheck.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_neighbor.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_neighbor_history.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_scores.t
BioPerl-1.6.1/t/Tools/EUtilities/epost.t
BioPerl-1.6.1/t/Tools/EUtilities/esearch.t
BioPerl-1.6.1/t/Tools/EUtilities/espell.t
BioPerl-1.6.1/t/Tools/EUtilities/esummary.t
BioPerl-1.6.1/t/Tools/EUtilities/EUtilParameters.t
BioPerl-1.6.1/t/Tools/Phylo
BioPerl-1.6.1/t/Tools/Phylo/Gerp.t
BioPerl-1.6.1/t/Tools/Phylo/Molphy.t
BioPerl-1.6.1/t/Tools/Phylo/PAML.t
BioPerl-1.6.1/t/Tools/Phylo/Phylip
BioPerl-1.6.1/t/Tools/Phylo/Phylip/ProtDist.t
BioPerl-1.6.1/t/Tools/Run
BioPerl-1.6.1/t/Tools/Run/RemoteBlast.t
BioPerl-1.6.1/t/Tools/Run/RemoteBlast_rpsblast.t
BioPerl-1.6.1/t/Tools/Run/StandAloneBlast.t
BioPerl-1.6.1/t/Tools/Run/WrapperBase.t
BioPerl-1.6.1/t/Tools/Signalp
BioPerl-1.6.1/t/Tools/Signalp/ExtendedSignalp.t
BioPerl-1.6.1/t/Tools/Spidey
BioPerl-1.6.1/t/Tools/Spidey/Spidey.t
BioPerl-1.6.1/t/Tree
BioPerl-1.6.1/t/Tree/Compatible.t
BioPerl-1.6.1/t/Tree/Node.t
BioPerl-1.6.1/t/Tree/RandomTreeFactory.t
BioPerl-1.6.1/t/Tree/Tree.t
BioPerl-1.6.1/t/Tree/TreeIO.t
BioPerl-1.6.1/t/Tree/TreeStatistics.t
BioPerl-1.6.1/t/Tree/PhyloNetwork
BioPerl-1.6.1/t/Tree/PhyloNetwork/Factory.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/GraphViz.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/MuVector.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/PhyloNetwork.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/RandomFactory.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/TreeFactory.t
BioPerl-1.6.1/t/Tree/TreeIO
BioPerl-1.6.1/t/Tree/TreeIO/lintree.t
BioPerl-1.6.1/t/Tree/TreeIO/newick.t
BioPerl-1.6.1/t/Tree/TreeIO/nexus.t
BioPerl-1.6.1/t/Tree/TreeIO/nhx.t
BioPerl-1.6.1/t/Tree/TreeIO/phyloxml.t
BioPerl-1.6.1/t/Tree/TreeIO/svggraph.t
BioPerl-1.6.1/t/Tree/TreeIO/tabtree.t
BioPerl-1.6.1/t/Variation
BioPerl-1.6.1/t/Variation/AAChange.t
BioPerl-1.6.1/t/Variation/AAReverseMutate.t
BioPerl-1.6.1/t/Variation/Allele.t
BioPerl-1.6.1/t/Variation/DNAMutation.t
BioPerl-1.6.1/t/Variation/RNAChange.t
BioPerl-1.6.1/t/Variation/SeqDiff.t
BioPerl-1.6.1/t/Variation/SNP.t
BioPerl-1.6.1/t/Variation/Variation_IO.t

  CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz

>>> C:\Perl-5.12\bin\perl.exe Makefile.PL
# running Build.PL 
 - ERROR: DB_File is not installed

(I think I'm being run by CPAN/CPANPLUS, so will rely on it to handle prerequisite installation)
   I'll get CPAN to prepend the installation of this
Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] Checking prerequisites...
  recommends:
    *  Optional prerequisite Ace is not installed
   (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace)
    *  Optional prerequisite Algorithm::Munkres is not installed
   (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork)
    *  Optional prerequisite Bio::ASN1::EntrezGene is not installed
   (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!])
    *  Optional prerequisite Convert::Binary::C is not installed
   (wanted for strider functionality, used by Bio::SeqIO::strider)
    *  Optional prerequisite GraphViz is not installed
   (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz)
    *  Optional prerequisite PostScript::TextBlock is not installed
   (wanted for EPS output, used by Bio::Tree::Draw::Cladogram)
    *  Optional prerequisite SVG::Graph is not installed
   (wanted for creating SVG images, used by Bio::TreeIO::svggraph)
    *  Optional prerequisite XML::SAX::Writer is not installed
   (wanted for writing xml, used by Bio::SeqIO::tigrxml)
    - DBD::mysql is not installed
    * This feature isn't supported under your OS (mswin)
    - DB_File is not installed
    - DBD::Pg is not installed

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

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

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] Encountered CODE ref, using dummy placeholder at C:/cpanfly-5.12/var/megalib/Data/Dumper.pm line 190.
  - will not run internet-requiring tests
Creating new 'MYMETA.yml' with configuration results
Creating new 'Build' script for 'BioPerl' version '1.006001'
---- Unsatisfied dependencies detected during ----
----       CJFIELDS/BioPerl-1.6.1.tar.gz      ----
    DB_File [requires]
Running make 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-1.820.tar.gz
Disabled via prefs file 'C:\cpanfly-5.12\etc\distroprefs\DB_File.yml' doc 0
  PMQS/DB_File-1.820.tar.gz
  [disabled] -- NA Disabled via prefs file 'C:\cpanfly-5.12\etc\distroprefs\DB_File.yml' doc 0
Running make for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
  Has already been unwrapped into directory C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR

  CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz

Warning: Prerequisite 'DB_File => 0' for 'CJFIELDS/BioPerl-1.6.1.tar.gz' failed when processing 'PMQS/DB_File-1.820.tar.gz' with 'unwrapped => NO Disabled via prefs file 'C:\cpanfly-5.12\etc\distroprefs\DB_File.yml' doc 0'. Continuing, but chances to succeed are limited.
>>> nmake

Microsoft (R) Program Maintenance Utility   Version 7.00.8882
Copyright (C) Microsoft Corp 1988-2000. All rights reserved.

	C:\Perl-5.12\bin\perl.exe Build --makefile_env_macros 1
Building BioPerl
blib\script\load_gff.PLS -> blib\script\bp_load_gff.pl
blib\script\search2alnblocks.PLS -> blib\script\bp_search2alnblocks.pl
blib\script\blast2tree.PLS -> blib\script\bp_blast2tree.pl
blib\script\bioflat_index.PLS -> blib\script\bp_bioflat_index.pl
blib\script\mask_by_search.PLS -> blib\script\bp_mask_by_search.pl
blib\script\bp_mrtrans.PLS -> blib\script\bp_mrtrans.pl
blib\script\bp_sreformat.PLS -> blib\script\bp_sreformat.pl
blib\script\search2gff.PLS -> blib\script\bp_search2gff.pl
blib\script\mutate.PLS -> blib\script\bp_mutate.pl
blib\script\chaos_plot.PLS -> blib\script\bp_chaos_plot.pl
blib\script\unflatten_seq.PLS -> blib\script\bp_unflatten_seq.pl
blib\script\hmmer_to_table.PLS -> blib\script\bp_hmmer_to_table.pl
blib\script\fast_load_gff.PLS -> blib\script\bp_fast_load_gff.pl
blib\script\bulk_load_gff.PLS -> blib\script\bp_bulk_load_gff.pl
blib\script\revtrans-motif.PLS -> blib\script\bp_revtrans-motif.pl
blib\script\seqconvert.PLS -> blib\script\bp_seqconvert.pl
blib\script\search2table.PLS -> blib\script\bp_search2table.pl
blib\script\flanks.PLS -> blib\script\bp_flanks.pl
blib\script\seq_length.PLS -> blib\script\bp_seq_length.pl
blib\script\bp_seqret.PLS -> blib\script\bp_seqret.pl
blib\script\composite_LD.PLS -> blib\script\bp_composite_LD.pl
blib\script\hivq.PLS -> blib\script\bp_hivq.pl
blib\script\genbank2gff.PLS -> blib\script\bp_genbank2gff.pl
blib\script\einfo.PLS -> blib\script\bp_einfo.pl
blib\script\bp_seqfeature_delete.PLS -> blib\script\bp_seqfeature_delete.pl
blib\script\process_gadfly.PLS -> blib\script\bp_process_gadfly.pl
blib\script\split_seq.PLS -> blib\script\bp_split_seq.pl
blib\script\biblio.PLS -> blib\script\bp_biblio.pl
blib\script\parse_hmmsearch.PLS -> blib\script\bp_parse_hmmsearch.pl
blib\script\bp_seqfeature_gff3.PLS -> blib\script\bp_seqfeature_gff3.pl
blib\script\process_wormbase.PLS -> blib\script\bp_process_wormbase.pl
blib\script\bp_seqfeature_load.PLS -> blib\script\bp_seqfeature_load.pl
blib\script\download_query_genbank.PLS -> blib\script\bp_download_query_genbank.pl
blib\script\extract_feature_seq.PLS -> blib\script\bp_extract_feature_seq.pl
blib\script\make_mrna_protein.PLS -> blib\script\bp_make_mrna_protein.pl
blib\script\biofetch_genbank_proxy.PLS -> blib\script\bp_biofetch_genbank_proxy.pl
blib\script\aacomp.PLS -> blib\script\bp_aacomp.pl
blib\script\nexus2nh.PLS -> blib\script\bp_nexus2nh.pl
blib\script\filter_search.PLS -> blib\script\bp_filter_search.pl
blib\script\bp_nrdb.PLS -> blib\script\bp_nrdb.pl
blib\script\bp_fetch.PLS -> blib\script\bp_fetch.pl
blib\script\heterogeneity_test.PLS -> blib\script\bp_heterogeneity_test.pl
blib\script\tree2pag.PLS -> blib\script\bp_tree2pag.pl
blib\script\taxid4species.PLS -> blib\script\bp_taxid4species.pl
blib\script\local_taxonomydb_query.PLS -> blib\script\bp_local_taxonomydb_query.pl
blib\script\taxonomy2tree.PLS -> blib\script\bp_taxonomy2tree.pl
blib\script\genbank2gff3.PLS -> blib\script\bp_genbank2gff3.pl
blib\script\search2BSML.PLS -> blib\script\bp_search2BSML.pl
blib\script\oligo_count.PLS -> blib\script\bp_oligo_count.pl
blib\script\meta_gff.PLS -> blib\script\bp_meta_gff.pl
blib\script\process_sgd.PLS -> blib\script\bp_process_sgd.pl
blib\script\seqretsplit.PLS -> blib\script\bp_seqretsplit.pl
blib\script\bp_index.PLS -> blib\script\bp_index.pl
blib\script\search2tribe.PLS -> blib\script\bp_search2tribe.pl
blib\script\generate_histogram.PLS -> blib\script\bp_generate_histogram.pl
blib\script\biogetseq.PLS -> blib\script\bp_biogetseq.pl
blib\script\gccalc.PLS -> blib\script\bp_gccalc.pl
blib\script\translate_seq.PLS -> blib\script\bp_translate_seq.pl
blib\script\query_entrez_taxa.PLS -> blib\script\bp_query_entrez_taxa.pl
blib\script\fastam9_to_table.PLS -> blib\script\bp_fastam9_to_table.pl
blib\script\classify_hits_kingdom.PLS -> blib\script\bp_classify_hits_kingdom.pl
blib\script\remote_blast.PLS -> blib\script\bp_remote_blast.pl
blib\script\dbsplit.PLS -> blib\script\bp_dbsplit.pl
blib\script\pairwise_kaks.PLS -> blib\script\Encountered CODE ref, using dummy placeholder at C:\cpanfly-5.12\var\megalib/Data/Dumper.pm line 190.
Build: blib\script\bp_bulk_load_gff.pl: cannot resolve L<fast_load_gff.pl> in paragraph 25.
Build: blib\script\bp_bulk_load_gff.pl: cannot resolve L<load_gff.pl> in paragraph 25.
Build: blib\script\bp_process_wormbase.pl: cannot resolve L<bulk_load_gff.pl> in paragraph 44.
Build: blib\script\bp_process_wormbase.pl: cannot resolve L<load_gff.pl> in paragraph 44.
Build: blib\script\bp_process_sgd.pl: cannot resolve L<bulk_load_gff.pl> in paragraph 29.
Build: blib\script\bp_process_sgd.pl: cannot resolve L<load_gff.pl> in paragraph 29.
Build: blib\script\bp_load_gff.pl: cannot resolve L<bulk_load_gff.pl> in paragraph 20.
Build: blib\script\bp_load_gff.pl: cannot resolve L<load_gff.pl> in paragraph 20.
Build: blib\script\bp_fast_load_gff.pl: cannot resolve L<bulk_load_gff.pl> in paragraph 25.
Build: blib\script\bp_fast_load_gff.pl: cannot resolve L<load_gff.pl> in paragraph 25.
Build: blib\script\bp_genbank2gff.pl: cannot resolve L<bulk_load_gff.pl> in paragraph 15.
Build: blib\script\bp_genbank2gff.pl: cannot resolve L<load_gff.pl> in paragraph 15.
Build: blib\script\bp_seqconvert.pl: cannot resolve L<bp_sreformat.PLS> in paragraph 19.
Build: blib\script\bp_process_gadfly.pl: cannot resolve L<bulk_load_gff.pl> in paragraph 39.
Build: blib\script\bp_process_gadfly.pl: cannot resolve L<load_gff.pl> in paragraph 39.
Build: blib\lib\Bio\DB\GFF\Adaptor\ace.pm: cannot resolve L<bioperl> in paragraph 8.
Build: blib\lib\Bio\DB\GFF\Adaptor\dbi\mysqlace.pm: cannot resolve L<bioperl> in paragraph 8.
Build: blib\lib\Bio\Variation\IO.pm: cannot resolve L<perltie> in paragraph 66.
Build: blib\lib\Bio\SeqIO.pm: cannot resolve L<perltie> in paragraph 75.
Build: blib\lib\Bio\DB\GFF\Adaptor\dbi\mysql.pm: cannot resolve L<bioperl> in paragraph 161.
Build: blib\lib\Bio\DB\SeqFeature.pm: cannot resolve L<bioperl> in paragraph 108.
Build: blib\lib\Bio\Restriction\Enzyme.pm: cannot resolve L<non_ambiguous_length> in paragraph 214.
Build: blib\lib\Bio\DB\SeqFeature\NormalizedTableFeatureI.pm: cannot resolve L<bioperl> in paragraph 13.
Build: blib\lib\Bio\DB\GFF\Adaptor\dbi\pg_fts.pm: cannot resolve L<mailto:bioperl-l@lists.open-bio.org> in paragraph 45.
Build: blib\lib\Bio\DB\GFF\Adaptor\dbi\pg_fts.pm: cannot resolve L<mailto:gmod-gbrowse@lists.sourceforge.net> in paragraph 45.
Build: blib\lib\Bio\DB\GFF\Featname.pm: cannot resolve L<bioperl> in paragraph 44.
Build: blib\lib\Bio\SearchIO\Writer\HTMLResultWriter.pm: cannot resolve L<remote_database> in paragraph 77.
Build: blib\lib\Bio\SearchIO\Writer\HTMLResultWriter.pm: cannot resolve L<remote_database> in paragraph 86.
Build: blib\lib\Bio\SearchIO\Writer\HTMLResultWriter.pm: cannot resolve L<remote_database> in paragraph 97.
Build: blib\lib\Bio\SeqIO\embldriver.pm: cannot resolve L<annotation()|annotation> in paragraph 23.
Build: blib\lib\Bio\Tools\Alignment\Consed.pm: cannot resolve L<get_quality_scalar()|get_quality_scalar> in paragraph 83.
Build: blib\lib\Bio\Tools\Alignment\Consed.pm: cannot resolve L<get_quality_array()|get_quality_array> in paragraph 89.
Build: blib\lib\Bio\Tools\Alignment\Consed.pm: cannot resolve L<get_contigs()|get_contigs> in paragraph 100.
Build: blib\lib\Bio\Tools\Alignment\Consed.pm: cannot resolve L<get_contigs()|get_contigs> in paragraph 105.
Build: blib\lib\Bio\Tools\Alignment\Consed.pm: cannot resolve L<get_contigs()|get_contigs> in paragraph 110.
Build: blib\lib\Bio\Tools\Alignment\Consed.pm: cannot resolve L<get_contigs()|get_contigs> in paragraph 115.
Build: blib\lib\Bio\Tools\Alignment\Consed.pm: cannot resolve L<sum_lets()|sum_lets> in paragraph 222.
Build: blib\lib\Bio\SeqIO\embl.pm: cannot resolve L<annotation()|annotation> in paragraph 23.
Build: blib\lib\Bio\DB\GFF\Adaptor\dbi\mysqlcmap.pm: cannot resolve L<bioperl> in paragraph 183.
Build: blib\lib\Bio\ClusterIO.pm: cannot resolve L<perltie> in paragraph 29.
Build: blib\lib\Bio\Search\Hit\HMMERHit.pm: cannot resolve L<score()|score> in paragraph 70.
Build: blib\lib\Bio\Search\Hit\HMMERHit.pm: cannot resolve L<hsp()|hsp> in paragraph 78.
Build: blib\lib\Bio\Search\Hit\PullHitI.pm: cannot resolve L<expect()|expect> in paragraph 142.
Build: blib\lib\Bio\Search\Hit\PullHitI.pm: cannot resolve L<signif()|signif> in paragraph 142.
Build: blib\lib\Bio\Seq\Quality.pm: cannot resolve L<force_flush> in paragraph 26.
Build: blib\lib\Bio\DB\GFF\Adaptor\memory.pm: cannot resolve L<bioperl> in paragraph 22.
Build: blib\lib\Bio\DB\GFF\Adaptor\dbi\caching_handle.pm: cannot resolve L<DBI> in paragraph 56.
Build: blib\lib\Bio\DB\GFF\Adaptor\dbi\caching_handle.pm: cannot resolve L<bioperl> in paragraph 56.
Build: blib\lib\Bio\Search\Hit\HmmpfamHit.pm: cannot resolve L<num_hsps> in paragraph 76.
Build: blib\lib\Bio\DB\SeqFeature\Store\Loader.pm: cannot resolve L<bioperl> in paragraph 178.
Build: blib\lib\Bio\Search\Hit\HitI.pm: cannot resolve L<expect()|expect> in paragraph 126.
Build: blib\lib\Bio\Search\Hit\HitI.pm: cannot resolve L<signif()|signif> in paragraph 126.
Build: blib\lib\Bio\Search\Hit\HitI.pm: cannot resolve L<frac_aligned_query()|frac_aligned_query> in paragraph 136.
Build: blib\lib\Bio\Search\Hit\HitI.pm: cannot resolve L<frac_aligned_hit()|frac_aligned_hit> in paragraph 136.
Build: blib\lib\Bio\FeatureIO.pm: cannot resolve L<perltie> in paragraph 55.
Build: blib\lib\Bio\DB\GFF\Adaptor\dbi\oracleace.pm: cannot resolve L<bioperl> in paragraph 8.
Build: blib\lib\Bio\Tools\Run\RemoteBlast.pm: cannot resolve L<FEEDBACK> in paragraph 36.
Build: blib\lib\Bio\Search\Result\HMMERResult.pm: cannot resolve L<next_models> in paragraph 9.
Build: blib\lib\Bio\Search\Hit\GenericHit.pm: cannot resolve L<expect()|expect> in paragraph 134.
Build: blib\lib\Bio\SeqIO\genbank.pm: cannot resolve L<annotation()|annotation> in paragraph 22.
Build: blib\lib\Bio\Structure\IO.pm: cannot resolve L<perltie> in paragraph 56.
Build: blib\lib\Bio\Search\Hit\ModelHit.pm: cannot resolve L<expect()|expect> in paragraph 105.
Build: blib\lib\Bio\Search\Hit\ModelHit.pm: cannot resolve L<signif()|signif> in paragraph 105.
Build: blib\lib\Bio\DB\SeqFeature\Store\berkeleydb3.pm: cannot resolve L<bioperl> in paragraph 15.
Build: blib\lib\Bio\DB\Fasta.pm: cannot resolve L<bioperl> in paragraph 123.
Build: blib\lib\Bio\DB\SeqFeature\Store\berkeleydb.pm: cannot resolve L<bioperl> in paragraph 264.
Build: blib\lib\Bio\DB\SeqFeature\Store\LoadHelper.pm: cannot resolve L<bioperl> in paragraph 10.
Build: blib\lib\Bio\DB\DBFetch.pm: cannot resolve L<http:E<sol>E<sol>www.ebi.ac.ukE<sol>cgi-binE<sol>dbfetch> in paragraph 8.
Build: blib\lib\Bio\DB\SeqFeature\NormalizedFeature.pm: cannot resolve L<bioperl> in paragraph 160.
Build: blib\lib\Bio\Search\Hit\BlastPullHit.pm: cannot resolve L<num_hsps> in paragraph 74.
Build: blib\lib\Bio\DB\GFF\Adaptor\dbi.pm: cannot resolve L<bioperl> in paragraph 447.
Build: blib\lib\Bio\Root\Root.pm: cannot resolve L<Error> in paragraph 22.
Build: blib\lib\Bio\Root\Root.pm: cannot resolve L<Error> in paragraph 23.
Build: blib\lib\Bio\Root\Root.pm: cannot resolve L<Error> in paragraph 23.
Build: blib\lib\Bio\Root\Root.pm: cannot resolve L<Error> in paragraph 37.
Build: blib\lib\Bio\Search\SearchUtils.pm: cannot resolve L<_adjust_contigs> in paragraph 16.
Build: blib\lib\Bio\DB\SeqFeature\Store\memory.pm: cannot resolve L<bioperl> in paragraph 121.
Build: blib\lib\Bio\DB\GFF\Homol.pm: cannot resolve L<bioperl> in paragraph 28.
Build: blib\lib\Bio\DB\GFF\RelSegment.pm: cannot resolve L<bioperl> in paragraph 251.
Build: blib\lib\Bio\DB\GFF\Segment.pm: cannot resolve L<bioperl> in paragraph 229.
Build: blib\lib\Bio\Seq\MetaI.pm: cannot resolve L<names_submeta> in paragraph 14.
Build: blib\lib\Bio\SeqEvolution\DNAPoint.pm: cannot resolve L<reset_sequence_counter> in paragraph 9.
Build: blib\lib\Bio\DB\GFF\Adaptor\dbi\mysqlopt.pm: cannot resolve L<bioperl> in paragraph 8.
Build: blib\lib\Bio\AlignIO.pm: cannot resolve L<print> in paragraph 51.
Build: blib\lib\Bio\AlignIO.pm: cannot resolve L<perltie> in paragraph 66.
Build: blib\lib\Bio\Search\HSP\ModelHSP.pm: cannot resolve L<seq_str()|seq_str> in paragraph 52.
Build: blib\lib\Bio\DB\GFF\Typename.pm: cannot resolve L<bioperl> in paragraph 49.
Build: blib\lib\Bio\DB\GFF\Adaptor\berkeleydb.pm: cannot resolve L<bioperl> in paragraph 34.
Build: blib\lib\Bio\DB\SeqFeature\NormalizedFeatureI.pm: cannot resolve L<bioperl> in paragraph 13.
Build: blib\lib\Bio\DB\GFF\Feature.pm: cannot resolve L<bioperl> in paragraph 295.
Build: blib\lib\Bio\Assembly\Contig.pm: cannot resolve L<Coordinate_Systems> in paragraph 120.
Build: blib\lib\Bio\Root\Exception.pm: cannot resolve L<Error.pm try|Error/try> in paragraph .
Build: blib\lib\Bio\Root\Exception.pm: cannot resolve L<Error.pm try|Error/try> in paragraph 12.
Build: blib\lib\Bio\Root\Exception.pm: cannot resolve L<Error> in paragraph 40.
Build: blib\lib\Bio\Root\Exception.pm: cannot resolve L<Error> in paragraph 46.
Build: blib\lib\Bio\Root\Exception.pm: cannot resolve L<pretty_format()|pretty_format> in paragraph 91.
Build: blib\lib\Bio\DB\SeqFeature\Segment.pm: cannot resolve L<bioperl> in paragraph 122.
Build: blib\lib\Bio\SeqIO\swiss.pm: cannot resolve L<annotation()|annotation> in paragraph 44.
Build: blib\lib\Bio\DB\SeqFeature\Store\GFF2Loader.pm: cannot resolve L<bioperl> in paragraph 181.
bp_pairwise_kaks.pl
  CJFIELDS/BioPerl-1.6.1.tar.gz
  nmake -- OK
Running make test
>>> nmake test TEST_VERBOSE=1

Microsoft (R) Program Maintenance Utility   Version 7.00.8882
Copyright (C) Microsoft Corp 1988-2000. All rights reserved.

	C:\Perl-5.12\bin\perl.exe Build --makefile_env_macros 1 test
Copying scripts\Bio-DB-GFF\load_gff.PLS -> blib\script\load_gff.PLS
Changing sharpbang in blib\script\load_gff.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\load_gff.PLS.bak
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Copying scripts\utilities\search2alnblocks.PLS -> blib\script\search2alnblocks.PLS
Changing sharpbang in blib\script\search2alnblocks.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\search2alnblocks.PLS.bak
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Copying scripts\tree\blast2tree.PLS -> blib\script\blast2tree.PLS
Changing sharpbang in blib\script\blast2tree.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\blast2tree.PLS.bak
blib\script\blast2tree.PLS -> blib\script\bp_blast2tree.pl
Copying scripts\DB\bioflat_index.PLS -> blib\script\bioflat_index.PLS
Changing sharpbang in blib\script\bioflat_index.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\bioflat_index.PLS.bak
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Copying scripts\utilities\mask_by_search.PLS -> blib\script\mask_by_search.PLS
Changing sharpbang in blib\script\mask_by_search.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\mask_by_search.PLS.bak
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Copying scripts\utilities\bp_mrtrans.PLS -> blib\script\bp_mrtrans.PLS
Changing sharpbang in blib\script\bp_mrtrans.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\bp_mrtrans.PLS.bak
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Copying scripts\utilities\bp_sreformat.PLS -> blib\script\bp_sreformat.PLS
Changing sharpbang in blib\script\bp_sreformat.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\bp_sreformat.PLS.bak
blib\script\bp_sreformat.PLS -> blib\script\bp_sreformat.pl
Copying scripts\utilities\search2gff.PLS -> blib\script\search2gff.PLS
Changing sharpbang in blib\script\search2gff.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\search2gff.PLS.bak
blib\script\search2gff.PLS -> blib\script\bp_search2gff.pl
Copying scripts\utilities\mutate.PLS -> blib\script\mutate.PLS
Changing sharpbang in blib\script\mutate.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\mutate.PLS.bak
blib\script\mutate.PLS -> blib\script\bp_mutate.pl
Copying scripts\seqstats\chaos_plot.PLS -> blib\script\chaos_plot.PLS
Changing sharpbang in blib\script\chaos_plot.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\chaos_plot.PLS.bak
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Copying scripts\seq\unflatten_seq.PLS -> blib\script\unflatten_seq.PLS
Changing sharpbang in blib\script\unflatten_seq.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\unflatten_seq.PLS.bak
blib\script\unflatten_seq.PLS -> blib\script\bp_unflatten_seq.pl
Copying scripts\searchio\hmmer_to_table.PLS -> blib\script\hmmer_to_table.PLS
Changing sharpbang in blib\script\hmmer_to_table.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\hmmer_to_table.PLS.bak
blib\script\hmmer_to_table.PLS -> blib\script\bp_hmmer_to_table.pl
Copying scripts\Bio-DB-GFF\fast_load_gff.PLS -> blib\script\fast_load_gff.PLS
Changing sharpbang in blib\script\fast_load_gff.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\fast_load_gff.PLS.bak
blib\script\fast_load_gff.PLS -> blib\script\bp_fast_load_gff.pl
Copying scripts\Bio-DB-GFF\bulk_load_gff.PLS -> blib\script\bulk_load_gff.PLS
Changing sharpbang in blib\script\bulk_load_gff.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\bulk_load_gff.PLS.bak
blib\script\bulk_load_gff.PLS -> blib\script\bp_bulk_load_gff.pl
Copying scripts\utilities\revtrans-motif.PLS -> blib\script\revtrans-motif.PLS
Changing sharpbang in blib\script\revtrans-motif.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\revtrans-motif.PLS.bak
blib\script\revtrans-motif.PLS -> blib\script\bp_revtrans-motif.pl
Copying scripts\seq\seqconvert.PLS -> blib\script\seqconvert.PLS
Changing sharpbang in blib\script\seqconvert.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\seqconvert.PLS.bak
blib\script\seqconvert.PLS -> blib\script\bp_seqconvert.pl
Copying scripts\searchio\search2table.PLS -> blib\script\search2table.PLS
Changing sharpbang in blib\script\search2table.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\search2table.PLS.bak
blib\script\search2table.PLS -> blib\script\bp_search2table.pl
Copying scripts\DB\flanks.PLS -> blib\script\flanks.PLS
Changing sharpbang in blib\script\flanks.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\flanks.PLS.bak
blib\script\flanks.PLS -> blib\script\bp_flanks.pl
Copying scripts\utilities\seq_length.PLS -> blib\script\seq_length.PLS
Changing sharpbang in blib\script\seq_length.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\seq_length.PLS.bak
blib\script\seq_length.PLS -> blib\script\bp_seq_length.pl
Copying scripts\index\bp_seqret.PLS -> blib\script\bp_seqret.PLS
Changing sharpbang in blib\script\bp_seqret.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\bp_seqret.PLS.bak
blib\script\bp_seqret.PLS -> blib\script\bp_seqret.pl
Copying scripts\popgen\composite_LD.PLS -> blib\script\composite_LD.PLS
Changing sharpbang in blib\script\composite_LD.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\composite_LD.PLS.bak
blib\script\composite_LD.PLS -> blib\script\bp_composite_LD.pl
Copying scripts\DB-HIV\hivq.PLS -> blib\script\hivq.PLS
Changing sharpbang in blib\script\hivq.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\hivq.PLS.bak
blib\script\hivq.PLS -> blib\script\bp_hivq.pl
Copying scripts\Bio-DB-GFF\genbank2gff.PLS -> blib\script\genbank2gff.PLS
Changing sharpbang in blib\script\genbank2gff.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\genbank2gff.PLS.bak
blib\script\genbank2gff.PLS -> blib\script\bp_genbank2gff.pl
Copying scripts\Bio-DB-EUtilities\einfo.PLS -> blib\script\einfo.PLS
Changing sharpbang in blib\script\einfo.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\einfo.PLS.bak
blib\script\einfo.PLS -> blib\script\bp_einfo.pl
Copying scripts\Bio-SeqFeature-Store\bp_seqfeature_delete.PLS -> blib\script\bp_seqfeature_delete.PLS
Changing sharpbang in blib\script\bp_seqfeature_delete.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\bp_seqfeature_delete.PLS.bak
blib\script\bp_seqfeature_delete.PLS -> blib\script\bp_seqfeature_delete.pl
Copying scripts\Bio-DB-GFF\process_gadfly.PLS -> blib\script\process_gadfly.PLS
Changing sharpbang in blib\script\process_gadfly.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\process_gadfly.PLS.bak
blib\script\process_gadfly.PLS -> blib\script\bp_process_gadfly.pl
Copying scripts\seq\split_seq.PLS -> blib\script\split_seq.PLS
Changing sharpbang in blib\script\split_seq.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\split_seq.PLS.bak
blib\script\split_seq.PLS -> blib\script\bp_split_seq.pl
Copying scripts\biblio\biblio.PLS -> blib\script\biblio.PLS
Changing sharpbang in blib\script\biblio.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\biblio.PLS.bak
blib\script\biblio.PLS -> blib\script\bp_biblio.pl
Copying scripts\searchio\parse_hmmsearch.PLS -> blib\script\parse_hmmsearch.PLS
Changing sharpbang in blib\script\parse_hmmsearch.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\parse_hmmsearch.PLS.bak
blib\script\parse_hmmsearch.PLS -> blib\script\bp_parse_hmmsearch.pl
Copying scripts\Bio-SeqFeature-Store\bp_seqfeature_gff3.PLS -> blib\script\bp_seqfeature_gff3.PLS
blib\script\bp_seqfeature_gff3.PLS -> blib\script\bp_seqfeature_gff3.pl
Copying scripts\Bio-DB-GFF\process_wormbase.PLS -> blib\script\process_wormbase.PLS
Changing sharpbang in blib\script\process_wormbase.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\process_wormbase.PLS.bak
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Copying scripts\Bio-SeqFeature-Store\bp_seqfeature_load.PLS -> blib\script\bp_seqfeature_load.PLS
Changing sharpbang in blib\script\bp_seqfeature_load.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\bp_seqfeature_load.PLS.bak
blib\script\bp_seqfeature_load.PLS -> blib\script\bp_seqfeature_load.pl
Copying scripts\utilities\download_query_genbank.PLS -> blib\script\download_query_genbank.PLS
Changing sharpbang in blib\script\download_query_genbank.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\download_query_genbank.PLS.bak
blib\script\download_query_genbank.PLS -> blib\script\bp_download_query_genbank.pl
Copying scripts\seq\extract_feature_seq.PLS -> blib\script\extract_feature_seq.PLS
Changing sharpbang in blib\script\extract_feature_seq.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\extract_feature_seq.PLS.bak
blib\script\extract_feature_seq.PLS -> blib\script\bp_extract_feature_seq.pl
Copying scripts\seq\make_mrna_protein.PLS -> blib\script\make_mrna_protein.PLS
Changing sharpbang in blib\script\make_mrna_protein.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\make_mrna_protein.PLS.bak
blib\script\make_mrna_protein.PLS -> blib\script\bp_make_mrna_protein.pl
Copying scripts\DB\biofetch_genbank_proxy.PLS -> blib\script\biofetch_genbank_proxy.PLS
Changing sharpbang in blib\script\biofetch_genbank_proxy.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\biofetch_genbank_proxy.PLS.bak
blib\script\biofetch_genbank_proxy.PLS -> blib\script\bp_biofetch_genbank_proxy.pl
Copying scripts\seqstats\aacomp.PLS -> blib\script\aacomp.PLS
Changing sharpbang in blib\script\aacomp.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\aacomp.PLS.bak
blib\script\aacomp.PLS -> blib\script\bp_aacomp.pl
Copying scripts\tree\nexus2nh.PLS -> blib\script\nexus2nh.PLS
Changing sharpbang in blib\script\nexus2nh.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\nexus2nh.PLS.bak
blib\script\nexus2nh.PLS -> blib\script\bp_nexus2nh.pl
Copying scripts\searchio\filter_search.PLS -> blib\script\filter_search.PLS
Changing sharpbang in blib\script\filter_search.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\filter_search.PLS.bak
blib\script\filter_search.PLS -> blib\script\bp_filter_search.pl
Copying scripts\utilities\bp_nrdb.PLS -> blib\script\bp_nrdb.PLS
Changing sharpbang in blib\script\bp_nrdb.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\bp_nrdb.PLS.bak
blib\script\bp_nrdb.PLS -> blib\script\bp_nrdb.pl
Copying scripts\index\bp_fetch.PLS -> blib\script\bp_fetch.PLS
Changing sharpbang in blib\script\bp_fetch.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\bp_fetch.PLS.bak
blib\script\bp_fetch.PLS -> blib\script\bp_fetch.pl
Copying scripts\popgen\heterogeneity_test.PLS -> blib\script\heterogeneity_test.PLS
Changing sharpbang in blib\script\heterogeneity_test.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\heterogeneity_test.PLS.bak
blib\script\heterogeneity_test.PLS -> blib\script\bp_heterogeneity_test.pl
Copying scripts\tree\tree2pag.PLS -> blib\script\tree2pag.PLS
Changing sharpbang in blib\script\tree2pag.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\tree2pag.PLS.bak
blib\script\tree2pag.PLS -> blib\script\bp_tree2pag.pl
Copying scripts\taxa\taxid4species.PLS -> blib\script\taxid4species.PLS
Changing sharpbang in blib\script\taxid4species.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\taxid4species.PLS.bak
blib\script\taxid4species.PLS -> blib\script\bp_taxid4species.pl
Copying scripts\taxa\local_taxonomydb_query.PLS -> blib\script\local_taxonomydb_query.PLS
Changing sharpbang in blib\script\local_taxonomydb_query.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\local_taxonomydb_query.PLS.bak
blib\script\local_taxonomydb_query.PLS -> blib\script\bp_local_taxonomydb_query.pl
Copying scripts\taxa\taxonomy2tree.PLS -> blib\script\taxonomy2tree.PLS
Changing sharpbang in blib\script\taxonomy2tree.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\taxonomy2tree.PLS.bak
blib\script\taxonomy2tree.PLS -> blib\script\bp_taxonomy2tree.pl
Copying scripts\Bio-DB-GFF\genbank2gff3.PLS -> blib\script\genbank2gff3.PLS
Changing sharpbang in blib\script\genbank2gff3.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\genbank2gff3.PLS.bak
blib\script\genbank2gff3.PLS -> blib\script\bp_genbank2gff3.pl
Copying scripts\utilities\search2BSML.PLS -> blib\script\search2BSML.PLS
Changing sharpbang in blib\script\search2BSML.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\search2BSML.PLS.bak
blib\script\search2BSML.PLS -> blib\script\bp_search2BSML.pl
Copying scripts\seqstats\oligo_count.PLS -> blib\script\oligo_count.PLS
Changing sharpbang in blib\script\oligo_count.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\oligo_count.PLS.bak
blib\script\oligo_count.PLS -> blib\script\bp_oligo_count.pl
Copying scripts\Bio-DB-GFF\meta_gff.PLS -> blib\script\meta_gff.PLS
Changing sharpbang in blib\script\meta_gff.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\meta_gff.PLS.bak
blib\script\meta_gff.PLS -> blib\script\bp_meta_gff.pl
Copying scripts\Bio-DB-GFF\process_sgd.PLS -> blib\script\process_sgd.PLS
Changing sharpbang in blib\script\process_sgd.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\process_sgd.PLS.bak
blib\script\process_sgd.PLS -> blib\script\bp_process_sgd.pl
Copying scripts\seq\seqretsplit.PLS -> blib\script\seqretsplit.PLS
Changing sharpbang in blib\script\seqretsplit.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\seqretsplit.PLS.bak
blib\script\seqretsplit.PLS -> blib\script\bp_seqretsplit.pl
Copying scripts\index\bp_index.PLS -> blib\script\bp_index.PLS
Changing sharpbang in blib\script\bp_index.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\bp_index.PLS.bak
blib\script\bp_index.PLS -> blib\script\bp_index.pl
Copying scripts\utilities\search2tribe.PLS -> blib\script\search2tribe.PLS
Changing sharpbang in blib\script\search2tribe.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\search2tribe.PLS.bak
blib\script\search2tribe.PLS -> blib\script\bp_search2tribe.pl
Copying scripts\Bio-DB-GFF\generate_histogram.PLS -> blib\script\generate_histogram.PLS
Changing sharpbang in blib\script\generate_histogram.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\generate_histogram.PLS.bak
blib\script\generate_histogram.PLS -> blib\script\bp_generate_histogram.pl
Copying scripts\DB\biogetseq.PLS -> blib\script\biogetseq.PLS
Changing sharpbang in blib\script\biogetseq.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\biogetseq.PLS.bak
blib\script\biogetseq.PLS -> blib\script\bp_biogetseq.pl
Copying scripts\seqstats\gccalc.PLS -> blib\script\gccalc.PLS
Changing sharpbang in blib\script\gccalc.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\gccalc.PLS.bak
blib\script\gccalc.PLS -> blib\script\bp_gccalc.pl
Copying scripts\seq\translate_seq.PLS -> blib\script\translate_seq.PLS
Changing sharpbang in blib\script\translate_seq.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\translate_seq.PLS.bak
blib\script\translate_seq.PLS -> blib\script\bp_translate_seq.pl
Copying scripts\taxa\query_entrez_taxa.PLS -> blib\script\query_entrez_taxa.PLS
Changing sharpbang in blib\script\query_entrez_taxa.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\query_entrez_taxa.PLS.bak
blib\script\query_entrez_taxa.PLS -> blib\script\bp_query_entrez_taxa.pl
Copying scripts\searchio\fastam9_to_table.PLS -> blib\script\fastam9_to_table.PLS
Changing sharpbang in blib\script\fastam9_to_table.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\fastam9_to_table.PLS.bak
blib\script\fastam9_to_table.PLS -> blib\script\bp_fastam9_to_table.pl
Copying scripts\taxa\classify_hits_kingdom.PLS -> blib\script\classify_hits_kingdom.PLS
Changing sharpbang in blib\script\classify_hits_kingdom.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\classify_hits_kingdom.PLS.bak
blib\script\classify_hits_kingdom.PLS -> blib\script\bp_classify_hits_kingdom.pl
Copying scripts\utilities\remote_blast.PLS -> blib\script\remote_blast.PLS
Changing sharpbang in blib\script\remote_blast.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\remote_blast.PLS.bak
blib\script\remote_blast.PLS -> blib\script\bp_remote_blast.pl
Copying scripts\utilities\dbsplit.PLS -> blib\script\dbsplit.PLS
Changing sharpbang in blib\script\dbsplit.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\dbsplit.PLS.bak
blib\script\dbsplit.PLS -> blib\script\bp_dbsplit.pl
Copying scripts\utilities\pairwise_kaks.PLS -> blib\script\pairwise_kaks.PLS
Changing sharpbang in blib\script\pairwise_kaks.PLS to C:\Perl-5.12\bin\perl.exe
Deleting blib\script\pairwise_kaks.PLS.bak
blib\script\pairwise_kaks.PLS -> blib\script\bp_pairwise_kaks.pl
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Align/AlignStats.t ......................... 
1..43
ok 1 - use Bio::Align::DNAStatistics;
ok 2 - use Bio::Align::ProteinStatistics;
ok 3 - use Bio::AlignIO;
ok 4 - The object isa Bio::Align::AlignI
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17 - The object isa Bio::Align::AlignI
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31 - The object isa Bio::Align::AlignI
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - The object isa Bio::Align::AlignI
ok 38 - The object isa Bio::Matrix::PhylipDist
ok 39
ok 40
ok 41
ok 42 - The object isa Bio::PrimarySeqI
ok 43
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Align/AlignUtil.t .......................... 
1..33
ok 1 - use Bio::Align::Utilities;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::SeqIO;
ok 4 - The object isa Bio::Align::AlignI
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine new redefined at Bio\Location\Simple.pm line 93, <GEN4> line 120.
Subroutine start redefined at Bio\Location\Simple.pm line 115, <GEN4> line 120.
Subroutine end redefined at Bio\Location\Simple.pm line 144, <GEN4> line 120.
Subroutine length redefined at Bio\Location\Simple.pm line 190, <GEN4> line 120.
Subroutine location_type redefined at Bio\Location\Simple.pm line 281, <GEN4> line 120.
Subroutine to_FTstring redefined at Bio\Location\Simple.pm line 328, <GEN4> line 120.
Subroutine trunc redefined at Bio\Location\Simple.pm line 370, <GEN4> line 120.
Subroutine new redefined at Bio\Location\Split.pm line 104, <GEN4> line 120.
Subroutine each_Location redefined at Bio\Location\Split.pm line 136, <GEN4> line 120.
Subroutine sub_Location redefined at Bio\Location\Split.pm line 165, <GEN4> line 120.
Subroutine add_sub_Location redefined at Bio\Location\Split.pm line 234, <GEN4> line 120.
Subroutine splittype redefined at Bio\Location\Split.pm line 258, <GEN4> line 120.
Subroutine is_single_sequence redefined at Bio\Location\Split.pm line 286, <GEN4> line 120.
Subroutine guide_strand redefined at Bio\Location\Split.pm line 311, <GEN4> line 120.
Subroutine strand redefined at Bio\Location\Split.pm line 339, <GEN4> line 120.
Subroutine flip_strand redefined at Bio\Location\Split.pm line 380, <GEN4> line 120.
Subroutine start redefined at Bio\Location\Split.pm line 401, <GEN4> line 120.
Subroutine end redefined at Bio\Location\Split.pm line 420, <GEN4> line 120.
Subroutine min_start redefined at Bio\Location\Split.pm line 439, <GEN4> line 120.
Subroutine max_start redefined at Bio\Location\Split.pm line 461, <GEN4> line 120.
Subroutine start_pos_type redefined at Bio\Location\Split.pm line 484, <GEN4> line 120.
Subroutine min_end redefined at Bio\Location\Split.pm line 505, <GEN4> line 120.
Subroutine max_end redefined at Bio\Location\Split.pm line 528, <GEN4> line 120.
Subroutine end_pos_type redefined at Bio\Location\Split.pm line 552, <GEN4> line 120.
Subroutine seq_id redefined at Bio\Location\Split.pm line 578, <GEN4> line 120.
Subroutine to_FTstring redefined at Bio\Location\Split.pm line 624, <GEN4> line 120.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118, <GEN4> line 120.
t/Align/SimpleAlign.t ........................ 
1..179
ok 1 - use Bio::SimpleAlign;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::SeqFeature::Generic;
ok 4 - use Bio::Location::Simple;
ok 5 - use Bio::Location::Split;
ok 6 - The object isa Bio::AlignIO
ok 7 - pfam input test
ok 8 - match_line
ok 9 - The object isa Bio::Align::AlignI
ok 10 - num_sequences
ok 11 - num_sequences
ok 12 - select_noncont
ok 13 - select_noncont
ok 14 - num_sequences
ok 15 - select_noncont
ok 16 - select_noncont
ok 17 - each_seq
ok 18 - get_nse
ok 19 - id
ok 20 - num_gaps
ok 21 - each_alphabetically
ok 22 - column_from_residue_number
ok 23 - display_name get/set
ok 24 - display_name get
ok 25 - consensus_string
ok 26 - consensus_string
ok 27 - consensus_string
ok 28
ok 29 - each_seq_with_id
ok 30 - is_flush
ok 31 - id get/set
ok 32 - length
ok 33 - num_residues
ok 34 - num_sequences
ok 35 - overall_percentage_identity
ok 36 - overall_percentage_identity
ok 37 - overall_percentage_identity
ok 38 - overall_percentage_identity
ok 39 - average_percentage_identity
ok 40
ok 41 - set_displayname_count
ok 42
ok 43 - set_displayname_flat
ok 44
ok 45 - set_displayname_normal
ok 46
ok 47
ok 48 - uppercase, map_chars
ok 49 - match_line
ok 50 - remove_seqs
ok 51 - remove_seqs
ok 52 - add_seq
ok 53 - add_seq
ok 54 - get_seq_by_pos
ok 55 - get_seq_by_pos
ok 56
ok 57
ok 58
ok 59 - purge
ok 60 - purge
ok 61 - IO::String consensus_iupac
ok 62 - IO::String write_aln normal
ok 63 - IO::String write_aln slice
ok 64 - IO::String write_aln slice
ok 65 - IO::String write_aln slice
ok 66 - IO::String write_aln slice
ok 67 - IO::String write_aln slice
ok 68
ok 69 - remove_columns by position
ok 70 - remove_columns by position (wrong order)
ok 71 - cigar_line
ok 72 - cigar_line
ok 73 - cigar_line
ok 74 - cigar_line
ok 75 - sort_alphabetically - before
ok 76
ok 77 - sort_alphabetically - after
ok 78 - remove_gaps
ok 79 - remove_gaps all_gaps_only
ok 80 - set_new_reference
ok 81 - set_new_reference
ok 82 - uniq_seq
ok 83 - bug 2099
ok 84 - bug 2099
ok 85 - bug 2793
ok 86 - bug 2793
ok 87 - bug 2793
ok 88 - bug 2793
ok 89 - Bad sequence, bad!
ok 90 - added 3 seqs
ok 91 - first 2 features added
ok 92 - 3rd feature added
not ok 93 # TODO This should pass but dies; see bug 2842

#   Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 1.  
# Overriding value [0] with value 1 for Bio::LocatableSeq::end().
# ?
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 94 - slice 1 len
ok 95 - correct masked seq
ok 96 - correct masked seq
ok 97 - correct masked seq
not ok 98 # TODO This should pass but dies; see bug 2842

#   Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 3.  
# Overriding value [2] with value 3 for Bio::LocatableSeq::end().
# ?
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 99 - slice 2 len
ok 100 - correct masked seq
ok 101 - correct masked seq
ok 102 - correct masked seq
not ok 103 # TODO This should pass but dies; see bug 2842

#   Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 3.  
# Overriding value [1] with value 3 for Bio::LocatableSeq::end().
# ??
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 104 - slice 3 len
ok 105 - correct masked seq
ok 106 - correct masked seq
ok 107 - correct masked seq
not ok 108 # TODO This should pass but dies; see bug 2842

#   Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 6.  
# Overriding value [4] with value 6 for Bio::LocatableSeq::end().
# ??
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 109 - slice 4 len
ok 110 - correct masked seq
ok 111 - correct masked seq
ok 112 - correct masked seq
ok 113 - initial display id ok
ok 114 - safe display id ok
ok 115 - restored display id ok
ok 116 - sort by list ok
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123 - BIC:GGATCCATT[C/C]CTACT
ok 124 - BIC:GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT
ok 125 - BIC:G[G/C]ATCCATT[C/G]CTACT
ok 126 - BIC:GGATCCATT[C/G]CTACT
ok 127 - BIC:GGATCCATT[C/G]CTAC[T/A]
ok 128 - BIC:GGATCCATT[C/G]CTA[C/G][T/A]
ok 129 - BIC:GGATCCATT[C/G]CTACT
ok 130 - BIC:GGATCCATT{C.C}CTACT
ok 131 - BIC:GGAT{C.-}{C.-}ATT{C.C}CT{A.C}CT
ok 132 - BIC:G{G.C}ATCCATT{C.G}CTACT
ok 133 - BIC:GGATCCATT{C.G}CTACT
ok 134 - BIC:GGATCCATT{C.G}CTAC{T.A}
ok 135 - BIC:GGATCCATT{C.G}CTA{C.G}{T.A}
ok 136 - BIC:GGATCCATT{C.G}CTACT
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174 - The object isa Bio::SimpleAlign
ok 175 - consensus string looks ok
ok 176 - looks like correct unmasked alignment (from clustalw)
ok 177 - looks like correct masked alignment (from clustalw)
ok 178
ok 179 - align after looks ok
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94
t/Align/TreeBuild.t .......................... 
1..13
ok 1 - use Bio::Align::DNAStatistics;
ok 2 - use Bio::Align::ProteinStatistics;
ok 3 - use Bio::Align::Utilities;
ok 4 - use Bio::AlignIO;
ok 5 - use Bio::Tree::DistanceFactory;
ok 6 - use Bio::TreeIO;
ok 7 - SimpleAlign object parsed out isa Bio::SimpleAlign
ok 8 - Protein distance matrix retrieved isa Bio::Matrix::MatrixI
ok 9 - Tree object gotten back isa Bio::Tree::TreeI
ok 10 - NJ calculated Branch length
ok 11 - NJ calculated Branch length
ok 12 - Make sure two nodes are sister
ok 13 - 10 replicates formulated
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Align/Utilities.t .......................... 
1..13
ok 1 - use Bio::Align::Utilities;
ok 2 - use Bio::SimpleAlign;
ok 3 - use Bio::PrimarySeq;
ok 4 - use Bio::LocatableSeq;
ok 5 - use Bio::AlignIO;
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine new redefined at Bio\Annotation\SimpleValue.pm line 97, <GEN24> line 86.
Subroutine as_text redefined at Bio\Annotation\SimpleValue.pm line 129, <GEN24> line 86.
Subroutine display_text redefined at Bio\Annotation\SimpleValue.pm line 154, <GEN24> line 86.
Subroutine hash_tree redefined at Bio\Annotation\SimpleValue.pm line 175, <GEN24> line 86.
Subroutine tagname redefined at Bio\Annotation\SimpleValue.pm line 200, <GEN24> line 86.
Subroutine value redefined at Bio\Annotation\SimpleValue.pm line 230, <GEN24> line 86.
Subroutine tag_term redefined at Bio\Annotation\SimpleValue.pm line 266, <GEN24> line 86.
Subroutine new redefined at Bio\Seq\Meta.pm line 226, <GEN52> line 64.
Subroutine meta redefined at Bio\Seq\Meta.pm line 270, <GEN52> line 64.
Subroutine meta_text redefined at Bio\Seq\Meta.pm line 285, <GEN52> line 64.
Subroutine named_meta redefined at Bio\Seq\Meta.pm line 301, <GEN52> line 64.
Subroutine _test_gap_positions redefined at Bio\Seq\Meta.pm line 348, <GEN52> line 64.
Subroutine named_meta_text redefined at Bio\Seq\Meta.pm line 378, <GEN52> line 64.
Subroutine submeta redefined at Bio\Seq\Meta.pm line 410, <GEN52> line 64.
Subroutine submeta_text redefined at Bio\Seq\Meta.pm line 426, <GEN52> line 64.
Subroutine named_submeta redefined at Bio\Seq\Meta.pm line 445, <GEN52> line 64.
Subroutine named_submeta_text redefined at Bio\Seq\Meta.pm line 504, <GEN52> line 64.
Subroutine meta_names redefined at Bio\Seq\Meta.pm line 519, <GEN52> line 64.
Subroutine meta_length redefined at Bio\Seq\Meta.pm line 541, <GEN52> line 64.
Subroutine named_meta_length redefined at Bio\Seq\Meta.pm line 557, <GEN52> line 64.
Subroutine force_flush redefined at Bio\Seq\Meta.pm line 578, <GEN52> line 64.
Subroutine _do_flush redefined at Bio\Seq\Meta.pm line 605, <GEN52> line 64.
Subroutine is_flush redefined at Bio\Seq\Meta.pm line 638, <GEN52> line 64.
Subroutine revcom redefined at Bio\Seq\Meta.pm line 680, <GEN52> line 64.
Subroutine trunc redefined at Bio\Seq\Meta.pm line 703, <GEN52> line 64.
Subroutine to_string redefined at Bio\Seq\Meta.pm line 727, <GEN52> line 64.
t/AlignIO/AlignIO.t .......................... 
1..28
ok 1 - use Bio::AlignIO;
ok 2 - input filehandle method test : metafasta
ok 3 - input filehandle method test : po
ok 4 - input filehandle method test : nexus
ok 5 - input filehandle method test : clustalw
ok 6 - input filehandle method test : prodom
ok 7 - input filehandle method test : fasta
ok 8 - input filehandle method test : arp
ok 9 - input filehandle method test : xmfa
ok 10 - input filehandle method test : mase
ok 11 - input filehandle method test : psi
ok 12 - input filehandle method test : phylip
ok 13 - input filehandle method test : pfam
ok 14 - input filehandle method test : selex
ok 15 - input filehandle method test : stockholm
ok 16 - input filehandle method test : msf
ok 17 - filehandle output test : metafasta
ok 18 - filehandle output test : po
ok 19 - filehandle output test : nexus
ok 20 - filehandle output test : clustalw
ok 21 - filehandle output test : fasta
ok 22 - filehandle output test : xmfa
ok 23 - filehandle output test : psi
ok 24 - filehandle output test : phylip
ok 25 - filehandle output test : pfam
ok 26 - filehandle output test : selex
ok 27 - filehandle output test : stockholm
ok 28 - filehandle output test : msf
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine next_aln redefined at Bio\AlignIO\arp.pm line 117.
Subroutine write_aln redefined at Bio\AlignIO\arp.pm line 200.
Subroutine _process_sequence redefined at Bio\AlignIO\arp.pm line 207.
Subroutine _process_annotation redefined at Bio\AlignIO\arp.pm line 218.
Subroutine new redefined at Bio\Annotation\SimpleValue.pm line 97, <GEN0> line 86.
Subroutine as_text redefined at Bio\Annotation\SimpleValue.pm line 129, <GEN0> line 86.
Subroutine display_text redefined at Bio\Annotation\SimpleValue.pm line 154, <GEN0> line 86.
Subroutine hash_tree redefined at Bio\Annotation\SimpleValue.pm line 175, <GEN0> line 86.
Subroutine tagname redefined at Bio\Annotation\SimpleValue.pm line 200, <GEN0> line 86.
Subroutine value redefined at Bio\Annotation\SimpleValue.pm line 230, <GEN0> line 86.
Subroutine tag_term redefined at Bio\Annotation\SimpleValue.pm line 266, <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
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine _initialize redefined at Bio\AlignIO\bl2seq.pm line 125.
Subroutine next_aln redefined at Bio\AlignIO\bl2seq.pm line 143.
Subroutine write_aln redefined at Bio\AlignIO\bl2seq.pm line 185.
Subroutine report_type redefined at Bio\AlignIO\bl2seq.pm line 201.
Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175.
Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 261.
Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 281.
Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 308.
Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 334.
Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 354.
Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 375.
Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 396.
Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 417.
Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 439.
Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 462.
Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 484.
Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 505.
Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 520.
Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 537.
Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 552.
Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 571.
Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 596.
Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 613.
Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 626.
Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 643.
Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 660.
Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 677.
Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 697.
Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 725.
Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 744.
Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 753.
Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 770.
Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 791.
Subroutine new redefined at Bio\SeqFeature\Similarity.pm line 86, <GEN0> line 64.
Subroutine significance redefined at Bio\SeqFeature\Similarity.pm line 123, <GEN0> line 64.
Subroutine bits redefined at Bio\SeqFeature\Similarity.pm line 139, <GEN0> line 64.
Subroutine frac_identical redefined at Bio\SeqFeature\Similarity.pm line 155, <GEN0> line 64.
Subroutine seqlength redefined at Bio\SeqFeature\Similarity.pm line 171, <GEN0> line 64.
Subroutine seqdesc redefined at Bio\SeqFeature\Similarity.pm line 191, <GEN0> line 64.
Subroutine new redefined at Bio\Location\Simple.pm line 93, <GEN0> line 64.
Subroutine start redefined at Bio\Location\Simple.pm line 115, <GEN0> line 64.
Subroutine end redefined at Bio\Location\Simple.pm line 144, <GEN0> line 64.
Subroutine length redefined at Bio\Location\Simple.pm line 190, <GEN0> line 64.
Subroutine location_type redefined at Bio\Location\Simple.pm line 281, <GEN0> line 64.
Subroutine to_FTstring redefined at Bio\Location\Simple.pm line 328, <GEN0> line 64.
Subroutine trunc redefined at Bio\Location\Simple.pm line 370, <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
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine _initialize redefined at Bio\AlignIO\clustalw.pm line 101.
Subroutine next_aln redefined at Bio\AlignIO\clustalw.pm line 122.
Subroutine write_aln redefined at Bio\AlignIO\clustalw.pm line 232.
Subroutine percentages redefined at Bio\AlignIO\clustalw.pm line 331.
Subroutine line_length redefined at Bio\AlignIO\clustalw.pm line 350.
t/AlignIO/clustalw.t ......................... 
1..6
ok 1 - use Bio::AlignIO::clustalw;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - clustalw consensus_string test
ok 4 - clustalw (.aln) output test
ok 5 - The object isa Bio::Align::AlignI
ok 6 - clustalw (.aln) input test
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine _initialize redefined at Bio\AlignIO\emboss.pm line 93.
Subroutine next_aln redefined at Bio\AlignIO\emboss.pm line 110.
Subroutine write_aln redefined at Bio\AlignIO\emboss.pm line 251.
t/AlignIO/emboss.t ........................... 
1..37
ok 1 - use Bio::AlignIO::emboss;
ok 2 - The object isa Bio::Align::AlignI
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10 - The object isa Bio::Align::AlignI
ok 11
ok 12
ok 13
ok 14 - The object isa Bio::Align::AlignI
ok 15
ok 16
ok 17
ok 18 - The object isa Bio::Align::AlignI
ok 19
ok 20
ok 21 - The object isa Bio::Align::AlignI
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32 - The object isa Bio::Align::AlignI
ok 33
ok 34
ok 35
ok 36
ok 37
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine next_aln redefined at Bio\AlignIO\fasta.pm line 81.
Subroutine write_aln redefined at Bio\AlignIO\fasta.pm line 182.
Subroutine _get_len redefined at Bio\AlignIO\fasta.pm line 225.
Subroutine width redefined at Bio\AlignIO\fasta.pm line 244.
t/AlignIO/fasta.t ............................ 
1..10
ok 1 - use Bio::AlignIO::fasta;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - fasta input test 
ok 4 - fasta input test for description
ok 5 - fasta input test for id
ok 6 - fasta input test for end
ok 7 - fasta input test for description
ok 8 - fasta output test
ok 9 - filehandle input test  
ok 10 - filehandle output test
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine _initialize redefined at Bio\AlignIO\largemultifasta.pm line 81.
Subroutine next_seq redefined at Bio\AlignIO\largemultifasta.pm line 102.
Subroutine next_aln redefined at Bio\AlignIO\largemultifasta.pm line 143.
Subroutine write_aln redefined at Bio\AlignIO\largemultifasta.pm line 176.
t/AlignIO/largemultifasta.t .................. 
1..7
ok 1 - use Bio::AlignIO::largemultifasta;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - fasta input test 
ok 4 - fasta input test for description
ok 5 - fasta input test for id
ok 6 - fasta input test for description
ok 7 - fasta output test
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine _initialize redefined at Bio\AlignIO\maf.pm line 103.
Subroutine next_aln redefined at Bio\AlignIO\maf.pm line 122.
Subroutine write_aln redefined at Bio\AlignIO\maf.pm line 186.
t/AlignIO/maf.t .............................. 
1..11
ok 1 - use Bio::AlignIO::maf;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - maf input test
ok 4
ok 5 - The object isa Bio::Align::AlignI
ok 6 - maf input test
ok 7
ok 8 - maf input test
ok 9
ok 10 - maf input test
ok 11
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine next_aln redefined at Bio\AlignIO\mase.pm line 83.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine next_aln redefined at Bio\AlignIO\mega.pm line 116.
Subroutine write_aln redefined at Bio\AlignIO\mega.pm line 189.
t/AlignIO/mega.t ............................. 
1..6
ok 1 - use Bio::AlignIO::mega;
ok 2 - The object isa Bio::Align::AlignI
ok 3
ok 4
ok 5
ok 6 - mega output test
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine next_aln redefined at Bio\AlignIO\meme.pm line 105.
Subroutine write_aln redefined at Bio\AlignIO\meme.pm line 197.
Subroutine _initialize redefined at Bio\AlignIO\meme.pm line 206.
t/AlignIO/meme.t ............................. 
1..14
ok 1 - use Bio::AlignIO::meme;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4
ok 5
ok 6
ok 7
ok 8 - The object isa Bio::AlignIO
ok 9 - The object isa Bio::Align::AlignI
ok 10
ok 11
ok 12
ok 13
ok 14
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine _initialize redefined at Bio\AlignIO\metafasta.pm line 90.
Subroutine next_aln redefined at Bio\AlignIO\metafasta.pm line 108.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine next_aln redefined at Bio\AlignIO\msf.pm line 91.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine _initialize redefined at Bio\AlignIO\nexus.pm line 104.
Subroutine next_aln redefined at Bio\AlignIO\nexus.pm line 143.
Subroutine _read_taxlabels redefined at Bio\AlignIO\nexus.pm line 344.
Subroutine write_aln redefined at Bio\AlignIO\nexus.pm line 372.
Subroutine flag redefined at Bio\AlignIO\nexus.pm line 468.
t/AlignIO/nexus.t ............................ 
1..43
ok 1 - use Bio::AlignIO::nexus;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4
ok 5 - nexus output test
ok 6 - The object isa Bio::AlignIO
ok 7 - The object isa Bio::Align::AlignI
ok 8 - The object isa Bio::AlignIO
ok 9 - The object isa Bio::Align::AlignI
ok 10 - The object isa Bio::AlignIO
ok 11 - The object isa Bio::Align::AlignI
ok 12 - The object isa Bio::AlignIO
ok 13 - The object isa Bio::Align::AlignI
ok 14 - The object isa Bio::AlignIO
ok 15 - The object isa Bio::Align::AlignI
ok 16 - The object isa Bio::AlignIO
ok 17 - The object isa Bio::Align::AlignI
ok 18 - The object isa Bio::AlignIO
ok 19 - The object isa Bio::Align::AlignI
ok 20 - The object isa Bio::AlignIO
ok 21 - The object isa Bio::Align::AlignI
ok 22 - The object isa Bio::AlignIO
ok 23 - The object isa Bio::Align::AlignI
ok 24 - The object isa Bio::AlignIO
ok 25 - The object isa Bio::Align::AlignI
ok 26 - The object isa Bio::AlignIO
ok 27 - The object isa Bio::Align::AlignI
ok 28 - The object isa Bio::AlignIO
ok 29 - The object isa Bio::Align::AlignI
ok 30 - The object isa Bio::AlignIO
ok 31 - The object isa Bio::Align::AlignI
ok 32 - The object isa Bio::AlignIO
ok 33 - The object isa Bio::Align::AlignI
ok 34 - The object isa Bio::AlignIO
ok 35 - The object isa Bio::Align::AlignI
ok 36 - The object isa Bio::AlignIO
ok 37 - The object isa Bio::Align::AlignI
ok 38 - The object isa Bio::AlignIO
ok 39 - The object isa Bio::Align::AlignI
ok 40 - The object isa Bio::AlignIO
ok 41 - The object isa Bio::Align::AlignI
ok 42 - The object isa Bio::AlignIO
ok 43 - The object isa Bio::Align::AlignI
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine next_aln redefined at Bio\AlignIO\pfam.pm line 82.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine _initialize redefined at Bio\AlignIO\phylip.pm line 135.
Subroutine next_aln redefined at Bio\AlignIO\phylip.pm line 172.
Subroutine write_aln redefined at Bio\AlignIO\phylip.pm line 312.
Subroutine interleaved redefined at Bio\AlignIO\phylip.pm line 432.
Subroutine flag_SI redefined at Bio\AlignIO\phylip.pm line 455.
Subroutine idlength redefined at Bio\AlignIO\phylip.pm line 475.
Subroutine line_length redefined at Bio\AlignIO\phylip.pm line 494.
Subroutine tag_length redefined at Bio\AlignIO\phylip.pm line 515.
Subroutine id_linebreak redefined at Bio\AlignIO\phylip.pm line 535.
Subroutine wrap_sequential redefined at Bio\AlignIO\phylip.pm line 555.
Subroutine longid redefined at Bio\AlignIO\phylip.pm line 574.
t/AlignIO/phylip.t ........................... 
1..11
ok 1 - use Bio::AlignIO::phylip;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4
ok 5 - phylip output test
ok 6 - The object isa Bio::Align::AlignI
ok 7
ok 8 - The object isa Bio::AlignIO
ok 9 - The object isa Bio::Align::AlignI
ok 10
ok 11
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine next_aln redefined at Bio\AlignIO\po.pm line 83.
Subroutine write_aln redefined at Bio\AlignIO\po.pm line 226.
t/AlignIO/po.t ............................... 
1..11
ok 1 - use Bio::AlignIO::po;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4
ok 5 - The object isa Bio::AlignIO
ok 6 - The object isa Bio::Align::AlignI
ok 7 - po output test
ok 8 - The object isa Bio::AlignIO
ok 9 - The object isa Bio::Align::AlignI
ok 10
ok 11
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine next_aln redefined at Bio\AlignIO\prodom.pm line 82.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine next_aln redefined at Bio\AlignIO\psi.pm line 108.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine next_aln redefined at Bio\AlignIO\selex.pm line 96.
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
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine _initialize redefined at Bio\AlignIO\stockholm.pm line 355.
Subroutine next_aln redefined at Bio\AlignIO\stockholm.pm line 380.
Subroutine write_aln redefined at Bio\AlignIO\stockholm.pm line 515.
Subroutine line_length redefined at Bio\AlignIO\stockholm.pm line 660.
Subroutine alphabet redefined at Bio\AlignIO\stockholm.pm line 678.
Subroutine spaces redefined at Bio\AlignIO\stockholm.pm line 698.
Subroutine alignhandler redefined at Bio\AlignIO\stockholm.pm line 714.
Subroutine _print_seqs redefined at Bio\AlignIO\stockholm.pm line 726.
Subroutine new redefined at Bio\Seq\Meta.pm line 226, <GEN0> line 64.
Subroutine meta redefined at Bio\Seq\Meta.pm line 270, <GEN0> line 64.
Subroutine meta_text redefined at Bio\Seq\Meta.pm line 285, <GEN0> line 64.
Subroutine named_meta redefined at Bio\Seq\Meta.pm line 301, <GEN0> line 64.
Subroutine _test_gap_positions redefined at Bio\Seq\Meta.pm line 348, <GEN0> line 64.
Subroutine named_meta_text redefined at Bio\Seq\Meta.pm line 378, <GEN0> line 64.
Subroutine submeta redefined at Bio\Seq\Meta.pm line 410, <GEN0> line 64.
Subroutine submeta_text redefined at Bio\Seq\Meta.pm line 426, <GEN0> line 64.
Subroutine named_submeta redefined at Bio\Seq\Meta.pm line 445, <GEN0> line 64.
Subroutine named_submeta_text redefined at Bio\Seq\Meta.pm line 504, <GEN0> line 64.
Subroutine meta_names redefined at Bio\Seq\Meta.pm line 519, <GEN0> line 64.
Subroutine meta_length redefined at Bio\Seq\Meta.pm line 541, <GEN0> line 64.
Subroutine named_meta_length redefined at Bio\Seq\Meta.pm line 557, <GEN0> line 64.
Subroutine force_flush redefined at Bio\Seq\Meta.pm line 578, <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 638, <GEN0> line 64.
Subroutine revcom redefined at Bio\Seq\Meta.pm line 680, <GEN0> line 64.
Subroutine trunc redefined at Bio\Seq\Meta.pm line 703, <GEN0> line 64.
Subroutine to_string redefined at Bio\Seq\Meta.pm line 727, <GEN0> line 64.
Subroutine new redefined at Bio\Location\Simple.pm line 93, <GEN2> line 196.
Subroutine start redefined at Bio\Location\Simple.pm line 115, <GEN2> line 196.
Subroutine end redefined at Bio\Location\Simple.pm line 144, <GEN2> line 196.
Subroutine length redefined at Bio\Location\Simple.pm line 190, <GEN2> line 196.
Subroutine location_type redefined at Bio\Location\Simple.pm line 281, <GEN2> line 196.
Subroutine to_FTstring redefined at Bio\Location\Simple.pm line 328, <GEN2> line 196.
Subroutine trunc redefined at Bio\Location\Simple.pm line 370, <GEN2> line 196.
t/AlignIO/stockholm.t ........................ 
1..83
ok 1 - use Bio::AlignIO::stockholm;
ok 2 - The object isa Bio::AlignIO
ok 3 - The object isa Bio::Align::AlignI
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9 - The object isa Bio::Annotation::Comment
ok 10 - Stockholm annotation
ok 11 - Stockholm annotation
ok 12 - stockholm output test
ok 13 - The object isa Bio::Align::AlignI
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20 - Stockholm annotation isa Bio::Annotation::Reference
ok 21 - Stockholm annotation
ok 22 - Stockholm annotation
ok 23 - Stockholm annotation
ok 24 - Stockholm annotation
ok 25 - The object isa Bio::Seq::MetaI
ok 26 - Rfam meta data
ok 27 - Rfam meta data
ok 28
ok 29 - The object isa Bio::Align::AlignI
ok 30
ok 31
ok 32
ok 33
ok 34 - The object isa Bio::Seq::MetaI
ok 35 - Rfam meta data
ok 36 - Rfam meta data
ok 37 - The object isa Bio::AlignIO
ok 38
ok 39 - The object isa Bio::Align::AlignI
ok 40
ok 41
ok 42
ok 43
ok 44 - The object isa Bio::Annotation::SimpleValue
ok 45 - Pfam annotation
ok 46
ok 47 - The object isa Bio::Align::AlignI
ok 48
ok 49
ok 50
ok 51
ok 52 - The object isa Bio::Align::AlignI
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58 - The object isa Bio::Seq::MetaI
ok 59 - Pfam aln meta data
ok 60 - Pfam aln meta data
ok 61 - Pfam aln meta data
ok 62 - Pfam aln meta data
ok 63 - Pfam aln meta data
ok 64 - Pfam aln meta data
ok 65 - Pfam seq meta data
ok 66 - Pfam seq meta data
ok 67 - Pfam seq meta data
ok 68 - Pfam seq meta data
ok 69
ok 70 - The object isa Bio::SeqFeatureI
ok 71 - The object isa Bio::Seq::Meta
ok 72 - The object isa Bio::AnnotationI
ok 73 - The object isa Bio::Annotation::DBLink
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine next_aln redefined at Bio\AlignIO\xmfa.pm line 88.
Subroutine write_aln redefined at Bio\AlignIO\xmfa.pm line 142.
Subroutine _get_len redefined at Bio\AlignIO\xmfa.pm line 195.
Subroutine width redefined at Bio\AlignIO\xmfa.pm line 213.
Subroutine _process_seq redefined at Bio\AlignIO\xmfa.pm line 222.
t/AlignIO/xmfa.t ............................. 
1..16
ok 1 - use Bio::AlignIO::xmfa;
ok 2 - The object isa Bio::Align::AlignI
ok 3 - xmfa input test 
ok 4 - xmfa input test for description
ok 5 - xmfa input test for id
ok 6 - xmfa input test for end
ok 7 - xmfa input test for end
ok 8 - xmfa alignment score
ok 9 - The object isa Bio::Align::AlignI
ok 10 - xmfa input test 
ok 11 - xmfa input test for description
ok 12 - xmfa input test for id
ok 13 - xmfa input test for end
ok 14 - xmfa input test for end
ok 15 - xmfa alignment score
ok 16 - xmfa output test
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Alphabet.t ................................. 
1..100
ok 1 - use Bio::Symbol::Alphabet;
ok 2 - use Bio::Symbol::Symbol;
ok 3 - use Bio::Symbol::DNAAlphabet;
ok 4 - use Bio::Symbol::ProteinAlphabet;
ok 5 - The object isa Bio::Symbol::Alphabet
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11 - The object isa Bio::Symbol::AlphabetI
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46 - The object isa Bio::Symbol::AlphabetI
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94
Subroutine new redefined at Bio\Annotation\SimpleValue.pm line 97.
Subroutine as_text redefined at Bio\Annotation\SimpleValue.pm line 129.
Subroutine display_text redefined at Bio\Annotation\SimpleValue.pm line 154.
Subroutine hash_tree redefined at Bio\Annotation\SimpleValue.pm line 175.
Subroutine tagname redefined at Bio\Annotation\SimpleValue.pm line 200.
Subroutine value redefined at Bio\Annotation\SimpleValue.pm line 230.
Subroutine tag_term redefined at Bio\Annotation\SimpleValue.pm line 266.
Subroutine new redefined at Bio\Annotation\OntologyTerm.pm line 129.
Subroutine as_text redefined at Bio\Annotation\OntologyTerm.pm line 173.
Subroutine display_text redefined at Bio\Annotation\OntologyTerm.pm line 198.
Subroutine hash_tree redefined at Bio\Annotation\OntologyTerm.pm line 219.
Subroutine tagname redefined at Bio\Annotation\OntologyTerm.pm line 247.
Subroutine term redefined at Bio\Annotation\OntologyTerm.pm line 275.
Subroutine identifier redefined at Bio\Annotation\OntologyTerm.pm line 298.
Subroutine name redefined at Bio\Annotation\OntologyTerm.pm line 314.
Subroutine definition redefined at Bio\Annotation\OntologyTerm.pm line 331.
Subroutine ontology redefined at Bio\Annotation\OntologyTerm.pm line 349.
Subroutine is_obsolete redefined at Bio\Annotation\OntologyTerm.pm line 365.
Subroutine comment redefined at Bio\Annotation\OntologyTerm.pm line 381.
Subroutine get_synonyms redefined at Bio\Annotation\OntologyTerm.pm line 395.
Subroutine add_synonym redefined at Bio\Annotation\OntologyTerm.pm line 411.
Subroutine remove_synonyms redefined at Bio\Annotation\OntologyTerm.pm line 426.
Subroutine get_dblinks redefined at Bio\Annotation\OntologyTerm.pm line 442.
Subroutine get_dbxrefs redefined at Bio\Annotation\OntologyTerm.pm line 458.
Subroutine add_dblink redefined at Bio\Annotation\OntologyTerm.pm line 478.
Subroutine add_dbxref redefined at Bio\Annotation\OntologyTerm.pm line 497.
Subroutine remove_dblinks redefined at Bio\Annotation\OntologyTerm.pm line 513.
Subroutine remove_dbxrefs redefined at Bio\Annotation\OntologyTerm.pm line 529.
Subroutine get_secondary_ids redefined at Bio\Annotation\OntologyTerm.pm line 547.
Subroutine add_secondary_id redefined at Bio\Annotation\OntologyTerm.pm line 564.
Subroutine remove_secondary_ids redefined at Bio\Annotation\OntologyTerm.pm line 579.
Subroutine new redefined at Bio\Annotation\Comment.pm line 65.
Subroutine as_text redefined at Bio\Annotation\Comment.pm line 93.
Subroutine display_text redefined at Bio\Annotation\Comment.pm line 118.
Subroutine hash_tree redefined at Bio\Annotation\Comment.pm line 139.
Subroutine tagname redefined at Bio\Annotation\Comment.pm line 167.
Subroutine text redefined at Bio\Annotation\Comment.pm line 194.
Subroutine type redefined at Bio\Annotation\Comment.pm line 232.
Subroutine Bio::Annotation::Comment::value redefined at Bio\Annotation\Comment.pm line 216.
Subroutine new redefined at Bio\Annotation\Target.pm line 68.
Subroutine as_text redefined at Bio\Annotation\Target.pm line 105.
Subroutine display_text redefined at Bio\Annotation\Target.pm line 135.
Subroutine tagname redefined at Bio\Annotation\Target.pm line 164.
Subroutine target_id redefined at Bio\Annotation\Target.pm line 199.
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 197.
Subroutine get_root_node redefined at Bio\Tree\Tree.pm line 231.
Subroutine set_root_node redefined at Bio\Tree\Tree.pm line 246.
Subroutine total_branch_length redefined at Bio\Tree\Tree.pm line 270.
Subroutine subtree_length redefined at Bio\Tree\Tree.pm line 284.
Subroutine id redefined at Bio\Tree\Tree.pm line 307.
Subroutine score redefined at Bio\Tree\Tree.pm line 328.
Subroutine as_text redefined at Bio\Tree\Tree.pm line 376.
Subroutine set_tag_value redefined at Bio\Tree\Tree.pm line 432.
Subroutine add_tag_value redefined at Bio\Tree\Tree.pm line 453.
Subroutine remove_tag redefined at Bio\Tree\Tree.pm line 473.
Subroutine remove_all_tags redefined at Bio\Tree\Tree.pm line 493.
Subroutine get_all_tags redefined at Bio\Tree\Tree.pm line 509.
Subroutine get_tag_values redefined at Bio\Tree\Tree.pm line 525.
Subroutine has_tag redefined at Bio\Tree\Tree.pm line 541.
Subroutine cleanup_tree redefined at Bio\Tree\Tree.pm line 548.
Subroutine new redefined at Bio\Tree\Node.pm line 113.
Subroutine create_node_on_branch redefined at Bio\Tree\Node.pm line 166.
Subroutine add_Descendent redefined at Bio\Tree\Node.pm line 224.
Subroutine each_Descendent redefined at Bio\Tree\Node.pm line 262.
Subroutine remove_Descendent redefined at Bio\Tree\Node.pm line 324.
Subroutine remove_all_Descendents redefined at Bio\Tree\Node.pm line 359.
Subroutine ancestor redefined at Bio\Tree\Node.pm line 393.
Subroutine branch_length redefined at Bio\Tree\Node.pm line 434.
Subroutine bootstrap redefined at Bio\Tree\Node.pm line 458.
Subroutine description redefined at Bio\Tree\Node.pm line 479.
Subroutine id redefined at Bio\Tree\Node.pm line 508.
Subroutine internal_id redefined at Bio\Tree\Node.pm line 550.
Subroutine _creation_id redefined at Bio\Tree\Node.pm line 564.
Subroutine is_Leaf redefined at Bio\Tree\Node.pm line 585.
Subroutine height redefined at Bio\Tree\Node.pm line 603.
Subroutine invalidate_height redefined at Bio\Tree\Node.pm line 628.
Subroutine set_tag_value redefined at Bio\Tree\Node.pm line 649.
Subroutine add_tag_value redefined at Bio\Tree\Node.pm line 671.
Subroutine remove_tag redefined at Bio\Tree\Node.pm line 692.
Subroutine remove_all_tags redefined at Bio\Tree\Node.pm line 712.
Subroutine get_all_tags redefined at Bio\Tree\Node.pm line 728.
Subroutine get_tag_values redefined at Bio\Tree\Node.pm line 746.
Subroutine has_tag redefined at Bio\Tree\Node.pm line 762.
Subroutine node_cleanup redefined at Bio\Tree\Node.pm line 767.
Subroutine reverse_edge redefined at Bio\Tree\Node.pm line 794.
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..158
ok 1 - use Bio::Annotation::Collection;
ok 2 - use Bio::Annotation::DBLink;
ok 3 - use Bio::Annotation::Comment;
ok 4 - use Bio::Annotation::Reference;
ok 5 - use Bio::Annotation::SimpleValue;
ok 6 - use Bio::Annotation::Target;
ok 7 - use Bio::Annotation::AnnotationFactory;
ok 8 - use Bio::Annotation::StructuredValue;
ok 9 - use Bio::Annotation::TagTree;
ok 10 - use Bio::Annotation::Tree;
ok 11 - use Bio::Seq;
ok 12 - use Bio::SimpleAlign;
ok 13 - use Bio::Cluster::UniGene;
ok 14 - The object isa Bio::AnnotationI
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21 - The object isa Bio::AnnotationI
ok 22
ok 23
ok 24
ok 25 - The object isa Bio::AnnotationCollectionI
ok 26
ok 27
ok 28 - The object isa Bio::AnnotationI
ok 29
ok 30 - The object isa Bio::AnnotationI
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53 - The object isa Bio::AnnotationI
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68 - The object isa Bio::AnnotationCollectionI
ok 69
ok 70
ok 71
ok 72
ok 73 - The object isa Bio::Annotation::StructuredValue
ok 74
ok 75
ok 76
ok 77
ok 78 - use Bio::Annotation::OntologyTerm;
ok 79 - The object isa Bio::Ontology::Term
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85 - The object isa Bio::AnnotatableI
ok 86 - isa SeqFeatureI isa Bio::SeqFeatureI
ok 87 - isa AnnotatableI isa Bio::AnnotatableI
ok 88 - isa SeqFeatureI isa Bio::SeqFeatureI
ok 89 - isa AnnotatableI isa Bio::AnnotatableI
ok 90 - The object isa Bio::AnnotatableI
ok 91 - The object isa Bio::AnnotatableI
ok 92 - The object isa Bio::Factory::ObjectFactoryI
ok 93 - The object isa Bio::Annotation::SimpleValue
ok 94
ok 95 - The object isa Bio::Annotation::OntologyTerm
ok 96 - Bio::Annotation::Comment
ok 97 - The object isa Bio::Annotation::Comment
ok 98
ok 99 - Bio::Annotation::Comment
ok 100 - The object isa Bio::Annotation::Comment
ok 101 - Bio::Annotation::Comment
ok 102 - The object isa Bio::Annotation::Comment
ok 103
ok 104 - The object isa Bio::Annotation::Target
ok 105
ok 106
ok 107 - The object isa Bio::AnnotationI
ok 108 - tree_id()
ok 109 - tagname()
ok 110 - The object isa Bio::AnnotatableI
ok 111 - add tree to AlignI
ok 112 - get seq from node id
ok 113
ok 114 - The object isa Bio::Annotation::Tree
ok 115 - The object isa Bio::AnnotationI
ok 116 - default itext
ok 117 - roundtrip
ok 118 - itext
ok 119 - spxr
ok 120 - indent
ok 121 - xml
ok 122 - The object isa Data::Stag::StagI
ok 123
ok 124 - child changes
ok 125 - The object isa Data::Stag::StagI
ok 126
ok 127 - child changes
ok 128 - The object isa Data::Stag::StagI
ok 129
ok 130 - child changes
ok 131 - child changes in parent node
ok 132 - no tags
ok 133 - before Stag node
ok 134 - after Stag node
ok 135 - both stag nodes
ok 136 - different instances
ok 137 - before TagTree
ok 138 - after TagTree
ok 139 - both stag nodes
ok 140 - different instances
ok 141 - before TagTree
ok 142 - after TagTree
ok 143 - stag nodes
ok 144 - same instance
ok 145 - before TagTree
ok 146 - after TagTree
ok 147 - stag nodes
ok 148 - different instance
ok 149 - The object isa Bio::AnnotationI
ok 150 - The object isa Data::Stag::StagI
ok 151 - child changes
ok 152 - The object isa Data::Stag::StagI
ok 153 - child changes
ok 154 - The object isa Data::Stag::StagI
ok 155 - child changes
ok 156
ok 157
ok 158 - The object isa Bio::Annotation::TagTree
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Annotation/AnnotationAdaptor.t ............. 
1..23
ok 1 - use Bio::SeqFeature::Generic;
ok 2 - use Bio::SeqFeature::AnnotationAdaptor;
ok 3 - use Bio::Annotation::DBLink;
ok 4 - use Bio::Annotation::Comment;
ok 5 - use Bio::Annotation::SimpleValue;
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok
t/Assembly/Assembly.t ........................ skipped: The optional module DB_File (or dependencies thereof) was not installed
Replacement list is longer than search list at Bio/Range.pm line 251.
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-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR\blib\lib C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR\blib\arch C:/cpanfly-5.12/var/cpan/build/BioPerl-1.6.1-M4bynR C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR C:\cpanfly-5.12\var\megalib C:\Perl-5.12\site\lib C:\Perl-5.12\lib C:/cpanfly-5.12/var/megalib C:/Perl-5.12/site/lib C:/Perl-5.12/lib) at Bio/SeqFeature/Collection.pm line 147.
BEGIN failed--compilation aborted at Bio/SeqFeature/Collection.pm line 147.
Compilation failed in require at Bio/Assembly/Contig.pm line 223.
BEGIN failed--compilation aborted at Bio/Assembly/Contig.pm line 223.
Compilation failed in require at Bio\Assembly\IO\tigr.pm line 236.
BEGIN failed--compilation aborted at Bio\Assembly\IO\tigr.pm line 236.
Compilation failed in require at Bio/Root/Root.pm line 439.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441
STACK: Bio::Assembly::IO::_load_format_module Bio/Assembly/IO.pm:192
STACK: Bio::Assembly::IO::new Bio/Assembly/IO.pm:133
STACK: t/Assembly/ContigSpectrum.t:11
-----------------------------------------------------------


#   Failed test 'The thing isa Bio::Assembly::IO'
#   at t/Assembly/ContigSpectrum.t line 15.
#     The thing isn't defined
Can't call method "next_assembly" on an undefined value at t/Assembly/ContigSpectrum.t line 16.
# Looks like you planned 134 tests but ran 3.
# Looks like you failed 1 test of 3 run.
# Looks like your test exited with 2 just after 3.
t/Assembly/ContigSpectrum.t .................. 
1..134
ok 1 - use Bio::Assembly::IO;
ok 2 - use Bio::Assembly::Tools::ContigSpectrum;
not ok 3 - The thing isa Bio::Assembly::IO
Dubious, test returned 2 (wstat 512, 0x200)
Failed 132/134 subtests 
defined(%hash) is deprecated at C:\cpanfly-5.12\var\megalib/SOAP/Lite.pm line 465.
	(Maybe you should just omit the defined()?)
defined(%hash) is deprecated at C:\cpanfly-5.12\var\megalib/SOAP/Lite.pm line 2203.
	(Maybe you should just omit the defined()?)
t/Biblio/Biblio.t ............................ 
1..24
ok 1 - use Bio::Biblio;
ok 2 - use Bio::Biblio::IO;
ok 3
ok 4
ok 5 - citation 1
ok 6 - citation 2
ok 7 - citation 3
ok 8 - in callback
ok 9 - in callback
ok 10 - in callback
ok 11 - calling callback
ok 12 - citation 1
ok 13 - citation 2
ok 14 - citation 1
ok 15 - citation 2
ok 16
ok 17 - citation 1
ok 18 - citation 2
ok 19 - citation 3
ok 20 - citation 4
ok 21 - filehandle test
ok 22 - filehandle test
ok 23 - filehandle test
ok 24 - filehandle test
ok
t/Biblio/References.t ........................ 
1..537
ok 1 - use Bio::Biblio::Article;
ok 2 - use Bio::Biblio::Book;
ok 3 - use Bio::Biblio::BookArticle;
ok 4 - use Bio::Biblio::Journal;
ok 5 - use Bio::Biblio::JournalArticle;
ok 6 - use Bio::Biblio::MedlineArticle;
ok 7 - use Bio::Biblio::MedlineBook;
ok 8 - use Bio::Biblio::MedlineBookArticle;
ok 9 - use Bio::Biblio::MedlineJournal;
ok 10 - use Bio::Biblio::MedlineJournalArticle;
ok 11 - use Bio::Biblio::Organisation;
ok 12 - use Bio::Biblio::Patent;
ok 13 - use Bio::Biblio::Person;
ok 14 - use Bio::Biblio::Proceeding;
ok 15 - use Bio::Biblio::Provider;
ok 16 - use Bio::Biblio::Ref;
ok 17 - use Bio::Biblio::Service;
ok 18 - use Bio::Biblio::TechReport;
ok 19 - use Bio::Biblio::Thesis;
ok 20 - use Bio::Biblio::WebResource;
ok 21 - use Bio::Biblio::PubmedArticle;
ok 22 - use Bio::Biblio::PubmedBookArticle;
ok 23 - use Bio::Biblio::PubmedJournalArticle;
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47 - set 'abstract'
ok 48 - get 'abstract'
ok 49 - set 'abstract_language'
ok 50 - get 'abstract_language'
ok 51 - set 'abstract_type'
ok 52 - get 'abstract_type'
ok 53 - set 'author_list_complete'
ok 54 - get 'author_list_complete'
ok 55 - set 'cross_references_list_complete'
ok 56 - get 'cross_references_list_complete'
ok 57 - set 'date'
ok 58 - get 'date'
ok 59 - set 'date_completed'
ok 60 - get 'date_completed'
ok 61 - set 'date_created'
ok 62 - get 'date_created'
ok 63 - set 'date_revised'
ok 64 - get 'date_revised'
ok 65 - set 'format'
ok 66 - get 'format'
ok 67 - set 'identifier'
ok 68 - get 'identifier'
ok 69 - set 'language'
ok 70 - get 'language'
ok 71 - set 'last_modified_date'
ok 72 - get 'last_modified_date'
ok 73 - set 'repository_subset'
ok 74 - get 'repository_subset'
ok 75 - set 'rights'
ok 76 - get 'rights'
ok 77 - set 'spatial_location'
ok 78 - get 'spatial_location'
ok 79 - set 'subject_headings_source'
ok 80 - get 'subject_headings_source'
ok 81 - set 'temporal_period'
ok 82 - get 'temporal_period'
ok 83 - set 'title'
ok 84 - get 'title'
ok 85 - set 'toc'
ok 86 - get 'toc'
ok 87 - set 'toc_type'
ok 88 - get 'toc_type'
ok 89 - set 'type'
ok 90 - get 'type'
ok 91 - set 'first_page'
ok 92 - get 'first_page'
ok 93 - set 'last_page'
ok 94 - get 'last_page'
ok 95 - set 'issue'
ok 96 - get 'issue'
ok 97 - set 'issue_supplement'
ok 98 - get 'issue_supplement'
ok 99 - set 'volume'
ok 100 - get 'volume'
ok 101 - set 'affiliation'
ok 102 - get 'affiliation'
ok 103 - set 'citation_owner'
ok 104 - get 'citation_owner'
ok 105 - set 'date_of_electronic_publication'
ok 106 - get 'date_of_electronic_publication'
ok 107 - set 'gene_symbols'
ok 108 - get 'gene_symbols'
ok 109 - set 'grant_list_complete'
ok 110 - get 'grant_list_complete'
ok 111 - set 'medline_date'
ok 112 - get 'medline_date'
ok 113 - set 'medline_id'
ok 114 - get 'medline_id'
ok 115 - set 'medline_page'
ok 116 - get 'medline_page'
ok 117 - set 'number_of_references'
ok 118 - get 'number_of_references'
ok 119 - set 'other_languages'
ok 120 - get 'other_languages'
ok 121 - set 'pmid'
ok 122 - get 'pmid'
ok 123 - set 'season'
ok 124 - get 'season'
ok 125 - set 'status'
ok 126 - get 'status'
ok 127 - set 'vernacular_title'
ok 128 - get 'vernacular_title'
ok 129
ok 130 - abstract
ok 131 - abstract_language
ok 132 - abstract_type
ok 133 - author_list_complete
ok 134 - cross_references_list_complete
ok 135 - date
ok 136 - date_completed
ok 137 - date_created
ok 138 - date_revised
ok 139 - format
ok 140 - identifier
ok 141 - language
ok 142 - last_modified_date
ok 143 - repository_subset
ok 144 - rights
ok 145 - spatial_location
ok 146 - subject_headings_source
ok 147 - temporal_period
ok 148 - title
ok 149 - toc
ok 150 - toc_type
ok 151 - type
ok 152 - first_page
ok 153 - last_page
ok 154 - issue
ok 155 - issue_supplement
ok 156 - volume
ok 157 - affiliation
ok 158 - citation_owner
ok 159 - date_of_electronic_publication
ok 160 - gene_symbols
ok 161 - grant_list_complete
ok 162 - medline_date
ok 163 - medline_id
ok 164 - medline_page
ok 165 - number_of_references
ok 166 - other_languages
ok 167 - pmid
ok 168 - season
ok 169 - status
ok 170 - vernacular_title
ok 171 - get 'authors'
ok 172 - get 'cross_references'
ok 173 - get 'codes'
ok 174 - get 'contributors'
ok 175 - get 'keywords'
ok 176 - get 'publisher'
ok 177 - get 'subject_headings'
ok 178 - get 'journal'
ok 179 - get 'chemicals'
ok 180 - get 'comment_ins'
ok 181 - get 'comment_ons'
ok 182 - get 'erratum_fors'
ok 183 - get 'erratum_ins'
ok 184 - get 'general_notes'
ok 185 - get 'grants'
ok 186 - get 'mesh_headings'
ok 187 - get 'original_report_ins'
ok 188 - get 'other_abstracts'
ok 189 - get 'other_ids'
ok 190 - get 'republished_froms'
ok 191 - get 'republished_ins'
ok 192 - get 'retraction_ins'
ok 193 - get 'retraction_ofs'
ok 194 - get 'summary_for_patients_ins'
ok 195 - get 'update_ins'
ok 196 - get 'update_ofs'
ok 197 - get 'journal'
ok 198 - add_author 1
ok 199 - add_author 2
ok 200 - get authors
ok 201 - add_contributor 1
ok 202 - add_contributor 2
ok 203 - get contributors
ok 204 - add_cross_reference 1
ok 205 - add_cross_reference 2
ok 206 - get cross_references
ok 207 - get cross_references
ok 208 - set 'abstract'
ok 209 - get 'abstract'
ok 210 - set 'abstract_language'
ok 211 - get 'abstract_language'
ok 212 - set 'abstract_type'
ok 213 - get 'abstract_type'
ok 214 - set 'author_list_complete'
ok 215 - get 'author_list_complete'
ok 216 - set 'cross_references_list_complete'
ok 217 - get 'cross_references_list_complete'
ok 218 - set 'date'
ok 219 - get 'date'
ok 220 - set 'date_completed'
ok 221 - get 'date_completed'
ok 222 - set 'date_created'
ok 223 - get 'date_created'
ok 224 - set 'date_revised'
ok 225 - get 'date_revised'
ok 226 - set 'format'
ok 227 - get 'format'
ok 228 - set 'identifier'
ok 229 - get 'identifier'
ok 230 - set 'language'
ok 231 - get 'language'
ok 232 - set 'last_modified_date'
ok 233 - get 'last_modified_date'
ok 234 - set 'repository_subset'
ok 235 - get 'repository_subset'
ok 236 - set 'rights'
ok 237 - get 'rights'
ok 238 - set 'spatial_location'
ok 239 - get 'spatial_location'
ok 240 - set 'subject_headings_source'
ok 241 - get 'subject_headings_source'
ok 242 - set 'temporal_period'
ok 243 - get 'temporal_period'
ok 244 - set 'title'
ok 245 - get 'title'
ok 246 - set 'toc'
ok 247 - get 'toc'
ok 248 - set 'toc_type'
ok 249 - get 'toc_type'
ok 250 - set 'type'
ok 251 - get 'type'
ok 252 - set 'first_page'
ok 253 - get 'first_page'
ok 254 - set 'last_page'
ok 255 - get 'last_page'
ok 256 - set 'affiliation'
ok 257 - get 'affiliation'
ok 258 - set 'citation_owner'
ok 259 - get 'citation_owner'
ok 260 - set 'date_of_electronic_publication'
ok 261 - get 'date_of_electronic_publication'
ok 262 - set 'gene_symbols'
ok 263 - get 'gene_symbols'
ok 264 - set 'grant_list_complete'
ok 265 - get 'grant_list_complete'
ok 266 - set 'medline_date'
ok 267 - get 'medline_date'
ok 268 - set 'medline_id'
ok 269 - get 'medline_id'
ok 270 - set 'medline_page'
ok 271 - get 'medline_page'
ok 272 - set 'number_of_references'
ok 273 - get 'number_of_references'
ok 274 - set 'other_languages'
ok 275 - get 'other_languages'
ok 276 - set 'pmid'
ok 277 - get 'pmid'
ok 278 - set 'season'
ok 279 - get 'season'
ok 280 - set 'status'
ok 281 - get 'status'
ok 282 - set 'vernacular_title'
ok 283 - get 'vernacular_title'
ok 284
ok 285 - abstract
ok 286 - abstract_language
ok 287 - abstract_type
ok 288 - author_list_complete
ok 289 - cross_references_list_complete
ok 290 - date
ok 291 - date_completed
ok 292 - date_created
ok 293 - date_revised
ok 294 - format
ok 295 - identifier
ok 296 - language
ok 297 - last_modified_date
ok 298 - repository_subset
ok 299 - rights
ok 300 - spatial_location
ok 301 - subject_headings_source
ok 302 - temporal_period
ok 303 - title
ok 304 - toc
ok 305 - toc_type
ok 306 - type
ok 307 - first_page
ok 308 - last_page
ok 309 - affiliation
ok 310 - citation_owner
ok 311 - date_of_electronic_publication
ok 312 - gene_symbols
ok 313 - grant_list_complete
ok 314 - medline_date
ok 315 - medline_id
ok 316 - medline_page
ok 317 - number_of_references
ok 318 - other_languages
ok 319 - pmid
ok 320 - season
ok 321 - status
ok 322 - vernacular_title
ok 323 - get 'authors'
ok 324 - get 'cross_references'
ok 325 - get 'codes'
ok 326 - get 'contributors'
ok 327 - get 'keywords'
ok 328 - get 'publisher'
ok 329 - get 'subject_headings'
ok 330 - get 'book'
ok 331 - get 'chemicals'
ok 332 - get 'comment_ins'
ok 333 - get 'comment_ons'
ok 334 - get 'erratum_fors'
ok 335 - get 'erratum_ins'
ok 336 - get 'general_notes'
ok 337 - get 'grants'
ok 338 - get 'mesh_headings'
ok 339 - get 'original_report_ins'
ok 340 - get 'other_abstracts'
ok 341 - get 'other_ids'
ok 342 - get 'republished_froms'
ok 343 - get 'republished_ins'
ok 344 - get 'retraction_ins'
ok 345 - get 'retraction_ofs'
ok 346 - get 'summary_for_patients_ins'
ok 347 - get 'update_ins'
ok 348 - get 'update_ofs'
ok 349 - get 'book'
ok 350 - set 'abstract'
ok 351 - get 'abstract'
ok 352 - set 'abstract_language'
ok 353 - get 'abstract_language'
ok 354 - set 'abstract_type'
ok 355 - get 'abstract_type'
ok 356 - set 'author_list_complete'
ok 357 - get 'author_list_complete'
ok 358 - set 'cross_references_list_complete'
ok 359 - get 'cross_references_list_complete'
ok 360 - set 'date'
ok 361 - get 'date'
ok 362 - set 'date_completed'
ok 363 - get 'date_completed'
ok 364 - set 'date_created'
ok 365 - get 'date_created'
ok 366 - set 'date_revised'
ok 367 - get 'date_revised'
ok 368 - set 'format'
ok 369 - get 'format'
ok 370 - set 'identifier'
ok 371 - get 'identifier'
ok 372 - set 'language'
ok 373 - get 'language'
ok 374 - set 'last_modified_date'
ok 375 - get 'last_modified_date'
ok 376 - set 'repository_subset'
ok 377 - get 'repository_subset'
ok 378 - set 'rights'
ok 379 - get 'rights'
ok 380 - set 'spatial_location'
ok 381 - get 'spatial_location'
ok 382 - set 'subject_headings_source'
ok 383 - get 'subject_headings_source'
ok 384 - set 'temporal_period'
ok 385 - get 'temporal_period'
ok 386 - set 'title'
ok 387 - get 'title'
ok 388 - set 'toc'
ok 389 - get 'toc'
ok 390 - set 'toc_type'
ok 391 - get 'toc_type'
ok 392 - set 'type'
ok 393 - get 'type'
ok 394 - set 'edition'
ok 395 - get 'edition'
ok 396 - set 'isbn'
ok 397 - get 'isbn'
ok 398 - set 'series'
ok 399 - get 'series'
ok 400 - set 'volume'
ok 401 - get 'volume'
ok 402
ok 403 - abstract
ok 404 - abstract_language
ok 405 - abstract_type
ok 406 - author_list_complete
ok 407 - cross_references_list_complete
ok 408 - date
ok 409 - date_completed
ok 410 - date_created
ok 411 - date_revised
ok 412 - format
ok 413 - identifier
ok 414 - language
ok 415 - last_modified_date
ok 416 - repository_subset
ok 417 - rights
ok 418 - spatial_location
ok 419 - subject_headings_source
ok 420 - temporal_period
ok 421 - title
ok 422 - toc
ok 423 - toc_type
ok 424 - type
ok 425 - edition
ok 426 - isbn
ok 427 - series
ok 428 - volume
ok 429 - get 'authors'
ok 430 - get 'cross_references'
ok 431 - get 'codes'
ok 432 - get 'contributors'
ok 433 - get 'keywords'
ok 434 - get 'publisher'
ok 435 - get 'subject_headings'
ok 436 - get 'editor'
ok 437 - set 'abbreviation'
ok 438 - get 'abbreviation'
ok 439 - set 'issn'
ok 440 - get 'issn'
ok 441 - set 'name'
ok 442 - get 'name'
ok 443 - set 'coden'
ok 444 - get 'coden'
ok 445 - set 'country'
ok 446 - get 'country'
ok 447 - set 'medline_code'
ok 448 - get 'medline_code'
ok 449 - set 'medline_ta'
ok 450 - get 'medline_ta'
ok 451 - set 'nlm_unique_id'
ok 452 - get 'nlm_unique_id'
ok 453
ok 454 - abbreviation
ok 455 - issn
ok 456 - name
ok 457 - coden
ok 458 - country
ok 459 - medline_code
ok 460 - medline_ta
ok 461 - nlm_unique_id
ok 462 - set 'doc_number'
ok 463 - get 'doc_number'
ok 464 - set 'doc_office'
ok 465 - get 'doc_office'
ok 466 - set 'doc_type'
ok 467 - get 'doc_type'
ok 468
ok 469 - doc_number
ok 470 - doc_office
ok 471 - doc_type
ok 472 - get 'applicants'
ok 473 - set 'url'
ok 474 - get 'url'
ok 475 - set 'estimated_size'
ok 476 - get 'estimated_size'
ok 477 - set 'cost'
ok 478 - get 'cost'
ok 479
ok 480 - url
ok 481 - estimated_size
ok 482 - cost
ok 483 - set 'type'
ok 484 - get 'type'
ok 485 - set 'affiliation'
ok 486 - get 'affiliation'
ok 487 - set 'email'
ok 488 - get 'email'
ok 489 - set 'firstname'
ok 490 - get 'firstname'
ok 491 - set 'forename'
ok 492 - get 'forename'
ok 493 - set 'initials'
ok 494 - get 'initials'
ok 495 - set 'lastname'
ok 496 - get 'lastname'
ok 497 - set 'middlename'
ok 498 - get 'middlename'
ok 499 - set 'postal_address'
ok 500 - get 'postal_address'
ok 501 - set 'suffix'
ok 502 - get 'suffix'
ok 503
ok 504 - type
ok 505 - affiliation
ok 506 - email
ok 507 - firstname
ok 508 - forename
ok 509 - initials
ok 510 - lastname
ok 511 - middlename
ok 512 - postal_address
ok 513 - suffix
ok 514 - set 'type'
ok 515 - get 'type'
ok 516 - set 'name'
ok 517 - get 'name'
ok 518
ok 519 - type
ok 520 - name
ok 521 - set 'type'
ok 522 - get 'type'
ok 523 - set 'name'
ok 524 - get 'name'
ok 525
ok 526 - type
ok 527 - name
ok 528 - set 'pubmed_status'
ok 529 - get 'pubmed_status'
ok 530 - set 'pubmed_provider_id'
ok 531 - get 'pubmed_provider_id'
ok 532
ok 533 - pubmed_status
ok 534 - pubmed_provider_id
ok 535 - get 'pubmed_history_list'
ok 536 - get 'pubmed_article_id_list'
ok 537 - get 'pubmed_url_list'
ok
t/Biblio/biofetch.t .......................... skipped: Network tests have not been requested
t/Biblio/eutils.t ............................ skipped: Network tests have not been requested
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94
t/ClusterIO/ClusterIO.t ...................... 
1..12
ok 1 - use Bio::ClusterIO;
ok 2 - use Bio::Cluster::ClusterFactory;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11 - The object isa Bio::Cluster::UniGeneI
ok 12 - The object isa Bio::Cluster::UniGeneI
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94
Subroutine new redefined at Bio\Location\Simple.pm line 93, <GEN0> line 70.
Subroutine start redefined at Bio\Location\Simple.pm line 115, <GEN0> line 70.
Subroutine end redefined at Bio\Location\Simple.pm line 144, <GEN0> line 70.
Subroutine length redefined at Bio\Location\Simple.pm line 190, <GEN0> line 70.
Subroutine location_type redefined at Bio\Location\Simple.pm line 281, <GEN0> line 70.
Subroutine to_FTstring redefined at Bio\Location\Simple.pm line 328, <GEN0> line 70.
Subroutine trunc redefined at Bio\Location\Simple.pm line 370, <GEN0> line 70.
Subroutine new redefined at Bio\Location\Fuzzy.pm line 147, <GEN0> line 142.
Subroutine location_type redefined at Bio\Location\Fuzzy.pm line 174, <GEN0> line 142.
Subroutine start redefined at Bio\Location\Fuzzy.pm line 236, <GEN0> line 142.
Subroutine end redefined at Bio\Location\Fuzzy.pm line 263, <GEN0> line 142.
Subroutine min_start redefined at Bio\Location\Fuzzy.pm line 290, <GEN0> line 142.
Subroutine max_start redefined at Bio\Location\Fuzzy.pm line 309, <GEN0> line 142.
Subroutine start_pos_type redefined at Bio\Location\Fuzzy.pm line 329, <GEN0> line 142.
Subroutine min_end redefined at Bio\Location\Fuzzy.pm line 359, <GEN0> line 142.
Subroutine max_end redefined at Bio\Location\Fuzzy.pm line 378, <GEN0> line 142.
Subroutine end_pos_type redefined at Bio\Location\Fuzzy.pm line 398, <GEN0> line 142.
Subroutine to_FTstring redefined at Bio\Location\Fuzzy.pm line 469, <GEN0> line 142.
Subroutine _fuzzypointdecode redefined at Bio\Location\Fuzzy.pm line 581, <GEN0> line 142.
t/ClusterIO/SequenceFamily.t ................. 
1..19
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::Cluster::SequenceFamily;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94
Subroutine new redefined at Bio\Cluster\UniGene.pm line 259.
Subroutine unigene_id redefined at Bio\Cluster\UniGene.pm line 321.
Subroutine title redefined at Bio\Cluster\UniGene.pm line 343.
Subroutine gene redefined at Bio\Cluster\UniGene.pm line 364.
Subroutine cytoband redefined at Bio\Cluster\UniGene.pm line 382.
Subroutine mgi redefined at Bio\Cluster\UniGene.pm line 399.
Subroutine locuslink redefined at Bio\Cluster\UniGene.pm line 427.
Subroutine homol redefined at Bio\Cluster\UniGene.pm line 456.
Subroutine restr_expr redefined at Bio\Cluster\UniGene.pm line 473.
Subroutine gnm_terminus redefined at Bio\Cluster\UniGene.pm line 491.
Subroutine scount redefined at Bio\Cluster\UniGene.pm line 507.
Subroutine express redefined at Bio\Cluster\UniGene.pm line 529.
Subroutine chromosome redefined at Bio\Cluster\UniGene.pm line 547.
Subroutine sts redefined at Bio\Cluster\UniGene.pm line 565.
Subroutine txmap redefined at Bio\Cluster\UniGene.pm line 583.
Subroutine protsim redefined at Bio\Cluster\UniGene.pm line 601.
Subroutine sequences redefined at Bio\Cluster\UniGene.pm line 624.
Subroutine species redefined at Bio\Cluster\UniGene.pm line 644.
Subroutine display_id redefined at Bio\Cluster\UniGene.pm line 676.
Subroutine description redefined at Bio\Cluster\UniGene.pm line 693.
Subroutine size redefined at Bio\Cluster\UniGene.pm line 711.
Subroutine cluster_score redefined at Bio\Cluster\UniGene.pm line 743.
Subroutine get_members redefined at Bio\Cluster\UniGene.pm line 766.
Subroutine annotation redefined at Bio\Cluster\UniGene.pm line 815.
Subroutine add_member redefined at Bio\Cluster\UniGene.pm line 847.
Subroutine remove_members redefined at Bio\Cluster\UniGene.pm line 877.
Subroutine next_locuslink redefined at Bio\Cluster\UniGene.pm line 906.
Subroutine next_express redefined at Bio\Cluster\UniGene.pm line 932.
Subroutine next_chromosome redefined at Bio\Cluster\UniGene.pm line 959.
Subroutine next_protsim redefined at Bio\Cluster\UniGene.pm line 986.
Subroutine next_sts redefined at Bio\Cluster\UniGene.pm line 1013.
Subroutine next_txmap redefined at Bio\Cluster\UniGene.pm line 1040.
Subroutine _next_element redefined at Bio\Cluster\UniGene.pm line 1053.
Subroutine object_id redefined at Bio\Cluster\UniGene.pm line 1090.
Subroutine version redefined at Bio\Cluster\UniGene.pm line 1112.
Subroutine authority redefined at Bio\Cluster\UniGene.pm line 1134.
Subroutine namespace redefined at Bio\Cluster\UniGene.pm line 1156.
Subroutine display_name redefined at Bio\Cluster\UniGene.pm line 1184.
Subroutine next_seq redefined at Bio\Cluster\UniGene.pm line 1235.
Subroutine sequence_factory redefined at Bio\Cluster\UniGene.pm line 1293.
Subroutine _annotation_value redefined at Bio\Cluster\UniGene.pm line 1321.
Subroutine _annotation_value_ary redefined at Bio\Cluster\UniGene.pm line 1362.
Subroutine _annotation_dblink redefined at Bio\Cluster\UniGene.pm line 1398.
Subroutine _remove_dblink redefined at Bio\Cluster\UniGene.pm line 1433.
Subroutine Bio::Cluster::UniGene::sequence redefined at Bio\Cluster\UniGene.pm line 1457.
Replacement list is longer than search list at Bio/Range.pm line 251, <GEN0> chunk 1.
t/ClusterIO/unigene.t ........................ 
1..73
ok 1 - use Bio::ClusterIO;
ok 2 - new Bio::ClusterIO object defined
ok 3
ok 4 - The object isa Bio::Cluster::UniGeneI
ok 5 - The object isa Bio::ClusterI
ok 6 - The object isa Bio::IdentifiableI
ok 7 - The object isa Bio::DescribableI
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48 - The object isa Bio::PrimarySeqI
ok 49
ok 50
ok 51 - annotation object defined
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66 - The object isa Bio::PrimarySeqI
ok 67
ok 68 - next cluster
ok 69
ok 70
ok 71
ok 72
ok 73
ok
t/Coordinate/CoordinateGraph.t ............... 
1..7
ok 1 - use Bio::Coordinate::Graph;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine new redefined at Bio\Location\Simple.pm line 93.
Subroutine start redefined at Bio\Location\Simple.pm line 115.
Subroutine end redefined at Bio\Location\Simple.pm line 144.
Subroutine length redefined at Bio\Location\Simple.pm line 190.
Subroutine location_type redefined at Bio\Location\Simple.pm line 281.
Subroutine to_FTstring redefined at Bio\Location\Simple.pm line 328.
Subroutine trunc redefined at Bio\Location\Simple.pm line 370.
Subroutine add_sub_Location redefined at Bio\Coordinate\Result.pm line 101.
Subroutine add_result redefined at Bio\Coordinate\Result.pm line 131.
Subroutine seq_id redefined at Bio\Coordinate\Result.pm line 155.
Subroutine each_gap redefined at Bio\Coordinate\Result.pm line 186.
Subroutine each_match redefined at Bio\Coordinate\Result.pm line 211.
Subroutine match redefined at Bio\Coordinate\Result.pm line 232.
Subroutine gap redefined at Bio\Coordinate\Result.pm line 255.
Subroutine purge_gaps redefined at Bio\Coordinate\Result.pm line 278.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Subroutine new redefined at Bio\Location\Split.pm line 104.
Subroutine each_Location redefined at Bio\Location\Split.pm line 136.
Subroutine sub_Location redefined at Bio\Location\Split.pm line 165.
Subroutine add_sub_Location redefined at Bio\Location\Split.pm line 234.
Subroutine splittype redefined at Bio\Location\Split.pm line 258.
Subroutine is_single_sequence redefined at Bio\Location\Split.pm line 286.
Subroutine guide_strand redefined at Bio\Location\Split.pm line 311.
Subroutine strand redefined at Bio\Location\Split.pm line 339.
Subroutine flip_strand redefined at Bio\Location\Split.pm line 380.
Subroutine start redefined at Bio\Location\Split.pm line 401.
Subroutine end redefined at Bio\Location\Split.pm line 420.
Subroutine min_start redefined at Bio\Location\Split.pm line 439.
Subroutine max_start redefined at Bio\Location\Split.pm line 461.
Subroutine start_pos_type redefined at Bio\Location\Split.pm line 484.
Subroutine min_end redefined at Bio\Location\Split.pm line 505.
Subroutine max_end redefined at Bio\Location\Split.pm line 528.
Subroutine end_pos_type redefined at Bio\Location\Split.pm line 552.
Subroutine seq_id redefined at Bio\Location\Split.pm line 578.
Subroutine to_FTstring redefined at Bio\Location\Split.pm line 624.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
t/Coordinate/CoordinateMapper.t .............. 
1..175
ok 1 - use Bio::Location::Simple;
ok 2 - use Bio::Coordinate::Pair;
ok 3 - use Bio::Coordinate::Result::Match;
ok 4 - use Bio::Coordinate::Result::Gap;
ok 5 - use Bio::Coordinate::Chain;
ok 6 - use Bio::Coordinate::Collection;
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14 - The object isa Bio::Coordinate::Result
ok 15 - The object isa Bio::Location::SplitLocationI
ok 16
ok 17
ok 18
ok 19 - The object isa Bio::LocationI
ok 20 - The object isa Bio::Coordinate::Result::Match
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - The object isa Bio::Coordinate::Result::Gap
ok 38 - The object isa Bio::LocationI
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106 - The object isa Bio::Coordinate::Result::Match
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138 - Match: |314696| Test: 314696|
ok 139
ok 140
ok 141
ok 142 - Match: |341| Test: 341|
ok 143
ok 144
ok 145
ok 146 - Match: |315843| Test: 315843|
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152 - Match: |627011| Test: 627011|
ok 153
ok 154
ok 155
ok 156 - Match: |chr1| Test: chr1|
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok
Subroutine new redefined at Bio\Location\Simple.pm line 93.
Subroutine start redefined at Bio\Location\Simple.pm line 115.
Subroutine end redefined at Bio\Location\Simple.pm line 144.
Subroutine length redefined at Bio\Location\Simple.pm line 190.
Subroutine location_type redefined at Bio\Location\Simple.pm line 281.
Subroutine to_FTstring redefined at Bio\Location\Simple.pm line 328.
Subroutine trunc redefined at Bio\Location\Simple.pm line 370.
Subroutine add_sub_Location redefined at Bio\Coordinate\Result.pm line 101.
Subroutine add_result redefined at Bio\Coordinate\Result.pm line 131.
Subroutine seq_id redefined at Bio\Coordinate\Result.pm line 155.
Subroutine each_gap redefined at Bio\Coordinate\Result.pm line 186.
Subroutine each_match redefined at Bio\Coordinate\Result.pm line 211.
Subroutine match redefined at Bio\Coordinate\Result.pm line 232.
Subroutine gap redefined at Bio\Coordinate\Result.pm line 255.
Subroutine purge_gaps redefined at Bio\Coordinate\Result.pm line 278.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Subroutine new redefined at Bio\Location\Split.pm line 104.
Subroutine each_Location redefined at Bio\Location\Split.pm line 136.
Subroutine sub_Location redefined at Bio\Location\Split.pm line 165.
Subroutine add_sub_Location redefined at Bio\Location\Split.pm line 234.
Subroutine splittype redefined at Bio\Location\Split.pm line 258.
Subroutine is_single_sequence redefined at Bio\Location\Split.pm line 286.
Subroutine guide_strand redefined at Bio\Location\Split.pm line 311.
Subroutine strand redefined at Bio\Location\Split.pm line 339.
Subroutine flip_strand redefined at Bio\Location\Split.pm line 380.
Subroutine start redefined at Bio\Location\Split.pm line 401.
Subroutine end redefined at Bio\Location\Split.pm line 420.
Subroutine min_start redefined at Bio\Location\Split.pm line 439.
Subroutine max_start redefined at Bio\Location\Split.pm line 461.
Subroutine start_pos_type redefined at Bio\Location\Split.pm line 484.
Subroutine min_end redefined at Bio\Location\Split.pm line 505.
Subroutine max_end redefined at Bio\Location\Split.pm line 528.
Subroutine end_pos_type redefined at Bio\Location\Split.pm line 552.
Subroutine seq_id redefined at Bio\Location\Split.pm line 578.
Subroutine to_FTstring redefined at Bio\Location\Split.pm line 624.
Use of uninitialized value $type in lc at Bio/Location/Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
Use of uninitialized value $type in lc at Bio\Location\Split.pm line 118.
t/Coordinate/GeneCoordinateMapper.t .......... 
1..116
ok 1 - use Bio::Location::Simple;
ok 2 - use Bio::Coordinate::Pair;
ok 3 - use Bio::Coordinate::ExtrapolatingPair;
ok 4 - use Bio::Coordinate::GeneMapper;
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14 - The object isa Bio::Location::Simple
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75 - The object isa Bio::Location::Simple
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok
t/LiveSeq/Chain.t ............................ 
1..45
ok 1 - use Bio::LiveSeq::Chain;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94
Subroutine new redefined at Bio\Location\Simple.pm line 93, <GEN0> line 48.
Subroutine start redefined at Bio\Location\Simple.pm line 115, <GEN0> line 48.
Subroutine end redefined at Bio\Location\Simple.pm line 144, <GEN0> line 48.
Subroutine length redefined at Bio\Location\Simple.pm line 190, <GEN0> line 48.
Subroutine location_type redefined at Bio\Location\Simple.pm line 281, <GEN0> line 48.
Subroutine to_FTstring redefined at Bio\Location\Simple.pm line 328, <GEN0> line 48.
Subroutine trunc redefined at Bio\Location\Simple.pm line 370, <GEN0> line 48.
Subroutine new redefined at Bio\Location\Fuzzy.pm line 147, <GEN0> line 57.
Subroutine location_type redefined at Bio\Location\Fuzzy.pm line 174, <GEN0> line 57.
Subroutine start redefined at Bio\Location\Fuzzy.pm line 236, <GEN0> line 57.
Subroutine end redefined at Bio\Location\Fuzzy.pm line 263, <GEN0> line 57.
Subroutine min_start redefined at Bio\Location\Fuzzy.pm line 290, <GEN0> line 57.
Subroutine max_start redefined at Bio\Location\Fuzzy.pm line 309, <GEN0> line 57.
Subroutine start_pos_type redefined at Bio\Location\Fuzzy.pm line 329, <GEN0> line 57.
Subroutine min_end redefined at Bio\Location\Fuzzy.pm line 359, <GEN0> line 57.
Subroutine max_end redefined at Bio\Location\Fuzzy.pm line 378, <GEN0> line 57.
Subroutine end_pos_type redefined at Bio\Location\Fuzzy.pm line 398, <GEN0> line 57.
Subroutine to_FTstring redefined at Bio\Location\Fuzzy.pm line 469, <GEN0> line 57.
Subroutine _fuzzypointdecode redefined at Bio\Location\Fuzzy.pm line 581, <GEN0> line 57.
Subroutine new redefined at Bio\Location\Split.pm line 104, <GEN0> line 74.
Subroutine each_Location redefined at Bio\Location\Split.pm line 136, <GEN0> line 74.
Subroutine sub_Location redefined at Bio\Location\Split.pm line 165, <GEN0> line 74.
Subroutine add_sub_Location redefined at Bio\Location\Split.pm line 234, <GEN0> line 74.
Subroutine splittype redefined at Bio\Location\Split.pm line 258, <GEN0> line 74.
Subroutine is_single_sequence redefined at Bio\Location\Split.pm line 286, <GEN0> line 74.
Subroutine guide_strand redefined at Bio\Location\Split.pm line 311, <GEN0> line 74.
Subroutine strand redefined at Bio\Location\Split.pm line 339, <GEN0> line 74.
Subroutine flip_strand redefined at Bio\Location\Split.pm line 380, <GEN0> line 74.
Subroutine start redefined at Bio\Location\Split.pm line 401, <GEN0> line 74.
Subroutine end redefined at Bio\Location\Split.pm line 420, <GEN0> line 74.
Subroutine min_start redefined at Bio\Location\Split.pm line 439, <GEN0> line 74.
Subroutine max_start redefined at Bio\Location\Split.pm line 461, <GEN0> line 74.
Subroutine start_pos_type redefined at Bio\Location\Split.pm line 484, <GEN0> line 74.
Subroutine min_end redefined at Bio\Location\Split.pm line 505, <GEN0> line 74.
Subroutine max_end redefined at Bio\Location\Split.pm line 528, <GEN0> line 74.
Subroutine end_pos_type redefined at Bio\Location\Split.pm line 552, <GEN0> line 74.
Subroutine seq_id redefined at Bio\Location\Split.pm line 578, <GEN0> line 74.
Subroutine to_FTstring redefined at Bio\Location\Split.pm line 624, <GEN0> line 74.
t/LiveSeq/LiveSeq.t .......................... 
1..48
ok 1 - use Bio::LiveSeq::IO::BioPerl;
ok 2
ok 3
ok 4 - Bio::LiveSeq::Gene
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok
t/LiveSeq/Mutation.t ......................... 
1..19
ok 1 - use Bio::LiveSeq::Mutation;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94
Subroutine new redefined at Bio\Location\Simple.pm line 93, <GEN0> line 40.
Subroutine start redefined at Bio\Location\Simple.pm line 115, <GEN0> line 40.
Subroutine end redefined at Bio\Location\Simple.pm line 144, <GEN0> line 40.
Subroutine length redefined at Bio\Location\Simple.pm line 190, <GEN0> line 40.
Subroutine location_type redefined at Bio\Location\Simple.pm line 281, <GEN0> line 40.
Subroutine to_FTstring redefined at Bio\Location\Simple.pm line 328, <GEN0> line 40.
Subroutine trunc redefined at Bio\Location\Simple.pm line 370, <GEN0> line 40.
Subroutine new redefined at Bio\Location\Split.pm line 104, <GEN1> line 67.
Subroutine each_Location redefined at Bio\Location\Split.pm line 136, <GEN1> line 67.
Subroutine sub_Location redefined at Bio\Location\Split.pm line 165, <GEN1> line 67.
Subroutine add_sub_Location redefined at Bio\Location\Split.pm line 234, <GEN1> line 67.
Subroutine splittype redefined at Bio\Location\Split.pm line 258, <GEN1> line 67.
Subroutine is_single_sequence redefined at Bio\Location\Split.pm line 286, <GEN1> line 67.
Subroutine guide_strand redefined at Bio\Location\Split.pm line 311, <GEN1> line 67.
Subroutine strand redefined at Bio\Location\Split.pm line 339, <GEN1> line 67.
Subroutine flip_strand redefined at Bio\Location\Split.pm line 380, <GEN1> line 67.
Subroutine start redefined at Bio\Location\Split.pm line 401, <GEN1> line 67.
Subroutine end redefined at Bio\Location\Split.pm line 420, <GEN1> line 67.
Subroutine min_start redefined at Bio\Location\Split.pm line 439, <GEN1> line 67.
Subroutine max_start redefined at Bio\Location\Split.pm line 461, <GEN1> line 67.
Subroutine start_pos_type redefined at Bio\Location\Split.pm line 484, <GEN1> line 67.
Subroutine min_end redefined at Bio\Location\Split.pm line 505, <GEN1> line 67.
Subroutine max_end redefined at Bio\Location\Split.pm line 528, <GEN1> line 67.
Subroutine end_pos_type redefined at Bio\Location\Split.pm line 552, <GEN1> line 67.
Subroutine seq_id redefined at Bio\Location\Split.pm line 578, <GEN1> line 67.
Subroutine to_FTstring redefined at Bio\Location\Split.pm line 624, <GEN1> line 67.
t/LiveSeq/Mutator.t .......................... 
1..24
ok 1 - use Bio::LiveSeq::Mutator;
ok 2 - use Bio::LiveSeq::IO::BioPerl;
ok 3 - use Bio::Variation::IO;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/LocalDB/BioDBGFF.t ......................... 
1..279
ok 1 - use Bio::DB::GFF;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103 # skip fetch_feature_by_gid() not implemented by this adaptor
ok 104 # skip fetch_feature_by_gid() not implemented by this adaptor
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134 # skip delete_groups() not implemented by this adaptor
ok 135 # skip delete_groups() not implemented by this adaptor
ok 136 # skip Not compatible with your Operating System
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok 176
ok 177
ok 178
ok 179
ok 180
ok 181
ok 182
ok 183
ok 184
ok 185
ok 186
ok 187
ok 188
ok 189
ok 190
ok 191
ok 192
ok 193
ok 194
ok 195
ok 196
ok 197
ok 198
ok 199
ok 200
ok 201
ok 202
ok 203
ok 204
ok 205
ok 206
ok 207
ok 208
ok 209
ok 210
ok 211
ok 212
ok 213
ok 214
ok 215
ok 216
ok 217
ok 218
ok 219
ok 220
ok 221
ok 222
ok 223
ok 224
ok 225
ok 226
ok 227
ok 228
ok 229
ok 230
ok 231
ok 232
ok 233
ok 234
ok 235
ok 236
ok 237
ok 238
ok 239
ok 240
ok 241
ok 242 # skip fetch_feature_by_gid() not implemented by this adaptor
ok 243 # skip fetch_feature_by_gid() not implemented by this adaptor
ok 244
ok 245
ok 246
ok 247
ok 248
ok 249
ok 250 # skip preferred groups are not supported by gff3
ok 251 # skip preferred groups are not supported by gff3
ok 252 # skip preferred groups are not supported by gff3
ok 253
ok 254
ok 255
ok 256
ok 257
ok 258
ok 259
ok 260
ok 261
ok 262
ok 263
ok 264
ok 265
ok 266
ok 267
ok 268
ok 269
ok 270
ok 271
ok 272
ok 273 # skip delete_groups() not implemented by this adaptor
ok 274 # skip delete_groups() not implemented by this adaptor
ok 275 # skip Not compatible with your Operating System
ok 276
ok 277
ok 278
ok 279
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Subroutine new redefined at Bio/Search/Result/GenericResult.pm line 175.
Subroutine algorithm redefined at Bio/Search/Result/GenericResult.pm line 261.
Subroutine algorithm_version redefined at Bio/Search/Result/GenericResult.pm line 281.
Subroutine next_hit redefined at Bio/Search/Result/GenericResult.pm line 308.
Subroutine query_name redefined at Bio/Search/Result/GenericResult.pm line 334.
Subroutine query_accession redefined at Bio/Search/Result/GenericResult.pm line 354.
Subroutine query_gi redefined at Bio/Search/Result/GenericResult.pm line 375.
Subroutine query_length redefined at Bio/Search/Result/GenericResult.pm line 396.
Subroutine query_description redefined at Bio/Search/Result/GenericResult.pm line 417.
Subroutine database_name redefined at Bio/Search/Result/GenericResult.pm line 439.
Subroutine database_letters redefined at Bio/Search/Result/GenericResult.pm line 462.
Subroutine database_entries redefined at Bio/Search/Result/GenericResult.pm line 484.
Subroutine get_parameter redefined at Bio/Search/Result/GenericResult.pm line 505.
Subroutine available_parameters redefined at Bio/Search/Result/GenericResult.pm line 520.
Subroutine get_statistic redefined at Bio/Search/Result/GenericResult.pm line 537.
Subroutine available_statistics redefined at Bio/Search/Result/GenericResult.pm line 552.
Subroutine add_hit redefined at Bio/Search/Result/GenericResult.pm line 571.
Subroutine hit_factory redefined at Bio/Search/Result/GenericResult.pm line 596.
Subroutine rewind redefined at Bio/Search/Result/GenericResult.pm line 613.
Subroutine _nexthitindex redefined at Bio/Search/Result/GenericResult.pm line 626.
Subroutine add_parameter redefined at Bio/Search/Result/GenericResult.pm line 643.
Subroutine add_statistic redefined at Bio/Search/Result/GenericResult.pm line 660.
Subroutine num_hits redefined at Bio/Search/Result/GenericResult.pm line 677.
Subroutine hits redefined at Bio/Search/Result/GenericResult.pm line 697.
Subroutine algorithm_reference redefined at Bio/Search/Result/GenericResult.pm line 725.
Subroutine program_reference redefined at Bio/Search/Result/GenericResult.pm line 744.
Subroutine no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 753.
Subroutine set_no_hits_found redefined at Bio/Search/Result/GenericResult.pm line 770.
Subroutine to_string redefined at Bio/Search/Result/GenericResult.pm line 791.
t/LocalDB/BlastIndex.t ....................... 
1..26
ok 1 - use Cwd;
ok 2 - use Bio::SearchIO;
ok 3 - use Bio::Index::Blast;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/LocalDB/DBFasta.t .......................... 
1..15
ok 1 - use Bio::Root::IO;
ok 2 - use File::Copy;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok
t/LocalDB/DBQual.t ........................... 
1..38
ok 1 - use Bio::Root::IO;
ok 2 - use File::Copy;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13 - The object isa Bio::Seq::PrimaryQual
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25 - The object isa Bio::Seq::PrimaryQual
ok 26
ok 27
ok 28 - The object isa Bio::Seq::PrimaryQual
ok 29
ok 30
ok 31
ok 32 - The object isa Bio::Seq::PrimaryQual
ok 33
ok 34 - The object isa Bio::Seq::PrimaryQual
ok 35
ok 36
ok 37
ok 38
ok
t/LocalDB/Flat.t ............................. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/LocalDB/Index.t ............................ skipped: The optional module DB_File (or dependencies thereof) was not installed
Replacement list is longer than search list at Bio/Range.pm line 251.
t/LocalDB/Registry.t ......................... 
1..14
ok 1 - use Bio::DB::Registry;
ok 2 - use Bio::DB::Flat;
ok 3
ok 4 # skip The optional module DB_File (or dependencies thereof) was not installed
ok 5 # skip The optional module DB_File (or dependencies thereof) was not installed
ok 6 # skip Network tests have not been requested
ok 7 # skip Network tests have not been requested
ok 8 # skip Network tests have not been requested
ok 9 # skip Network tests have not been requested
ok 10 # skip Network tests have not been requested
ok 11 # skip Network tests have not been requested
ok 12 # skip Network tests have not been requested
ok 13 # skip Network tests have not been requested
ok 14 # skip Network tests have not been requested
ok
Replacement list is longer than search list at Bio/Range.pm line 251.

#   Failed test 'use Bio::DB::SeqFeature::Store::GFF3Loader;'
#   at t/LocalDB/SeqFeature.t line 17.
#     Tried to use 'Bio::DB::SeqFeature::Store::GFF3Loader'.
#     Error:  Can't locate DB_File.pm in @INC (@INC contains: . /home/lstein/projects/bioperl-live C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR\blib\lib C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR\blib\arch C:/cpanfly-5.12/var/cpan/build/BioPerl-1.6.1-M4bynR C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR C:\cpanfly-5.12\var\megalib C:\Perl-5.12\site\lib C:\Perl-5.12\lib C:/cpanfly-5.12/var/megalib C:/Perl-5.12/site/lib C:/Perl-5.12/lib) at Bio/DB/SeqFeature/Store/LoadHelper.pm line 39.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/LoadHelper.pm line 39.
# Compilation failed in require at Bio/DB/SeqFeature/Store/GFF3Loader.pm line 73.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/GFF3Loader.pm line 73.
# Compilation failed in require at (eval 49) line 2.
# BEGIN failed--compilation aborted at (eval 49) line 2.
# Looks like you failed 1 test of 69.
t/LocalDB/SeqFeature.t ....................... 
1..69
ok 1 - use Bio::DB::SeqFeature::Store;
not ok 2 - use Bio::DB::SeqFeature::Store::GFF3Loader;
ok 3 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 4 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 5 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 6 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 7 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 8 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 9 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 10 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 11 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 12 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 13 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 14 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 15 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 16 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 17 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 18 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 19 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 20 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 21 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 22 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 23 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 24 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 25 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 26 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 27 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 28 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 29 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 30 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 31 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 32 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 33 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 34 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 35 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 36 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 37 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 38 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 39 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 40 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 41 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 42 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 43 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 44 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 45 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 46 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 47 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 48 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 49 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 50 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 51 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 52 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 53 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 54 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 55 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 56 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 57 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 58 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 59 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 60 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 61 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 62 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 63 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 64 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 65 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 66 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 67 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 68 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
ok 69 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 50) line 2.
#  at t/LocalDB/SeqFeature.t line 28
# 
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/69 subtests 
	(less 67 skipped subtests: 1 okay)
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94

------------- 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-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR\blib\lib C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR\blib\arch C:/cpanfly-5.12/var/cpan/build/BioPerl-1.6.1-M4bynR C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR C:\cpanfly-5.12\var\megalib C:\Perl-5.12\site\lib C:\Perl-5.12\lib C:/cpanfly-5.12/var/megalib C:/Perl-5.12/site/lib C:/Perl-5.12/lib) at Bio\DB\Taxonomy\flatfile.pm line 90.
BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 90.
Compilation failed in require at Bio/Root/Root.pm line 439.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441
STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:264
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:115
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-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR\blib\lib C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR\blib\arch C:/cpanfly-5.12/var/cpan/build/BioPerl-1.6.1-M4bynR C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR C:\cpanfly-5.12\var\megalib C:\Perl-5.12\site\lib C:\Perl-5.12\lib C:/cpanfly-5.12/var/megalib C:/Perl-5.12/site/lib C:/Perl-5.12/lib) at Bio\DB\Taxonomy\flatfile.pm line 90.
BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 90.
Compilation failed in require at Bio/Root/Root.pm line 439.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441
STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:264
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:115
STACK: t/LocalDB/transfac_pro.t:18
-----------------------------------------------------------

For more information about the Bio::DB::Taxonomy system please see
the Bio::DB::Taxonomy docs.  This includes ways of checking for 
formats at compile time, not run time.
Replacement list is longer than search list at Bio/Range.pm line 251.

------------- 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-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR\blib\lib C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR\blib\arch C:/cpanfly-5.12/var/cpan/build/BioPerl-1.6.1-M4bynR C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR C:\cpanfly-5.12\var\megalib C:\Perl-5.12\site\lib C:\Perl-5.12\lib C:/cpanfly-5.12/var/megalib C:/Perl-5.12/site/lib C:/Perl-5.12/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 439.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441
STACK: Bio::DB::TFBS::_load_tax_module Bio/DB/TFBS.pm:151
STACK: Bio::DB::TFBS::new Bio/DB/TFBS.pm:130
STACK: t/LocalDB/transfac_pro.t:25
-----------------------------------------------------------
Bio::DB::TFBS: transfac_pro cannot be found
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::TFBS::transfac_pro. Can't locate DB_File.pm in @INC (@INC contains: . C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR\blib\lib C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR\blib\arch C:/cpanfly-5.12/var/cpan/build/BioPerl-1.6.1-M4bynR C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR C:\cpanfly-5.12\var\megalib C:\Perl-5.12\site\lib C:\Perl-5.12\lib C:/cpanfly-5.12/var/megalib C:/Perl-5.12/site/lib C:/Perl-5.12/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 439.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441
STACK: Bio::DB::TFBS::_load_tax_module Bio/DB/TFBS.pm:151
STACK: Bio::DB::TFBS::new Bio/DB/TFBS.pm:130
STACK: t/LocalDB/transfac_pro.t:25
-----------------------------------------------------------

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

#   Failed test at t/LocalDB/transfac_pro.t line 25.
Can't call method "get_reference_ids" on an undefined value at t/LocalDB/transfac_pro.t line 33.
# Looks like you planned 115 tests but ran 4.
# Looks like you failed 1 test of 4 run.
# Looks like your test exited with 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 
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Map/Cyto.t ................................. 
1..110
ok 1 - use Bio::Map::CytoMap;
ok 2 - use Bio::Map::CytoPosition;
ok 3 - use Bio::Map::CytoMarker;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14 - The object isa Bio::Map::CytoPosition
ok 15
ok 16
ok 17
ok 18 - The object isa Bio::Range
ok 19
ok 20
ok 21
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ok 104
ok 105
ok 106
ok 107
ok 108
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ok
t/Map/Linkage.t .............................. 
1..18
ok 1 - use Bio::Map::LinkagePosition;
ok 2 - use Bio::Map::Microsatellite;
ok 3 - use Bio::Map::LinkageMap;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
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
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ok 18
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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
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ok 248
ok 249 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 250 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 251 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 252 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 253 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 254 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 255 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 256 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 257 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 258 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 259 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 260 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 261 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 262 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 263 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 264 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 265 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 266 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 267 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok
Replacement list is longer than search list at Bio/Range.pm line 251, <GEN1> line 16.
t/Map/MapIO.t ................................ 
1..51
ok 1 - use Bio::MapIO;
ok 2
ok 3 - The object isa Bio::Map::MapI
ok 4
ok 5
ok 6
ok 7
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ok 51
ok
t/Map/MicrosatelliteMarker.t ................. 
1..8
ok 1 - use Bio::Map::SimpleMap;
ok 2 - use Bio::Map::Position;
ok 3 - use Bio::Map::Microsatellite;
ok 4
ok 5
ok 6
ok 7
ok 8
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Map/Physical.t ............................. 
1..39
ok 1 - use Bio::Map::Physical;
ok 2 - use Bio::MapIO;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12 - code holds and returns a string, definition requires a boolean
ok 13 - code holds and returns a string, definition requires a boolean
ok 14
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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
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ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Matrix/IO/psm.t ............................ 
1..63
ok 1 - use Bio::Matrix::PSM::IO;
ok 2
ok 3
ok 4
ok 5
ok 6
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ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Matrix/InstanceSite.t ...................... 
1..6
ok 1 - use Bio::Matrix::PSM::InstanceSite;
ok 2
ok 3
ok 4
ok 5
ok 6
ok
t/Matrix/Matrix.t ............................ 
1..77
ok 1 - use Bio::Matrix::Generic;
ok 2 - use Bio::Matrix::IO;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
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ok 10
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ok 13
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ok 30 - The object isa Bio::Matrix::Scoring
ok 31
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ok 42 - The object isa Bio::Matrix::Scoring
ok 43
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ok 75
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ok 77
ok
t/Matrix/ProtMatrix.t ........................ 
1..14
ok 1 - use Bio::Matrix::PSM::ProtMatrix;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Matrix/ProtPsm.t ........................... 
1..14
ok 1 - use Bio::Matrix::PSM::IO;
ok 2
ok 3
ok 4
ok 5 # skip TODO: Module incomplete
ok 6 # skip TODO: Module incomplete
ok 7 # skip TODO: Module incomplete
ok 8 # skip TODO: Module incomplete
ok 9 # skip TODO: Module incomplete
ok 10 # skip TODO: Module incomplete
ok 11 # skip TODO: Module incomplete
ok 12 # skip TODO: Module incomplete
ok 13 # skip TODO: Module incomplete
ok 14 # skip TODO: Module incomplete
ok
t/Matrix/SiteMatrix.t ........................ 
1..14
ok 1 - use Bio::Matrix::PSM::SiteMatrix;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok
t/Ontology/GOterm.t .......................... 
1..62
ok 1 - use Bio::Ontology::GOterm;
ok 2 - use Bio::Ontology::Ontology;
ok 3 - use Bio::Annotation::DBLink;
ok 4 - The object isa Bio::Ontology::GOterm
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
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ok 50
ok 51
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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
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ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok
t/Ontology/IO/go.t ........................... 
1..102
ok 1 - use Bio::OntologyIO;
ok 2
ok 3 - The object isa Bio::Ontology::OntologyI
ok 4
ok 5 - The object isa Bio::Ontology::OntologyEngineI
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
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ok 97
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ok 99
ok 100
ok 101
ok 102
ok
t/Ontology/IO/interpro.t ..................... 
1..47
ok 1 - use Bio::OntologyIO;
ok 2
ok 3
ok 4
ok 5
ok 6 - term Integrins alpha chain in ontology InterPro
ok 7
ok 8 - term post-translational modification in ontology InterPro
ok 9
ok 10 - term Repeat in ontology InterPro
ok 11
ok 12 - term Binding Site in ontology InterPro
ok 13
ok 14 - term Cdc20/Fizzy in ontology InterPro
ok 15
ok 16 - term Kringle in ontology InterPro
ok 17
ok 18 - term Helix-turn-helix, AraC type  in ontology InterPro
ok 19
ok 20 - term Active Site in ontology InterPro
ok 21
ok 22 - term Active Site in ontology InterPro
ok 23
ok 24 - term Binding Site in ontology InterPro
ok 25
ok 26 - term Domain in ontology InterPro
ok 27
ok 28 - term Family in ontology InterPro
ok 29
ok 30 - term Repeat in ontology InterPro
ok 31
ok 32 - term post-translational modification in ontology InterPro
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok
t/Ontology/IO/obo.t .......................... 
1..83
ok 1 - use Bio::OntologyIO;
ok 2 - use Bio::Ontology::RelationshipType;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46 - got a ontology IO handler isa Bio::OntologyIO
ok 47 - got ontology parser2 isa Bio::Ontology::Ontology
ok 48 - got OBO engine object isa Bio::Ontology::OBOEngine
ok 49 - got ontology parser2 isa Bio::Ontology::Ontology
ok 50 - got OBO engine object isa Bio::Ontology::OBOEngine
ok 51 - got ontology parser2 isa Bio::Ontology::Ontology
ok 52 - got OBO engine object isa Bio::Ontology::OBOEngine
ok 53 - Gene ontology
ok 54 - biological process
ok 55 - molecular function
ok 56 - Got root
ok 57 - Got root
ok 58 - Got regulates
# 	 from gene_ontology
ok 59 - Got
# 	 positively regulates from gene_ontology
ok 60 - Got
# 	  regulates from biological_process
ok 61 - Got
# 	 positively regulates from biological_process
ok 62 - Got predicates for gene_ontology
ok 63 - Got predicates for biological_process
ok 64 - Got regulates predicate
ok 65 - Got positively regulates predicate
ok 66 - Got relationships for biological_process
ok 67 - Got relationships for molecular_function
ok 68 - Got is a relationship from
# 	 molecular_function
ok 69 - Got term object isa Bio::Ontology::Term
ok 70 - Got term id
ok 71 - Got term name
ok 72 - Got regulated object isa Bio::Ontology::Term
ok 73 - Got regulated term1 id
ok 74 - Got term1 object isa Bio::Ontology::Term
ok 75 - Got back the child
ok 76 - Got term object isa Bio::Ontology::Term
ok 77 - Got term id
ok 78 - Got term name
ok 79 - Got regulated object isa Bio::Ontology::Term
ok 80 - Got regulated term1 id
ok 81 - Got identical regulation
ok 82 - Got term1 object isa Bio::Ontology::Term
ok 83 - Got back the child
ok
t/Ontology/Ontology.t ........................ 
1..52
ok 1 - use Bio::OntologyIO;
ok 2 - use Bio::Ontology::RelationshipType;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok
Subroutine new redefined at Bio\Ontology\Relationship.pm line 140.
Subroutine init redefined at Bio\Ontology\Relationship.pm line 191.
Subroutine identifier redefined at Bio\Ontology\Relationship.pm line 216.
Subroutine subject_term redefined at Bio\Ontology\Relationship.pm line 246.
Subroutine object_term redefined at Bio\Ontology\Relationship.pm line 277.
Subroutine predicate_term redefined at Bio\Ontology\Relationship.pm line 308.
Subroutine ontology redefined at Bio\Ontology\Relationship.pm line 334.
Subroutine to_string redefined at Bio\Ontology\Relationship.pm line 362.
Subroutine _check_class redefined at Bio\Ontology\Relationship.pm line 384.
Subroutine Bio::Ontology::Relationship::child_term redefined at Bio\Ontology\Relationship.pm line 410.
Subroutine Bio::Ontology::Relationship::parent_term redefined at Bio\Ontology\Relationship.pm line 411.
Subroutine Bio::Ontology::Relationship::relationship_type redefined at Bio\Ontology\Relationship.pm line 412.
t/Ontology/OntologyEngine.t .................. 
1..27
ok 1 - use Bio::Ontology::Term;
ok 2 - use Bio::Ontology::Relationship;
ok 3 - use Bio::Ontology::RelationshipType;
ok 4 - use Bio::Ontology::SimpleOntologyEngine;
ok 5 - use Bio::Ontology::Ontology;
ok 6 - The object isa Bio::Ontology::OntologyEngineI
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok
t/Ontology/OntologyStore.t ................... skipped: Network tests have not been requested
t/Ontology/Relationship.t .................... 
1..12
ok 1 - use Bio::Ontology::Relationship;
ok 2 - use Bio::Ontology::GOterm;
ok 3 - use Bio::Ontology::RelationshipType;
ok 4 - The object isa Bio::Ontology::RelationshipType
ok 5 - The object isa Bio::Ontology::GOterm
ok 6 - The object isa Bio::Ontology::GOterm
ok 7 - The object isa Bio::Ontology::Relationship
ok 8
ok 9
ok 10
ok 11
ok 12
ok
t/Ontology/RelationshipType.t ................ 
1..23
ok 1 - use Bio::Ontology::RelationshipType;
ok 2 - use Bio::Ontology::Ontology;
ok 3 - The object isa Bio::Ontology::RelationshipType
ok 4 - The object isa Bio::Ontology::TermI
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok
Constant subroutine Bio::Ontology::Term::TRUE redefined at C:\Perl-5.12\lib/constant.pm line 130.
Constant subroutine Bio::Ontology::Term::FALSE redefined at C:\Perl-5.12\lib/constant.pm line 130.
Subroutine new redefined at Bio\Ontology\Term.pm line 146.
Subroutine init redefined at Bio\Ontology\Term.pm line 196.
Subroutine identifier redefined at Bio\Ontology\Term.pm line 227.
Subroutine name redefined at Bio\Ontology\Term.pm line 247.
Subroutine definition redefined at Bio\Ontology\Term.pm line 267.
Subroutine ontology redefined at Bio\Ontology\Term.pm line 295.
Subroutine version redefined at Bio\Ontology\Term.pm line 325.
Subroutine is_obsolete redefined at Bio\Ontology\Term.pm line 344.
Subroutine comment redefined at Bio\Ontology\Term.pm line 364.
Subroutine get_synonyms redefined at Bio\Ontology\Term.pm line 381.
Subroutine add_synonym redefined at Bio\Ontology\Term.pm line 401.
Subroutine remove_synonyms redefined at Bio\Ontology\Term.pm line 425.
Subroutine get_dblinks redefined at Bio\Ontology\Term.pm line 448.
Subroutine get_dbxrefs redefined at Bio\Ontology\Term.pm line 474.
Subroutine get_dblink_context redefined at Bio\Ontology\Term.pm line 499.
Subroutine get_dbxref_context redefined at Bio\Ontology\Term.pm line 515.
Subroutine add_dblink redefined at Bio\Ontology\Term.pm line 535.
Subroutine add_dbxref redefined at Bio\Ontology\Term.pm line 562.
Subroutine has_dblink redefined at Bio\Ontology\Term.pm line 598.
Subroutine has_dbxref redefined at Bio\Ontology\Term.pm line 616.
Subroutine add_dblink_context redefined at Bio\Ontology\Term.pm line 647.
Subroutine remove_dblinks redefined at Bio\Ontology\Term.pm line 668.
Subroutine remove_dbxrefs redefined at Bio\Ontology\Term.pm line 685.
Subroutine get_references redefined at Bio\Ontology\Term.pm line 707.
Subroutine add_reference redefined at Bio\Ontology\Term.pm line 723.
Subroutine remove_references redefined at Bio\Ontology\Term.pm line 746.
Subroutine get_secondary_ids redefined at Bio\Ontology\Term.pm line 767.
Subroutine add_secondary_id redefined at Bio\Ontology\Term.pm line 787.
Subroutine remove_secondary_ids redefined at Bio\Ontology\Term.pm line 811.
Subroutine _is_true_or_false redefined at Bio\Ontology\Term.pm line 825.
Subroutine object_id redefined at Bio\Ontology\Term.pm line 850.
Subroutine authority redefined at Bio\Ontology\Term.pm line 871.
Subroutine namespace redefined at Bio\Ontology\Term.pm line 900.
Subroutine display_name redefined at Bio\Ontology\Term.pm line 924.
Subroutine description redefined at Bio\Ontology\Term.pm line 948.
Subroutine each_dblink redefined at Bio\Ontology\Term.pm line 962.
Subroutine add_dblinks redefined at Bio\Ontology\Term.pm line 963.
Subroutine Bio::Ontology::Term::each_synonym redefined at Bio\Ontology\Term.pm line 964.
Subroutine Bio::Ontology::Term::add_synonyms redefined at Bio\Ontology\Term.pm line 965.
t/Ontology/Term.t ............................ 
1..54
ok 1 - use Bio::Ontology::Term;
ok 2 - use Bio::Ontology::TermFactory;
ok 3 - use Bio::Annotation::DBLink;
ok 4 - The object isa Bio::Ontology::TermI
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44 - The object isa Bio::Ontology::TermI
ok 45
ok 46 - The object isa Bio::Ontology::TermI
ok 47 - The object isa Bio::Ontology::GOterm
ok 48
ok 49
ok 50 - The object isa Bio::Ontology::TermI
ok 51 - The object isa Bio::AnnotationI
ok 52
ok 53
ok 54
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
Replacement list is longer than search list at Bio/Perl.pm line 627.
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94
Subroutine new redefined at Bio\Location\Simple.pm line 93, <GEN1> line 31.
Subroutine start redefined at Bio\Location\Simple.pm line 115, <GEN1> line 31.
Subroutine end redefined at Bio\Location\Simple.pm line 144, <GEN1> line 31.
Subroutine length redefined at Bio\Location\Simple.pm line 190, <GEN1> line 31.
Subroutine location_type redefined at Bio\Location\Simple.pm line 281, <GEN1> line 31.
Subroutine to_FTstring redefined at Bio\Location\Simple.pm line 328, <GEN1> line 31.
Subroutine trunc redefined at Bio\Location\Simple.pm line 370, <GEN1> line 31.
Subroutine new redefined at Bio\Location\Split.pm line 104, <GEN1> line 42.
Subroutine each_Location redefined at Bio\Location\Split.pm line 136, <GEN1> line 42.
Subroutine sub_Location redefined at Bio\Location\Split.pm line 165, <GEN1> line 42.
Subroutine add_sub_Location redefined at Bio\Location\Split.pm line 234, <GEN1> line 42.
Subroutine splittype redefined at Bio\Location\Split.pm line 258, <GEN1> line 42.
Subroutine is_single_sequence redefined at Bio\Location\Split.pm line 286, <GEN1> line 42.
Subroutine guide_strand redefined at Bio\Location\Split.pm line 311, <GEN1> line 42.
Subroutine strand redefined at Bio\Location\Split.pm line 339, <GEN1> line 42.
Subroutine flip_strand redefined at Bio\Location\Split.pm line 380, <GEN1> line 42.
Subroutine start redefined at Bio\Location\Split.pm line 401, <GEN1> line 42.
Subroutine end redefined at Bio\Location\Split.pm line 420, <GEN1> line 42.
Subroutine min_start redefined at Bio\Location\Split.pm line 439, <GEN1> line 42.
Subroutine max_start redefined at Bio\Location\Split.pm line 461, <GEN1> line 42.
Subroutine start_pos_type redefined at Bio\Location\Split.pm line 484, <GEN1> line 42.
Subroutine min_end redefined at Bio\Location\Split.pm line 505, <GEN1> line 42.
Subroutine max_end redefined at Bio\Location\Split.pm line 528, <GEN1> line 42.
Subroutine end_pos_type redefined at Bio\Location\Split.pm line 552, <GEN1> line 42.
Subroutine seq_id redefined at Bio\Location\Split.pm line 578, <GEN1> line 42.
Subroutine to_FTstring redefined at Bio\Location\Split.pm line 624, <GEN1> line 42.
Subroutine new redefined at Bio\Location\Fuzzy.pm line 147, <GEN1> line 42.
Subroutine location_type redefined at Bio\Location\Fuzzy.pm line 174, <GEN1> line 42.
Subroutine start redefined at Bio\Location\Fuzzy.pm line 236, <GEN1> line 42.
Subroutine end redefined at Bio\Location\Fuzzy.pm line 263, <GEN1> line 42.
Subroutine min_start redefined at Bio\Location\Fuzzy.pm line 290, <GEN1> line 42.
Subroutine max_start redefined at Bio\Location\Fuzzy.pm line 309, <GEN1> line 42.
Subroutine start_pos_type redefined at Bio\Location\Fuzzy.pm line 329, <GEN1> line 42.
Subroutine min_end redefined at Bio\Location\Fuzzy.pm line 359, <GEN1> line 42.
Subroutine max_end redefined at Bio\Location\Fuzzy.pm line 378, <GEN1> line 42.
Subroutine end_pos_type redefined at Bio\Location\Fuzzy.pm line 398, <GEN1> line 42.
Subroutine to_FTstring redefined at Bio\Location\Fuzzy.pm line 469, <GEN1> line 42.
Subroutine _fuzzypointdecode redefined at Bio\Location\Fuzzy.pm line 581, <GEN1> line 42.
t/Perl.t ..................................... 
1..29
ok 1 - use Bio::Perl;
ok 2
ok 3 - The object isa Bio::SeqI
ok 4
ok 5 - The object isa Bio::SeqI
ok 6
ok 7 - The object isa Bio::SeqI
ok 8 - The object isa Bio::SeqI
ok 9
ok 10
ok 11 - The object isa Bio::SeqI
ok 12
ok 13 - The object isa Bio::SeqI
ok 14
ok 15 - The object isa Bio::PrimarySeqI
ok 16
ok 17
ok 18
ok 19
ok 20 # skip Network tests have not been requested
ok 21 # skip Network tests have not been requested
ok 22 # skip Network tests have not been requested
ok 23 # skip Network tests have not been requested
ok 24 # skip Network tests have not been requested
ok 25 # skip Network tests have not been requested
ok 26 # skip Network tests have not been requested
ok 27 # skip Network tests have not been requested
ok 28 # skip Network tests have not been requested
ok 29 # skip Network tests have not been requested
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94
t/Phenotype/Correlate.t ...................... 
1..17
ok 1 - use Bio::Phenotype::Correlate;
ok 2 - use Bio::Species;
ok 3 - The object isa Bio::Phenotype::Correlate
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok
t/Phenotype/MeSH.t ........................... 
1..24
ok 1 - use Bio::Phenotype::MeSH::Term;
ok 2 - use Bio::Phenotype::MeSH::Twig;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok
t/Phenotype/Measure.t ........................ 
1..21
ok 1 - use Bio::Phenotype::Measure;
ok 2 - The object isa Bio::Phenotype::Measure
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok
t/Phenotype/MiniMIMentry.t ................... 
1..15
ok 1 - use Bio::Phenotype::OMIM::MiniMIMentry;
ok 2 - The object isa Bio::Phenotype::OMIM::MiniMIMentry
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Phenotype/OMIMentry.t ...................... 
1..153
ok 1 - use Bio::Phenotype::OMIM::OMIMentry;
ok 2 - use Bio::Phenotype::OMIM::MiniMIMentry;
ok 3 - use Bio::Species;
ok 4 - use Bio::Annotation::Reference;
ok 5 - use Bio::Map::CytoPosition;
ok 6 - use Bio::Phenotype::Correlate;
ok 7 - use Bio::Phenotype::Measure;
ok 8 - use Bio::Annotation::DBLink;
ok 9 - The object isa Bio::Phenotype::OMIM::OMIMentry
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79 - operator overloading in AnnotationI is deprecated
ok 80 - operator overloading in AnnotationI is deprecated
ok 81
ok 82
ok 83 - operator overloading in AnnotationI is deprecated
ok 84 - operator overloading in AnnotationI is deprecated
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136 - operator overloading in AnnotationI is deprecated
ok 137 - operator overloading in AnnotationI is deprecated
ok 138
ok 139
ok 140 - operator overloading in AnnotationI is deprecated
ok 141 - operator overloading in AnnotationI is deprecated
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok
t/Phenotype/OMIMentryAllelicVariant.t ........ 
1..27
ok 1 - use Bio::Phenotype::OMIM::OMIMentryAllelicVariant;
ok 2 - The object isa Bio::Phenotype::OMIM::OMIMentryAllelicVariant
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Phenotype/OMIMparser.t ..................... 
1..175
ok 1 - use Bio::Phenotype::OMIM::OMIMparser;
ok 2 - The object isa Bio::Phenotype::OMIM::OMIMparser
ok 3 - The object isa Bio::Phenotype::OMIM::OMIMentry
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19 - The object isa Bio::Phenotype::OMIM::MiniMIMentry
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89 - The object isa Bio::Phenotype::OMIM::OMIMentry
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105 - The object isa Bio::Phenotype::OMIM::MiniMIMentry
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175 - missing linebreak caught
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94
Replacement list is longer than search list at Bio/Range.pm line 251.
t/Phenotype/Phenotype.t ...................... 
1..116
ok 1 - use Bio::Phenotype::Phenotype;
ok 2 - use Bio::Species;
ok 3 - use Bio::Annotation::Reference;
ok 4 - use Bio::Map::CytoPosition;
ok 5 - use Bio::Phenotype::Correlate;
ok 6 - use Bio::Phenotype::Measure;
ok 7 - use Bio::Annotation::DBLink;
ok 8 - The object isa Bio::Phenotype::PhenotypeI
ok 9 - The object isa Bio::Phenotype::Phenotype
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42 - operator overloading in AnnotationI is deprecated
ok 43 - operator overloading in AnnotationI is deprecated
ok 44
ok 45
ok 46 - operator overloading in AnnotationI is deprecated
ok 47 - operator overloading in AnnotationI is deprecated
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99 - operator overloading in AnnotationI is deprecated
ok 100 - operator overloading in AnnotationI is deprecated
ok 101
ok 102
ok 103 - operator overloading in AnnotationI is deprecated
ok 104 - operator overloading in AnnotationI is deprecated
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok
t/PodSyntax.t ................................ 
1..999
ok 1 - POD test for Bio\AlignIO.pm
ok 2 - POD test for Bio\AnalysisI.pm
ok 3 - POD test for Bio\AnalysisParserI.pm
ok 4 - POD test for Bio\AnalysisResultI.pm
ok 5 - POD test for Bio\AnnotatableI.pm
ok 6 - POD test for Bio\AnnotationCollectionI.pm
ok 7 - POD test for Bio\AnnotationI.pm
ok 8 - POD test for Bio\Biblio.pm
ok 9 - POD test for Bio\ClusterI.pm
ok 10 - POD test for Bio\ClusterIO.pm
ok 11 - POD test for Bio\DasI.pm
ok 12 - POD test for Bio\DBLinkContainerI.pm
ok 13 - POD test for Bio\DescribableI.pm
ok 14 - POD test for Bio\FeatureHolderI.pm
ok 15 - POD test for Bio\FeatureIO.pm
ok 16 - POD test for Bio\HandlerBaseI.pm
ok 17 - POD test for Bio\IdCollectionI.pm
ok 18 - POD test for Bio\IdentifiableI.pm
ok 19 - POD test for Bio\LocatableSeq.pm
ok 20 - POD test for Bio\LocationI.pm
ok 21 - POD test for Bio\MapIO.pm
ok 22 - POD test for Bio\OntologyIO.pm
ok 23 - POD test for Bio\ParameterBaseI.pm
ok 24 - POD test for Bio\Perl.pm
ok 25 - POD test for Bio\PhyloNetwork.pm
ok 26 - POD test for Bio\PrimarySeq.pm
ok 27 - POD test for Bio\PrimarySeqI.pm
ok 28 - POD test for Bio\PullParserI.pm
ok 29 - POD test for Bio\Range.pm
ok 30 - POD test for Bio\RangeI.pm
ok 31 - POD test for Bio\SearchDist.pm
ok 32 - POD test for Bio\SearchIO.pm
ok 33 - POD test for Bio\Seq.pm
ok 34 - POD test for Bio\SeqAnalysisParserI.pm
ok 35 - POD test for Bio\SeqFeatureI.pm
ok 36 - POD test for Bio\SeqI.pm
ok 37 - POD test for Bio\SeqIO.pm
ok 38 - POD test for Bio\SeqUtils.pm
ok 39 - POD test for Bio\SimpleAlign.pm
ok 40 - POD test for Bio\SimpleAnalysisI.pm
ok 41 - POD test for Bio\Species.pm
ok 42 - POD test for Bio\Taxon.pm
ok 43 - POD test for Bio\Taxonomy.pm
ok 44 - POD test for Bio\TreeIO.pm
ok 45 - POD test for Bio\UpdateableSeqI.pm
ok 46 - POD test for Bio\WebAgent.pm
ok 47 - POD test for examples\bioperl.pl (no pod)
ok 48 - POD test for examples\generate_random_seq.pl (no pod)
ok 49 - POD test for examples\longorf.pl
ok 50 - POD test for examples\make_primers.pl (no pod)
ok 51 - POD test for examples\revcom_dir.pl (no pod)
ok 52 - POD test for examples\rev_and_trans.pl (no pod)
ok 53 - POD test for examples\subsequence.cgi (no pod)
ok 54 - POD test for maintenance\authors.pl
ok 55 - POD test for maintenance\check_NAME.pl
ok 56 - POD test for maintenance\check_URLs.pl
ok 57 - POD test for maintenance\cvs2cl_by_file.pl
ok 58 - POD test for maintenance\dependencies.pl
ok 59 - POD test for maintenance\deprecated.pl
ok 60 - POD test for maintenance\modules.pl
ok 61 - POD test for maintenance\module_usage.pl (no pod)
ok 62 - POD test for maintenance\ncbi_blast_switches.pl (no pod)
ok 63 - POD test for maintenance\pod.pl
ok 64 - POD test for maintenance\symlink_script.pl
ok 65 - POD test for maintenance\version.pl
ok 66 - POD test for Bio\Align\AlignI.pm
ok 67 - POD test for Bio\Align\DNAStatistics.pm
ok 68 - POD test for Bio\Align\PairwiseStatistics.pm
ok 69 - POD test for Bio\Align\ProteinStatistics.pm
ok 70 - POD test for Bio\Align\StatisticsI.pm
ok 71 - POD test for Bio\Align\Utilities.pm
ok 72 - POD test for Bio\AlignIO\arp.pm
ok 73 - POD test for Bio\AlignIO\bl2seq.pm
ok 74 - POD test for Bio\AlignIO\clustalw.pm
ok 75 - POD test for Bio\AlignIO\emboss.pm
ok 76 - POD test for Bio\AlignIO\fasta.pm
ok 77 - POD test for Bio\AlignIO\largemultifasta.pm
ok 78 - POD test for Bio\AlignIO\maf.pm
ok 79 - POD test for Bio\AlignIO\mase.pm
ok 80 - POD test for Bio\AlignIO\mega.pm
ok 81 - POD test for Bio\AlignIO\meme.pm
ok 82 - POD test for Bio\AlignIO\metafasta.pm
ok 83 - POD test for Bio\AlignIO\msf.pm
ok 84 - POD test for Bio\AlignIO\nexus.pm
ok 85 - POD test for Bio\AlignIO\pfam.pm
ok 86 - POD test for Bio\AlignIO\phylip.pm
ok 87 - POD test for Bio\AlignIO\po.pm
ok 88 - POD test for Bio\AlignIO\proda.pm
ok 89 - POD test for Bio\AlignIO\prodom.pm
ok 90 - POD test for Bio\AlignIO\psi.pm
ok 91 - POD test for Bio\AlignIO\selex.pm
ok 92 - POD test for Bio\AlignIO\stockholm.pm
ok 93 - POD test for Bio\AlignIO\xmfa.pm
ok 94 - POD test for Bio\Annotation\AnnotationFactory.pm
ok 95 - POD test for Bio\Annotation\Collection.pm
ok 96 - POD test for Bio\Annotation\Comment.pm
ok 97 - POD test for Bio\Annotation\DBLink.pm
ok 98 - POD test for Bio\Annotation\OntologyTerm.pm
ok 99 - POD test for Bio\Annotation\Reference.pm
ok 100 - POD test for Bio\Annotation\Relation.pm
ok 101 - POD test for Bio\Annotation\SimpleValue.pm
ok 102 - POD test for Bio\Annotation\StructuredValue.pm
ok 103 - POD test for Bio\Annotation\TagTree.pm
ok 104 - POD test for Bio\Annotation\Target.pm
ok 105 - POD test for Bio\Annotation\Tree.pm
ok 106 - POD test for Bio\Annotation\TypeManager.pm
ok 107 - POD test for Bio\Assembly\Contig.pm
ok 108 - POD test for Bio\Assembly\ContigAnalysis.pm
ok 109 - POD test for Bio\Assembly\IO.pm
ok 110 - POD test for Bio\Assembly\Scaffold.pm
ok 111 - POD test for Bio\Assembly\ScaffoldI.pm
ok 112 - POD test for Bio\Assembly\Singlet.pm
ok 113 - POD test for Bio\Biblio\Article.pm
ok 114 - POD test for Bio\Biblio\BiblioBase.pm
ok 115 - POD test for Bio\Biblio\Book.pm
ok 116 - POD test for Bio\Biblio\BookArticle.pm
ok 117 - POD test for Bio\Biblio\IO.pm
ok 118 - POD test for Bio\Biblio\Journal.pm
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ok 938 - POD test for Bio\DB\GFF\Util\Rearrange.pm
ok 939 - POD test for Bio\DB\SeqFeature\Store\bdb.pm
ok 940 - POD test for Bio\DB\SeqFeature\Store\berkeleydb.pm
ok 941 - POD test for Bio\DB\SeqFeature\Store\berkeleydb3.pm
ok 942 - POD test for Bio\DB\SeqFeature\Store\FeatureFileLoader.pm
ok 943 - POD test for Bio\DB\SeqFeature\Store\GFF2Loader.pm
ok 944 - POD test for Bio\DB\SeqFeature\Store\GFF3Loader.pm
ok 945 - POD test for Bio\DB\SeqFeature\Store\Loader.pm
ok 946 - POD test for Bio\DB\SeqFeature\Store\LoadHelper.pm
ok 947 - POD test for Bio\DB\SeqFeature\Store\memory.pm
ok 948 - POD test for Bio\Matrix\PSM\IO\mast.pm
ok 949 - POD test for Bio\Matrix\PSM\IO\masta.pm
ok 950 - POD test for Bio\Matrix\PSM\IO\meme.pm
ok 951 - POD test for Bio\Matrix\PSM\IO\psiblast.pm
ok 952 - POD test for Bio\Matrix\PSM\IO\transfac.pm
ok 953 - POD test for Bio\Structure\SecStr\DSSP\Res.pm
ok 954 - POD test for Bio\Structure\SecStr\STRIDE\Res.pm
ok 955 - POD test for Bio\Tools\Analysis\DNA\ESEfinder.pm
ok 956 - POD test for Bio\Tools\Analysis\Protein\Domcut.pm
ok 957 - POD test for Bio\Tools\Analysis\Protein\ELM.pm
ok 958 - POD test for Bio\Tools\Analysis\Protein\GOR4.pm
ok 959 - POD test for Bio\Tools\Analysis\Protein\HNN.pm
ok 960 - POD test for Bio\Tools\Analysis\Protein\Mitoprot.pm
ok 961 - POD test for Bio\Tools\Analysis\Protein\NetPhos.pm
ok 962 - POD test for Bio\Tools\Analysis\Protein\Scansite.pm
ok 963 - POD test for Bio\Tools\Analysis\Protein\Sopma.pm
ok 964 - POD test for Bio\Tools\EUtilities\Info\FieldInfo.pm
ok 965 - POD test for Bio\Tools\EUtilities\Info\LinkInfo.pm
ok 966 - POD test for Bio\Tools\EUtilities\Link\LinkSet.pm
ok 967 - POD test for Bio\Tools\EUtilities\Link\UrlLink.pm
ok 968 - POD test for Bio\Tools\EUtilities\Query\GlobalQuery.pm
ok 969 - POD test for Bio\Tools\EUtilities\Summary\DocSum.pm
ok 970 - POD test for Bio\Tools\EUtilities\Summary\Item.pm
ok 971 - POD test for Bio\Tools\EUtilities\Summary\ItemContainerI.pm
ok 972 - POD test for Bio\Tools\Phylo\Molphy\Result.pm
ok 973 - POD test for Bio\Tools\Phylo\PAML\ModelResult.pm
ok 974 - POD test for Bio\Tools\Phylo\PAML\Result.pm
ok 975 - POD test for Bio\Tools\Phylo\Phylip\ProtDist.pm
ok 976 - POD test for Bio\Tools\Primer\Assessor\Base.pm
ok 977 - POD test for Bio\Tools\SiRNA\Ruleset\saigo.pm
ok 978 - POD test for Bio\Tools\SiRNA\Ruleset\tuschl.pm
ok 979 - POD test for examples\root\lib\Bio\PrimarySeq.pm
ok 980 - POD test for examples\root\lib\Bio\PrimarySeqI.pm
ok 981 - POD test for examples\root\lib\Bio\Seq.pm
ok 982 - POD test for examples\root\lib\Bio\SeqI.pm
ok 983 - POD test for Bio\DB\GFF\Adaptor\berkeleydb\iterator.pm
ok 984 - POD test for Bio\DB\GFF\Adaptor\dbi\caching_handle.pm
ok 985 - POD test for Bio\DB\GFF\Adaptor\dbi\iterator.pm
ok 986 - POD test for Bio\DB\GFF\Adaptor\dbi\mysql.pm
ok 987 - POD test for Bio\DB\GFF\Adaptor\dbi\mysqlace.pm
ok 988 - POD test for Bio\DB\GFF\Adaptor\dbi\mysqlcmap.pm
ok 989 - POD test for Bio\DB\GFF\Adaptor\dbi\mysqlopt.pm
ok 990 - POD test for Bio\DB\GFF\Adaptor\dbi\oracle.pm
ok 991 - POD test for Bio\DB\GFF\Adaptor\dbi\oracleace.pm
ok 992 - POD test for Bio\DB\GFF\Adaptor\dbi\pg.pm
ok 993 - POD test for Bio\DB\GFF\Adaptor\dbi\pg_fts.pm
ok 994 - POD test for Bio\DB\GFF\Adaptor\memory\feature_serializer.pm
ok 995 - POD test for Bio\DB\GFF\Adaptor\memory\iterator.pm
ok 996 - POD test for Bio\DB\SeqFeature\Store\DBI\Iterator.pm
ok 997 - POD test for Bio\DB\SeqFeature\Store\DBI\mysql.pm
ok 998 - POD test for Bio\DB\SeqFeature\Store\DBI\Pg.pm
ok 999 - POD test for Bio\DB\SeqFeature\Store\DBI\SQLite.pm
ok
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94
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 197.
Subroutine get_root_node redefined at Bio\Tree\Tree.pm line 231.
Subroutine set_root_node redefined at Bio\Tree\Tree.pm line 246.
Subroutine total_branch_length redefined at Bio\Tree\Tree.pm line 270.
Subroutine subtree_length redefined at Bio\Tree\Tree.pm line 284.
Subroutine id redefined at Bio\Tree\Tree.pm line 307.
Subroutine score redefined at Bio\Tree\Tree.pm line 328.
Subroutine as_text redefined at Bio\Tree\Tree.pm line 376.
Subroutine set_tag_value redefined at Bio\Tree\Tree.pm line 432.
Subroutine add_tag_value redefined at Bio\Tree\Tree.pm line 453.
Subroutine remove_tag redefined at Bio\Tree\Tree.pm line 473.
Subroutine remove_all_tags redefined at Bio\Tree\Tree.pm line 493.
Subroutine get_all_tags redefined at Bio\Tree\Tree.pm line 509.
Subroutine get_tag_values redefined at Bio\Tree\Tree.pm line 525.
Subroutine has_tag redefined at Bio\Tree\Tree.pm line 541.
Subroutine cleanup_tree redefined at Bio\Tree\Tree.pm line 548.
Subroutine new redefined at Bio\Tree\Node.pm line 113.
Subroutine create_node_on_branch redefined at Bio\Tree\Node.pm line 166.
Subroutine add_Descendent redefined at Bio\Tree\Node.pm line 224.
Subroutine each_Descendent redefined at Bio\Tree\Node.pm line 262.
Subroutine remove_Descendent redefined at Bio\Tree\Node.pm line 324.
Subroutine remove_all_Descendents redefined at Bio\Tree\Node.pm line 359.
Subroutine ancestor redefined at Bio\Tree\Node.pm line 393.
Subroutine branch_length redefined at Bio\Tree\Node.pm line 434.
Subroutine bootstrap redefined at Bio\Tree\Node.pm line 458.
Subroutine description redefined at Bio\Tree\Node.pm line 479.
Subroutine id redefined at Bio\Tree\Node.pm line 508.
Subroutine internal_id redefined at Bio\Tree\Node.pm line 550.
Subroutine _creation_id redefined at Bio\Tree\Node.pm line 564.
Subroutine is_Leaf redefined at Bio\Tree\Node.pm line 585.
Subroutine height redefined at Bio\Tree\Node.pm line 603.
Subroutine invalidate_height redefined at Bio\Tree\Node.pm line 628.
Subroutine set_tag_value redefined at Bio\Tree\Node.pm line 649.
Subroutine add_tag_value redefined at Bio\Tree\Node.pm line 671.
Subroutine remove_tag redefined at Bio\Tree\Node.pm line 692.
Subroutine remove_all_tags redefined at Bio\Tree\Node.pm line 712.
Subroutine get_all_tags redefined at Bio\Tree\Node.pm line 728.
Subroutine get_tag_values redefined at Bio\Tree\Node.pm line 746.
Subroutine has_tag redefined at Bio\Tree\Node.pm line 762.
Subroutine node_cleanup redefined at Bio\Tree\Node.pm line 767.
Subroutine reverse_edge redefined at Bio\Tree\Node.pm line 794.
t/PopGen/Coalescent.t ........................ 
1..13
ok 1 - use Bio::PopGen::Simulation::Coalescent;
ok 2 - use Bio::PopGen::Statistics;
ok 3 - use Bio::TreeIO;
ok 4
ok 5
ok 6 - pi
ok 7 - theta
ok 8 - tajimaD
ok 9 - all the mutations should be polymorphic (by definition)
ok 10 - fu and li D
ok 11 - fu and li D*
ok 12 - fu and li F
ok 13 - fu and li F
ok
t/PopGen/HtSNP.t ............................. 
1..8
ok 1 - use Bio::PopGen::HtSNP;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/PopGen/MK.t ................................ 
1..46
ok 1 - use Bio::AlignIO;
ok 2 - use Bio::PopGen::Statistics;
ok 3 - use Bio::PopGen::Utilities;
ok 4 - The object isa Bio::PopGen::Statistics
ok 5 - The object isa Bio::SimpleAlign
ok 6 - The object isa Bio::PopGen::Population
ok 7 - Marker Names
ok 8 - Number of Inds
ok 9 - number of ingroup sequences
ok 10 - number of outgroup1 sequences
ok 11 - number of outgroup2 sequences
ok 12 - NSpoly
ok 13 - NSfixed
ok 14 - Spoly
ok 15 - Sfixed
ok 16 - McDonald Kreitman
ok 17 - NSpoly
ok 18 - NSfixed
ok 19 - Spoly
ok 20 - Sfixed
ok 21 - McDonald Kreitman
ok 22 - NSpoly
ok 23 - NSfixed
ok 24 - Spoly
ok 25 - Sfixed
ok 26 - The object isa Bio::SimpleAlign
ok 27 - The object isa Bio::PopGen::Population
ok 28 - Marker Names
ok 29 - Number of Inds
ok 30 - number of ingroup sequences
ok 31 - number of outgroup1 sequences
ok 32 - number of outgroup2 sequences
ok 33 - NSpoly
ok 34 - NSfixed
ok 35 - Spoly
ok 36 - Sfixed
ok 37 - McDonald Kreitman
ok 38 - NSpoly
ok 39 - NSfixed
ok 40 - Spoly
ok 41 - Sfixed
ok 42 - McDonald Kreitman
ok 43 - NSpoly
ok 44 - NSfixed
ok 45 - Spoly
ok 46 - Sfixed
ok
Replacement list is longer than search list at Bio/Range.pm line 251.
t/PopGen/PopGen.t ............................ 
1..100
ok 1 - use Bio::PopGen::Individual;
ok 2 - use Bio::PopGen::Genotype;
ok 3 - use Bio::PopGen::Population;
ok 4 - use Bio::PopGen::IO;
ok 5 - use Bio::PopGen::PopStats;
ok 6 - use Bio::AlignIO;
ok 7 - use Bio::PopGen::Statistics;
ok 8 - use Bio::PopGen::Utilities;
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - mrsa,mssa aflp1
ok 38 - all pops, aflp1
ok 39 - mrsa,envpop aflp1,aflp2
ok 40
ok 41
ok 42
ok 43 - mssa,mrsa all_bands
ok 44 - env,mssa mkr1
ok 45 - env,mssa,mrsa all bands
ok 46 - env,mssa,mrsa mkr2
ok 47 - mrsa,nc all_bands
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99 - Pi on 3-allele data
ok 100 - Theta on 3-allele data
ok
t/PopGen/PopGenSims.t ........................ 
1..23
ok 1 - use Bio::PopGen::Simulation::GeneticDrift;
ok 2 - Allele freqs should sum to 1
ok 3 - Allele freqs should sum to 1
ok 4 - Allele freqs should sum to 1
ok 5 - Allele freqs should sum to 1
ok 6 - Allele freqs should sum to 1
ok 7 - Allele freqs should sum to 1
ok 8 - Allele freqs should sum to 1
ok 9 - Allele freqs should sum to 1
ok 10 - Allele freqs should sum to 1
ok 11 - Allele freqs should sum to 1
ok 12
ok 13 - All frequencies should be <= 1
ok 14 - Allele freqs should sum to 1
ok 15 - Allele freqs should sum to 1
ok 16 - Allele freqs should sum to 1
ok 17 - Allele freqs should sum to 1
ok 18 - Allele freqs should sum to 1
ok 19 - Allele freqs should sum to 1
ok 20 - Allele freqs should sum to 1
ok 21 - Allele freqs should sum to 1
ok 22 - Allele freqs should sum to 1
ok 23 - Allele freqs should sum to 1
ok
t/PopGen/TagHaplotype.t ...................... 
1..3
ok 1 - use Bio::PopGen::TagHaplotype;
ok 2
ok 3
ok
t/RemoteDB/BioFetch.t ........................ skipped: Network tests have not been requested
Replacement list is longer than search list at Bio/Range.pm line 251.
t/RemoteDB/CUTG.t ............................ 
1..37
ok 1 - use Bio::DB::CUTG;
ok 2 - use Bio::CodonUsage::Table;
ok 3 - use Bio::CodonUsage::IO;
ok 4 - use Bio::SeqIO;
ok 5 - use Bio::Tools::SeqStats;
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24 # skip Network tests have not been requested
ok 25 # skip Network tests have not been requested
ok 26 # skip Network tests have not been requested
ok 27 # skip Network tests have not been requested
ok 28 # skip Network tests have not been requested
ok 29 # skip Network tests have not been requested
ok 30 # skip Network tests have not been requested
ok 31 # skip Network tests have not been requested
ok 32 # skip Network tests have not been requested
ok 33 # skip Network tests have not been requested
ok 34 # skip Network tests have not been requested
ok 35 # skip Network tests have not been requested
ok 36 # skip Network tests have not been requested
ok 37 # skip Network tests have not been requested
ok
t/RemoteDB/EMBL.t ............................ skipped: Network tests have not been requested
t/RemoteDB/EUtilities.t ...................... skipped: Network tests have not been requested
t/RemoteDB/EntrezGene.t ...................... skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed
t/RemoteDB/GenBank.t ......................... skipped: Network tests have not been requested
t/RemoteDB/GenPept.t ......................... skipped: Network tests have not been requested
t/RemoteDB/HIV/HIV.t ......................... 
1..30
ok 1 - use Bio::DB::HIV;
ok 2 - use Bio::DB::WebDBSeqI;
ok 3 - use Bio::DB::HIV::HIVAnnotProcessor;
ok 4 - The object isa Bio::DB::HIV
ok 5 - The object isa Bio::Root::Root
ok 6 - Bio::DB::HIV->can(...)
ok 7 - Bio::DB::HIV->can(...)
ok 8 - Bio::DB::HIV->can(...)
ok 9 - lanl_base set in default object
ok 10 - map_db set in default object
ok 11 - make_search_if set in default object
ok 12 - search_ set in default object
ok 13 - url_base_address set in default object
ok 14 - default sequence request format (fasta)
ok 15 - sorry till implemented
ok 16 - sorry till implemented
ok 17 - HIVQuery type exception check
ok 18 # skip Network tests have not been requested
ok 19 # skip Network tests have not been requested
ok 20 # skip Network tests have not been requested
ok 21 # skip Network tests have not been requested
ok 22 # skip Network tests have not been requested
ok 23 # skip Network tests have not been requested
ok 24 # skip Network tests have not been requested
ok 25 # skip Network tests have not been requested
ok 26 # skip Network tests have not been requested
ok 27 # skip Network tests have not been requested
ok 28 # skip Network tests have not been requested
ok 29 # skip Network tests have not been requested
ok 30 # skip Network tests have not been requested
ok
Replacement list is longer than search list at C:\cpanfly-5.12\var\cpan\build\BioPerl-1.6.1-M4bynR\blib\lib/Bio/Range.pm line 251.
t/RemoteDB/HIV/HIVAnnotProcessor.t ........... 
1..11
ok 1 - use Bio::Seq;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::DB::HIV::HIVAnnotProcessor;
ok 4 - The object isa Bio::DB::HIV::HIVAnnotProcessor
ok 5 - The object isa Bio::Root::Root
ok 6 - Bio::DB::HIV::HIVAnnotProcessor->can(...)
ok 7 - Bio::DB::HIV::HIVAnnotProcessor->can('hiv_query')
ok 8 - bad type set exception
ok 9 - attach stream
ok 10 - write exception
ok 11 - access stream
ok
Use of uninitialized value $rest[0] in join or string at (eval 74) line 15.
t/RemoteDB/HIV/HIVQuery.t .................... 
1..41
ok 1 - use Bio::DB::Query::HIVQuery;
ok 2 - use Bio::DB::HIV;
ok 3 - use Bio::Annotation::Collection;
ok 4 - use Bio::Annotation::Comment;
ok 5 - use Bio::Annotation::Reference;
ok 6 - use Bio::DB::HIV::HIVQueryHelper;
ok 7 - The object isa Bio::DB::Query::HIVQuery
ok 8 - The object isa Bio::Root::Root
ok 9 - Bio::DB::Query::HIVQuery->can(...)
ok 10 - Bio::DB::Query::HIVQuery->can(...)
ok 11 - Bio::DB::Query::HIVQuery->can(...)
ok 12 - _map_db_uri set in default object
ok 13 - _make_search_if_uri set in default object
ok 14 - _search_uri set in default object
ok 15 - _schema_file set in default object
ok 16 - _run_option set in default object
ok 17 - annotations container available
ok 18 - query syntax check 1
ok 19 - query syntax check 2
ok 20 - query syntax check 3
ok 21 - query parser check
ok 22 - multiquery parse check
ok 23 - use HTML::Parser;
ok 24 - help html to file
ok 25 - help html parsed
ok 26 - bad field exception check
ok 27 - bad match data exception check
ok 28 - empty field not ok exception check
ok 29 - uninitialized schema exception check
ok 30 - query not run (level 1) warning check
ok 31 - query not run (level 2) warning check
ok 32 # skip Network tests have not been requested
ok 33 # skip Network tests have not been requested
ok 34 # skip Network tests have not been requested
ok 35 # skip Network tests have not been requested
ok 36 # skip Network tests have not been requested
ok 37 # skip Network tests have not been requested
ok 38 # skip Network tests have not been requested
ok 39 # skip Network tests have not been requested
ok 40 # skip Network tests have not been requested
ok 41 # skip Network tests have not been requested
ok
t/RemoteDB/HIV/HIVQueryHelper.t .............. 
1..40
ok 1 - use Bio::DB::HIV::HIVQueryHelper;
ok 2 - The object isa HIVSchema
ok 3 - The object isa QRY
ok 4 - The object isa R
ok 5 - The object isa Q
ok 6 - schema load
ok 7 - HIVSchema->can(...)
ok 8 - fields complete
ok 9 - tables complete
ok 10 - aliases complete
ok 11
ok 12 - test field syntax ok
ok 13 - test field syntax ok
ok 14 - test alias by field name
ok 15 - correct primary key for SequenceEntry
ok 16 - correct number of foreign keys for AUthor
ok 17 - correct foreign table for au_pub_id
ok 18 - correct annotation key hash
ok 19 - QRY->can(...)
ok 20 - R->can(...)
ok 21 - Q->can(...)
ok 22 - null QRY
ok 23 - null R (request object)
ok 24 - null Q (atomic query object)
ok 25 - R obj create and init (1)
ok 26 - R obj create and init (2)
ok 27 - R::In
ok 28 - !R::In
ok 29 - R::Eq
ok 30 - QRY obj create and init (1)
ok 31 - QRY obj create and init (2)
ok 32 - QRY obj create and init (3)
ok 33 - QRY overload |
ok 34 - QRY overload &
ok 35 - QRY nontrivial &
ok 36 - parse: ('odds bodkins', a)[X] m[Y] u[Z] OR 'b'[X] {A B [C] [D]} 
ok 37 - make: 2 queries returned
ok 38 - {annotation fields} parsed correctly
ok 39 - parse: ('odds bodkins', a)[X] m[Y] u[Z] AND b[X] {A B [C] [D]} 
ok 40 - above query is null
ok
t/RemoteDB/MeSH.t ............................ skipped: Network tests have not been requested
t/RemoteDB/Query/GenBank.t ................... skipped: Network tests have not been requested
t/RemoteDB/RefSeq.t .......................... 
1..16
ok 1 - use Bio::DB::RefSeq;
ok 2 - use Bio::DB::GenBank;
ok 3 - use Bio::DB::EMBL;
ok 4
ok 5
ok 6
ok 7 # skip Network tests have not been requested
ok 8 # skip Network tests have not been requested
ok 9 # skip Network tests have not been requested
ok 10 # skip Network tests have not been requested
ok 11 # skip Network tests have not been requested
ok 12 # skip Network tests have not been requested
ok 13 # skip Network tests have not been requested
ok 14 # skip Network tests have not been requested
ok 15 # skip Network tests have not been requested
ok 16 # skip Network tests have not been requested
ok
t/RemoteDB/SeqHound.t ........................ skipped: Network tests have not been requested
t/RemoteDB/SeqRead_fail.t .................... skipped: Network tests have not been requested

Timeout (max run time is 300s)
C:\Perl-5.12\bin\perl.exe exits with 37