PATH=C:\mingw\bin;C:\cygwin\bin;C:\cpanfly-5.18\var\megalib\bin;C:\Perl64-5.18\site\bin;C:\Perl64-5.18\bin;C:\cygwin\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\PROGRA~2\Perforce;C:\instantclient_11_2;C:\cygwin\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\PROGRA~2\Perforce;C:\mysql\bin
Start 2014-02-27T11:23:27
ActivePerl-1800 CPAN-2.00
PATH=C:\mingw\bin;C:\cygwin\bin;C:\CPANFL~1.18\var\megalib\bin;C:\Perl64-5.18\site\bin;C:\Perl64-5.18\bin;C:\cygwin\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WINDOW~1\v1.0;C:\PROGRA~2\Perforce;C:\INSTAN~1;C:\cygwin\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WINDOW~1\v1.0;C:\PROGRA~2\Perforce;C:\mysql\bin
Reading 'C:\cpanfly-5.18\var\cpan\Metadata'
  Database was generated on Thu, 27 Feb 2014 15:06:12 GMT
Running make for C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz
Fetching with LWP:
http://cpan.nas1.activestate.com/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz
Checksum for C:\cpanfly-5.18\var\cpan\sources\authors\id\C\CJ\CJFIELDS\BioPerl-1.6.901.tar.gz ok
BioPerl-1.6.901
BioPerl-1.6.901/AUTHORS
BioPerl-1.6.901/BioPerl.pm
BioPerl-1.6.901/BUGS
BioPerl-1.6.901/Build.PL
BioPerl-1.6.901/Changes
BioPerl-1.6.901/DEPENDENCIES
BioPerl-1.6.901/DEPRECATED
BioPerl-1.6.901/INSTALL
BioPerl-1.6.901/INSTALL.SKIP
BioPerl-1.6.901/INSTALL.WIN
BioPerl-1.6.901/LICENSE
BioPerl-1.6.901/MANIFEST
BioPerl-1.6.901/META.json
BioPerl-1.6.901/META.yml
BioPerl-1.6.901/README
BioPerl-1.6.901/Bio
BioPerl-1.6.901/Bio/AlignIO.pm
BioPerl-1.6.901/Bio/AnalysisI.pm
BioPerl-1.6.901/Bio/AnalysisParserI.pm
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BioPerl-1.6.901/Bio/AlignIO/msf.pm
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BioPerl-1.6.901/Bio/Annotation/TagTree.pm
BioPerl-1.6.901/Bio/Annotation/Target.pm
BioPerl-1.6.901/Bio/Annotation/Tree.pm
BioPerl-1.6.901/Bio/Annotation/TypeManager.pm
BioPerl-1.6.901/Bio/Assembly
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BioPerl-1.6.901/Bio/Assembly/ContigAnalysis.pm
BioPerl-1.6.901/Bio/Assembly/IO.pm
BioPerl-1.6.901/Bio/Assembly/Scaffold.pm
BioPerl-1.6.901/Bio/Assembly/ScaffoldI.pm
BioPerl-1.6.901/Bio/Assembly/Singlet.pm
BioPerl-1.6.901/Bio/Assembly/IO
BioPerl-1.6.901/Bio/Assembly/IO/ace.pm
BioPerl-1.6.901/Bio/Assembly/IO/bowtie.pm
BioPerl-1.6.901/Bio/Assembly/IO/maq.pm
BioPerl-1.6.901/Bio/Assembly/IO/phrap.pm
BioPerl-1.6.901/Bio/Assembly/IO/sam.pm
BioPerl-1.6.901/Bio/Assembly/IO/tigr.pm
BioPerl-1.6.901/Bio/Assembly/Tools
BioPerl-1.6.901/Bio/Assembly/Tools/ContigSpectrum.pm
BioPerl-1.6.901/Bio/Biblio
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BioPerl-1.6.901/Bio/Biblio/Journal.pm
BioPerl-1.6.901/Bio/Biblio/JournalArticle.pm
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BioPerl-1.6.901/Bio/Biblio/MedlineBook.pm
BioPerl-1.6.901/Bio/Biblio/MedlineBookArticle.pm
BioPerl-1.6.901/Bio/Biblio/MedlineJournal.pm
BioPerl-1.6.901/Bio/Biblio/MedlineJournalArticle.pm
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BioPerl-1.6.901/Bio/Biblio/PubmedArticle.pm
BioPerl-1.6.901/Bio/Biblio/PubmedBookArticle.pm
BioPerl-1.6.901/Bio/Biblio/PubmedJournalArticle.pm
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BioPerl-1.6.901/Bio/Biblio/TechReport.pm
BioPerl-1.6.901/Bio/Biblio/Thesis.pm
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BioPerl-1.6.901/Bio/Biblio/IO
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BioPerl-1.6.901/Bio/Biblio/IO/medlinexml.pm
BioPerl-1.6.901/Bio/Biblio/IO/pubmed2ref.pm
BioPerl-1.6.901/Bio/Biblio/IO/pubmedxml.pm
BioPerl-1.6.901/Bio/Cluster
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BioPerl-1.6.901/Bio/CodonUsage
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BioPerl-1.6.901/Bio/Coordinate/Graph.pm
BioPerl-1.6.901/Bio/Coordinate/MapperI.pm
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BioPerl-1.6.901/Bio/DB/EMBL.pm
BioPerl-1.6.901/Bio/DB/EntrezGene.pm
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BioPerl-1.6.901/Bio/DB/Failover.pm
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BioPerl-1.6.901/Bio/DB/Qual.pm
BioPerl-1.6.901/Bio/DB/QueryI.pm
BioPerl-1.6.901/Bio/DB/RandomAccessI.pm
BioPerl-1.6.901/Bio/DB/ReferenceI.pm
BioPerl-1.6.901/Bio/DB/RefSeq.pm
BioPerl-1.6.901/Bio/DB/Registry.pm
BioPerl-1.6.901/Bio/DB/SeqFeature.pm
BioPerl-1.6.901/Bio/DB/SeqHound.pm
BioPerl-1.6.901/Bio/DB/SeqI.pm
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BioPerl-1.6.901/Bio/DB/Universal.pm
BioPerl-1.6.901/Bio/DB/UpdateableSeqI.pm
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BioPerl-1.6.901/Bio/DB/Biblio
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BioPerl-1.6.901/Bio/DB/Biblio/soap.pm
BioPerl-1.6.901/Bio/DB/Expression
BioPerl-1.6.901/Bio/DB/Expression/geo.pm
BioPerl-1.6.901/Bio/DB/Flat
BioPerl-1.6.901/Bio/DB/Flat/BDB.pm
BioPerl-1.6.901/Bio/DB/Flat/BinarySearch.pm
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BioPerl-1.6.901/Bio/DB/Flat/BDB/embl.pm
BioPerl-1.6.901/Bio/DB/Flat/BDB/fasta.pm
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BioPerl-1.6.901/Bio/DB/GFF/Typename.pm
BioPerl-1.6.901/Bio/DB/GFF/Adaptor
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BioPerl-1.6.901/Bio/DB/GFF/Adaptor/dbi
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BioPerl-1.6.901/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
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BioPerl-1.6.901/Bio/DB/GFF/Aggregator/orf.pm
BioPerl-1.6.901/Bio/DB/GFF/Aggregator/processed_transcript.pm
BioPerl-1.6.901/Bio/DB/GFF/Aggregator/so_transcript.pm
BioPerl-1.6.901/Bio/DB/GFF/Aggregator/transcript.pm
BioPerl-1.6.901/Bio/DB/GFF/Aggregator/ucsc_acembly.pm
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BioPerl-1.6.901/Bio/DB/GFF/Aggregator/ucsc_softberry.pm
BioPerl-1.6.901/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
BioPerl-1.6.901/Bio/DB/GFF/Aggregator/ucsc_unigene.pm
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BioPerl-1.6.901/Bio/DB/GFF/Util/Binning.pm
BioPerl-1.6.901/Bio/DB/GFF/Util/Rearrange.pm
BioPerl-1.6.901/Bio/DB/HIV
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BioPerl-1.6.901/Bio/DB/HIV/HIVQueryHelper.pm
BioPerl-1.6.901/Bio/DB/HIV/lanl-schema.xml
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BioPerl-1.6.901/Bio/DB/Query/GenBank.pm
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BioPerl-1.6.901/Bio/DB/SeqFeature/Segment.pm
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BioPerl-1.6.901/Bio/DB/SeqFeature/Store/DBI/SQLite.pm
BioPerl-1.6.901/Bio/DB/SeqVersion
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BioPerl-1.6.901/Bio/DB/Taxonomy
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BioPerl-1.6.901/Bio/DB/TFBS/transfac_pro.pm
BioPerl-1.6.901/Bio/Draw
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BioPerl-1.6.901/Bio/Event
BioPerl-1.6.901/Bio/Event/EventGeneratorI.pm
BioPerl-1.6.901/Bio/Event/EventHandlerI.pm
BioPerl-1.6.901/Bio/Factory
BioPerl-1.6.901/Bio/Factory/AnalysisI.pm
BioPerl-1.6.901/Bio/Factory/ApplicationFactoryI.pm
BioPerl-1.6.901/Bio/Factory/DriverFactory.pm
BioPerl-1.6.901/Bio/Factory/FTLocationFactory.pm
BioPerl-1.6.901/Bio/Factory/LocationFactoryI.pm
BioPerl-1.6.901/Bio/Factory/MapFactoryI.pm
BioPerl-1.6.901/Bio/Factory/ObjectBuilderI.pm
BioPerl-1.6.901/Bio/Factory/ObjectFactory.pm
BioPerl-1.6.901/Bio/Factory/ObjectFactoryI.pm
BioPerl-1.6.901/Bio/Factory/SeqAnalysisParserFactory.pm
BioPerl-1.6.901/Bio/Factory/SeqAnalysisParserFactoryI.pm
BioPerl-1.6.901/Bio/Factory/SequenceFactoryI.pm
BioPerl-1.6.901/Bio/Factory/SequenceProcessorI.pm
BioPerl-1.6.901/Bio/Factory/SequenceStreamI.pm
BioPerl-1.6.901/Bio/Factory/TreeFactoryI.pm
BioPerl-1.6.901/Bio/FeatureIO
BioPerl-1.6.901/Bio/FeatureIO/bed.pm
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BioPerl-1.6.901/Bio/Tree
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BioPerl-1.6.901/Bio/TreeIO
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BioPerl-1.6.901/Bio/Variation
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BioPerl-1.6.901/Bio/Variation/IO.pm
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BioPerl-1.6.901/doc
BioPerl-1.6.901/doc/makedoc.PL
BioPerl-1.6.901/doc/README
BioPerl-1.6.901/doc/Deobfuscator
BioPerl-1.6.901/doc/Deobfuscator/Build.PL
BioPerl-1.6.901/doc/Deobfuscator/Changes
BioPerl-1.6.901/doc/Deobfuscator/excluded_modules.txt
BioPerl-1.6.901/doc/Deobfuscator/LICENSE
BioPerl-1.6.901/doc/Deobfuscator/Makefile.PL
BioPerl-1.6.901/doc/Deobfuscator/MANIFEST
BioPerl-1.6.901/doc/Deobfuscator/META.yml
BioPerl-1.6.901/doc/Deobfuscator/README
BioPerl-1.6.901/doc/Deobfuscator/bin
BioPerl-1.6.901/doc/Deobfuscator/bin/deob_index.pl
BioPerl-1.6.901/doc/Deobfuscator/cgi-bin
BioPerl-1.6.901/doc/Deobfuscator/cgi-bin/deob_detail.cgi
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BioPerl-1.6.901/doc/Deobfuscator/cgi-bin/deob_help.html
BioPerl-1.6.901/doc/Deobfuscator/cgi-bin/deob_interface.cgi
BioPerl-1.6.901/doc/Deobfuscator/lib
BioPerl-1.6.901/doc/Deobfuscator/lib/Deobfuscator.pm
BioPerl-1.6.901/doc/Deobfuscator/t
BioPerl-1.6.901/doc/Deobfuscator/t/00.load.t
BioPerl-1.6.901/doc/Deobfuscator/t/pod.t
BioPerl-1.6.901/examples
BioPerl-1.6.901/examples/bioperl.pl
BioPerl-1.6.901/examples/generate_random_seq.pl
BioPerl-1.6.901/examples/longorf.pl
BioPerl-1.6.901/examples/make_primers.pl
BioPerl-1.6.901/examples/rev_and_trans.pl
BioPerl-1.6.901/examples/revcom_dir.pl
BioPerl-1.6.901/examples/subsequence.cgi
BioPerl-1.6.901/examples/align
BioPerl-1.6.901/examples/align/align_on_codons.pl
BioPerl-1.6.901/examples/align/aligntutorial.pl
BioPerl-1.6.901/examples/align/clustalw.pl
BioPerl-1.6.901/examples/align/simplealign.pl
BioPerl-1.6.901/examples/biblio
BioPerl-1.6.901/examples/biblio/biblio-eutils-example.pl
BioPerl-1.6.901/examples/biblio/biblio-soap-example.pl
BioPerl-1.6.901/examples/biblio/biblio_soap.pl
BioPerl-1.6.901/examples/Bio-DB-GFF
BioPerl-1.6.901/examples/Bio-DB-GFF/load_ucsc.pl
BioPerl-1.6.901/examples/cluster
BioPerl-1.6.901/examples/cluster/dbsnp.pl
BioPerl-1.6.901/examples/contributed
BioPerl-1.6.901/examples/contributed/nmrpdb_parse.pl
BioPerl-1.6.901/examples/contributed/prosite2perl.pl
BioPerl-1.6.901/examples/contributed/rebase2list.pl
BioPerl-1.6.901/examples/db
BioPerl-1.6.901/examples/db/dbfetch
BioPerl-1.6.901/examples/db/est_tissue_query.pl
BioPerl-1.6.901/examples/db/gb2features.pl
BioPerl-1.6.901/examples/db/get_seqs.pl
BioPerl-1.6.901/examples/db/getGenBank.pl
BioPerl-1.6.901/examples/db/rfetch.pl
BioPerl-1.6.901/examples/db/use_registry.pl
BioPerl-1.6.901/examples/liveseq
BioPerl-1.6.901/examples/liveseq/change_gene.pl
BioPerl-1.6.901/examples/popgen
BioPerl-1.6.901/examples/popgen/parse_calc_stats.pl
BioPerl-1.6.901/examples/quality
BioPerl-1.6.901/examples/quality/svgtrace.pl
BioPerl-1.6.901/examples/root
BioPerl-1.6.901/examples/root/exceptions1.pl
BioPerl-1.6.901/examples/root/exceptions2.pl
BioPerl-1.6.901/examples/root/exceptions3.pl
BioPerl-1.6.901/examples/root/exceptions4.pl
BioPerl-1.6.901/examples/root/README
BioPerl-1.6.901/examples/root/lib
BioPerl-1.6.901/examples/root/lib/TestInterface.pm
BioPerl-1.6.901/examples/root/lib/TestObject.pm
BioPerl-1.6.901/examples/searchio
BioPerl-1.6.901/examples/searchio/blast_example.pl
BioPerl-1.6.901/examples/searchio/custom_writer.pl
BioPerl-1.6.901/examples/searchio/hitwriter.pl
BioPerl-1.6.901/examples/searchio/hspwriter.pl
BioPerl-1.6.901/examples/searchio/htmlwriter.pl
BioPerl-1.6.901/examples/searchio/psiblast_features.pl
BioPerl-1.6.901/examples/searchio/psiblast_iterations.pl
BioPerl-1.6.901/examples/searchio/rawwriter.pl
BioPerl-1.6.901/examples/searchio/resultwriter.pl
BioPerl-1.6.901/examples/searchio/waba2gff.pl
BioPerl-1.6.901/examples/searchio/waba2gff3.pl
BioPerl-1.6.901/examples/sirna
BioPerl-1.6.901/examples/sirna/rnai_finder.cgi
BioPerl-1.6.901/examples/sirna/TAG
BioPerl-1.6.901/examples/structure
BioPerl-1.6.901/examples/structure/structure-io.pl
BioPerl-1.6.901/examples/tk
BioPerl-1.6.901/examples/tk/gsequence.pl
BioPerl-1.6.901/examples/tk/hitdisplay.pl
BioPerl-1.6.901/examples/tools
BioPerl-1.6.901/examples/tools/extract_genes.pl
BioPerl-1.6.901/examples/tools/gb_to_gff.pl
BioPerl-1.6.901/examples/tools/gff2ps.pl
BioPerl-1.6.901/examples/tools/parse_codeml.pl
BioPerl-1.6.901/examples/tools/psw.pl
BioPerl-1.6.901/examples/tools/reverse-translate.pl
BioPerl-1.6.901/examples/tools/run_genscan.pl
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BioPerl-1.6.901/examples/tools/seq_pattern.pl
BioPerl-1.6.901/examples/tools/standaloneblast.pl
BioPerl-1.6.901/examples/tree
BioPerl-1.6.901/examples/tree/paup2phylip.pl
BioPerl-1.6.901/ide
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BioPerl-1.6.901/maintenance/check_NAME.pl
BioPerl-1.6.901/maintenance/check_URLs.pl
BioPerl-1.6.901/maintenance/cvs2cl_by_file.pl
BioPerl-1.6.901/maintenance/dependencies.pl
BioPerl-1.6.901/maintenance/deprecated.pl
BioPerl-1.6.901/maintenance/find_mod_deps.pl
BioPerl-1.6.901/maintenance/module_usage.pl
BioPerl-1.6.901/maintenance/modules.pl
BioPerl-1.6.901/maintenance/ncbi_blast_switches.pl
BioPerl-1.6.901/maintenance/perltidy.conf
BioPerl-1.6.901/maintenance/pod.pl
BioPerl-1.6.901/maintenance/README
BioPerl-1.6.901/maintenance/symlink_script.pl
BioPerl-1.6.901/maintenance/version.pl
BioPerl-1.6.901/maintenance/big_split
BioPerl-1.6.901/maintenance/big_split/file_classification.csv
BioPerl-1.6.901/maintenance/big_split/rbuels_notes.txt
BioPerl-1.6.901/models
BioPerl-1.6.901/models/biblio.dia
BioPerl-1.6.901/models/bio_liveseq_variation.dia
BioPerl-1.6.901/models/bio_map.dia
BioPerl-1.6.901/models/bio_restriction.dia
BioPerl-1.6.901/models/bioperl.dia
BioPerl-1.6.901/models/coordinatemapper.dia
BioPerl-1.6.901/models/map_proposal.txt
BioPerl-1.6.901/models/maps_and_markers.dia
BioPerl-1.6.901/models/popgen.dia
BioPerl-1.6.901/models/population_proposal.txt
BioPerl-1.6.901/models/README
BioPerl-1.6.901/scripts
BioPerl-1.6.901/scripts/README
BioPerl-1.6.901/scripts/biblio
BioPerl-1.6.901/scripts/biblio/biblio.PLS
BioPerl-1.6.901/scripts/biblio/TAG
BioPerl-1.6.901/scripts/Bio-DB-EUtilities
BioPerl-1.6.901/scripts/Bio-DB-EUtilities/einfo.PLS
BioPerl-1.6.901/scripts/Bio-DB-GFF
BioPerl-1.6.901/scripts/Bio-DB-GFF/bulk_load_gff.PLS
BioPerl-1.6.901/scripts/Bio-DB-GFF/fast_load_gff.PLS
BioPerl-1.6.901/scripts/Bio-DB-GFF/genbank2gff.PLS
BioPerl-1.6.901/scripts/Bio-DB-GFF/genbank2gff3.PLS
BioPerl-1.6.901/scripts/Bio-DB-GFF/generate_histogram.PLS
BioPerl-1.6.901/scripts/Bio-DB-GFF/load_gff.PLS
BioPerl-1.6.901/scripts/Bio-DB-GFF/meta_gff.PLS
BioPerl-1.6.901/scripts/Bio-DB-GFF/process_gadfly.PLS
BioPerl-1.6.901/scripts/Bio-DB-GFF/process_sgd.PLS
BioPerl-1.6.901/scripts/Bio-DB-GFF/process_wormbase.PLS
BioPerl-1.6.901/scripts/Bio-DB-GFF/README
BioPerl-1.6.901/scripts/Bio-DB-SeqFeature-Store
BioPerl-1.6.901/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.PLS
BioPerl-1.6.901/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.PLS
BioPerl-1.6.901/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.PLS
BioPerl-1.6.901/scripts/das
BioPerl-1.6.901/scripts/das/das_server.pl
BioPerl-1.6.901/scripts/das/README
BioPerl-1.6.901/scripts/das/TAG
BioPerl-1.6.901/scripts/DB
BioPerl-1.6.901/scripts/DB/biofetch_genbank_proxy.PLS
BioPerl-1.6.901/scripts/DB/bioflat_index.PLS
BioPerl-1.6.901/scripts/DB/biogetseq.PLS
BioPerl-1.6.901/scripts/DB/flanks.PLS
BioPerl-1.6.901/scripts/DB/TAG
BioPerl-1.6.901/scripts/DB-HIV
BioPerl-1.6.901/scripts/DB-HIV/hivq.PLS
BioPerl-1.6.901/scripts/index
BioPerl-1.6.901/scripts/index/bp_fetch.PLS
BioPerl-1.6.901/scripts/index/bp_index.PLS
BioPerl-1.6.901/scripts/index/bp_seqret.PLS
BioPerl-1.6.901/scripts/index/TAG
BioPerl-1.6.901/scripts/popgen
BioPerl-1.6.901/scripts/popgen/composite_LD.PLS
BioPerl-1.6.901/scripts/popgen/heterogeneity_test.PLS
BioPerl-1.6.901/scripts/searchio
BioPerl-1.6.901/scripts/searchio/fastam9_to_table.PLS
BioPerl-1.6.901/scripts/searchio/filter_search.PLS
BioPerl-1.6.901/scripts/searchio/hmmer_to_table.PLS
BioPerl-1.6.901/scripts/searchio/parse_hmmsearch.PLS
BioPerl-1.6.901/scripts/searchio/README
BioPerl-1.6.901/scripts/searchio/search2table.PLS
BioPerl-1.6.901/scripts/searchio/TAG
BioPerl-1.6.901/scripts/seq
BioPerl-1.6.901/scripts/seq/extract_feature_seq.PLS
BioPerl-1.6.901/scripts/seq/make_mrna_protein.PLS
BioPerl-1.6.901/scripts/seq/seqconvert.PLS
BioPerl-1.6.901/scripts/seq/seqretsplit.PLS
BioPerl-1.6.901/scripts/seq/split_seq.PLS
BioPerl-1.6.901/scripts/seq/TAG
BioPerl-1.6.901/scripts/seq/translate_seq.PLS
BioPerl-1.6.901/scripts/seq/unflatten_seq.PLS
BioPerl-1.6.901/scripts/seqstats
BioPerl-1.6.901/scripts/seqstats/aacomp.PLS
BioPerl-1.6.901/scripts/seqstats/chaos_plot.PLS
BioPerl-1.6.901/scripts/seqstats/gccalc.PLS
BioPerl-1.6.901/scripts/seqstats/oligo_count.PLS
BioPerl-1.6.901/scripts/seqstats/TAG
BioPerl-1.6.901/scripts/taxa
BioPerl-1.6.901/scripts/taxa/classify_hits_kingdom.PLS
BioPerl-1.6.901/scripts/taxa/local_taxonomydb_query.PLS
BioPerl-1.6.901/scripts/taxa/query_entrez_taxa.PLS
BioPerl-1.6.901/scripts/taxa/TAG
BioPerl-1.6.901/scripts/taxa/taxid4species.PLS
BioPerl-1.6.901/scripts/taxa/taxonomy2tree.PLS
BioPerl-1.6.901/scripts/tree
BioPerl-1.6.901/scripts/tree/blast2tree.PLS
BioPerl-1.6.901/scripts/tree/nexus2nh.PLS
BioPerl-1.6.901/scripts/tree/TAG
BioPerl-1.6.901/scripts/tree/tree2pag.PLS
BioPerl-1.6.901/scripts/utilities
BioPerl-1.6.901/scripts/utilities/bp_mrtrans.PLS
BioPerl-1.6.901/scripts/utilities/bp_netinstall.PLS
BioPerl-1.6.901/scripts/utilities/bp_nrdb.PLS
BioPerl-1.6.901/scripts/utilities/bp_sreformat.PLS
BioPerl-1.6.901/scripts/utilities/dbsplit.PLS
BioPerl-1.6.901/scripts/utilities/download_query_genbank.PLS
BioPerl-1.6.901/scripts/utilities/mask_by_search.PLS
BioPerl-1.6.901/scripts/utilities/mutate.PLS
BioPerl-1.6.901/scripts/utilities/pairwise_kaks.PLS
BioPerl-1.6.901/scripts/utilities/README
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BioPerl-1.6.901/scripts/utilities/revtrans-motif.PLS
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BioPerl-1.6.901/scripts/utilities/search2BSML.PLS
BioPerl-1.6.901/scripts/utilities/search2gff.PLS
BioPerl-1.6.901/scripts/utilities/search2tribe.PLS
BioPerl-1.6.901/scripts/utilities/seq_length.PLS
BioPerl-1.6.901/scripts/utilities/TAG
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BioPerl-1.6.901/t/Map/Linkage.t
BioPerl-1.6.901/t/Map/Map.t
BioPerl-1.6.901/t/Map/MapIO.t
BioPerl-1.6.901/t/Map/MicrosatelliteMarker.t
BioPerl-1.6.901/t/Map/Physical.t
BioPerl-1.6.901/t/Matrix
BioPerl-1.6.901/t/Matrix/InstanceSite.t
BioPerl-1.6.901/t/Matrix/Matrix.t
BioPerl-1.6.901/t/Matrix/ProtMatrix.t
BioPerl-1.6.901/t/Matrix/ProtPsm.t
BioPerl-1.6.901/t/Matrix/SiteMatrix.t
BioPerl-1.6.901/t/Matrix/IO
BioPerl-1.6.901/t/Matrix/IO/masta.t
BioPerl-1.6.901/t/Matrix/IO/psm.t
BioPerl-1.6.901/t/Ontology
BioPerl-1.6.901/t/Ontology/GOterm.t
BioPerl-1.6.901/t/Ontology/GraphAdaptor.t
BioPerl-1.6.901/t/Ontology/Ontology.t
BioPerl-1.6.901/t/Ontology/OntologyEngine.t
BioPerl-1.6.901/t/Ontology/OntologyStore.t
BioPerl-1.6.901/t/Ontology/Relationship.t
BioPerl-1.6.901/t/Ontology/RelationshipType.t
BioPerl-1.6.901/t/Ontology/Term.t
BioPerl-1.6.901/t/Ontology/IO
BioPerl-1.6.901/t/Ontology/IO/go.t
BioPerl-1.6.901/t/Ontology/IO/interpro.t
BioPerl-1.6.901/t/Ontology/IO/obo.t
BioPerl-1.6.901/t/Phenotype
BioPerl-1.6.901/t/Phenotype/Correlate.t
BioPerl-1.6.901/t/Phenotype/Measure.t
BioPerl-1.6.901/t/Phenotype/MeSH.t
BioPerl-1.6.901/t/Phenotype/MiniMIMentry.t
BioPerl-1.6.901/t/Phenotype/OMIMentry.t
BioPerl-1.6.901/t/Phenotype/OMIMentryAllelicVariant.t
BioPerl-1.6.901/t/Phenotype/OMIMparser.t
BioPerl-1.6.901/t/Phenotype/Phenotype.t
BioPerl-1.6.901/t/PopGen
BioPerl-1.6.901/t/PopGen/Coalescent.t
BioPerl-1.6.901/t/PopGen/HtSNP.t
BioPerl-1.6.901/t/PopGen/MK.t
BioPerl-1.6.901/t/PopGen/PopGen.t
BioPerl-1.6.901/t/PopGen/PopGenSims.t
BioPerl-1.6.901/t/PopGen/TagHaplotype.t
BioPerl-1.6.901/t/RemoteDB
BioPerl-1.6.901/t/RemoteDB/BioFetch.t
BioPerl-1.6.901/t/RemoteDB/CUTG.t
BioPerl-1.6.901/t/RemoteDB/EMBL.t
BioPerl-1.6.901/t/RemoteDB/EntrezGene.t
BioPerl-1.6.901/t/RemoteDB/EUtilities.t
BioPerl-1.6.901/t/RemoteDB/GenBank.t
BioPerl-1.6.901/t/RemoteDB/GenPept.t
BioPerl-1.6.901/t/RemoteDB/MeSH.t
BioPerl-1.6.901/t/RemoteDB/RefSeq.t
BioPerl-1.6.901/t/RemoteDB/SeqHound.t
BioPerl-1.6.901/t/RemoteDB/SeqRead_fail.t
BioPerl-1.6.901/t/RemoteDB/SeqVersion.t
BioPerl-1.6.901/t/RemoteDB/SwissProt.t
BioPerl-1.6.901/t/RemoteDB/Taxonomy.t
BioPerl-1.6.901/t/RemoteDB/HIV
BioPerl-1.6.901/t/RemoteDB/HIV/HIV.t
BioPerl-1.6.901/t/RemoteDB/HIV/HIVAnnotProcessor.t
BioPerl-1.6.901/t/RemoteDB/HIV/HIVQuery.t
BioPerl-1.6.901/t/RemoteDB/HIV/HIVQueryHelper.t
BioPerl-1.6.901/t/RemoteDB/Query
BioPerl-1.6.901/t/RemoteDB/Query/GenBank.t
BioPerl-1.6.901/t/Restriction
BioPerl-1.6.901/t/Restriction/Analysis-refac.t
BioPerl-1.6.901/t/Restriction/Analysis.t
BioPerl-1.6.901/t/Restriction/Gel.t
BioPerl-1.6.901/t/Restriction/IO.t
BioPerl-1.6.901/t/Root
BioPerl-1.6.901/t/Root/Exception.t
BioPerl-1.6.901/t/Root/HTTPget.t
BioPerl-1.6.901/t/Root/RootI.t
BioPerl-1.6.901/t/Root/RootIO.t
BioPerl-1.6.901/t/Root/Storable.t
BioPerl-1.6.901/t/Root/Tempfile.t
BioPerl-1.6.901/t/Root/Utilities.t
BioPerl-1.6.901/t/SearchIO
BioPerl-1.6.901/t/SearchIO/axt.t
BioPerl-1.6.901/t/SearchIO/blast.t
BioPerl-1.6.901/t/SearchIO/blast_pull.t
BioPerl-1.6.901/t/SearchIO/blasttable.t
BioPerl-1.6.901/t/SearchIO/blastxml.t
BioPerl-1.6.901/t/SearchIO/CigarString.t
BioPerl-1.6.901/t/SearchIO/cross_match.t
BioPerl-1.6.901/t/SearchIO/erpin.t
BioPerl-1.6.901/t/SearchIO/exonerate.t
BioPerl-1.6.901/t/SearchIO/fasta.t
BioPerl-1.6.901/t/SearchIO/gmap_f9.t
BioPerl-1.6.901/t/SearchIO/hmmer.t
BioPerl-1.6.901/t/SearchIO/hmmer_pull.t
BioPerl-1.6.901/t/SearchIO/infernal.t
BioPerl-1.6.901/t/SearchIO/megablast.t
BioPerl-1.6.901/t/SearchIO/psl.t
BioPerl-1.6.901/t/SearchIO/rnamotif.t
BioPerl-1.6.901/t/SearchIO/SearchIO.t
BioPerl-1.6.901/t/SearchIO/sim4.t
BioPerl-1.6.901/t/SearchIO/SimilarityPair.t
BioPerl-1.6.901/t/SearchIO/Tiling.t
BioPerl-1.6.901/t/SearchIO/waba.t
BioPerl-1.6.901/t/SearchIO/wise.t
BioPerl-1.6.901/t/SearchIO/Writer
BioPerl-1.6.901/t/SearchIO/Writer/GbrowseGFF.t
BioPerl-1.6.901/t/SearchIO/Writer/HitTableWriter.t
BioPerl-1.6.901/t/SearchIO/Writer/HSPTableWriter.t
BioPerl-1.6.901/t/SearchIO/Writer/HTMLWriter.t
BioPerl-1.6.901/t/SearchIO/Writer/TextWriter.t
BioPerl-1.6.901/t/Seq
BioPerl-1.6.901/t/Seq/DBLink.t
BioPerl-1.6.901/t/Seq/EncodedSeq.t
BioPerl-1.6.901/t/Seq/LargeLocatableSeq.t
BioPerl-1.6.901/t/Seq/LargePSeq.t
BioPerl-1.6.901/t/Seq/LocatableSeq.t
BioPerl-1.6.901/t/Seq/MetaSeq.t
BioPerl-1.6.901/t/Seq/PrimaryQual.t
BioPerl-1.6.901/t/Seq/PrimarySeq.t
BioPerl-1.6.901/t/Seq/PrimedSeq.t
BioPerl-1.6.901/t/Seq/Quality.t
BioPerl-1.6.901/t/Seq/Seq.t
BioPerl-1.6.901/t/Seq/WithQuality.t
BioPerl-1.6.901/t/SeqFeature
BioPerl-1.6.901/t/SeqFeature/Clone.t
BioPerl-1.6.901/t/SeqFeature/FeatureIO.t
BioPerl-1.6.901/t/SeqFeature/Location.t
BioPerl-1.6.901/t/SeqFeature/LocationFactory.t
BioPerl-1.6.901/t/SeqFeature/Primer.t
BioPerl-1.6.901/t/SeqFeature/Range.t
BioPerl-1.6.901/t/SeqFeature/RangeI.t
BioPerl-1.6.901/t/SeqFeature/SeqAnalysisParser.t
BioPerl-1.6.901/t/SeqFeature/SeqFeatAnnotated.t
BioPerl-1.6.901/t/SeqFeature/SeqFeatCollection.t
BioPerl-1.6.901/t/SeqFeature/SeqFeature.t
BioPerl-1.6.901/t/SeqFeature/SeqFeaturePrimer.t
BioPerl-1.6.901/t/SeqFeature/Unflattener.t
BioPerl-1.6.901/t/SeqFeature/Unflattener2.t
BioPerl-1.6.901/t/SeqIO
BioPerl-1.6.901/t/SeqIO/abi.t
BioPerl-1.6.901/t/SeqIO/ace.t
BioPerl-1.6.901/t/SeqIO/agave.t
BioPerl-1.6.901/t/SeqIO/alf.t
BioPerl-1.6.901/t/SeqIO/asciitree.t
BioPerl-1.6.901/t/SeqIO/bsml.t
BioPerl-1.6.901/t/SeqIO/bsml_sax.t
BioPerl-1.6.901/t/SeqIO/chadoxml.t
BioPerl-1.6.901/t/SeqIO/chaos.t
BioPerl-1.6.901/t/SeqIO/chaosxml.t
BioPerl-1.6.901/t/SeqIO/ctf.t
BioPerl-1.6.901/t/SeqIO/embl.t
BioPerl-1.6.901/t/SeqIO/entrezgene.t
BioPerl-1.6.901/t/SeqIO/excel.t
BioPerl-1.6.901/t/SeqIO/exp.t
BioPerl-1.6.901/t/SeqIO/fasta.t
BioPerl-1.6.901/t/SeqIO/fastq.t
BioPerl-1.6.901/t/SeqIO/flybase_chadoxml.t
BioPerl-1.6.901/t/SeqIO/game.t
BioPerl-1.6.901/t/SeqIO/gbxml.t
BioPerl-1.6.901/t/SeqIO/gcg.t
BioPerl-1.6.901/t/SeqIO/genbank.t
BioPerl-1.6.901/t/SeqIO/Handler.t
BioPerl-1.6.901/t/SeqIO/interpro.t
BioPerl-1.6.901/t/SeqIO/kegg.t
BioPerl-1.6.901/t/SeqIO/largefasta.t
BioPerl-1.6.901/t/SeqIO/lasergene.t
BioPerl-1.6.901/t/SeqIO/locuslink.t
BioPerl-1.6.901/t/SeqIO/mbsout.t
BioPerl-1.6.901/t/SeqIO/metafasta.t
BioPerl-1.6.901/t/SeqIO/msout.t
BioPerl-1.6.901/t/SeqIO/MultiFile.t
BioPerl-1.6.901/t/SeqIO/Multiple_fasta.t
BioPerl-1.6.901/t/SeqIO/nexml.t
BioPerl-1.6.901/t/SeqIO/phd.t
BioPerl-1.6.901/t/SeqIO/pir.t
BioPerl-1.6.901/t/SeqIO/pln.t
BioPerl-1.6.901/t/SeqIO/qual.t
BioPerl-1.6.901/t/SeqIO/raw.t
BioPerl-1.6.901/t/SeqIO/scf.t
BioPerl-1.6.901/t/SeqIO/SeqBuilder.t
BioPerl-1.6.901/t/SeqIO/SeqIO.t
BioPerl-1.6.901/t/SeqIO/seqxml.t
BioPerl-1.6.901/t/SeqIO/Splicedseq.t
BioPerl-1.6.901/t/SeqIO/strider.t
BioPerl-1.6.901/t/SeqIO/swiss.t
BioPerl-1.6.901/t/SeqIO/tab.t
BioPerl-1.6.901/t/SeqIO/table.t
BioPerl-1.6.901/t/SeqIO/tigr.t
BioPerl-1.6.901/t/SeqIO/tigrxml.t
BioPerl-1.6.901/t/SeqIO/tinyseq.t
BioPerl-1.6.901/t/SeqIO/ztr.t
BioPerl-1.6.901/t/SeqTools
BioPerl-1.6.901/t/SeqTools/Backtranslate.t
BioPerl-1.6.901/t/SeqTools/CodonTable.t
BioPerl-1.6.901/t/SeqTools/ECnumber.t
BioPerl-1.6.901/t/SeqTools/GuessSeqFormat.t
BioPerl-1.6.901/t/SeqTools/OddCodes.t
BioPerl-1.6.901/t/SeqTools/SeqPattern.t
BioPerl-1.6.901/t/SeqTools/SeqStats.t
BioPerl-1.6.901/t/SeqTools/SeqUtils.t
BioPerl-1.6.901/t/SeqTools/SeqWords.t
BioPerl-1.6.901/t/Structure
BioPerl-1.6.901/t/Structure/IO.t
BioPerl-1.6.901/t/Structure/Structure.t
BioPerl-1.6.901/t/Tools
BioPerl-1.6.901/t/Tools/ePCR.t
BioPerl-1.6.901/t/Tools/Est2Genome.t
BioPerl-1.6.901/t/Tools/FootPrinter.t
BioPerl-1.6.901/t/Tools/Geneid.t
BioPerl-1.6.901/t/Tools/Genewise.t
BioPerl-1.6.901/t/Tools/Genomewise.t
BioPerl-1.6.901/t/Tools/Genpred.t
BioPerl-1.6.901/t/Tools/GFF.t
BioPerl-1.6.901/t/Tools/GuessSeqFormat.t
BioPerl-1.6.901/t/Tools/Hmmer.t
BioPerl-1.6.901/t/Tools/IUPAC.t
BioPerl-1.6.901/t/Tools/Lucy.t
BioPerl-1.6.901/t/Tools/Match.t
BioPerl-1.6.901/t/Tools/pICalculator.t
BioPerl-1.6.901/t/Tools/Primer3.t
BioPerl-1.6.901/t/Tools/Promoterwise.t
BioPerl-1.6.901/t/Tools/Pseudowise.t
BioPerl-1.6.901/t/Tools/QRNA.t
BioPerl-1.6.901/t/Tools/RandDistFunctions.t
BioPerl-1.6.901/t/Tools/RepeatMasker.t
BioPerl-1.6.901/t/Tools/rnamotif.t
BioPerl-1.6.901/t/Tools/Seg.t
BioPerl-1.6.901/t/Tools/Sigcleave.t
BioPerl-1.6.901/t/Tools/Signalp.t
BioPerl-1.6.901/t/Tools/Sim4.t
BioPerl-1.6.901/t/Tools/SiRNA.t
BioPerl-1.6.901/t/Tools/TandemRepeatsFinder.t
BioPerl-1.6.901/t/Tools/TargetP.t
BioPerl-1.6.901/t/Tools/Tmhmm.t
BioPerl-1.6.901/t/Tools/tRNAscanSE.t
BioPerl-1.6.901/t/Tools/Alignment
BioPerl-1.6.901/t/Tools/Alignment/Consed.t
BioPerl-1.6.901/t/Tools/Analysis
BioPerl-1.6.901/t/Tools/Analysis/DNA
BioPerl-1.6.901/t/Tools/Analysis/DNA/ESEfinder.t
BioPerl-1.6.901/t/Tools/Analysis/Protein
BioPerl-1.6.901/t/Tools/Analysis/Protein/Domcut.t
BioPerl-1.6.901/t/Tools/Analysis/Protein/ELM.t
BioPerl-1.6.901/t/Tools/Analysis/Protein/GOR4.t
BioPerl-1.6.901/t/Tools/Analysis/Protein/HNN.t
BioPerl-1.6.901/t/Tools/Analysis/Protein/Mitoprot.t
BioPerl-1.6.901/t/Tools/Analysis/Protein/NetPhos.t
BioPerl-1.6.901/t/Tools/Analysis/Protein/Scansite.t
BioPerl-1.6.901/t/Tools/Analysis/Protein/Sopma.t
BioPerl-1.6.901/t/Tools/EMBOSS
BioPerl-1.6.901/t/Tools/EMBOSS/Palindrome.t
BioPerl-1.6.901/t/Tools/EUtilities
BioPerl-1.6.901/t/Tools/EUtilities/egquery.t
BioPerl-1.6.901/t/Tools/EUtilities/einfo.t
BioPerl-1.6.901/t/Tools/EUtilities/elink_acheck.t
BioPerl-1.6.901/t/Tools/EUtilities/elink_lcheck.t
BioPerl-1.6.901/t/Tools/EUtilities/elink_llinks.t
BioPerl-1.6.901/t/Tools/EUtilities/elink_ncheck.t
BioPerl-1.6.901/t/Tools/EUtilities/elink_neighbor.t
BioPerl-1.6.901/t/Tools/EUtilities/elink_neighbor_history.t
BioPerl-1.6.901/t/Tools/EUtilities/elink_scores.t
BioPerl-1.6.901/t/Tools/EUtilities/epost.t
BioPerl-1.6.901/t/Tools/EUtilities/esearch.t
BioPerl-1.6.901/t/Tools/EUtilities/espell.t
BioPerl-1.6.901/t/Tools/EUtilities/esummary.t
BioPerl-1.6.901/t/Tools/EUtilities/EUtilParameters.t
BioPerl-1.6.901/t/Tools/Phylo
BioPerl-1.6.901/t/Tools/Phylo/Gerp.t
BioPerl-1.6.901/t/Tools/Phylo/Molphy.t
BioPerl-1.6.901/t/Tools/Phylo/PAML.t
BioPerl-1.6.901/t/Tools/Phylo/Phylip
BioPerl-1.6.901/t/Tools/Phylo/Phylip/ProtDist.t
BioPerl-1.6.901/t/Tools/Run
BioPerl-1.6.901/t/Tools/Run/Dummy.pm
BioPerl-1.6.901/t/Tools/Run/RemoteBlast.t
BioPerl-1.6.901/t/Tools/Run/RemoteBlast_rpsblast.t
BioPerl-1.6.901/t/Tools/Run/StandAloneBlast.t
BioPerl-1.6.901/t/Tools/Run/WBCommandExts.t
BioPerl-1.6.901/t/Tools/Run/WrapperBase.t
BioPerl-1.6.901/t/Tools/Run/Dummy
BioPerl-1.6.901/t/Tools/Run/Dummy/Config.pm
BioPerl-1.6.901/t/Tools/Signalp
BioPerl-1.6.901/t/Tools/Signalp/ExtendedSignalp.t
BioPerl-1.6.901/t/Tools/Spidey
BioPerl-1.6.901/t/Tools/Spidey/Spidey.t
BioPerl-1.6.901/t/Tree
BioPerl-1.6.901/t/Tree/Compatible.t
BioPerl-1.6.901/t/Tree/Node.t
BioPerl-1.6.901/t/Tree/RandomTreeFactory.t
BioPerl-1.6.901/t/Tree/Tree.t
BioPerl-1.6.901/t/Tree/TreeIO.t
BioPerl-1.6.901/t/Tree/TreeStatistics.t
BioPerl-1.6.901/t/Tree/PhyloNetwork
BioPerl-1.6.901/t/Tree/PhyloNetwork/Factory.t
BioPerl-1.6.901/t/Tree/PhyloNetwork/GraphViz.t
BioPerl-1.6.901/t/Tree/PhyloNetwork/MuVector.t
BioPerl-1.6.901/t/Tree/PhyloNetwork/PhyloNetwork.t
BioPerl-1.6.901/t/Tree/PhyloNetwork/RandomFactory.t
BioPerl-1.6.901/t/Tree/PhyloNetwork/TreeFactory.t
BioPerl-1.6.901/t/Tree/TreeIO
BioPerl-1.6.901/t/Tree/TreeIO/lintree.t
BioPerl-1.6.901/t/Tree/TreeIO/newick.t
BioPerl-1.6.901/t/Tree/TreeIO/nexml.t
BioPerl-1.6.901/t/Tree/TreeIO/nexus.t
BioPerl-1.6.901/t/Tree/TreeIO/nhx.t
BioPerl-1.6.901/t/Tree/TreeIO/phyloxml.t
BioPerl-1.6.901/t/Tree/TreeIO/svggraph.t
BioPerl-1.6.901/t/Tree/TreeIO/tabtree.t
BioPerl-1.6.901/t/Variation
BioPerl-1.6.901/t/Variation/AAChange.t
BioPerl-1.6.901/t/Variation/AAReverseMutate.t
BioPerl-1.6.901/t/Variation/Allele.t
BioPerl-1.6.901/t/Variation/DNAMutation.t
BioPerl-1.6.901/t/Variation/RNAChange.t
BioPerl-1.6.901/t/Variation/SeqDiff.t
BioPerl-1.6.901/t/Variation/SNP.t
BioPerl-1.6.901/t/Variation/Variation_IO.t

  CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz

>>> C:\Perl64-5.18\bin\perl.exe Build.PL
could not find ParserDetails.ini in C:/cpanfly-5.18/var/megalib/XML/SAX
Checking prerequisites...
  requires:
    !  DB_File is not installed
  recommends:
    *  Convert::Binary::C is not installed
    *  GraphViz is not installed
    *  PostScript::TextBlock is not installed
    *  SOAP::Lite is not installed
    *  XML::DOM::XPath is not installed

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

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

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

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

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

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

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

Do you want to run tests that require connection to servers across the internet
(likely to cause some failures)? y/n [n]   - will not run internet-requiring tests
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'BioPerl' version '1.006901'
---- Unsatisfied dependencies detected during ----
----      CJFIELDS/BioPerl-1.6.901.tar.gz     ----
    DB_File [requires]
Running Build test
  Delayed until after prerequisites
Running test for module 'DB_File'

______________________ D i s t r o P r e f s ______________________
                           DB_File.yml[0]                           
Running make for P/PM/PMQS/DB_File-1.831.tar.gz
Disabled via prefs file 'C:\cpanfly-5.18\etc\distroprefs\DB_File.yml' doc 0
  PMQS/DB_File-1.831.tar.gz
  [disabled] -- NA Disabled via prefs file 'C:\cpanfly-5.18\etc\distroprefs\DB_File.yml' doc 0
Running Build for C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz
  Has already been unwrapped into directory C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt

  CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz

Warning: Prerequisite 'DB_File => 0' for 'CJFIELDS/BioPerl-1.6.901.tar.gz' failed when processing 'PMQS/DB_File-1.831.tar.gz' with 'unwrapped => NO Disabled via prefs file 'C:\cpanfly-5.18\etc\distroprefs\DB_File.yml' doc 0'. Continuing, but chances to succeed are limited.
>>> C:\Perl64-5.18\bin\perl.exe ./Build
Building BioPerl
  CJFIELDS/BioPerl-1.6.901.tar.gz
  C:\Perl64-5.18\bin\perl.exe ./Build -- OK
Running Build test
>>> C:\Perl64-5.18\bin\perl.exe ./Build test verbose=1
Copying scripts\das\das_server.pl -> blib\script\das_server.pl
Changing sharpbang in blib\script\das_server.pl to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\das_server.pl.bak
Copying scripts\DB\flanks.PLS -> blib\script\flanks.PLS
Changing sharpbang in blib\script\flanks.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\flanks.PLS.bak
Copying scripts\seqstats\chaos_plot.PLS -> blib\script\chaos_plot.PLS
Changing sharpbang in blib\script\chaos_plot.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\chaos_plot.PLS.bak
Copying scripts\searchio\fastam9_to_table.PLS -> blib\script\fastam9_to_table.PLS
Changing sharpbang in blib\script\fastam9_to_table.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\fastam9_to_table.PLS.bak
Copying scripts\seq\extract_feature_seq.PLS -> blib\script\extract_feature_seq.PLS
Changing sharpbang in blib\script\extract_feature_seq.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\extract_feature_seq.PLS.bak
Copying scripts\biblio\biblio.PLS -> blib\script\biblio.PLS
Changing sharpbang in blib\script\biblio.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\biblio.PLS.bak
Copying scripts\Bio-DB-GFF\process_sgd.PLS -> blib\script\process_sgd.PLS
Changing sharpbang in blib\script\process_sgd.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\process_sgd.PLS.bak
Copying scripts\Bio-DB-EUtilities\einfo.PLS -> blib\script\einfo.PLS
Changing sharpbang in blib\script\einfo.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\einfo.PLS.bak
Copying scripts\popgen\heterogeneity_test.PLS -> blib\script\heterogeneity_test.PLS
Changing sharpbang in blib\script\heterogeneity_test.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\heterogeneity_test.PLS.bak
Copying scripts\utilities\download_query_genbank.PLS -> blib\script\download_query_genbank.PLS
Changing sharpbang in blib\script\download_query_genbank.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\download_query_genbank.PLS.bak
Copying scripts\seq\seqretsplit.PLS -> blib\script\seqretsplit.PLS
Changing sharpbang in blib\script\seqretsplit.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\seqretsplit.PLS.bak
Copying scripts\utilities\bp_mrtrans.PLS -> blib\script\bp_mrtrans.PLS
Changing sharpbang in blib\script\bp_mrtrans.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\bp_mrtrans.PLS.bak
Copying scripts\seq\split_seq.PLS -> blib\script\split_seq.PLS
Changing sharpbang in blib\script\split_seq.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\split_seq.PLS.bak
Copying scripts\tree\nexus2nh.PLS -> blib\script\nexus2nh.PLS
Changing sharpbang in blib\script\nexus2nh.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\nexus2nh.PLS.bak
Copying scripts\utilities\mutate.PLS -> blib\script\mutate.PLS
Changing sharpbang in blib\script\mutate.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\mutate.PLS.bak
Copying scripts\seq\seqconvert.PLS -> blib\script\seqconvert.PLS
Changing sharpbang in blib\script\seqconvert.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\seqconvert.PLS.bak
Copying scripts\Bio-DB-GFF\generate_histogram.PLS -> blib\script\generate_histogram.PLS
Changing sharpbang in blib\script\generate_histogram.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\generate_histogram.PLS.bak
Copying scripts\searchio\search2table.PLS -> blib\script\search2table.PLS
Changing sharpbang in blib\script\search2table.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\search2table.PLS.bak
Copying scripts\taxa\taxonomy2tree.PLS -> blib\script\taxonomy2tree.PLS
Changing sharpbang in blib\script\taxonomy2tree.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\taxonomy2tree.PLS.bak
Copying scripts\utilities\revtrans-motif.PLS -> blib\script\revtrans-motif.PLS
Changing sharpbang in blib\script\revtrans-motif.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\revtrans-motif.PLS.bak
Copying scripts\seq\unflatten_seq.PLS -> blib\script\unflatten_seq.PLS
Changing sharpbang in blib\script\unflatten_seq.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\unflatten_seq.PLS.bak
Copying scripts\tree\blast2tree.PLS -> blib\script\blast2tree.PLS
Changing sharpbang in blib\script\blast2tree.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\blast2tree.PLS.bak
Copying scripts\index\bp_fetch.PLS -> blib\script\bp_fetch.PLS
Changing sharpbang in blib\script\bp_fetch.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\bp_fetch.PLS.bak
Copying scripts\DB\biofetch_genbank_proxy.PLS -> blib\script\biofetch_genbank_proxy.PLS
Changing sharpbang in blib\script\biofetch_genbank_proxy.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\biofetch_genbank_proxy.PLS.bak
Copying scripts\popgen\composite_LD.PLS -> blib\script\composite_LD.PLS
Changing sharpbang in blib\script\composite_LD.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\composite_LD.PLS.bak
Copying scripts\utilities\dbsplit.PLS -> blib\script\dbsplit.PLS
Changing sharpbang in blib\script\dbsplit.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\dbsplit.PLS.bak
Copying scripts\index\bp_index.PLS -> blib\script\bp_index.PLS
Changing sharpbang in blib\script\bp_index.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\bp_index.PLS.bak
Copying scripts\utilities\search2gff.PLS -> blib\script\search2gff.PLS
Changing sharpbang in blib\script\search2gff.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\search2gff.PLS.bak
Copying scripts\seqstats\aacomp.PLS -> blib\script\aacomp.PLS
Changing sharpbang in blib\script\aacomp.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\aacomp.PLS.bak
Copying scripts\DB\bioflat_index.PLS -> blib\script\bioflat_index.PLS
Changing sharpbang in blib\script\bioflat_index.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\bioflat_index.PLS.bak
Copying scripts\utilities\mask_by_search.PLS -> blib\script\mask_by_search.PLS
Changing sharpbang in blib\script\mask_by_search.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\mask_by_search.PLS.bak
Copying scripts\Bio-DB-GFF\process_wormbase.PLS -> blib\script\process_wormbase.PLS
Changing sharpbang in blib\script\process_wormbase.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\process_wormbase.PLS.bak
Copying scripts\Bio-DB-GFF\genbank2gff3.PLS -> blib\script\genbank2gff3.PLS
Changing sharpbang in blib\script\genbank2gff3.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\genbank2gff3.PLS.bak
Copying scripts\tree\tree2pag.PLS -> blib\script\tree2pag.PLS
Changing sharpbang in blib\script\tree2pag.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\tree2pag.PLS.bak
Copying scripts\utilities\search2tribe.PLS -> blib\script\search2tribe.PLS
Changing sharpbang in blib\script\search2tribe.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\search2tribe.PLS.bak
Copying scripts\taxa\taxid4species.PLS -> blib\script\taxid4species.PLS
Changing sharpbang in blib\script\taxid4species.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\taxid4species.PLS.bak
Copying scripts\Bio-DB-SeqFeature-Store\bp_seqfeature_delete.PLS -> blib\script\bp_seqfeature_delete.PLS
Changing sharpbang in blib\script\bp_seqfeature_delete.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\bp_seqfeature_delete.PLS.bak
Copying scripts\seqstats\gccalc.PLS -> blib\script\gccalc.PLS
Changing sharpbang in blib\script\gccalc.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\gccalc.PLS.bak
Copying scripts\searchio\filter_search.PLS -> blib\script\filter_search.PLS
Changing sharpbang in blib\script\filter_search.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\filter_search.PLS.bak
Copying scripts\Bio-DB-GFF\load_gff.PLS -> blib\script\load_gff.PLS
Changing sharpbang in blib\script\load_gff.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\load_gff.PLS.bak
Copying scripts\utilities\search2alnblocks.PLS -> blib\script\search2alnblocks.PLS
Changing sharpbang in blib\script\search2alnblocks.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\search2alnblocks.PLS.bak
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:\Perl64-5.18\bin\perl.exe
Deleting blib\script\bulk_load_gff.PLS.bak
Copying scripts\Bio-DB-SeqFeature-Store\bp_seqfeature_gff3.PLS -> blib\script\bp_seqfeature_gff3.PLS
Copying scripts\taxa\query_entrez_taxa.PLS -> blib\script\query_entrez_taxa.PLS
Changing sharpbang in blib\script\query_entrez_taxa.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\query_entrez_taxa.PLS.bak
Copying scripts\searchio\parse_hmmsearch.PLS -> blib\script\parse_hmmsearch.PLS
Changing sharpbang in blib\script\parse_hmmsearch.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\parse_hmmsearch.PLS.bak
Copying scripts\Bio-DB-GFF\meta_gff.PLS -> blib\script\meta_gff.PLS
Changing sharpbang in blib\script\meta_gff.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\meta_gff.PLS.bak
Copying scripts\utilities\bp_nrdb.PLS -> blib\script\bp_nrdb.PLS
Changing sharpbang in blib\script\bp_nrdb.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\bp_nrdb.PLS.bak
Copying scripts\taxa\classify_hits_kingdom.PLS -> blib\script\classify_hits_kingdom.PLS
Changing sharpbang in blib\script\classify_hits_kingdom.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\classify_hits_kingdom.PLS.bak
Copying scripts\utilities\remote_blast.PLS -> blib\script\remote_blast.PLS
Changing sharpbang in blib\script\remote_blast.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\remote_blast.PLS.bak
Copying scripts\seq\translate_seq.PLS -> blib\script\translate_seq.PLS
Changing sharpbang in blib\script\translate_seq.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\translate_seq.PLS.bak
Copying scripts\Bio-DB-GFF\fast_load_gff.PLS -> blib\script\fast_load_gff.PLS
Changing sharpbang in blib\script\fast_load_gff.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\fast_load_gff.PLS.bak
Copying scripts\Bio-DB-SeqFeature-Store\bp_seqfeature_load.PLS -> blib\script\bp_seqfeature_load.PLS
Changing sharpbang in blib\script\bp_seqfeature_load.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\bp_seqfeature_load.PLS.bak
Copying scripts\seqstats\oligo_count.PLS -> blib\script\oligo_count.PLS
Changing sharpbang in blib\script\oligo_count.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\oligo_count.PLS.bak
Copying scripts\utilities\bp_sreformat.PLS -> blib\script\bp_sreformat.PLS
Changing sharpbang in blib\script\bp_sreformat.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\bp_sreformat.PLS.bak
Copying scripts\index\bp_seqret.PLS -> blib\script\bp_seqret.PLS
Changing sharpbang in blib\script\bp_seqret.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\bp_seqret.PLS.bak
Copying scripts\DB\biogetseq.PLS -> blib\script\biogetseq.PLS
Changing sharpbang in blib\script\biogetseq.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\biogetseq.PLS.bak
Copying scripts\Bio-DB-GFF\genbank2gff.PLS -> blib\script\genbank2gff.PLS
Changing sharpbang in blib\script\genbank2gff.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\genbank2gff.PLS.bak
Copying scripts\utilities\bp_netinstall.PLS -> blib\script\bp_netinstall.PLS
Changing sharpbang in blib\script\bp_netinstall.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\bp_netinstall.PLS.bak
Copying scripts\utilities\pairwise_kaks.PLS -> blib\script\pairwise_kaks.PLS
Changing sharpbang in blib\script\pairwise_kaks.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\pairwise_kaks.PLS.bak
Copying scripts\utilities\seq_length.PLS -> blib\script\seq_length.PLS
Changing sharpbang in blib\script\seq_length.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\seq_length.PLS.bak
Copying scripts\seq\make_mrna_protein.PLS -> blib\script\make_mrna_protein.PLS
Changing sharpbang in blib\script\make_mrna_protein.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\make_mrna_protein.PLS.bak
Copying scripts\DB-HIV\hivq.PLS -> blib\script\hivq.PLS
Changing sharpbang in blib\script\hivq.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\hivq.PLS.bak
Copying scripts\utilities\search2BSML.PLS -> blib\script\search2BSML.PLS
Changing sharpbang in blib\script\search2BSML.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\search2BSML.PLS.bak
Copying scripts\searchio\hmmer_to_table.PLS -> blib\script\hmmer_to_table.PLS
Changing sharpbang in blib\script\hmmer_to_table.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\hmmer_to_table.PLS.bak
Copying scripts\Bio-DB-GFF\process_gadfly.PLS -> blib\script\process_gadfly.PLS
Changing sharpbang in blib\script\process_gadfly.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\process_gadfly.PLS.bak
Copying scripts\taxa\local_taxonomydb_query.PLS -> blib\script\local_taxonomydb_query.PLS
Changing sharpbang in blib\script\local_taxonomydb_query.PLS to C:\Perl64-5.18\bin\perl.exe
Deleting blib\script\local_taxonomydb_query.PLS.bak
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Align/AlignStats.t ......................... 
1..45
ok 1 - use Bio::Align::DNAStatistics;
ok 2 - use Bio::Align::ProteinStatistics;
ok 3 - use Bio::AlignIO;
ok 4 - An object of class 'Bio::SimpleAlign' 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 - An object of class 'Bio::SimpleAlign' 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 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 38 - An object of class 'Bio::Matrix::PhylipDist' isa 'Bio::Matrix::PhylipDist'
ok 39
ok 40
ok 41
ok 42 - An object of class 'Bio::Seq' isa 'Bio::PrimarySeqI'
ok 43
ok 44 - Warn if seqs don't overlap
ok 45
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Align/AlignUtil.t .......................... 
1..33
ok 1 - use Bio::Align::Utilities;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::SeqIO;
ok 4 - An object of class 'Bio::SimpleAlign' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Align/Graphics.t ........................... 
1..41
ok 1 - use Bio::Align::Graphics;
ok 2 - require Bio::Align::Graphics;
ok 3 - Bio::Align::Graphics->can(...)
ok 4 - input is defined
ok 5 - AlignIO object is defined
ok 6 - An object of class 'Bio::AlignIO::clustalw' isa 'Bio::AlignIO'
ok 7 - alignment is there and defined
ok 8 - all starts are present
ok 9 - all ends are present
ok 10 - all colors are present
ok 11 - first end is further than first start
ok 12 - second end is further than second start
ok 13 - third end is further than third start
ok 14 - domain labels are present
ok 15 - domain starts are present
ok 16 - domain ends are present
ok 17 - domain colors are present
ok 18 - label - first end is further than first start
ok 19 - label - second end is further than second start
ok 20 - label - third end is further than third start
ok 21 - first label start is within domain range
ok 22 - second label start is within domain range
ok 23 - third label start is within domain range
ok 24 - first label end is within domain range
ok 25 - second label end is within domain range
ok 26 - third label end is within domain range
ok 27 - individual labels work
ok 28 - An object of class 'Bio::Align::Graphics' isa 'Bio::Align::Graphics'
ok 29 - new object is defined
ok 30 -   pad_bottom is right
ok 31 -   default pad_top is right
ok 32 -   start point loaded
ok 33 -   end point loaded
ok 34 -   color of domain loaded
ok 35 -   domain labels loaded
ok 36 -   label starts loaded
ok 37 -   label ends loaded
ok 38 -   label colors loaded
ok 39 -   labels loaded
ok 40 -   output file is png
ok 41 -   wrapping length is not zero
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Align/SimpleAlign.t ........................ 
1..199
ok 1 - use Bio::SimpleAlign;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::SeqFeature::Generic;
ok 4 - use Bio::Location::Simple;
ok 5 - use Bio::Location::Split;
ok 6 - An object of class 'Bio::AlignIO::pfam' isa 'Bio::AlignIO'
ok 7 - pfam input test
ok 8 - match_line
ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 10 - num_sequences
ok 11 - num_sequences
ok 12 - select_noncont
ok 13 - select_noncont
ok 14 - num_sequences
ok 15 - select_noncont
ok 16 - select_noncont
ok 17 - each_seq
ok 18 - get_nse
ok 19 - id
ok 20 - num_gaps
ok 21 - each_alphabetically
ok 22 - column_from_residue_number
ok 23 - display_name get/set
ok 24 - display_name get
ok 25 - consensus_string
ok 26 - consensus_string
ok 27 - consensus_string
ok 28
ok 29 - each_seq_with_id
ok 30 - is_flush
ok 31 - id get/set
ok 32 - length
ok 33 - num_residues
ok 34 - num_sequences
ok 35 - overall_percentage_identity
ok 36 - overall_percentage_identity (align)
ok 37 - overall_percentage_identity (short)
ok 38 - overall_percentage_identity (long)
ok 39 - average_percentage_identity
ok 40
ok 41 - set_displayname_count
ok 42
ok 43 - set_displayname_flat
ok 44
ok 45 - set_displayname_normal
ok 46
ok 47
ok 48 - uppercase, map_chars
ok 49 - match_line
ok 50 - remove_seqs
ok 51 - remove_seqs
ok 52 - add_seq
ok 53 - add_seq
ok 54 - get_seq_by_pos
ok 55 - get_seq_by_pos
ok 56
ok 57
ok 58
ok 59 - purge
ok 60 - purge
ok 61 - IO::String consensus_iupac
ok 62 - IO::String write_aln normal
ok 63 - IO::String write_aln slice
ok 64 - IO::String write_aln slice
ok 65 - IO::String write_aln slice
ok 66 - IO::String write_aln slice
ok 67 - IO::String write_aln slice
ok 68
ok 69 - remove_columns by position
ok 70 - remove_columns by position (wrong order)
ok 71 - cigar_line
ok 72 - cigar_line
ok 73 - cigar_line
ok 74 - cigar_line
ok 75 - sort_alphabetically - before
ok 76
ok 77 - sort_alphabetically - after
ok 78 - remove_gaps
ok 79 - remove_gaps all_gaps_only
ok 80 - set_new_reference
ok 81 - set_new_reference
ok 82 - uniq_seq
ok 83 - bug 2099
ok 84 - bug 2099
ok 85 - bug 2793
ok 86 - bug 2793
ok 87 - bug 2793
ok 88 - bug 2793
ok 89 - Bad sequence, bad!
ok 90 - added 3 seqs
ok 91 - first 2 features added
ok 92 - 3rd feature added
not ok 93 # TODO This should pass but dies; see bug 2842

#   Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 1.  
# Overriding value [0] with value 1 for Bio::LocatableSeq::end().
# ?
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:195
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1146
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 94 - slice 1 len
ok 95 - correct masked seq
ok 96 - correct masked seq
ok 97 - correct masked seq
not ok 98 # TODO This should pass but dies; see bug 2842

#   Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 3.  
# Overriding value [2] with value 3 for Bio::LocatableSeq::end().
# ?
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:195
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1146
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 99 - slice 2 len
ok 100 - correct masked seq
ok 101 - correct masked seq
ok 102 - correct masked seq
not ok 103 # TODO This should pass but dies; see bug 2842

#   Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 3.  
# Overriding value [1] with value 3 for Bio::LocatableSeq::end().
# ??
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:195
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1146
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 104 - slice 3 len
ok 105 - correct masked seq
ok 106 - correct masked seq
ok 107 - correct masked seq
not ok 108 # TODO This should pass but dies; see bug 2842

#   Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 6.  
# Overriding value [4] with value 6 for Bio::LocatableSeq::end().
# ??
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:195
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1146
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 109 - slice 4 len
ok 110 - correct masked seq
ok 111 - correct masked seq
ok 112 - correct masked seq
ok 113 - initial display id ok
ok 114 - safe display id ok
ok 115 - restored display id ok
ok 116 - sort by list ok
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123 - BIC:GGATCCATT[C/C]CTACT
ok 124 - BIC:GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT
ok 125 - BIC:G[G/C]ATCCATT[C/G]CTACT
ok 126 - BIC:GGATCCATT[C/G]CTACT
ok 127 - BIC:GGATCCATT[C/G]CTAC[T/A]
ok 128 - BIC:GGATCCATT[C/G]CTA[C/G][T/A]
ok 129 - BIC:GGATCCATT[C/G]CTACT
ok 130 - BIC:GGATCCATT{C.C}CTACT
ok 131 - BIC:GGAT{C.-}{C.-}ATT{C.C}CT{A.C}CT
ok 132 - BIC:G{G.C}ATCCATT{C.G}CTACT
ok 133 - BIC:GGATCCATT{C.G}CTACT
ok 134 - BIC:GGATCCATT{C.G}CTAC{T.A}
ok 135 - BIC:GGATCCATT{C.G}CTA{C.G}{T.A}
ok 136 - BIC:GGATCCATT{C.G}CTACT
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok 176
ok 177
ok 178
ok 179
ok 180
ok 181
ok 182
ok 183
ok 184
ok 185
ok 186
ok 187
ok 188
ok 189
ok 190
ok 191
ok 192
ok 193
ok 194 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 195 - consensus string looks ok
ok 196 - looks like correct unmasked alignment (from clustalw)
ok 197 - looks like correct masked alignment (from clustalw)
ok 198
ok 199 - align after looks ok
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/AlignIO.t .......................... 
1..28
ok 1 - use Bio::AlignIO;
ok 2 - input filehandle method test : nexus
ok 3 - input filehandle method test : mase
ok 4 - input filehandle method test : metafasta
ok 5 - input filehandle method test : pfam
ok 6 - input filehandle method test : stockholm
ok 7 - input filehandle method test : xmfa
ok 8 - input filehandle method test : msf
ok 9 - input filehandle method test : arp
ok 10 - input filehandle method test : prodom
ok 11 - input filehandle method test : clustalw
ok 12 - input filehandle method test : po
ok 13 - input filehandle method test : fasta
ok 14 - input filehandle method test : psi
ok 15 - input filehandle method test : phylip
ok 16 - input filehandle method test : selex
ok 17 - filehandle output test : nexus
ok 18 - filehandle output test : metafasta
ok 19 - filehandle output test : pfam
ok 20 - filehandle output test : stockholm
ok 21 - filehandle output test : xmfa
ok 22 - filehandle output test : msf
ok 23 - filehandle output test : clustalw
ok 24 - filehandle output test : po
ok 25 - filehandle output test : fasta
ok 26 - filehandle output test : psi
ok 27 - filehandle output test : phylip
ok 28 - filehandle output test : selex
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/arp.t .............................. 
1..48
ok 1 - use Bio::AlignIO::arp;
ok 2 - An object of class 'Bio::AlignIO::arp' isa 'Bio::AlignIO'
ok 3 - An object of class 'Bio::SimpleAlign' 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 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI'
ok 10 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI'
ok 11
ok 12
ok 13
ok 14
ok 15 - An object of class 'Bio::AlignIO::arp' isa 'Bio::AlignIO'
ok 16 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 17 - ARP get_nse()
ok 18 - ARP num_sequences()
ok 19 - ARP id()
ok 20 - ARP description()
ok 21 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI'
ok 22 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI'
ok 23
ok 24
ok 25
ok 26
ok 27 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 28 - ARP get_nse()
ok 29 - ARP num_sequences()
ok 30 - ARP id()
ok 31 - ARP description()
ok 32 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI'
ok 33 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI'
ok 34
ok 35
ok 36
ok 37
ok 38 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 39 - ARP get_nse()
ok 40 - ARP num_sequences()
ok 41 - ARP id()
ok 42 - ARP description()
ok 43 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI'
ok 44 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI'
ok 45
ok 46
ok 47
ok 48
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/bl2seq.t ........................... 
1..3
ok 1 - use Bio::AlignIO::bl2seq;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3 - BLAST bl2seq format test
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/clustalw.t ......................... 
1..6
ok 1 - use Bio::AlignIO::clustalw;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3 - clustalw consensus_string test
ok 4 - clustalw (.aln) output test
ok 5 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 6 - clustalw (.aln) input test
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/emboss.t ........................... 
1..37
ok 1 - use Bio::AlignIO::emboss;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 11
ok 12
ok 13
ok 14 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 15
ok 16
ok 17
ok 18 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 19
ok 20
ok 21 - An object of class 'Bio::SimpleAlign' 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 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 33
ok 34
ok 35
ok 36
ok 37
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/fasta.t ............................ 
1..10
ok 1 - use Bio::AlignIO::fasta;
ok 2 - An object of class 'Bio::SimpleAlign' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/largemultifasta.t .................. 
1..7
ok 1 - use Bio::AlignIO::largemultifasta;
ok 2 - An object of class 'Bio::SimpleAlign' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/maf.t .............................. 
1..11
ok 1 - use Bio::AlignIO::maf;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3 - maf input test
ok 4
ok 5 - An object of class 'Bio::SimpleAlign' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/mase.t ............................. 
1..3
ok 1 - use Bio::AlignIO::mase;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3 - mase input test 
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/mega.t ............................. 
1..6
ok 1 - use Bio::AlignIO::mega;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3
ok 4
ok 5
ok 6 - mega output test
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/meme.t ............................. 
1..14
ok 1 - use Bio::AlignIO::meme;
ok 2 - An object of class 'Bio::AlignIO::meme' isa 'Bio::AlignIO'
ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 4
ok 5
ok 6
ok 7
ok 8 - An object of class 'Bio::AlignIO::meme' isa 'Bio::AlignIO'
ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 10
ok 11
ok 12
ok 13
ok 14
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/metafasta.t ........................ 
1..4
ok 1 - use Bio::AlignIO::metafasta;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3 - consensus_string on metafasta
ok 4 - symbol_chars() using metafasta
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/msf.t .............................. 
1..4
ok 1 - use Bio::AlignIO::msf;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3 - msf input test
ok 4 - msf output test
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
# WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support
t/AlignIO/nexml.t ............................ 
1..125
ok 1 - use Bio::AlignIO::nexml;
ok 2 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 3 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 4 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 5 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 6 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 7 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 8 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 9 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 10 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 11 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 12 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 13 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 14 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 15 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 16 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 17 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 18 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 19 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 20 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 21 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 22 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 23 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 24 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 25 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 26 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 27 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 28 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 29 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 30 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 31 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 32 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 33 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 34 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 35 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 36 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 37 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 38 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 39 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 40 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 41 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 42 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 43 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 44 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 45 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 46 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 47 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 48 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 49 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 50 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 51 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 52 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 53 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 54 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 55 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 56 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 57 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 58 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 59 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 60 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 61 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 62 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 63 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 64 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 65 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 66 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 67 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 68 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 69 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 70 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 71 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 72 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 73 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 74 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 75 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 76 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 77 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 78 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 79 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 80 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 81 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 82 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 83 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 84 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 85 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 86 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 87 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 88 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 89 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 90 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 91 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 92 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 93 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 94 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 95 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 96 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 97 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 98 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 99 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 100 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 101 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 102 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 103 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 104 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 105 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 106 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 107 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 108 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 109 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 110 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 111 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 112 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 113 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 114 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 115 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 116 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 117 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 118 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 119 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 120 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 121 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 122 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 123 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 124 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok 125 # skip NeXML parsing for NeXML v0.9 is currently very experimental support
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/nexus.t ............................ 
1..43
ok 1 - use Bio::AlignIO::nexus;
ok 2 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 4
ok 5 - nexus output test
ok 6 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 8 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 10 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 11 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 12 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 13 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 14 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 15 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 16 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 17 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 18 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 19 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 20 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 21 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 22 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 23 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 24 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 25 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 26 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 27 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 28 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 29 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 30 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 31 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 32 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 33 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 34 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 35 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 36 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 37 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 38 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 39 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 40 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 41 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 42 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 43 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/pfam.t ............................. 
1..5
ok 1 - use Bio::AlignIO::pfam;
ok 2 - An object of class 'Bio::AlignIO::pfam' isa 'Bio::AlignIO'
ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 4
ok 5 -  pfam output test
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/phylip.t ........................... 
1..16
ok 1 - use Bio::AlignIO::phylip;
ok 2 - An object of class 'Bio::AlignIO::phylip' isa 'Bio::AlignIO'
ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 4
ok 5 - phylip output test
ok 6
ok 7
ok 8
not ok 9 # TODO problems with default strand, length?

#   Failed (TODO) test at t/AlignIO/phylip.t line 44.
#          got: undef
#     expected: '0'
not ok 10 # TODO problems with default strand, length?

#   Failed (TODO) test at t/AlignIO/phylip.t line 45.
#          got: '50'
#     expected: '47'
ok 11 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 12
ok 13 - An object of class 'Bio::AlignIO::phylip' isa 'Bio::AlignIO'
ok 14 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 15
ok 16
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/po.t ............................... 
1..11
ok 1 - use Bio::AlignIO::po;
ok 2 - An object of class 'Bio::AlignIO::po' isa 'Bio::AlignIO'
ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 4
ok 5 - An object of class 'Bio::AlignIO::clustalw' isa 'Bio::AlignIO'
ok 6 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 7 - po output test
ok 8 - An object of class 'Bio::AlignIO::po' isa 'Bio::AlignIO'
ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 10
ok 11
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/prodom.t ........................... 
1..3
ok 1 - use Bio::AlignIO::prodom;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3 - prodom input test 
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/psi.t .............................. 
1..5
ok 1 - use Bio::AlignIO::psi;
ok 2 - An object of class 'Bio::AlignIO::psi' isa 'Bio::AlignIO'
ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 4
ok 5
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/selex.t ............................ 
1..4
ok 1 - use Bio::AlignIO::selex;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3 - selex format test 
ok 4 - selex output test
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/stockholm.t ........................ 
1..84
ok 1 - use Bio::AlignIO::stockholm;
ok 2 - An object of class 'Bio::AlignIO::stockholm' isa 'Bio::AlignIO'
ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment'
ok 10 - Stockholm annotation
ok 11 - Stockholm annotation
ok 12 - stockholm output test
ok 13 - An object of class 'Bio::SimpleAlign' 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 - An object of class 'Bio::Seq::Meta' isa 'Bio::Seq::MetaI'
ok 26 - Rfam meta data
ok 27 - Rfam meta data
ok 28
ok 29 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35 - An object of class 'Bio::Seq::Meta' isa 'Bio::Seq::MetaI'
ok 36 - Rfam meta data
ok 37 - Rfam meta data
ok 38 - An object of class 'Bio::AlignIO::stockholm' isa 'Bio::AlignIO'
ok 39
ok 40 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 41
ok 42
ok 43
ok 44
ok 45 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue'
ok 46 - Pfam annotation
ok 47
ok 48 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 49
ok 50
ok 51
ok 52
ok 53 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59 - An object of class 'Bio::Seq::Meta' isa 'Bio::Seq::MetaI'
ok 60 - Pfam aln meta data
ok 61 - Pfam aln meta data
ok 62 - Pfam aln meta data
ok 63 - Pfam aln meta data
ok 64 - Pfam aln meta data
ok 65 - Pfam aln meta data
ok 66 - Pfam seq meta data
ok 67 - Pfam seq meta data
ok 68 - Pfam seq meta data
ok 69 - Pfam seq meta data
ok 70
ok 71 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeatureI'
ok 72 - An object of class 'Bio::Seq::Meta' isa 'Bio::Seq::Meta'
ok 73 - An object of class 'Bio::Annotation::Target' isa 'Bio::AnnotationI'
ok 74 - An object of class 'Bio::Annotation::Target' isa 'Bio::Annotation::DBLink'
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/xmfa.t ............................. 
1..30
ok 1 - use Bio::AlignIO::xmfa;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3 - xmfa input test 
ok 4 - xmfa input test for start
ok 5 - xmfa input test for end
ok 6 - xmfa strand test
ok 7 - xmfa input test for id
ok 8 - xmfa input test for id
ok 9 - xmfa input test 
ok 10 - xmfa input test for start
ok 11 - xmfa input test for end
ok 12 - xmfa strand test
ok 13 - xmfa input test for id
ok 14 - xmfa input test for id
ok 15 - xmfa input test 
ok 16 - xmfa input test for start
ok 17 - xmfa input test for end
ok 18 - xmfa strand test
ok 19 - xmfa input test for id
ok 20 - xmfa input test for id
ok 21 - xmfa alignment score
ok 22 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 23 - xmfa input test 
ok 24 - xmfa strand
ok 25 - xmfa input test for description
ok 26 - xmfa input test for id
ok 27 - xmfa input test for end
ok 28 - xmfa input test for end
ok 29 - xmfa alignment score
ok 30 - xmfa output test
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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 - An object of class 'Bio::Symbol::Alphabet' isa 'Bio::Symbol::Alphabet'
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11 - An object of class 'Bio::Symbol::DNAAlphabet' 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 - An object of class 'Bio::Symbol::ProteinAlphabet' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Annotation/Annotation.t .................... 
1..159
ok 1 - use Bio::Annotation::Collection;
ok 2 - use Bio::Annotation::DBLink;
ok 3 - use Bio::Annotation::Comment;
ok 4 - use Bio::Annotation::Reference;
ok 5 - use Bio::Annotation::SimpleValue;
ok 6 - use Bio::Annotation::Target;
ok 7 - use Bio::Annotation::AnnotationFactory;
ok 8 - use Bio::Annotation::StructuredValue;
ok 9 - use Bio::Annotation::TagTree;
ok 10 - use Bio::Annotation::Tree;
ok 11 - use Bio::Seq;
ok 12 - use Bio::SimpleAlign;
ok 13 - use Bio::Cluster::UniGene;
ok 14 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::AnnotationI'
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21 - An object of class 'Bio::Annotation::DBLink' isa 'Bio::AnnotationI'
ok 22
ok 23
ok 24
ok 25 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI'
ok 26
ok 27
ok 28 - An object of class 'Bio::Annotation::Target' isa 'Bio::AnnotationI'
ok 29
ok 30 - An object of class 'Bio::Annotation::Reference' 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 - An object of class 'Bio::Annotation::StructuredValue' 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 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI'
ok 69
ok 70
ok 71
ok 72
ok 73 - An object of class 'Bio::Annotation::StructuredValue' isa 'Bio::Annotation::StructuredValue'
ok 74
ok 75
ok 76
ok 77
ok 78 - use Bio::Annotation::OntologyTerm;
ok 79 - An object of class 'Bio::Ontology::Term' isa 'Bio::Ontology::Term'
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85 - An object of class 'Bio::Seq' 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 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::AnnotatableI'
ok 91 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::AnnotatableI'
ok 92 - An object of class 'Bio::Annotation::AnnotationFactory' isa 'Bio::Factory::ObjectFactoryI'
ok 93 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue'
ok 94
ok 95 - An object of class 'Bio::Annotation::OntologyTerm' isa 'Bio::Annotation::OntologyTerm'
ok 96 - Bio::Annotation::Comment
ok 97 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment'
ok 98
ok 99 - Bio::Annotation::Comment
ok 100 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment'
ok 101 - Bio::Annotation::Comment
ok 102 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment'
ok 103
ok 104 - An object of class 'Bio::Annotation::Target' isa 'Bio::Annotation::Target'
ok 105
ok 106
ok 107 - An object of class 'Bio::Annotation::Tree' isa 'Bio::AnnotationI'
ok 108 - tree_id()
ok 109 - tagname()
ok 110 - An object of class 'Bio::SimpleAlign' isa 'Bio::AnnotatableI'
ok 111
ok 112 - add tree to AlignI
ok 113 - get seq from node id
ok 114
ok 115 - An object of class 'Bio::Annotation::Tree' isa 'Bio::Annotation::Tree'
ok 116 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI'
ok 117 - default itext
ok 118 - roundtrip
ok 119 - itext
ok 120 - spxr
ok 121 - indent
ok 122 - xml
ok 123 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI'
ok 124
ok 125 - child changes
ok 126 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI'
ok 127
ok 128 - child changes
ok 129 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI'
ok 130
ok 131 - child changes
ok 132 - child changes in parent node
ok 133 - no tags
ok 134 - before Stag node
ok 135 - after Stag node
ok 136 - both stag nodes
ok 137 - different instances
ok 138 - before TagTree
ok 139 - after TagTree
ok 140 - both stag nodes
ok 141 - different instances
ok 142 - before TagTree
ok 143 - after TagTree
ok 144 - stag nodes
ok 145 - same instance
ok 146 - before TagTree
ok 147 - after TagTree
ok 148 - stag nodes
ok 149 - different instance
ok 150 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI'
ok 151 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI'
ok 152 - child changes
ok 153 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI'
ok 154 - child changes
ok 155 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI'
ok 156 - child changes
ok 157
ok 158
ok 159 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::Annotation::TagTree'
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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 (you may need to install the DB_File module) (@INC contains: . C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt\blib\lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt\blib\arch C:/cpanfly-5.18/var/cpan/build/BioPerl-1.6.901-pnEgJt C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt C:\cpanfly-5.18\var\megalib C:/cpanfly-5.18/var/megalib C:/Perl64-5.18/site/lib C:/Perl64-5.18/lib) at Bio/SeqFeature/Collection.pm line 146.
BEGIN failed--compilation aborted at Bio/SeqFeature/Collection.pm line 146.
Compilation failed in require at Bio/Assembly/Singlet.pm line 91.
BEGIN failed--compilation aborted at Bio/Assembly/Singlet.pm line 91.
Compilation failed in require at Bio\Assembly\IO\tigr.pm line 237.
BEGIN failed--compilation aborted at Bio\Assembly\IO\tigr.pm line 237.
Compilation failed in require at Bio/Root/Root.pm line 543.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545
STACK: Bio::Assembly::IO::_load_format_module Bio/Assembly/IO.pm:296
STACK: Bio::Assembly::IO::new Bio/Assembly/IO.pm:138
STACK: t/Assembly/ContigSpectrum.t:12
-----------------------------------------------------------


#   Failed test 'undef isa 'Bio::Assembly::IO''
#   at t/Assembly/ContigSpectrum.t line 16.
#     undef isn't defined
Can't call method "next_assembly" on an undefined value at t/Assembly/ContigSpectrum.t line 17.
# Looks like you planned 236 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..236
ok 1 - use Bio::Assembly::IO;
ok 2 - use Bio::Assembly::Tools::ContigSpectrum;
not ok 3 - undef isa 'Bio::Assembly::IO'
Dubious, test returned 2 (wstat 512, 0x200)
Failed 234/236 subtests 
t/Assembly/IO/bowtie.t ....................... skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Assembly/IO/sam.t .......................... skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Assembly/core.t ............................ skipped: The optional module DB_File (or dependencies thereof) was not installed
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Biblio/Biblio.t ............................ 
1..24
ok 1 - use Bio::Biblio;
ok 2 - use Bio::Biblio::IO;
ok 3 # skip The optional module SOAP::Lite (or dependencies thereof) was not installed
ok 4
ok 5 - citation 1
ok 6 - citation 2
ok 7 - citation 3
ok 8 - in callback
ok 9 - in callback
ok 10 - in callback
ok 11 - calling callback
ok 12 - citation 1
ok 13 - citation 2
ok 14 - citation 1
ok 15 - citation 2
ok 16
ok 17 - citation 1
ok 18 - citation 2
ok 19 - citation 3
ok 20 - citation 4
ok 21 - filehandle test
ok 22 - filehandle test
ok 23 - filehandle test
ok 24 - filehandle test
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::Cluster::UniGeneI'
ok 12 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::Cluster::UniGeneI'
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/ClusterIO/unigene.t ........................ 
1..73
ok 1 - use Bio::ClusterIO;
ok 2 - new Bio::ClusterIO object defined
ok 3
ok 4 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::Cluster::UniGeneI'
ok 5 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::ClusterI'
ok 6 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::IdentifiableI'
ok 7 - An object of class 'Bio::Cluster::UniGene' 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 - An object of class 'Bio::Seq::RichSeq' 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 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::PrimarySeqI'
ok 67
ok 68 - next cluster
ok 69
ok 70
ok 71
ok 72
ok 73
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Coordinate/CoordinateBoundaryTest.t ........ 
1..174
ok 1 - use Bio::Location::Simple;
ok 2 - use Bio::Coordinate::Pair;
ok 3
ok 4 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple'
ok 5
ok 6 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple'
ok 7
ok 8 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple'
ok 9
ok 10 - An object of class 'Bio::Coordinate::Pair' isa 'Bio::Coordinate::Pair'
ok 11
ok 12 - An object of class 'Bio::Coordinate::Pair' isa 'Bio::Coordinate::Pair'
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32 - An object of class 'Bio::Location::Simple' isa 'Bio::LocationI'
ok 33
ok 34 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
ok 35
ok 36 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50 - An object of class 'Bio::Location::Simple' isa 'Bio::LocationI'
ok 51
ok 52 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
ok 53
ok 54 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68 - An object of class 'Bio::Location::Simple' isa 'Bio::LocationI'
ok 69
ok 70 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
ok 71
ok 72 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88 - An object of class 'Bio::Location::Simple' isa 'Bio::LocationI'
ok 89
ok 90 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
ok 91
ok 92 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple'
ok 109
ok 110 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple'
ok 111
ok 112 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple'
ok 113
ok 114 - An object of class 'Bio::Coordinate::Pair' isa 'Bio::Coordinate::Pair'
ok 115
ok 116 - An object of class 'Bio::Coordinate::Pair' isa 'Bio::Coordinate::Pair'
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
ok 133
ok 134 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
ok 143
ok 144 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
ok 153
ok 154 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
ok 165
ok 166 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
ok 15 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Location::SplitLocationI'
ok 16
ok 17
ok 18
ok 19 - An object of class 'Bio::Coordinate::Result::Match' isa 'Bio::LocationI'
ok 20 - An object of class 'Bio::Coordinate::Result::Match' 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 - An object of class 'Bio::Coordinate::Result::Gap' isa 'Bio::Coordinate::Result::Gap'
ok 38 - An object of class 'Bio::Coordinate::Result::Gap' 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 - An object of class 'Bio::Coordinate::Result::Match' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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 - An object of class 'Bio::Coordinate::Result::Match' 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 - An object of class 'Bio::Coordinate::Result::Match' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Draw/Pictogram.t ........................... 
1..6
ok 1 - use Bio::Draw::Pictogram;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::Matrix::PSM::IO;
ok 4 - An object of class 'Bio::Draw::Pictogram' isa 'Bio::Draw::Pictogram'
ok 5
ok 6
ok
t/LiveSeq/Chain.t ............................ 
1..45
ok 1 - use Bio::LiveSeq::Chain;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/LiveSeq/Mutator.t .......................... 
1..24
ok 1 - use Bio::LiveSeq::Mutator;
ok 2 - use Bio::LiveSeq::IO::BioPerl;
ok 3 - use Bio::Variation::IO;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok
t/LocalDB/BioDBGFF.t ......................... skipped: Not compatible with your Operating System
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/LocalDB/DBFasta.t .......................... 
1..17
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8 - bug 3126
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17 - threw Regexp ((?^:FASTA header doesn't match))
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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 - An object of class 'Bio::Seq::PrimaryQual::Qual' 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 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual'
ok 26
ok 27
ok 28 - An object of class 'Bio::Seq::PrimaryQual' isa 'Bio::Seq::PrimaryQual'
ok 29
ok 30
ok 31
ok 32 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual'
ok 33
ok 34 - An object of class 'Bio::Seq::PrimaryQual::Qual' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/LocalDB/Index/Blast.t ...................... 
1..26
ok 1 - use Cwd;
ok 2 - use Bio::SearchIO;
ok 3 - use Bio::Index::Blast;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29

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

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

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

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

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

---------------------------------------------------
t/LocalDB/Index/BlastTable.t ................. 
1..27
ok 1 - use Cwd;
ok 2 - use Bio::SearchIO;
ok 3 - use Bio::Index::BlastTable;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok
t/LocalDB/Index/Index.t ...................... skipped: The optional module DB_File (or dependencies thereof) was not installed
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29

#   Failed test 'use Bio::DB::SeqFeature::Store::GFF3Loader;'
#   in t/LocalDB/SeqFeature.t at line 16.
#     Tried to use 'Bio::DB::SeqFeature::Store::GFF3Loader'.
#     Error:  Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: . .. ./t/lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt\blib\lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt\blib\arch C:/cpanfly-5.18/var/cpan/build/BioPerl-1.6.901-pnEgJt C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt C:\cpanfly-5.18\var\megalib C:/cpanfly-5.18/var/megalib C:/Perl64-5.18/site/lib C:/Perl64-5.18/lib) at Bio/DB/SeqFeature/Store/LoadHelper.pm line 38.
# BEGIN failed--compilation aborted at t/LocalDB/SeqFeature.t line 16.
# Compilation failed in require at Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72.
# Compilation failed in require at (eval 116) line 2.
# BEGIN failed--compilation aborted at (eval 116) line 2.
# Looks like you planned 116 tests but ran 1 extra.
# Looks like you failed 1 test of 117 run.
t/LocalDB/SeqFeature.t ....................... 
1..116
ok 1 - use Bio::SeqFeature::Generic;
ok 2 - use Bio::DB::SeqFeature::Store;
not ok 3 - use Bio::DB::SeqFeature::Store::GFF3Loader;
ok 4 - use Bio::Root::IO;
ok 5 - use Bio::DB::Fasta;
ok 6 - use File::Copy;
ok 7 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 8 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 9 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 10 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 11 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 12 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 13 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 14 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 15 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 16 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 17 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 18 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 19 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 20 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 21 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 22 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 23 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 24 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 25 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 26 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 27 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 28 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 29 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 30 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 31 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 32 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 33 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 34 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 35 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 36 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 37 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 38 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 39 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 40 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 41 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 42 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 43 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 44 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 45 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 46 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 47 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 48 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 49 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 50 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 51 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 52 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 53 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 54 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 55 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 56 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 57 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 58 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 59 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 60 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 61 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 62 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 63 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 64 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 65 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 66 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 67 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 68 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 69 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 70 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 71 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 72 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 73 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 74 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 75 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 76 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 77 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 78 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 79 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 80 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 81 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 82 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 83 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 84 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 85 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 86 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 87 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 88 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 89 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 90 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 91 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 92 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 93 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 94 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 95 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 96 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 97 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 98 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 99 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 100 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 101 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 102 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 103 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 104 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 105 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 106 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 107 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 108 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 109 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 110 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 111 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 112 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 113 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 114 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 115 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 116 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
ok 117 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124.
# Compilation failed in require at (eval 130) line 2.
#  at t/LocalDB/SeqFeature.t line 32.
# 
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/116 subtests 
	(less 111 skipped subtests: 4 okay)
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: . C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt\blib\lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt\blib\arch C:/cpanfly-5.18/var/cpan/build/BioPerl-1.6.901-pnEgJt C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt C:\cpanfly-5.18\var\megalib C:/cpanfly-5.18/var/megalib C:/Perl64-5.18/site/lib C:/Perl64-5.18/lib) at Bio\DB\Taxonomy\flatfile.pm line 89.
BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 89.
Compilation failed in require at Bio/Root/Root.pm line 543.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545
STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:263
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:114
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 (you may need to install the DB_File module) (@INC contains: . C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt\blib\lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt\blib\arch C:/cpanfly-5.18/var/cpan/build/BioPerl-1.6.901-pnEgJt C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt C:\cpanfly-5.18\var\megalib C:/cpanfly-5.18/var/megalib C:/Perl64-5.18/site/lib C:/Perl64-5.18/lib) at Bio\DB\Taxonomy\flatfile.pm line 89.
BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 89.
Compilation failed in require at Bio/Root/Root.pm line 543.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545
STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:263
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:114
STACK: t/LocalDB/transfac_pro.t:18
-----------------------------------------------------------

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

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::TFBS::transfac_pro. Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: . C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt\blib\lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt\blib\arch C:/cpanfly-5.18/var/cpan/build/BioPerl-1.6.901-pnEgJt C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt C:\cpanfly-5.18\var\megalib C:/cpanfly-5.18/var/megalib C:/Perl64-5.18/site/lib C:/Perl64-5.18/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 543.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545
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 (you may need to install the DB_File module) (@INC contains: . C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt\blib\lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt\blib\arch C:/cpanfly-5.18/var/cpan/build/BioPerl-1.6.901-pnEgJt C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt C:\cpanfly-5.18\var\megalib C:/cpanfly-5.18/var/megalib C:/Perl64-5.18/site/lib C:/Perl64-5.18/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 543.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545
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 
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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 - An object of class 'Bio::Map::CytoPosition' isa 'Bio::Map::CytoPosition'
ok 15
ok 16
ok 17
ok 18 - An object of class 'Bio::Range' isa 'Bio::Range'
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Map/Map.t .................................. 
1..267
ok 1 - use Bio::Map::SimpleMap;
ok 2 - use Bio::Map::Marker;
ok 3 - use Bio::Map::Position;
ok 4 - use Bio::Map::Relative;
ok 5 - use Bio::Map::Mappable;
ok 6
ok 7
ok 8
ok 9
ok 10 - Length is 0
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151 - use Bio::Map::Gene;
ok 152 - use Bio::Map::GeneMap;
ok 153 - use Bio::Map::TranscriptionFactor;
ok 154 - use Bio::Map::GeneRelative;
ok 155 - use Bio::Map::GenePosition;
ok 156 - use Bio::Map::Prediction;
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok 176
ok 177
ok 178
ok 179
ok 180
ok 181
ok 182
ok 183
ok 184
ok 185
ok 186
ok 187
ok 188
ok 189
ok 190
ok 191
ok 192
ok 193
ok 194
ok 195
ok 196
ok 197
ok 198
ok 199
ok 200
ok 201
ok 202
ok 203
ok 204
ok 205
ok 206
ok 207
ok 208
ok 209
ok 210
ok 211
ok 212
ok 213
ok 214
ok 215
ok 216
ok 217
ok 218
ok 219
ok 220
ok 221
ok 222
ok 223
ok 224
ok 225
ok 226
ok 227
ok 228
ok 229
ok 230
ok 231
ok 232
ok 233
ok 234
ok 235
ok 236
ok 237
ok 238
ok 239
ok 240
ok 241
ok 242
ok 243
ok 244
ok 245
ok 246
ok 247
ok 248
ok 249 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 250 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 251 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 252 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 253 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 254 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 255 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 256 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 257 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 258 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 259 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 260 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 261 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 262 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 263 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 264 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 265 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 266 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 267 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Map/MapIO.t ................................ 
1..51
ok 1 - use Bio::MapIO;
ok 2
ok 3 - An object of class 'Bio::Map::SimpleMap' isa 'Bio::Map::MapI'
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Map/Physical.t ............................. 
1..39
ok 1 - use Bio::Map::Physical;
ok 2 - use Bio::MapIO;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12 - code holds and returns a string, definition requires a boolean
ok 13 - code holds and returns a string, definition requires a boolean
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Matrix/IO/masta.t .......................... 
1..16
ok 1 - use Bio::Matrix::PSM::IO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Matrix/IO/psm.t ............................ 
1..63
ok 1 - use Bio::Matrix::PSM::IO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Matrix/InstanceSite.t ...................... 
1..6
ok 1 - use Bio::Matrix::PSM::InstanceSite;
ok 2
ok 3
ok 4
ok 5
ok 6
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Matrix/Matrix.t ............................ 
1..77
ok 1 - use Bio::Matrix::Generic;
ok 2 - use Bio::Matrix::IO;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30 - An object of class 'Bio::Matrix::Scoring' isa 'Bio::Matrix::Scoring'
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42 - An object of class 'Bio::Matrix::Scoring' isa 'Bio::Matrix::Scoring'
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::GOterm'
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Ontology/GraphAdaptor.t .................... 
1..28
ok 1 - use Bio::Ontology::SimpleGOEngine::GraphAdaptor;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Ontology/IO/go.t ........................... 
1..102
ok 1 - use Bio::OntologyIO;
ok 2
ok 3 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::OntologyI'
ok 4
ok 5 - An object of class 'Bio::Ontology::OBOEngine' isa 'Bio::Ontology::OntologyEngineI'
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Ontology/IO/interpro.t ..................... 
1..69
ok 1 - use Bio::OntologyIO;
ok 2 - An object of class 'Bio::OntologyIO::InterProParser' isa 'Bio::OntologyIO::InterProParser'
ok 3
ok 4 - get_dbxrefs on leaf terms is non-empty
ok 5 - get_dbxrefs(member_list) on leaf terms is non-empty
ok 6 - get_dbxrefs(sec_list) on leaf terms is non-empty
ok 7 - get_dbxrefs(class_list) on leaf terms is non-empty
ok 8 - get_dbxrefs(pub_list) on leaf terms is non-empty
ok 9 - get_dbxrefs(example_list) on leaf terms is non-empty
ok 10 - get_dbxrefs(external_doc_list) on leaf terms is non-empty
ok 11 - get_members on leaf terms is non-empty
ok 12 - class_list on leaf terms is non-empty
ok 13 - get_examples on leaf terms is non-empty
ok 14 - get_external_documents on leaf terms is non-empty
ok 15 - get_references on leaf terms is non-empty
ok 16 - protein_count on leaf terms is non-empty
ok 17 - to_string looks reasonable
ok 18 - There are 8 root InterPro terms
ok 19 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 20 - term Cdc20/Fizzy in ontology InterPro
ok 21 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 22 - term Binding Site in ontology InterPro
ok 23 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 24 - term Repeat in ontology InterPro
ok 25 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 26 - term Helix-turn-helix, AraC type  in ontology InterPro
ok 27 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 28 - term Active Site in ontology InterPro
ok 29 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 30 - term Conserved Site in ontology InterPro
ok 31 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 32 - term Kringle in ontology InterPro
ok 33 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 34 - term post-translational modification in ontology InterPro
ok 35 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 36 - term Region in ontology InterPro
ok 37 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 38 - term Integrins alpha chain in ontology InterPro
ok 39 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 40 - term Active Site in ontology InterPro
ok 41 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 42 - term Binding Site in ontology InterPro
ok 43 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 44 - term Conserved Site in ontology InterPro
ok 45 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 46 - term Domain in ontology InterPro
ok 47 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 48 - term Family in ontology InterPro
ok 49 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 50 - term Region in ontology InterPro
ok 51 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 52 - term Repeat in ontology InterPro
ok 53 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 54 - term post-translational modification in ontology InterPro
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61 - Cdc20/Fizzy term has one parent
ok 62 - Cdc20/Fizzy term has one ancestor
ok 63 - Helix-turn-helix, AraC type  term has one parent
ok 64 - Helix-turn-helix, AraC type  term has one ancestor
ok 65 - Kringle term has one parent
ok 66 - Kringle term has one ancestor
ok 67 - Integrins alpha chain term has one parent
ok 68 - Integrins alpha chain term has one ancestor
ok 69 - secondary accession map has 2 keys
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Ontology/IO/obo.t .......................... 
1..92
ok 1 - use Bio::OntologyIO;
ok 2 - use Bio::Ontology::RelationshipType;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46 - 'got a ontology IO handler' isa 'Bio::OntologyIO'
ok 47 - 'got ontology parser2' isa 'Bio::Ontology::Ontology'
ok 48 - 'got OBO engine object' isa 'Bio::Ontology::OBOEngine'
ok 49 - 'got ontology parser2' isa 'Bio::Ontology::Ontology'
ok 50 - 'got OBO engine object' isa 'Bio::Ontology::OBOEngine'
ok 51 - 'got ontology parser2' isa 'Bio::Ontology::Ontology'
ok 52 - 'got OBO engine object' isa 'Bio::Ontology::OBOEngine'
ok 53 - Gene ontology
ok 54 - biological process
ok 55 - molecular function
ok 56 - Got root
ok 57 - Got root
ok 58 - Got regulates
# 	 from gene_ontology
ok 59 - Got
# 	 positively regulates from gene_ontology
ok 60 - Got
# 	  regulates from biological_process
ok 61 - Got
# 	 positively regulates from biological_process
ok 62 - Got predicates for gene_ontology
ok 63 - Got predicates for biological_process
ok 64 - Got regulates predicate
ok 65 - Got positively regulates predicate
ok 66 - Got relationships for biological_process
ok 67 - Got relationships for molecular_function
ok 68 - Got is a relationship from
# 	 molecular_function
ok 69 - 'Got term object' isa 'Bio::Ontology::Term'
ok 70 - Got term id
ok 71 - Got term name
ok 72 - 'Got regulated object' isa 'Bio::Ontology::Term'
ok 73 - Got regulated term1 id
ok 74 - 'Got term1 object' isa 'Bio::Ontology::Term'
ok 75 - Got back the child
ok 76 - 'Got term object' isa 'Bio::Ontology::Term'
ok 77 - Got term id
ok 78 - Got term name
ok 79 - 'Got regulated object' isa 'Bio::Ontology::Term'
ok 80 - Got regulated term1 id
ok 81 - Got identical regulation
ok 82 - 'Got term1 object' isa 'Bio::Ontology::Term'
ok 83 - Got back the child
ok 84 - 'got a ontology IO handler' isa 'Bio::OntologyIO'
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Ontology/Ontology.t ........................ 
1..55
ok 1 - use Bio::OntologyIO;
ok 2 - use Bio::Ontology::RelationshipType;
ok 3 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53 - Interpro XML file interpro.xml can be parsed
ok 54 - Interpro XML file interpro_sample.xml can be parsed
ok 55 - Interpro XML file interpro_relationship.xml can be parsed
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Ontology/OntologyEngine.t .................. 
1..31
ok 1 - use Bio::Ontology::Term;
ok 2 - use Bio::Ontology::Relationship;
ok 3 - use Bio::Ontology::RelationshipType;
ok 4 - use Bio::Ontology::SimpleOntologyEngine;
ok 5 - use Bio::Ontology::Ontology;
ok 6 - An object of class 'Bio::Ontology::SimpleOntologyEngine' isa 'Bio::Ontology::OntologyEngineI'
ok 7
ok 8 - adding a relationship with an undef object term fails
ok 9 - adding a relationship with an undef object term fails
ok 10 - adding a relationship with an undef subject term fails
ok 11 - adding a relationship with an undef subject term fails
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok
t/Ontology/OntologyStore.t ................... skipped: Network tests have not been requested
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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 - An object of class 'Bio::Ontology::RelationshipType' isa 'Bio::Ontology::RelationshipType'
ok 5 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::GOterm'
ok 6 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::GOterm'
ok 7 - An object of class 'Bio::Ontology::Relationship' isa 'Bio::Ontology::Relationship'
ok 8
ok 9
ok 10
ok 11
ok 12
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Ontology/RelationshipType.t ................ 
1..23
ok 1 - use Bio::Ontology::RelationshipType;
ok 2 - use Bio::Ontology::Ontology;
ok 3 - An object of class 'Bio::Ontology::RelationshipType' isa 'Bio::Ontology::RelationshipType'
ok 4 - An object of class 'Bio::Ontology::RelationshipType' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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 - An object of class 'Bio::Ontology::Term' 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 - An object of class 'Bio::Ontology::Term' isa 'Bio::Ontology::TermI'
ok 45
ok 46 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::TermI'
ok 47 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::GOterm'
ok 48
ok 49
ok 50 - An object of class 'Bio::Annotation::OntologyTerm' isa 'Bio::Ontology::TermI'
ok 51 - An object of class 'Bio::Annotation::OntologyTerm' isa 'Bio::AnnotationI'
ok 52
ok 53
ok 54
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Perl.t ..................................... 
1..31
ok 1 - use Bio::Perl;
ok 2
ok 3 - An object of class 'Bio::Seq' isa 'Bio::SeqI'
ok 4
ok 5 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::SeqI'
ok 6
ok 7 - An object of class 'Bio::Seq' isa 'Bio::SeqI'
ok 8 - An object of class 'Bio::Seq' isa 'Bio::SeqI'
ok 9
ok 10
ok 11 - An object of class 'Bio::Seq' isa 'Bio::SeqI'
ok 12
ok 13 - An object of class 'Bio::Seq' isa 'Bio::SeqI'
ok 14
ok 15 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeqI'
ok 16
ok 17
ok 18
ok 19
ok 20 # skip Network tests have not been requested
ok 21 # skip Network tests have not been requested
ok 22 # skip Network tests have not been requested
ok 23 # skip Network tests have not been requested
ok 24 # skip Network tests have not been requested
ok 25 # skip Network tests have not been requested
ok 26 # skip Network tests have not been requested
ok 27 # skip Network tests have not been requested
ok 28 # skip Network tests have not been requested
ok 29 # skip Network tests have not been requested
ok 30 # skip Network tests have not been requested
ok 31 # skip Network tests have not been requested
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Phenotype/Correlate.t ...................... 
1..17
ok 1 - use Bio::Phenotype::Correlate;
ok 2 - use Bio::Species;
ok 3 - An object of class 'Bio::Phenotype::Correlate' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Phenotype/Measure.t ........................ 
1..21
ok 1 - use Bio::Phenotype::Measure;
ok 2 - An object of class 'Bio::Phenotype::Measure' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Phenotype/MiniMIMentry.t ................... 
1..15
ok 1 - use Bio::Phenotype::OMIM::MiniMIMentry;
ok 2 - An object of class 'Bio::Phenotype::OMIM::MiniMIMentry' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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 - An object of class 'Bio::Phenotype::OMIM::OMIMentry' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Phenotype/OMIMentryAllelicVariant.t ........ 
1..27
ok 1 - use Bio::Phenotype::OMIM::OMIMentryAllelicVariant;
ok 2 - An object of class 'Bio::Phenotype::OMIM::OMIMentryAllelicVariant' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Phenotype/OMIMparser.t ..................... 
1..175
ok 1 - use Bio::Phenotype::OMIM::OMIMparser;
ok 2 - An object of class 'Bio::Phenotype::OMIM::OMIMparser' isa 'Bio::Phenotype::OMIM::OMIMparser'
ok 3 - An object of class 'Bio::Phenotype::OMIM::OMIMentry' 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 - An object of class 'Bio::Phenotype::OMIM::MiniMIMentry' 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 - An object of class 'Bio::Phenotype::OMIM::OMIMentry' 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 - An object of class 'Bio::Phenotype::OMIM::MiniMIMentry' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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 - An object of class 'Bio::Phenotype::Phenotype' isa 'Bio::Phenotype::PhenotypeI'
ok 9 - An object of class 'Bio::Phenotype::Phenotype' isa 'Bio::Phenotype::Phenotype'
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42 - operator overloading in AnnotationI is deprecated
ok 43 - operator overloading in AnnotationI is deprecated
ok 44
ok 45
ok 46 - operator overloading in AnnotationI is deprecated
ok 47 - operator overloading in AnnotationI is deprecated
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99 - operator overloading in AnnotationI is deprecated
ok 100 - operator overloading in AnnotationI is deprecated
ok 101
ok 102
ok 103 - operator overloading in AnnotationI is deprecated
ok 104 - operator overloading in AnnotationI is deprecated
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok

#   Failed test 'POD test for Bio/Tools/Geneid.pm'
#   at C:\cpanfly-5.18\var\megalib/Test/Pod.pm line 186.
# Bio/Tools/Geneid.pm (37): Non-ASCII character seen before =encoding in 'Guigó'. Assuming ISO8859-1

#   Failed test 'POD test for Bio/Tools/GuessSeqFormat.pm'
#   at C:\cpanfly-5.18\var\megalib/Test/Pod.pm line 186.
# Bio/Tools/GuessSeqFormat.pm (233): Non-ASCII character seen before =encoding in 'Kähäri,'. Assuming ISO8859-1

#   Failed test 'POD test for Bio/Tools/Run/WrapperBase.pm'
#   at C:\cpanfly-5.18\var\megalib/Test/Pod.pm line 186.
# Bio/Tools/Run/WrapperBase.pm (181): Non-ASCII character seen before =encoding in 'NB:ÊThis'. Assuming ISO8859-1

#   Failed test 'POD test for Bio/Tree/Statistics.pm'
#   at C:\cpanfly-5.18\var\megalib/Test/Pod.pm line 186.
Wide character in print at C:\cpanfly-5.18\var\megalib/Test/Builder.pm line 1821.
# Bio/Tree/Statistics.pm (214): Non-ASCII character seen before =encoding in 'de�ning'. Assuming UTF-8

#   Failed test 'POD test for examples/biblio/biblio-eutils-example.pl'
#   at C:\cpanfly-5.18\var\megalib/Test/Pod.pm line 186.
# examples/biblio/biblio-eutils-example.pl (108): Non-ASCII character seen before =encoding in '<LastName>Kubícková</LastName>'. Assuming ISO8859-1
# Looks like you failed 5 tests of 1011.
t/PodSyntax.t ................................ 
1..1011
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/NexmlIO.pm
ok 23 - POD test for Bio/OntologyIO.pm
ok 24 - POD test for Bio/ParameterBaseI.pm
ok 25 - POD test for Bio/Perl.pm
ok 26 - POD test for Bio/PhyloNetwork.pm
ok 27 - POD test for Bio/PrimarySeq.pm
ok 28 - POD test for Bio/PrimarySeqI.pm
ok 29 - POD test for Bio/PullParserI.pm
ok 30 - POD test for Bio/Range.pm
ok 31 - POD test for Bio/RangeI.pm
ok 32 - POD test for Bio/SearchDist.pm
ok 33 - POD test for Bio/SearchIO.pm
ok 34 - POD test for Bio/Seq.pm
ok 35 - POD test for Bio/SeqAnalysisParserI.pm
ok 36 - POD test for Bio/SeqFeatureI.pm
ok 37 - POD test for Bio/SeqI.pm
ok 38 - POD test for Bio/SeqIO.pm
ok 39 - POD test for Bio/SeqUtils.pm
ok 40 - POD test for Bio/SimpleAlign.pm
ok 41 - POD test for Bio/SimpleAnalysisI.pm
ok 42 - POD test for Bio/Species.pm
ok 43 - POD test for Bio/Taxon.pm
ok 44 - POD test for Bio/Taxonomy.pm
ok 45 - POD test for Bio/TreeIO.pm
ok 46 - POD test for Bio/UpdateableSeqI.pm
ok 47 - POD test for Bio/WebAgent.pm
ok 48 - POD test for Bio/Align/AlignI.pm
ok 49 - POD test for Bio/Align/DNAStatistics.pm
ok 50 - POD test for Bio/Align/Graphics.pm
ok 51 - POD test for Bio/Align/PairwiseStatistics.pm
ok 52 - POD test for Bio/Align/ProteinStatistics.pm
ok 53 - POD test for Bio/Align/StatisticsI.pm
ok 54 - POD test for Bio/Align/Utilities.pm
ok 55 - POD test for Bio/AlignIO/arp.pm
ok 56 - POD test for Bio/AlignIO/bl2seq.pm
ok 57 - POD test for Bio/AlignIO/clustalw.pm
ok 58 - POD test for Bio/AlignIO/emboss.pm
ok 59 - POD test for Bio/AlignIO/fasta.pm
ok 60 - POD test for Bio/AlignIO/largemultifasta.pm
ok 61 - POD test for Bio/AlignIO/maf.pm
ok 62 - POD test for Bio/AlignIO/mase.pm
ok 63 - POD test for Bio/AlignIO/mega.pm
ok 64 - POD test for Bio/AlignIO/meme.pm
ok 65 - POD test for Bio/AlignIO/metafasta.pm
ok 66 - POD test for Bio/AlignIO/msf.pm
ok 67 - POD test for Bio/AlignIO/nexml.pm
ok 68 - POD test for Bio/AlignIO/nexus.pm
ok 69 - POD test for Bio/AlignIO/pfam.pm
ok 70 - POD test for Bio/AlignIO/phylip.pm
ok 71 - POD test for Bio/AlignIO/po.pm
ok 72 - POD test for Bio/AlignIO/proda.pm
ok 73 - POD test for Bio/AlignIO/prodom.pm
ok 74 - POD test for Bio/AlignIO/psi.pm
ok 75 - POD test for Bio/AlignIO/selex.pm
ok 76 - POD test for Bio/AlignIO/stockholm.pm
ok 77 - POD test for Bio/AlignIO/xmfa.pm
ok 78 - POD test for Bio/AlignIO/Handler/GenericAlignHandler.pm
ok 79 - POD test for Bio/Annotation/AnnotationFactory.pm
ok 80 - POD test for Bio/Annotation/Collection.pm
ok 81 - POD test for Bio/Annotation/Comment.pm
ok 82 - POD test for Bio/Annotation/DBLink.pm
ok 83 - POD test for Bio/Annotation/OntologyTerm.pm
ok 84 - POD test for Bio/Annotation/Reference.pm
ok 85 - POD test for Bio/Annotation/Relation.pm
ok 86 - POD test for Bio/Annotation/SimpleValue.pm
ok 87 - POD test for Bio/Annotation/StructuredValue.pm
ok 88 - POD test for Bio/Annotation/TagTree.pm
ok 89 - POD test for Bio/Annotation/Target.pm
ok 90 - POD test for Bio/Annotation/Tree.pm
ok 91 - POD test for Bio/Annotation/TypeManager.pm
ok 92 - POD test for Bio/Assembly/Contig.pm
ok 93 - POD test for Bio/Assembly/ContigAnalysis.pm
ok 94 - POD test for Bio/Assembly/IO.pm
ok 95 - POD test for Bio/Assembly/Scaffold.pm
ok 96 - POD test for Bio/Assembly/ScaffoldI.pm
ok 97 - POD test for Bio/Assembly/Singlet.pm
ok 98 - POD test for Bio/Assembly/IO/ace.pm
ok 99 - POD test for Bio/Assembly/IO/bowtie.pm
ok 100 - POD test for Bio/Assembly/IO/maq.pm
ok 101 - POD test for Bio/Assembly/IO/phrap.pm
ok 102 - POD test for Bio/Assembly/IO/sam.pm
ok 103 - POD test for Bio/Assembly/IO/tigr.pm
ok 104 - POD test for Bio/Assembly/Tools/ContigSpectrum.pm
ok 105 - POD test for Bio/Biblio/Article.pm
ok 106 - POD test for Bio/Biblio/BiblioBase.pm
ok 107 - POD test for Bio/Biblio/Book.pm
ok 108 - POD test for Bio/Biblio/BookArticle.pm
ok 109 - POD test for Bio/Biblio/IO.pm
ok 110 - POD test for Bio/Biblio/Journal.pm
ok 111 - POD test for Bio/Biblio/JournalArticle.pm
ok 112 - POD test for Bio/Biblio/MedlineArticle.pm
ok 113 - POD test for Bio/Biblio/MedlineBook.pm
ok 114 - POD test for Bio/Biblio/MedlineBookArticle.pm
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ok 531 - POD test for Bio/Search/Iteration/GenericIteration.pm
ok 532 - POD test for Bio/Search/Iteration/IterationI.pm
ok 533 - POD test for Bio/Search/Result/BlastPullResult.pm
ok 534 - POD test for Bio/Search/Result/BlastResult.pm
ok 535 - POD test for Bio/Search/Result/CrossMatchResult.pm
ok 536 - POD test for Bio/Search/Result/GenericResult.pm
ok 537 - POD test for Bio/Search/Result/hmmer3Result.pm
ok 538 - POD test for Bio/Search/Result/HMMERResult.pm
ok 539 - POD test for Bio/Search/Result/HmmpfamResult.pm
ok 540 - POD test for Bio/Search/Result/PullResultI.pm
ok 541 - POD test for Bio/Search/Result/ResultFactory.pm
ok 542 - POD test for Bio/Search/Result/ResultI.pm
ok 543 - POD test for Bio/Search/Result/WABAResult.pm
ok 544 - POD test for Bio/Search/Tiling/MapTileUtils.pm
ok 545 - POD test for Bio/Search/Tiling/MapTiling.pm
ok 546 - POD test for Bio/Search/Tiling/TilingI.pm
ok 547 - POD test for Bio/SearchIO/axt.pm
ok 548 - POD test for Bio/SearchIO/blast.pm
ok 549 - POD test for Bio/SearchIO/blasttable.pm
ok 550 - POD test for Bio/SearchIO/blastxml.pm
ok 551 - POD test for Bio/SearchIO/blast_pull.pm
ok 552 - POD test for Bio/SearchIO/cross_match.pm
ok 553 - POD test for Bio/SearchIO/erpin.pm
ok 554 - POD test for Bio/SearchIO/EventHandlerI.pm
ok 555 - POD test for Bio/SearchIO/exonerate.pm
ok 556 - POD test for Bio/SearchIO/fasta.pm
ok 557 - POD test for Bio/SearchIO/FastHitEventBuilder.pm
ok 558 - POD test for Bio/SearchIO/gmap_f9.pm
ok 559 - POD test for Bio/SearchIO/hmmer.pm
ok 560 - POD test for Bio/SearchIO/hmmer2.pm
ok 561 - POD test for Bio/SearchIO/hmmer3.pm
ok 562 - POD test for Bio/SearchIO/hmmer_pull.pm
ok 563 - POD test for Bio/SearchIO/infernal.pm
ok 564 - POD test for Bio/SearchIO/IteratedSearchResultEventBuilder.pm
ok 565 - POD test for Bio/SearchIO/megablast.pm
ok 566 - POD test for Bio/SearchIO/psl.pm
ok 567 - POD test for Bio/SearchIO/rnamotif.pm
ok 568 - POD test for Bio/SearchIO/SearchResultEventBuilder.pm
ok 569 - POD test for Bio/SearchIO/SearchWriterI.pm
ok 570 - POD test for Bio/SearchIO/sim4.pm
ok 571 - POD test for Bio/SearchIO/waba.pm
ok 572 - POD test for Bio/SearchIO/wise.pm
ok 573 - POD test for Bio/SearchIO/Writer/BSMLResultWriter.pm
ok 574 - POD test for Bio/SearchIO/Writer/GbrowseGFF.pm
ok 575 - POD test for Bio/SearchIO/Writer/HitTableWriter.pm
ok 576 - POD test for Bio/SearchIO/Writer/HSPTableWriter.pm
ok 577 - POD test for Bio/SearchIO/Writer/HTMLResultWriter.pm
ok 578 - POD test for Bio/SearchIO/Writer/ResultTableWriter.pm
ok 579 - POD test for Bio/SearchIO/Writer/TextResultWriter.pm
ok 580 - POD test for Bio/SearchIO/XML/BlastHandler.pm
ok 581 - POD test for Bio/SearchIO/XML/PsiBlastHandler.pm
ok 582 - POD test for Bio/Seq/BaseSeqProcessor.pm
ok 583 - POD test for Bio/Seq/EncodedSeq.pm
ok 584 - POD test for Bio/Seq/LargeLocatableSeq.pm
ok 585 - POD test for Bio/Seq/LargePrimarySeq.pm
ok 586 - POD test for Bio/Seq/LargeSeq.pm
ok 587 - POD test for Bio/Seq/LargeSeqI.pm
ok 588 - POD test for Bio/Seq/Meta.pm
ok 589 - POD test for Bio/Seq/MetaI.pm
ok 590 - POD test for Bio/Seq/PrimaryQual.pm
ok 591 - POD test for Bio/Seq/PrimedSeq.pm
ok 592 - POD test for Bio/Seq/QualI.pm
ok 593 - POD test for Bio/Seq/Quality.pm
ok 594 - POD test for Bio/Seq/RichSeq.pm
ok 595 - POD test for Bio/Seq/RichSeqI.pm
ok 596 - POD test for Bio/Seq/SeqBuilder.pm
ok 597 - POD test for Bio/Seq/SeqFactory.pm
ok 598 - POD test for Bio/Seq/SeqFastaSpeedFactory.pm
ok 599 - POD test for Bio/Seq/SequenceTrace.pm
ok 600 - POD test for Bio/Seq/SeqWithQuality.pm
ok 601 - POD test for Bio/Seq/TraceI.pm
ok 602 - POD test for Bio/Seq/Meta/Array.pm
ok 603 - POD test for Bio/SeqEvolution/DNAPoint.pm
ok 604 - POD test for Bio/SeqEvolution/EvolutionI.pm
ok 605 - POD test for Bio/SeqEvolution/Factory.pm
ok 606 - POD test for Bio/SeqFeature/Annotated.pm
ok 607 - POD test for Bio/SeqFeature/AnnotationAdaptor.pm
ok 608 - POD test for Bio/SeqFeature/Collection.pm
ok 609 - POD test for Bio/SeqFeature/CollectionI.pm
ok 610 - POD test for Bio/SeqFeature/Computation.pm
ok 611 - POD test for Bio/SeqFeature/FeaturePair.pm
ok 612 - POD test for Bio/SeqFeature/Generic.pm
ok 613 - POD test for Bio/SeqFeature/Lite.pm
ok 614 - POD test for Bio/SeqFeature/PositionProxy.pm
ok 615 - POD test for Bio/SeqFeature/Primer.pm
ok 616 - POD test for Bio/SeqFeature/Similarity.pm
ok 617 - POD test for Bio/SeqFeature/SimilarityPair.pm
ok 618 - POD test for Bio/SeqFeature/TypedSeqFeatureI.pm
ok 619 - POD test for Bio/SeqFeature/Gene/Exon.pm
ok 620 - POD test for Bio/SeqFeature/Gene/ExonI.pm
ok 621 - POD test for Bio/SeqFeature/Gene/GeneStructure.pm
ok 622 - POD test for Bio/SeqFeature/Gene/GeneStructureI.pm
ok 623 - POD test for Bio/SeqFeature/Gene/Intron.pm
ok 624 - POD test for Bio/SeqFeature/Gene/NC_Feature.pm
ok 625 - POD test for Bio/SeqFeature/Gene/Poly_A_site.pm
ok 626 - POD test for Bio/SeqFeature/Gene/Promoter.pm
ok 627 - POD test for Bio/SeqFeature/Gene/Transcript.pm
ok 628 - POD test for Bio/SeqFeature/Gene/TranscriptI.pm
ok 629 - POD test for Bio/SeqFeature/Gene/UTR.pm
ok 630 - POD test for Bio/SeqFeature/SiRNA/Oligo.pm
ok 631 - POD test for Bio/SeqFeature/SiRNA/Pair.pm
ok 632 - POD test for Bio/SeqFeature/Tools/FeatureNamer.pm
ok 633 - POD test for Bio/SeqFeature/Tools/IDHandler.pm
ok 634 - POD test for Bio/SeqFeature/Tools/TypeMapper.pm
ok 635 - POD test for Bio/SeqFeature/Tools/Unflattener.pm
ok 636 - POD test for Bio/SeqIO/abi.pm
ok 637 - POD test for Bio/SeqIO/ace.pm
ok 638 - POD test for Bio/SeqIO/agave.pm
ok 639 - POD test for Bio/SeqIO/alf.pm
ok 640 - POD test for Bio/SeqIO/asciitree.pm
ok 641 - POD test for Bio/SeqIO/bsml.pm
ok 642 - POD test for Bio/SeqIO/bsml_sax.pm
ok 643 - POD test for Bio/SeqIO/chadoxml.pm
ok 644 - POD test for Bio/SeqIO/chaos.pm
ok 645 - POD test for Bio/SeqIO/chaosxml.pm
ok 646 - POD test for Bio/SeqIO/ctf.pm
ok 647 - POD test for Bio/SeqIO/embl.pm
ok 648 - POD test for Bio/SeqIO/embldriver.pm
ok 649 - POD test for Bio/SeqIO/entrezgene.pm
ok 650 - POD test for Bio/SeqIO/excel.pm
ok 651 - POD test for Bio/SeqIO/exp.pm
ok 652 - POD test for Bio/SeqIO/fasta.pm
ok 653 - POD test for Bio/SeqIO/fastq.pm
ok 654 - POD test for Bio/SeqIO/flybase_chadoxml.pm
ok 655 - POD test for Bio/SeqIO/FTHelper.pm
ok 656 - POD test for Bio/SeqIO/game.pm
ok 657 - POD test for Bio/SeqIO/gbdriver.pm
ok 658 - POD test for Bio/SeqIO/gbxml.pm
ok 659 - POD test for Bio/SeqIO/gcg.pm
ok 660 - POD test for Bio/SeqIO/genbank.pm
ok 661 - POD test for Bio/SeqIO/interpro.pm
ok 662 - POD test for Bio/SeqIO/kegg.pm
ok 663 - POD test for Bio/SeqIO/largefasta.pm
ok 664 - POD test for Bio/SeqIO/lasergene.pm
ok 665 - POD test for Bio/SeqIO/locuslink.pm
ok 666 - POD test for Bio/SeqIO/mbsout.pm
ok 667 - POD test for Bio/SeqIO/metafasta.pm
ok 668 - POD test for Bio/SeqIO/msout.pm
ok 669 - POD test for Bio/SeqIO/MultiFile.pm
ok 670 - POD test for Bio/SeqIO/nexml.pm
ok 671 - POD test for Bio/SeqIO/phd.pm
ok 672 - POD test for Bio/SeqIO/pir.pm
ok 673 - POD test for Bio/SeqIO/pln.pm
ok 674 - POD test for Bio/SeqIO/qual.pm
ok 675 - POD test for Bio/SeqIO/raw.pm
ok 676 - POD test for Bio/SeqIO/scf.pm
ok 677 - POD test for Bio/SeqIO/seqxml.pm
ok 678 - POD test for Bio/SeqIO/strider.pm
ok 679 - POD test for Bio/SeqIO/swiss.pm
ok 680 - POD test for Bio/SeqIO/swissdriver.pm
ok 681 - POD test for Bio/SeqIO/tab.pm
ok 682 - POD test for Bio/SeqIO/table.pm
ok 683 - POD test for Bio/SeqIO/tigr.pm
ok 684 - POD test for Bio/SeqIO/tigrxml.pm
ok 685 - POD test for Bio/SeqIO/tinyseq.pm
ok 686 - POD test for Bio/SeqIO/ztr.pm
ok 687 - POD test for Bio/SeqIO/game/featHandler.pm
ok 688 - POD test for Bio/SeqIO/game/gameHandler.pm
ok 689 - POD test for Bio/SeqIO/game/gameSubs.pm
ok 690 - POD test for Bio/SeqIO/game/gameWriter.pm
ok 691 - POD test for Bio/SeqIO/game/seqHandler.pm
ok 692 - POD test for Bio/SeqIO/Handler/GenericRichSeqHandler.pm
ok 693 - POD test for Bio/SeqIO/tinyseq/tinyseqHandler.pm
ok 694 - POD test for Bio/Structure/Atom.pm
ok 695 - POD test for Bio/Structure/Chain.pm
ok 696 - POD test for Bio/Structure/Entry.pm
ok 697 - POD test for Bio/Structure/IO.pm
ok 698 - POD test for Bio/Structure/Model.pm
ok 699 - POD test for Bio/Structure/Residue.pm
ok 700 - POD test for Bio/Structure/StructureI.pm
ok 701 - POD test for Bio/Structure/IO/pdb.pm
ok 702 - POD test for Bio/Structure/SecStr/DSSP/Res.pm
ok 703 - POD test for Bio/Structure/SecStr/STRIDE/Res.pm
ok 704 - POD test for Bio/Symbol/Alphabet.pm
ok 705 - POD test for Bio/Symbol/AlphabetI.pm
ok 706 - POD test for Bio/Symbol/DNAAlphabet.pm
ok 707 - POD test for Bio/Symbol/ProteinAlphabet.pm
ok 708 - POD test for Bio/Symbol/Symbol.pm
ok 709 - POD test for Bio/Symbol/SymbolI.pm
ok 710 - POD test for Bio/Taxonomy/FactoryI.pm
ok 711 - POD test for Bio/Taxonomy/Node.pm
ok 712 - POD test for Bio/Taxonomy/Taxon.pm
ok 713 - POD test for Bio/Taxonomy/Tree.pm
ok 714 - POD test for Bio/Tools/AlignFactory.pm
ok 715 - POD test for Bio/Tools/AnalysisResult.pm
ok 716 - POD test for Bio/Tools/Blat.pm
ok 717 - POD test for Bio/Tools/CodonTable.pm
ok 718 - POD test for Bio/Tools/Coil.pm
ok 719 - POD test for Bio/Tools/dpAlign.pm
ok 720 - POD test for Bio/Tools/ECnumber.pm
ok 721 - POD test for Bio/Tools/EPCR.pm
ok 722 - POD test for Bio/Tools/Eponine.pm
ok 723 - POD test for Bio/Tools/ERPIN.pm
ok 724 - POD test for Bio/Tools/Est2Genome.pm
ok 725 - POD test for Bio/Tools/ESTScan.pm
ok 726 - POD test for Bio/Tools/EUtilities.pm
ok 727 - POD test for Bio/Tools/Fgenesh.pm
ok 728 - POD test for Bio/Tools/FootPrinter.pm
ok 729 - POD test for Bio/Tools/Gel.pm
not ok 730 - POD test for Bio/Tools/Geneid.pm
ok 731 - POD test for Bio/Tools/Genemark.pm
ok 732 - POD test for Bio/Tools/Genewise.pm
ok 733 - POD test for Bio/Tools/Genomewise.pm
ok 734 - POD test for Bio/Tools/Genscan.pm
ok 735 - POD test for Bio/Tools/GFF.pm
ok 736 - POD test for Bio/Tools/Glimmer.pm
ok 737 - POD test for Bio/Tools/Grail.pm
not ok 738 - POD test for Bio/Tools/GuessSeqFormat.pm
ok 739 - POD test for Bio/Tools/Hmmpfam.pm
ok 740 - POD test for Bio/Tools/Infernal.pm
ok 741 - POD test for Bio/Tools/ipcress.pm
ok 742 - POD test for Bio/Tools/isPcr.pm
ok 743 - POD test for Bio/Tools/IUPAC.pm
ok 744 - POD test for Bio/Tools/Lucy.pm
ok 745 - POD test for Bio/Tools/Match.pm
ok 746 - POD test for Bio/Tools/MZEF.pm
ok 747 - POD test for Bio/Tools/OddCodes.pm
ok 748 - POD test for Bio/Tools/pICalculator.pm
ok 749 - POD test for Bio/Tools/Primer3.pm
ok 750 - POD test for Bio/Tools/Prints.pm
ok 751 - POD test for Bio/Tools/Profile.pm
ok 752 - POD test for Bio/Tools/Promoterwise.pm
ok 753 - POD test for Bio/Tools/PrositeScan.pm
ok 754 - POD test for Bio/Tools/Protparam.pm
ok 755 - POD test for Bio/Tools/Pseudowise.pm
ok 756 - POD test for Bio/Tools/pSW.pm
ok 757 - POD test for Bio/Tools/QRNA.pm
ok 758 - POD test for Bio/Tools/RandomDistFunctions.pm
ok 759 - POD test for Bio/Tools/RepeatMasker.pm
ok 760 - POD test for Bio/Tools/RNAMotif.pm
ok 761 - POD test for Bio/Tools/Seg.pm
ok 762 - POD test for Bio/Tools/SeqPattern.pm
ok 763 - POD test for Bio/Tools/SeqStats.pm
ok 764 - POD test for Bio/Tools/SeqWords.pm
ok 765 - POD test for Bio/Tools/Sigcleave.pm
ok 766 - POD test for Bio/Tools/Signalp.pm
ok 767 - POD test for Bio/Tools/SiRNA.pm
ok 768 - POD test for Bio/Tools/TandemRepeatsFinder.pm
ok 769 - POD test for Bio/Tools/TargetP.pm
ok 770 - POD test for Bio/Tools/Tmhmm.pm
ok 771 - POD test for Bio/Tools/tRNAscanSE.pm
ok 772 - POD test for Bio/Tools/Alignment/Consed.pm
ok 773 - POD test for Bio/Tools/Alignment/Trim.pm
ok 774 - POD test for Bio/Tools/Analysis/SimpleAnalysisBase.pm
ok 775 - POD test for Bio/Tools/Analysis/DNA/ESEfinder.pm
ok 776 - POD test for Bio/Tools/Analysis/Protein/Domcut.pm
ok 777 - POD test for Bio/Tools/Analysis/Protein/ELM.pm
ok 778 - POD test for Bio/Tools/Analysis/Protein/GOR4.pm
ok 779 - POD test for Bio/Tools/Analysis/Protein/HNN.pm
ok 780 - POD test for Bio/Tools/Analysis/Protein/Mitoprot.pm
ok 781 - POD test for Bio/Tools/Analysis/Protein/NetPhos.pm
ok 782 - POD test for Bio/Tools/Analysis/Protein/Scansite.pm
ok 783 - POD test for Bio/Tools/Analysis/Protein/Sopma.pm
ok 784 - POD test for Bio/Tools/EMBOSS/Palindrome.pm
ok 785 - POD test for Bio/Tools/EUtilities/EUtilDataI.pm
ok 786 - POD test for Bio/Tools/EUtilities/EUtilParameters.pm
ok 787 - POD test for Bio/Tools/EUtilities/History.pm
ok 788 - POD test for Bio/Tools/EUtilities/HistoryI.pm
ok 789 - POD test for Bio/Tools/EUtilities/Info.pm
ok 790 - POD test for Bio/Tools/EUtilities/Link.pm
ok 791 - POD test for Bio/Tools/EUtilities/Query.pm
ok 792 - POD test for Bio/Tools/EUtilities/Summary.pm
ok 793 - POD test for Bio/Tools/EUtilities/Info/FieldInfo.pm
ok 794 - POD test for Bio/Tools/EUtilities/Info/LinkInfo.pm
ok 795 - POD test for Bio/Tools/EUtilities/Link/LinkSet.pm
ok 796 - POD test for Bio/Tools/EUtilities/Link/UrlLink.pm
ok 797 - POD test for Bio/Tools/EUtilities/Query/GlobalQuery.pm
ok 798 - POD test for Bio/Tools/EUtilities/Summary/DocSum.pm
ok 799 - POD test for Bio/Tools/EUtilities/Summary/Item.pm
ok 800 - POD test for Bio/Tools/EUtilities/Summary/ItemContainerI.pm
ok 801 - POD test for Bio/Tools/HMMER/Domain.pm
ok 802 - POD test for Bio/Tools/HMMER/Results.pm
ok 803 - POD test for Bio/Tools/HMMER/Set.pm
ok 804 - POD test for Bio/Tools/Phylo/Gerp.pm
ok 805 - POD test for Bio/Tools/Phylo/Gumby.pm
ok 806 - POD test for Bio/Tools/Phylo/Molphy.pm
ok 807 - POD test for Bio/Tools/Phylo/PAML.pm
ok 808 - POD test for Bio/Tools/Phylo/Molphy/Result.pm
ok 809 - POD test for Bio/Tools/Phylo/PAML/Codeml.pm
ok 810 - POD test for Bio/Tools/Phylo/PAML/ModelResult.pm
ok 811 - POD test for Bio/Tools/Phylo/PAML/Result.pm
ok 812 - POD test for Bio/Tools/Phylo/Phylip/ProtDist.pm
ok 813 - POD test for Bio/Tools/Prediction/Exon.pm
ok 814 - POD test for Bio/Tools/Prediction/Gene.pm
ok 815 - POD test for Bio/Tools/Primer/AssessorI.pm
ok 816 - POD test for Bio/Tools/Primer/Feature.pm
ok 817 - POD test for Bio/Tools/Primer/Pair.pm
ok 818 - POD test for Bio/Tools/Primer/Assessor/Base.pm
ok 819 - POD test for Bio/Tools/Run/GenericParameters.pm
ok 820 - POD test for Bio/Tools/Run/hmmer3.pm (no pod)
ok 821 - POD test for Bio/Tools/Run/ParametersI.pm
ok 822 - POD test for Bio/Tools/Run/RemoteBlast.pm
ok 823 - POD test for Bio/Tools/Run/StandAloneBlast.pm
ok 824 - POD test for Bio/Tools/Run/StandAloneNCBIBlast.pm
ok 825 - POD test for Bio/Tools/Run/StandAloneWUBlast.pm
not ok 826 - POD test for Bio/Tools/Run/WrapperBase.pm
ok 827 - POD test for Bio/Tools/Run/WrapperBase/CommandExts.pm
ok 828 - POD test for Bio/Tools/SeqPattern/Backtranslate.pm
ok 829 - POD test for Bio/Tools/Signalp/ExtendedSignalp.pm
ok 830 - POD test for Bio/Tools/Sim4/Exon.pm
ok 831 - POD test for Bio/Tools/Sim4/Results.pm
ok 832 - POD test for Bio/Tools/SiRNA/Ruleset/saigo.pm
ok 833 - POD test for Bio/Tools/SiRNA/Ruleset/tuschl.pm
ok 834 - POD test for Bio/Tools/Spidey/Exon.pm
ok 835 - POD test for Bio/Tools/Spidey/Results.pm
ok 836 - POD test for Bio/Tree/AlleleNode.pm
ok 837 - POD test for Bio/Tree/AnnotatableNode.pm
ok 838 - POD test for Bio/Tree/Compatible.pm
ok 839 - POD test for Bio/Tree/DistanceFactory.pm
ok 840 - POD test for Bio/Tree/Node.pm
ok 841 - POD test for Bio/Tree/NodeI.pm
ok 842 - POD test for Bio/Tree/NodeNHX.pm
ok 843 - POD test for Bio/Tree/RandomFactory.pm
not ok 844 - POD test for Bio/Tree/Statistics.pm
ok 845 - POD test for Bio/Tree/Tree.pm
ok 846 - POD test for Bio/Tree/TreeFunctionsI.pm
ok 847 - POD test for Bio/Tree/TreeI.pm
ok 848 - POD test for Bio/Tree/Draw/Cladogram.pm
ok 849 - POD test for Bio/TreeIO/cluster.pm
ok 850 - POD test for Bio/TreeIO/lintree.pm
ok 851 - POD test for Bio/TreeIO/newick.pm
ok 852 - POD test for Bio/TreeIO/NewickParser.pm
ok 853 - POD test for Bio/TreeIO/nexml.pm
ok 854 - POD test for Bio/TreeIO/nexus.pm
ok 855 - POD test for Bio/TreeIO/nhx.pm
ok 856 - POD test for Bio/TreeIO/pag.pm
ok 857 - POD test for Bio/TreeIO/phyloxml.pm
ok 858 - POD test for Bio/TreeIO/svggraph.pm
ok 859 - POD test for Bio/TreeIO/tabtree.pm
ok 860 - POD test for Bio/TreeIO/TreeEventBuilder.pm
ok 861 - POD test for Bio/Variation/AAChange.pm
ok 862 - POD test for Bio/Variation/AAReverseMutate.pm
ok 863 - POD test for Bio/Variation/Allele.pm
ok 864 - POD test for Bio/Variation/DNAMutation.pm
ok 865 - POD test for Bio/Variation/IO.pm
ok 866 - POD test for Bio/Variation/RNAChange.pm
ok 867 - POD test for Bio/Variation/SeqDiff.pm
ok 868 - POD test for Bio/Variation/SNP.pm
ok 869 - POD test for Bio/Variation/VariantI.pm
ok 870 - POD test for Bio/Variation/IO/flat.pm
ok 871 - POD test for Bio/Variation/IO/xml.pm
ok 872 - POD test for scripts/biblio/biblio.PLS
ok 873 - POD test for scripts/Bio-DB-EUtilities/einfo.PLS
ok 874 - POD test for scripts/Bio-DB-GFF/bulk_load_gff.PLS
ok 875 - POD test for scripts/Bio-DB-GFF/fast_load_gff.PLS
ok 876 - POD test for scripts/Bio-DB-GFF/genbank2gff.PLS
ok 877 - POD test for scripts/Bio-DB-GFF/genbank2gff3.PLS
ok 878 - POD test for scripts/Bio-DB-GFF/generate_histogram.PLS
ok 879 - POD test for scripts/Bio-DB-GFF/load_gff.PLS
ok 880 - POD test for scripts/Bio-DB-GFF/meta_gff.PLS
ok 881 - POD test for scripts/Bio-DB-GFF/process_gadfly.PLS
ok 882 - POD test for scripts/Bio-DB-GFF/process_sgd.PLS
ok 883 - POD test for scripts/Bio-DB-GFF/process_wormbase.PLS
ok 884 - POD test for scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.PLS (no pod)
ok 885 - POD test for scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.PLS (no pod)
ok 886 - POD test for scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.PLS
ok 887 - POD test for scripts/das/das_server.pl (no pod)
ok 888 - POD test for scripts/DB/biofetch_genbank_proxy.PLS
ok 889 - POD test for scripts/DB/bioflat_index.PLS
ok 890 - POD test for scripts/DB/biogetseq.PLS
ok 891 - POD test for scripts/DB/flanks.PLS
ok 892 - POD test for scripts/DB-HIV/hivq.PLS
ok 893 - POD test for scripts/index/bp_fetch.PLS
ok 894 - POD test for scripts/index/bp_index.PLS
ok 895 - POD test for scripts/index/bp_seqret.PLS
ok 896 - POD test for scripts/popgen/composite_LD.PLS
ok 897 - POD test for scripts/popgen/heterogeneity_test.PLS
ok 898 - POD test for scripts/searchio/fastam9_to_table.PLS
ok 899 - POD test for scripts/searchio/filter_search.PLS
ok 900 - POD test for scripts/searchio/hmmer_to_table.PLS
ok 901 - POD test for scripts/searchio/parse_hmmsearch.PLS
ok 902 - POD test for scripts/searchio/search2table.PLS
ok 903 - POD test for scripts/seq/extract_feature_seq.PLS
ok 904 - POD test for scripts/seq/make_mrna_protein.PLS
ok 905 - POD test for scripts/seq/seqconvert.PLS
ok 906 - POD test for scripts/seq/seqretsplit.PLS
ok 907 - POD test for scripts/seq/split_seq.PLS
ok 908 - POD test for scripts/seq/translate_seq.PLS
ok 909 - POD test for scripts/seq/unflatten_seq.PLS
ok 910 - POD test for scripts/seqstats/aacomp.PLS
ok 911 - POD test for scripts/seqstats/chaos_plot.PLS
ok 912 - POD test for scripts/seqstats/gccalc.PLS
ok 913 - POD test for scripts/seqstats/oligo_count.PLS
ok 914 - POD test for scripts/taxa/classify_hits_kingdom.PLS
ok 915 - POD test for scripts/taxa/local_taxonomydb_query.PLS
ok 916 - POD test for scripts/taxa/query_entrez_taxa.PLS
ok 917 - POD test for scripts/taxa/taxid4species.PLS
ok 918 - POD test for scripts/taxa/taxonomy2tree.PLS
ok 919 - POD test for scripts/tree/blast2tree.PLS
ok 920 - POD test for scripts/tree/nexus2nh.PLS
ok 921 - POD test for scripts/tree/tree2pag.PLS
ok 922 - POD test for scripts/utilities/bp_mrtrans.PLS
ok 923 - POD test for scripts/utilities/bp_netinstall.PLS
ok 924 - POD test for scripts/utilities/bp_nrdb.PLS
ok 925 - POD test for scripts/utilities/bp_sreformat.PLS
ok 926 - POD test for scripts/utilities/dbsplit.PLS
ok 927 - POD test for scripts/utilities/download_query_genbank.PLS
ok 928 - POD test for scripts/utilities/mask_by_search.PLS
ok 929 - POD test for scripts/utilities/mutate.PLS
ok 930 - POD test for scripts/utilities/pairwise_kaks.PLS
ok 931 - POD test for scripts/utilities/remote_blast.PLS
ok 932 - POD test for scripts/utilities/revtrans-motif.PLS
ok 933 - POD test for scripts/utilities/search2alnblocks.PLS
ok 934 - POD test for scripts/utilities/search2BSML.PLS
ok 935 - POD test for scripts/utilities/search2gff.PLS
ok 936 - POD test for scripts/utilities/search2tribe.PLS
ok 937 - POD test for scripts/utilities/seq_length.PLS
ok 938 - POD test for examples/bioperl.pl (no pod)
ok 939 - POD test for examples/generate_random_seq.pl (no pod)
ok 940 - POD test for examples/longorf.pl
ok 941 - POD test for examples/make_primers.pl (no pod)
ok 942 - POD test for examples/revcom_dir.pl (no pod)
ok 943 - POD test for examples/rev_and_trans.pl (no pod)
ok 944 - POD test for examples/subsequence.cgi (no pod)
ok 945 - POD test for examples/align/aligntutorial.pl (no pod)
ok 946 - POD test for examples/align/align_on_codons.pl (no pod)
ok 947 - POD test for examples/align/clustalw.pl (no pod)
ok 948 - POD test for examples/align/simplealign.pl (no pod)
not ok 949 - POD test for examples/biblio/biblio-eutils-example.pl
ok 950 - POD test for examples/biblio/biblio-soap-example.pl
ok 951 - POD test for examples/biblio/biblio_soap.pl (no pod)
ok 952 - POD test for examples/Bio-DB-GFF/load_ucsc.pl (no pod)
ok 953 - POD test for examples/cluster/dbsnp.pl (no pod)
ok 954 - POD test for examples/contributed/nmrpdb_parse.pl (no pod)
ok 955 - POD test for examples/contributed/prosite2perl.pl (no pod)
ok 956 - POD test for examples/contributed/rebase2list.pl (no pod)
ok 957 - POD test for examples/db/dbfetch
ok 958 - POD test for examples/db/est_tissue_query.pl (no pod)
ok 959 - POD test for examples/db/gb2features.pl (no pod)
ok 960 - POD test for examples/db/getGenBank.pl (no pod)
ok 961 - POD test for examples/db/get_seqs.pl (no pod)
ok 962 - POD test for examples/db/rfetch.pl (no pod)
ok 963 - POD test for examples/db/use_registry.pl (no pod)
ok 964 - POD test for examples/liveseq/change_gene.pl (no pod)
ok 965 - POD test for examples/popgen/parse_calc_stats.pl (no pod)
ok 966 - POD test for examples/quality/svgtrace.pl (no pod)
ok 967 - POD test for examples/root/exceptions1.pl (no pod)
ok 968 - POD test for examples/root/exceptions2.pl (no pod)
ok 969 - POD test for examples/root/exceptions3.pl (no pod)
ok 970 - POD test for examples/root/exceptions4.pl (no pod)
ok 971 - POD test for examples/root/lib/TestInterface.pm
ok 972 - POD test for examples/root/lib/TestObject.pm
ok 973 - POD test for examples/searchio/blast_example.pl (no pod)
ok 974 - POD test for examples/searchio/custom_writer.pl (no pod)
ok 975 - POD test for examples/searchio/hitwriter.pl (no pod)
ok 976 - POD test for examples/searchio/hspwriter.pl (no pod)
ok 977 - POD test for examples/searchio/htmlwriter.pl (no pod)
ok 978 - POD test for examples/searchio/psiblast_features.pl (no pod)
ok 979 - POD test for examples/searchio/psiblast_iterations.pl (no pod)
ok 980 - POD test for examples/searchio/rawwriter.pl (no pod)
ok 981 - POD test for examples/searchio/resultwriter.pl (no pod)
ok 982 - POD test for examples/searchio/waba2gff.pl (no pod)
ok 983 - POD test for examples/searchio/waba2gff3.pl
ok 984 - POD test for examples/sirna/rnai_finder.cgi
ok 985 - POD test for examples/structure/structure-io.pl (no pod)
ok 986 - POD test for examples/tk/gsequence.pl (no pod)
ok 987 - POD test for examples/tk/hitdisplay.pl (no pod)
ok 988 - POD test for examples/tools/extract_genes.pl
ok 989 - POD test for examples/tools/gb_to_gff.pl (no pod)
ok 990 - POD test for examples/tools/gff2ps.pl
ok 991 - POD test for examples/tools/parse_codeml.pl (no pod)
ok 992 - POD test for examples/tools/psw.pl (no pod)
ok 993 - POD test for examples/tools/reverse-translate.pl
ok 994 - POD test for examples/tools/run_genscan.pl (no pod)
ok 995 - POD test for examples/tools/run_primer3.pl
ok 996 - POD test for examples/tools/seq_pattern.pl (no pod)
ok 997 - POD test for examples/tools/standaloneblast.pl (no pod)
ok 998 - POD test for examples/tree/paup2phylip.pl (no pod)
ok 999 - POD test for maintenance/authors.pl
ok 1000 - POD test for maintenance/check_NAME.pl
ok 1001 - POD test for maintenance/check_URLs.pl
ok 1002 - POD test for maintenance/cvs2cl_by_file.pl
ok 1003 - POD test for maintenance/dependencies.pl
ok 1004 - POD test for maintenance/deprecated.pl
ok 1005 - POD test for maintenance/find_mod_deps.pl
ok 1006 - POD test for maintenance/modules.pl
ok 1007 - POD test for maintenance/module_usage.pl (no pod)
ok 1008 - POD test for maintenance/ncbi_blast_switches.pl (no pod)
ok 1009 - POD test for maintenance/pod.pl
ok 1010 - POD test for maintenance/symlink_script.pl
ok 1011 - POD test for maintenance/version.pl
Dubious, test returned 5 (wstat 1280, 0x500)
Failed 5/1011 subtests 
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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 - An object of class 'Bio::PopGen::Statistics' isa 'Bio::PopGen::Statistics'
ok 5 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 6 - An object of class 'Bio::PopGen::Population' 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 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 27 - An object of class 'Bio::PopGen::Population' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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: Valid email not provided; required for tests
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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 - An object of class 'Bio::DB::HIV' isa 'Bio::DB::HIV'
ok 5 - An object of class 'Bio::DB::HIV' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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 - An object of class 'Bio::DB::HIV::HIVAnnotProcessor' isa 'Bio::DB::HIV::HIVAnnotProcessor'
ok 5 - An object of class 'Bio::DB::HIV::HIVAnnotProcessor' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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 - An object of class 'Bio::DB::Query::HIVQuery' isa 'Bio::DB::Query::HIVQuery'
ok 8 - An object of class 'Bio::DB::Query::HIVQuery' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/RemoteDB/HIV/HIVQueryHelper.t .............. 
1..40
ok 1 - use Bio::DB::HIV::HIVQueryHelper;
ok 2 - An object of class 'HIVSchema' isa 'HIVSchema'
ok 3 - An object of class 'QRY' isa 'QRY'
ok 4 - An object of class 'R' isa 'R'
ok 5 - An object of class 'Q' 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/RemoteDB/SeqVersion.t ...................... 
1..10
ok 1 - use Bio::DB::SeqVersion;
ok 2
ok 3 # skip Network tests have not been requested
ok 4 # skip Network tests have not been requested
ok 5 # skip Network tests have not been requested
ok 6 # skip Network tests have not been requested
ok 7 # skip Network tests have not been requested
ok 8 # skip Network tests have not been requested
ok 9 # skip Network tests have not been requested
ok 10 # skip Network tests have not been requested
ok
t/RemoteDB/SwissProt.t ....................... skipped: Network tests have not been requested
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: . C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt\blib\lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt\blib\arch C:/cpanfly-5.18/var/cpan/build/BioPerl-1.6.901-pnEgJt C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt C:\cpanfly-5.18\var\megalib C:/cpanfly-5.18/var/megalib C:/Perl64-5.18/site/lib C:/Perl64-5.18/lib) at Bio\DB\Taxonomy\flatfile.pm line 89.
BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 89.
Compilation failed in require at Bio/Root/Root.pm line 543.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545
STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:263
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:114
STACK: t/RemoteDB/Taxonomy.t:24
-----------------------------------------------------------
Bio::DB::Taxonomy: flatfile cannot be found
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: . C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt\blib\lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt\blib\arch C:/cpanfly-5.18/var/cpan/build/BioPerl-1.6.901-pnEgJt C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-pnEgJt C:\cpanfly-5.18\var\megalib C:/cpanfly-5.18/var/megalib C:/Perl64-5.18/site/lib C:/Perl64-5.18/lib) at Bio\DB\Taxonomy\flatfile.pm line 89.
BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 89.
Compilation failed in require at Bio/Root/Root.pm line 543.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545
STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:263
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:114
STACK: t/RemoteDB/Taxonomy.t:24
-----------------------------------------------------------

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

#   Failed test at t/RemoteDB/Taxonomy.t line 24.
Can't call method "get_taxon" on an undefined value at t/RemoteDB/Taxonomy.t line 124.
# Looks like you planned 103 tests but ran 82.
# Looks like you failed 1 test of 82 run.
# Looks like your test exited with 255 just after 82.
t/RemoteDB/Taxonomy.t ........................ 
1..103
ok 1 - use Bio::DB::Taxonomy;
ok 2 - use Bio::Tree::Tree;
ok 3
not ok 4
ok 5 # skip Network tests have not been requested
ok 6 # skip Network tests have not been requested
ok 7 # skip Network tests have not been requested
ok 8 # skip Network tests have not been requested
ok 9 # skip Network tests have not been requested
ok 10 # skip Network tests have not been requested
ok 11 # skip Network tests have not been requested
ok 12 # skip Network tests have not been requested
ok 13 # skip Network tests have not been requested
ok 14 # skip Network tests have not been requested
ok 15 # skip Network tests have not been requested
ok 16 # skip Network tests have not been requested
ok 17 # skip Network tests have not been requested
ok 18 # skip Network tests have not been requested
ok 19 # skip Network tests have not been requested
ok 20 # skip Network tests have not been requested
ok 21 # skip Network tests have not been requested
ok 22 # skip Network tests have not been requested
ok 23 # skip Network tests have not been requested
ok 24 # skip Network tests have not been requested
ok 25 # skip Network tests have not been requested
ok 26 # skip Network tests have not been requested
ok 27 # skip Network tests have not been requested
ok 28 # skip Network tests have not been requested
ok 29 # skip Network tests have not been requested
ok 30 # skip Network tests have not been requested
ok 31 # skip Network tests have not been requested
ok 32 # skip Network tests have not been requested
ok 33 # skip Network tests have not been requested
ok 34 # skip Network tests have not been requested
ok 35 # skip Network tests have not been requested
ok 36 # skip Network tests have not been requested
ok 37 # skip Network tests have not been requested
ok 38 # skip Network tests have not been requested
ok 39 # skip Network tests have not been requested
ok 40 # skip Network tests have not been requested
ok 41 # skip Network tests have not been requested
ok 42 # skip Network tests have not been requested
ok 43 # skip Unable to connect to entrez database; no network or server busy?
ok 44 # skip Unable to connect to entrez database; no network or server busy?
ok 45 # skip Unable to connect to entrez database; no network or server busy?
ok 46 # skip Unable to connect to entrez database; no network or server busy?
ok 47 # skip Unable to connect to entrez database; no network or server busy?
ok 48 # skip Unable to connect to entrez database; no network or server busy?
ok 49 # skip Unable to connect to entrez database; no network or server busy?
ok 50 # skip Unable to connect to entrez database; no network or server busy?
ok 51 # skip Unable to connect to entrez database; no network or server busy?
ok 52 # skip Unable to connect to entrez database; no network or server busy?
ok 53 # skip Unable to connect to entrez database; no network or server busy?
ok 54 # skip Unable to connect to entrez database; no network or server busy?
ok 55 # skip Unable to connect to entrez database; no network or server busy?
ok 56 # skip Unable to connect to entrez database; no network or server busy?
ok 57 # skip Unable to connect to entrez database; no network or server busy?
ok 58 # skip Unable to connect to entrez database; no network or server busy?
ok 59 # skip Unable to connect to entrez database; no network or server busy?
ok 60 # skip Unable to connect to entrez database; no network or server busy?
ok 61 # skip Unable to connect to entrez database; no network or server busy?
ok 62 # skip Unable to connect to entrez database; no network or server busy?
ok 63 # skip Unable to connect to entrez database; no network or server busy?
ok 64 # skip Unable to connect to entrez database; no network or server busy?
ok 65 # skip Unable to connect to entrez database; no network or server busy?
ok 66 # skip Unable to connect to entrez database; no network or server busy?
ok 67 # skip Unable to connect to entrez database; no network or server busy?
ok 68 # skip Unable to connect to entrez database; no network or server busy?
ok 69 # skip Unable to connect to entrez database; no network or server busy?
ok 70 # skip Unable to connect to entrez database; no network or server busy?
ok 71 # skip Unable to connect to entrez database; no network or server busy?
ok 72 # skip Unable to connect to entrez database; no network or server busy?
ok 73 # skip Unable to connect to entrez database; no network or server busy?
ok 74 # skip Unable to connect to entrez database; no network or server busy?
ok 75 # skip Unable to connect to entrez database; no network or server busy?
ok 76 # skip Unable to connect to entrez database; no network or server busy?
ok 77 # skip Unable to connect to entrez database; no network or server busy?
ok 78 # skip Unable to connect to entrez database; no network or server busy?
ok 79 # skip Unable to connect to entrez database; no network or server busy?
ok 80 # skip Unable to connect to entrez database; no network or server busy?
ok 81
ok 82
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 22/103 subtests 
	(less 76 skipped subtests: 5 okay)
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Restriction/Analysis-refac.t ............... 
1..91
ok 1 - use Bio::Restriction::IO;
ok 2 - use Bio::Restriction::Analysis;
ok 3 - use Bio::Restriction::EnzymeCollection;
ok 4 - use Bio::Restriction::Enzyme;
ok 5 - read withrefm file
ok 6 - parse withrefm file
ok 7 - HindIII: nonambiguous intrasite cutter
ok 8 - AarI: nonambiguous extrasite cutter
ok 9 - AasI: ambiguous intrasite cutter
ok 10 - BceSI: ambiguous extrasite cutter
ok 11 - AjuI: cutter with central recog site
ok 12 - TaqII: multi-extrasite cutter
ok 13
ok 14 - HindIII plus
ok 15 - HindIII minus
ok 16 - AasI plus
ok 17 - AasI  minus
ok 18 - AarI plus
ok 19 - AarI  minus
ok 20 - BceSI plus
ok 21 - BceSI  minus
ok 22 - AjuI plus
ok 23 - AjuI minus
ok 24 - TaqII plus
ok 25 - TaqII minus
ok 26 - build real B:R::Analysis object
ok 27 - 13 fragments
ok 28 - circularize
ok 29 - recut
ok 30 - circ: AasI
# site at origin
ok 31 - circ: still 13 fragments (cut site at origin)
ok 32 - use Bio::Restriction::IO;
ok 33 - use Bio::Restriction::Analysis;
ok 34 - read withrefm file
ok 35 - parse withrefm file
ok 36 - Collection initiated
ok 37 - AbeI: found ok into collection
ok 38 - AccBSI: found ok into collection
ok 39 - AciI: found ok into collection
ok 40 - Asp26HI: found ok into collection
ok 41 - BmgBI: found ok into collection
ok 42 - AbeI plus
ok 43 - AbeI minus
ok 44 - AbeI fragment
ok 45 - AbeI positions
ok 46 - AbeI Overhang
ok 47 - AbeI name
ok 48 - AbeI site
ok 49 - AbeI revcom_site
ok 50 - AbeI cut
ok 51 - AbeI complementary_cut
ok 52 - AccBSI plus
ok 53 - AccBSI minus
ok 54 - AccBSI fragment
ok 55 - AccBSI positions
ok 56 - AccBSI Overhang
ok 57 - AccBSI name
ok 58 - AccBSI site
ok 59 - AccBSI revcom_site
ok 60 - AccBSI cut
ok 61 - AccBSI complementary_cut
ok 62 - AciI plus
ok 63 - AciI minus
ok 64 - AciI fragment
ok 65 - AciI positions
ok 66 - AciI Overhang
ok 67 - AciI name
ok 68 - AciI site
ok 69 - AciI revcom_site
ok 70 - AciI cut
ok 71 - AciI complementary_cut
ok 72 - Asp26HI plus
ok 73 - Asp26HI minus
ok 74 - Asp26HI fragment
ok 75 - Asp26HI positions
ok 76 - Asp26HI Overhang
ok 77 - Asp26HI name
ok 78 - Asp26HI site
ok 79 - Asp26HI revcom_site
ok 80 - Asp26HI cut
ok 81 - Asp26HI complementary_cut
ok 82 - BmgBI plus
ok 83 - BmgBI minus
ok 84 - BmgBI fragment
ok 85 - BmgBI positions
ok 86 - BmgBI Overhang
ok 87 - BmgBI name
ok 88 - BmgBI site
ok 89 - BmgBI revcom_site
ok 90 - BmgBI cut
ok 91 - BmgBI complementary_cut
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Restriction/Analysis.t ..................... 
1..182
ok 1 - use Bio::Restriction::Enzyme;
ok 2 - use Bio::Restriction::Enzyme::MultiCut;
ok 3 - use Bio::Restriction::Enzyme::MultiSite;
ok 4 - use Bio::Restriction::EnzymeCollection;
ok 5 - use Bio::Restriction::Analysis;
ok 6 - use Bio::SeqIO;
ok 7
ok 8 - An object of class 'Bio::Restriction::Enzyme' isa 'Bio::Restriction::EnzymeI'
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeqI'
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56 - bug 2179
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76 - An object of class 'Bio::Restriction::Enzyme::MultiSite' isa 'Bio::Restriction::EnzymeI'
ok 77 - An object of class 'Bio::Restriction::Enzyme::MultiSite' isa 'Bio::Restriction::EnzymeI'
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87 - An object of class 'Bio::Restriction::Enzyme::MultiCut' isa 'Bio::Restriction::EnzymeI'
ok 88 - An object of class 'Bio::Restriction::Enzyme::MultiCut' isa 'Bio::Restriction::EnzymeI'
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99 - An object of class 'Bio::Restriction::Enzyme' isa 'Bio::Restriction::Enzyme'
ok 100
ok 101
ok 102 - An object of class 'Bio::Restriction::Enzyme' isa 'Bio::Restriction::Enzyme'
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118 - number of unique cutters
ok 119 - number of RsaI fragments
ok 120 - number of maximum cutters
ok 121 - number of zero cutters
ok 122 - number of cutters
ok 123 - number of 3x cutters
ok 124 - 4 MseI fragments
ok 125 - 3 MseI cut sites
ok 126 - expected 2 PspEI fragments
ok 127
ok 128
ok 129 - expected 2 sizes for PspEI
ok 130
ok 131 - expected 2 sizes for PspEI
ok 132
ok 133 - not circular expected 1 fragments for MwoI as it doesnt cut
ok 134
ok 135
ok 136 - number of RsaI fragments
ok 137 - 3 circular MseI fragments
ok 138 - 3 circular MseI cut sites
ok 139 - number for AciI a non-palindromic enzyme
ok 140 - 1 fragment for MwoI as it cuts across the circ point
ok 141
ok 142
ok 143
ok 144
ok 145 - 7 fragments in the multiple digest
ok 146 - 7 positions in the multiple digest
ok 147 - 7 sizes in the multiple digest
ok 148
ok 149 -  expected 9 cuts for HindI
ok 150 - expect 9 fragment maps for HindI
ok 151 - sequence for GT
ok 152 - start at 40
ok 153 - end at 41
ok 154 - sequence for GGATTAAAAAAAGAGT
ok 155 - start at 42
ok 156 - end at 57
ok 157 - sequence for GTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGT
ok 158 - start at 58
ok 159 - end at 92
ok 160 - sequence for GAGTAAATTAAAATTTTATTGACTTAGGTCA
ok 161 - start at 93
ok 162 - end at 123
ok 163 - sequence for CTAAATACTTTAACCAATATAGGCATAGCGCA
ok 164 - start at 124
ok 165 - end at 155
ok 166 - sequence for CAGACAGATAAAAATTACAGAGTACA
ok 167 - start at 156
ok 168 - end at 181
ok 169 - sequence for CAACATCCATGAAACGCATTAGCA
ok 170 - start at 182
ok 171 - end at 205
ok 172 - sequence for CCA
ok 173 - start at 206
ok 174 - end at 208
ok 175 - sequence for CCAGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGT
ok 176 - start at 209
ok 177 - end at 39
ok 178
ok 179 - bug 2139
ok 180 - number of HindIII fragments
ok 181 - number of EcoRI fragments
ok 182 - number of RsaI fragments
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Restriction/Gel.t .......................... 
1..9
ok 1 - use Bio::PrimarySeq;
ok 2 - use Bio::Restriction::Analysis;
ok 3 - use Bio::Tools::Gel;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Restriction/IO.t ........................... 
1..18
ok 1 - use Bio::Restriction::IO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
not ok 8 # TODO writing to a file doesn't seem to work? prints to STDOUT!

#   Failed (TODO) test at t/Restriction/IO.t line 31.
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16 # skip Network tests have not been requested
ok 17 # skip Network tests have not been requested
ok 18 # skip Network tests have not been requested
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Root/Exception.t ........................... 
1..8
ok 1 - use TestObject;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok
t/Root/HTTPget.t ............................. skipped: Network tests have not been requested
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Root/RootI.t ............................... 
1..63
ok 1 - use Bio::Root::Root;
ok 2 - use Bio::Seq;
ok 3
ok 4 - An object of class 'Bio::Root::Root' isa 'Bio::Root::RootI'
ok 5 - threw Regexp ((?^:Testing throw))
ok 6 - threw Regexp ((?^:EXCEPTION: Bio::Root::NotImplemented))
ok 7 - threw Regexp ((?^:EXCEPTION ))
ok 8 - threw Regexp ((?^:Testing throw))
ok 9
ok 10 - threw Regexp ((?^:Testing throw))
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16 - simple
ok 17 - simple
ok 18 - warns for versions below current version 1.006901
ok 19 - warns for versions below current version 1.006901
ok 20 - throws for versions above 1.006901
ok 21 - throws for versions above 1.006901
ok 22 - throws for versions equal to 1.006901
ok 23 - simple
ok 24 - simple
ok 25 - warns for versions below current version 1.006901
ok 26 - warns for versions below current version 1.006901
ok 27 - throws for versions above 1.006901
ok 28 - throws for versions above 1.006901
ok 29 - arg callable since method was created
ok 30 - mal-formed arg callable since method was created with good name
ok 31 - Bio::Foo2->can('t3')
ok 32 - Methods don't pollute original Bio::Root::Root namespace
ok 33 - Bio::Foo2->can('test_4')
ok 34 - Methods don't pollute original Bio::Root::Root namespace
ok 35 - Bio::Foo3->can('t5')
ok 36 - arg not in method list not created
ok 37 - Bio::Foo3->can('t5')
ok 38 - Methods don't pollute original Bio::Root::Root namespace
ok 39 - verbose was set correctly
ok 40 - synonym was set correctly
ok 41 - real method of synonym was set correctly
ok 42 - mal-formed arg correctly resolved to created method
ok 43 - synonym of set method was set correctly
ok 44 - Bio::Foo4->can('t7')
ok 45 - Methods don't pollute original Bio::Root::Root namespace
ok 46 - Bio::Foo4->can('test7')
ok 47 - Methods don't pollute original Bio::Root::Root namespace
ok 48 - Bio::Foo4->can('test_8')
ok 49 - Methods don't pollute original Bio::Root::Root namespace
ok 50 - Bio::Foo4->can('t8')
ok 51 - Methods don't pollute original Bio::Root::Root namespace
ok 52 - clone
ok 53 - clone
ok 54 - clone
ok 55 - clone changed, original didn't
ok 56 - parameters passed to clone() modify object
ok 57 - original is not modified
ok 58 - must use proper versioning scheme
ok 59 - warns for versions >= 1.006901
ok 60 - warns for versions >= 1.006901
ok 61 - throws for versions >= 1.006901
ok 62 - throws for versions >= 1.006901
ok 63 - No warnings/exceptions below 1.006901
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29

#   Failed test 'executable file'
#   at t/Root/RootIO.t line 55.
Can't do inplace edit without backup at Bio/Root/IO.pm line 513.
# Looks like you planned 67 tests but ran 43.
# Looks like you failed 1 test of 43 run.
# Looks like your test exited with 25 just after 43.
Error removing C:/cpanfly-5.18/var/tmp/CPn0vH3n4S at C:\cpanfly-5.18\var\megalib/File/Temp.pm line 762.
t/Root/RootIO.t .............................. 
1..67
ok 1 - use Bio::Root::IO;
ok 2
ok 3 - throw()
ok 4 - throw() verbose(-1)
ok 5 - warn()
ok 6 - throw() verbose(1)
ok 7 - stack_trace()
ok 8 - set verbosity to 1
ok 9
ok 10
not ok 11 - executable file
ok 12 - non-executable file
ok 13 - executable dir
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19 - filename, read
ok 20
ok 21
ok 22 - filename, write
ok 23
ok 24
ok 25
ok 26
ok 27 - handle, read
ok 28
ok 29
ok 30 - handle, write
ok 31
ok 32 - is a write handle
ok 33 - no warnings
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42 - _print
ok 43
Dubious, test returned 25 (wstat 6400, 0x1900)
Failed 25/67 subtests 
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Root/Storable.t ............................ 
1..35
ok 1 - use Bio::Root::Storable;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Root/Tempfile.t ............................ 
1..18
ok 1 - use Bio::Root::IO;
ok 2
ok 3 - An object of class 'Bio::Root::IO' isa 'Bio::Root::IO'
ok 4
ok 5
ok 6 - auto UNLINK => 1
ok 7
ok 8
ok 9 - tempfile deleted
ok 10
ok 11 - UNLINK => 0
ok 12
ok 13
ok 14
ok 15 - tempfile suffix
ok 16
ok 17 - tempfile() in scalar context
ok 18
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Root/Utilities.t ........................... 
1..56
ok 1 - use Bio::Root::Utilities;
ok 2 - An object of class 'Bio::Root::Utilities' isa 'Bio::Root::Utilities'
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - file_date()
ok 38 - unix (\n or 012 or ^J)
ok 39 - date format
ok 40 - date format
ok 41 - date format
ok 42 - date format
ok 43 - date format
ok 44
ok 45 # skip gzip not found, skipping gzip tests
ok 46 # skip gzip not found, skipping gzip tests
ok 47 # skip gzip not found, skipping gzip tests
ok 48 # skip gzip not found, skipping gzip tests
ok 49 # skip gzip not found, skipping gzip tests
ok 50 # skip gzip not found, skipping gzip tests
ok 51 # skip gzip not found, skipping gzip tests
ok 52 # skip gzip not found, skipping gzip tests
ok 53 # skip gzip not found, skipping gzip tests
ok 54 # skip gzip not found, skipping gzip tests
ok 55 # skip gzip not found, skipping gzip tests
ok 56 # skip gzip not found, skipping gzip tests
ok
t/SearchDist.t ............................... skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/SearchIO/CigarString.t ..................... 
1..4
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok 4
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/SearchIO/SearchIO.t ........................ 
1..19
ok 1 - use Bio::SearchIO;
ok 2 - fasta for f.fasta
ok 3 - blast for f.blx
ok 4 - blast for f.tblx
ok 5 - blast for filename.blast
ok 6 - fasta for f.fy
ok 7 - blastxml for f.blastxml
ok 8 - fasta for f.m9
ok 9 - fasta for f.psearch
ok 10 - fasta for f.osearch
ok 11 - exonerate for f.exon
ok 12 - exonerate for f.exonerate
ok 13 - fasta for f.SSEARCH.m9
ok 14 - fasta for f.fx
ok 15 - blast for fast.bls
ok 16 - blastxml for f.xml
ok 17 - blast for filename.bls
ok 18 - fasta for f.fa
ok 19 - fasta for f.ssearch
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/SearchIO/SimilarityPair.t .................. 
1..12
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::SeqIO;
ok 3
ok 4 - An object of class 'Bio::Seq' isa 'Bio::SeqI'
ok 5
ok 6 - An object of class 'Bio::SearchIO::blast' isa 'Bio::SearchIO'
ok 7
ok 8 - An object of class 'Bio::Search::Hit::BlastHit' isa 'Bio::Search::Hit::HitI'
ok 9
ok 10 - An object of class 'Bio::Search::HSP::GenericHSP' isa 'Bio::SeqFeatureI'
ok 11
ok 12
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/SearchIO/Tiling.t .......................... 
1..1141
ok 1 - use Bio::Search::Tiling::MapTiling;
ok 2 - use Bio::Search::Tiling::MapTileUtils;
ok 3 - use Bio::SearchIO;
ok 4 - use Bio::Search::Hit::BlastHit;
ok 5 - use File::Spec;
ok 6 - parse data file
ok 7 - got test hit
ok 8 - create tiling
ok 9 - An object of class 'Bio::Search::Tiling::MapTiling' isa 'Bio::Search::Tiling::TilingI'
ok 10 - implements 'next_tiling'
ok 11 - implements 'rewind_tilings'
ok 12 - implements 'identities'
ok 13 - implements 'conserved'
ok 14 - implements 'length'
ok 15 - identities regression test
ok 16 - conserved regression test
ok 17 - tiling iterator regression test(1)
ok 18 - tiling iterator regression test(2)
ok 19 - tiling iterator regression test(3, rewind)
ok 20 - ecolitst.wublastp
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29 - dnaEbsub_ecoli.wublastx
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36 - tricky.wublast
ok 37 - tricky.wublast(1)
ok 38 - tricky.wublast(2)
ok 39 - tricky.wublast(3)
ok 40 - tricky.wublast(4)
ok 41 - ecolitst.bls
ok 42 - tile ecolitst.bls hit 1 \#hsps 1
ok 43 - q id: est (0.98293) = fast (0.98293)
ok 44 - q cn: est (0.98293) = fast (0.98293)
ok 45 - h id: est (0.98293) = fast (0.98293)
ok 46 - h cn: est (0.98293) = fast (0.98293)
ok 47 - tile ecolitst.bls hit 2 \#hsps 1
ok 48 - q id: est (0.30074) = fast (0.30074)
ok 49 - q cn: est (0.49876) = fast (0.49876)
ok 50 - h id: est (0.30759) = fast (0.30759)
ok 51 - h cn: est (0.51013) = fast (0.51013)
ok 52 - tile ecolitst.bls hit 3 \#hsps 1
ok 53 - q id: est (0.31004) = fast (0.31004)
ok 54 - q cn: est (0.49782) = fast (0.49782)
ok 55 - h id: est (0.32054) = fast (0.32054)
ok 56 - h cn: est (0.51467) = fast (0.51467)
ok 57 - tile ecolitst.bls hit 4 \#hsps 1
ok 58 - q id: est (0.30435) = fast (0.30435)
ok 59 - q cn: est (0.47826) = fast (0.47826)
ok 60 - h id: est (0.29787) = fast (0.29787)
ok 61 - h cn: est (0.46809) = fast (0.46809)
ok 62 - tricky.wublast
ok 63 - tile tricky.wublast hit 1 \#hsps 7
ok 64 - q id: exact (0.22153) ~ est (0.22153)
ok 65 - q id: exact (0.22153) <= max (0.22153)
ok 66 - q cn: exact (0.42760) ~ est (0.42760)
ok 67 - q cn: exact (0.42760) <= max (0.42760)
ok 68 - h id: exact (0.22704) ~ est (0.22704)
ok 69 - h id: exact (0.22704) <= max (0.22704)
ok 70 - h cn: exact (0.43335) ~ est (0.43335)
ok 71 - h cn: exact (0.43335) <= max (0.43335)
ok 72 - a_thaliana.blastn
ok 73 - tile a_thaliana.blastn hit 1 \#hsps 1
ok 74 - q id: est (0.96667) = fast (0.96667)
ok 75 - q cn: est (0.96667) = fast (0.96667)
ok 76 - h id: est (0.98305) = fast (0.98305)
ok 77 - h cn: est (0.98305) = fast (0.98305)
ok 78 - tile a_thaliana.blastn hit 2 \#hsps 1
ok 79 - q id: est (0.96667) = fast (0.96667)
ok 80 - q cn: est (0.96667) = fast (0.96667)
ok 81 - h id: est (0.98305) = fast (0.98305)
ok 82 - h cn: est (0.98305) = fast (0.98305)
ok 83 - tile a_thaliana.blastn hit 3 \#hsps 1
ok 84 - q id: est (1.00000) = fast (1.00000)
ok 85 - q cn: est (1.00000) = fast (1.00000)
ok 86 - h id: est (1.00000) = fast (1.00000)
ok 87 - h cn: est (1.00000) = fast (1.00000)
ok 88 - tile a_thaliana.blastn hit 4 \#hsps 1
ok 89 - q id: est (1.00000) = fast (1.00000)
ok 90 - q cn: est (1.00000) = fast (1.00000)
ok 91 - h id: est (1.00000) = fast (1.00000)
ok 92 - h cn: est (1.00000) = fast (1.00000)
ok 93 - tile a_thaliana.blastn hit 5 \#hsps 1
ok 94 - q id: est (0.92308) = fast (0.92308)
ok 95 - q cn: est (0.92308) = fast (0.92308)
ok 96 - h id: est (0.92308) = fast (0.92308)
ok 97 - h cn: est (0.92308) = fast (0.92308)
ok 98 - tile a_thaliana.blastn hit 6 \#hsps 1
ok 99 - q id: est (1.00000) = fast (1.00000)
ok 100 - q cn: est (1.00000) = fast (1.00000)
ok 101 - h id: est (1.00000) = fast (1.00000)
ok 102 - h cn: est (1.00000) = fast (1.00000)
ok 103 - tile a_thaliana.blastn hit 7 \#hsps 1
ok 104 - q id: est (1.00000) = fast (1.00000)
ok 105 - q cn: est (1.00000) = fast (1.00000)
ok 106 - h id: est (1.00000) = fast (1.00000)
ok 107 - h cn: est (1.00000) = fast (1.00000)
ok 108 - tile a_thaliana.blastn hit 8 \#hsps 1
ok 109 - q id: est (1.00000) = fast (1.00000)
ok 110 - q cn: est (1.00000) = fast (1.00000)
ok 111 - h id: est (1.00000) = fast (1.00000)
ok 112 - h cn: est (1.00000) = fast (1.00000)
ok 113 - tile a_thaliana.blastn hit 9 \#hsps 1
ok 114 - q id: est (1.00000) = fast (1.00000)
ok 115 - q cn: est (1.00000) = fast (1.00000)
ok 116 - h id: est (1.00000) = fast (1.00000)
ok 117 - h cn: est (1.00000) = fast (1.00000)
ok 118 - tile a_thaliana.blastn hit 10 \#hsps 1
ok 119 - q id: est (1.00000) = fast (1.00000)
ok 120 - q cn: est (1.00000) = fast (1.00000)
ok 121 - h id: est (1.00000) = fast (1.00000)
ok 122 - h cn: est (1.00000) = fast (1.00000)
ok 123 - tile a_thaliana.blastn hit 11 \#hsps 1
ok 124 - q id: est (1.00000) = fast (1.00000)
ok 125 - q cn: est (1.00000) = fast (1.00000)
ok 126 - h id: est (1.00000) = fast (1.00000)
ok 127 - h cn: est (1.00000) = fast (1.00000)
ok 128 - tile a_thaliana.blastn hit 12 \#hsps 1
ok 129 - q id: est (1.00000) = fast (1.00000)
ok 130 - q cn: est (1.00000) = fast (1.00000)
ok 131 - h id: est (1.00000) = fast (1.00000)
ok 132 - h cn: est (1.00000) = fast (1.00000)
ok 133 - tile a_thaliana.blastn hit 13 \#hsps 1
ok 134 - q id: est (1.00000) = fast (1.00000)
ok 135 - q cn: est (1.00000) = fast (1.00000)
ok 136 - h id: est (1.00000) = fast (1.00000)
ok 137 - h cn: est (1.00000) = fast (1.00000)
ok 138 - tile a_thaliana.blastn hit 14 \#hsps 1
ok 139 - q id: est (1.00000) = fast (1.00000)
ok 140 - q cn: est (1.00000) = fast (1.00000)
ok 141 - h id: est (1.00000) = fast (1.00000)
ok 142 - h cn: est (1.00000) = fast (1.00000)
ok 143 - tile a_thaliana.blastn hit 15 \#hsps 1
ok 144 - q id: est (1.00000) = fast (1.00000)
ok 145 - q cn: est (1.00000) = fast (1.00000)
ok 146 - h id: est (1.00000) = fast (1.00000)
ok 147 - h cn: est (1.00000) = fast (1.00000)
ok 148 - tile a_thaliana.blastn hit 16 \#hsps 1
ok 149 - q id: est (1.00000) = fast (1.00000)
ok 150 - q cn: est (1.00000) = fast (1.00000)
ok 151 - h id: est (1.00000) = fast (1.00000)
ok 152 - h cn: est (1.00000) = fast (1.00000)
ok 153 - tile a_thaliana.blastn hit 17 \#hsps 1
ok 154 - q id: est (1.00000) = fast (1.00000)
ok 155 - q cn: est (1.00000) = fast (1.00000)
ok 156 - h id: est (1.00000) = fast (1.00000)
ok 157 - h cn: est (1.00000) = fast (1.00000)
ok 158 - tile a_thaliana.blastn hit 18 \#hsps 1
ok 159 - q id: est (1.00000) = fast (1.00000)
ok 160 - q cn: est (1.00000) = fast (1.00000)
ok 161 - h id: est (1.00000) = fast (1.00000)
ok 162 - h cn: est (1.00000) = fast (1.00000)
ok 163 - tile a_thaliana.blastn hit 19 \#hsps 1
ok 164 - q id: est (1.00000) = fast (1.00000)
ok 165 - q cn: est (1.00000) = fast (1.00000)
ok 166 - h id: est (1.00000) = fast (1.00000)
ok 167 - h cn: est (1.00000) = fast (1.00000)
ok 168 - tile a_thaliana.blastn hit 20 \#hsps 1
ok 169 - q id: est (0.95238) = fast (0.95238)
ok 170 - q cn: est (0.95238) = fast (0.95238)
ok 171 - h id: est (0.95238) = fast (0.95238)
ok 172 - h cn: est (0.95238) = fast (0.95238)
ok 173 - tile a_thaliana.blastn hit 21 \#hsps 1
ok 174 - q id: est (1.00000) = fast (1.00000)
ok 175 - q cn: est (1.00000) = fast (1.00000)
ok 176 - h id: est (1.00000) = fast (1.00000)
ok 177 - h cn: est (1.00000) = fast (1.00000)
ok 178 - tile a_thaliana.blastn hit 22 \#hsps 1
ok 179 - q id: est (0.95238) = fast (0.95238)
ok 180 - q cn: est (0.95238) = fast (0.95238)
ok 181 - h id: est (0.95238) = fast (0.95238)
ok 182 - h cn: est (0.95238) = fast (0.95238)
ok 183 - tile a_thaliana.blastn hit 23 \#hsps 1
ok 184 - q id: est (1.00000) = fast (1.00000)
ok 185 - q cn: est (1.00000) = fast (1.00000)
ok 186 - h id: est (1.00000) = fast (1.00000)
ok 187 - h cn: est (1.00000) = fast (1.00000)
ok 188 - tile a_thaliana.blastn hit 24 \#hsps 1
ok 189 - q id: est (0.95238) = fast (0.95238)
ok 190 - q cn: est (0.95238) = fast (0.95238)
ok 191 - h id: est (0.95238) = fast (0.95238)
ok 192 - h cn: est (0.95238) = fast (0.95238)
ok 193 - tile a_thaliana.blastn hit 25 \#hsps 1
ok 194 - q id: est (1.00000) = fast (1.00000)
ok 195 - q cn: est (1.00000) = fast (1.00000)
ok 196 - h id: est (1.00000) = fast (1.00000)
ok 197 - h cn: est (1.00000) = fast (1.00000)
ok 198 - tile a_thaliana.blastn hit 26 \#hsps 1
ok 199 - q id: est (1.00000) = fast (1.00000)
ok 200 - q cn: est (1.00000) = fast (1.00000)
ok 201 - h id: est (1.00000) = fast (1.00000)
ok 202 - h cn: est (1.00000) = fast (1.00000)
ok 203 - tile a_thaliana.blastn hit 27 \#hsps 1
ok 204 - q id: est (1.00000) = fast (1.00000)
ok 205 - q cn: est (1.00000) = fast (1.00000)
ok 206 - h id: est (1.00000) = fast (1.00000)
ok 207 - h cn: est (1.00000) = fast (1.00000)
ok 208 - tile a_thaliana.blastn hit 28 \#hsps 1
ok 209 - q id: est (1.00000) = fast (1.00000)
ok 210 - q cn: est (1.00000) = fast (1.00000)
ok 211 - h id: est (1.00000) = fast (1.00000)
ok 212 - h cn: est (1.00000) = fast (1.00000)
ok 213 - tile a_thaliana.blastn hit 29 \#hsps 1
ok 214 - q id: est (1.00000) = fast (1.00000)
ok 215 - q cn: est (1.00000) = fast (1.00000)
ok 216 - h id: est (1.00000) = fast (1.00000)
ok 217 - h cn: est (1.00000) = fast (1.00000)
ok 218 - tile a_thaliana.blastn hit 30 \#hsps 1
ok 219 - q id: est (1.00000) = fast (1.00000)
ok 220 - q cn: est (1.00000) = fast (1.00000)
ok 221 - h id: est (1.00000) = fast (1.00000)
ok 222 - h cn: est (1.00000) = fast (1.00000)
ok 223 - tile a_thaliana.blastn hit 31 \#hsps 1
ok 224 - q id: est (1.00000) = fast (1.00000)
ok 225 - q cn: est (1.00000) = fast (1.00000)
ok 226 - h id: est (1.00000) = fast (1.00000)
ok 227 - h cn: est (1.00000) = fast (1.00000)
ok 228 - brassica_ATH.WUBLASTN
ok 229 - tile brassica_ATH.WUBLASTN hit 1 \#hsps 3
ok 230 - q id: exact (0.82465) ~ est (0.82343)
ok 231 - q id: exact (0.82465) <= max (0.83333)
ok 232 - q cn: exact (0.85590) ~ est (0.85312)
ok 233 - q cn: exact (0.85590) <= max (0.86458)
ok 234 - h id: exact (0.83920) ~ est (0.83920)
ok 235 - h id: exact (0.83920) <= max (0.83920)
ok 236 - h cn: exact (0.86935) ~ est (0.86935)
ok 237 - h cn: exact (0.86935) <= max (0.86935)
ok 238 - tile brassica_ATH.WUBLASTN hit 2 \#hsps 2
ok 239 - q id: exact (0.82486) ~ est (0.82486)
ok 240 - q id: exact (0.82486) <= max (0.82486)
ok 241 - q cn: exact (0.85122) ~ est (0.85122)
ok 242 - q cn: exact (0.85122) <= max (0.85122)
ok 243 - h id: exact (0.82955) ~ est (0.82955)
ok 244 - h id: exact (0.82955) <= max (0.82955)
ok 245 - h cn: exact (0.85606) ~ est (0.85606)
ok 246 - h cn: exact (0.85606) <= max (0.85606)
ok 247 - no_hsps.blastp
ok 248 - tile no_hsps.blastp hit 1 \#hsps 0
ok 249 - tile no_hsps.blastp hit 2 \#hsps 0
ok 250 - tile no_hsps.blastp hit 3 \#hsps 0
ok 251 - tile no_hsps.blastp hit 4 \#hsps 0
ok 252 - tile no_hsps.blastp hit 5 \#hsps 0
ok 253 - tile no_hsps.blastp hit 6 \#hsps 0
ok 254 - tile no_hsps.blastp hit 7 \#hsps 0
ok 255 - tile no_hsps.blastp hit 8 \#hsps 0
ok 256 - tile no_hsps.blastp hit 9 \#hsps 0
ok 257 - tile no_hsps.blastp hit 10 \#hsps 0
ok 258 - tile no_hsps.blastp hit 11 \#hsps 0
ok 259 - tile no_hsps.blastp hit 12 \#hsps 0
ok 260 - tile no_hsps.blastp hit 13 \#hsps 0
ok 261 - tile no_hsps.blastp hit 14 \#hsps 0
ok 262 - tile no_hsps.blastp hit 15 \#hsps 0
ok 263 - tile no_hsps.blastp hit 16 \#hsps 0
ok 264 - tile no_hsps.blastp hit 17 \#hsps 0
ok 265 - tile no_hsps.blastp hit 18 \#hsps 0
ok 266 - tile no_hsps.blastp hit 19 \#hsps 0
ok 267 - tile no_hsps.blastp hit 20 \#hsps 0
ok 268 - tile no_hsps.blastp hit 21 \#hsps 0
ok 269 - tile no_hsps.blastp hit 22 \#hsps 0
ok 270 - tile no_hsps.blastp hit 23 \#hsps 0
ok 271 - tile no_hsps.blastp hit 24 \#hsps 0
ok 272 - tile no_hsps.blastp hit 25 \#hsps 0
ok 273 - tile no_hsps.blastp hit 26 \#hsps 0
ok 274 - tile no_hsps.blastp hit 27 \#hsps 0
ok 275 - tile no_hsps.blastp hit 28 \#hsps 0
ok 276 - tile no_hsps.blastp hit 29 \#hsps 0
ok 277 - tile no_hsps.blastp hit 30 \#hsps 0
ok 278 - tile no_hsps.blastp hit 31 \#hsps 0
ok 279 - tile no_hsps.blastp hit 32 \#hsps 0
ok 280 - tile no_hsps.blastp hit 33 \#hsps 0
ok 281 - tile no_hsps.blastp hit 34 \#hsps 0
ok 282 - tile no_hsps.blastp hit 35 \#hsps 0
ok 283 - tile no_hsps.blastp hit 36 \#hsps 0
ok 284 - tile no_hsps.blastp hit 37 \#hsps 0
ok 285 - tile no_hsps.blastp hit 38 \#hsps 0
ok 286 - tile no_hsps.blastp hit 39 \#hsps 0
ok 287 - tile no_hsps.blastp hit 40 \#hsps 0
ok 288 - tile no_hsps.blastp hit 41 \#hsps 0
ok 289 - tile no_hsps.blastp hit 42 \#hsps 0
ok 290 - tile no_hsps.blastp hit 43 \#hsps 0
ok 291 - tile no_hsps.blastp hit 44 \#hsps 0
ok 292 - tile no_hsps.blastp hit 45 \#hsps 0
ok 293 - tile no_hsps.blastp hit 46 \#hsps 0
ok 294 - tile no_hsps.blastp hit 47 \#hsps 0
ok 295 - tile no_hsps.blastp hit 48 \#hsps 0
ok 296 - tile no_hsps.blastp hit 49 \#hsps 0
ok 297 - tile no_hsps.blastp hit 50 \#hsps 0
ok 298 - tile no_hsps.blastp hit 51 \#hsps 0
ok 299 - tile no_hsps.blastp hit 52 \#hsps 0
ok 300 - tile no_hsps.blastp hit 53 \#hsps 0
ok 301 - tile no_hsps.blastp hit 54 \#hsps 0
ok 302 - tile no_hsps.blastp hit 55 \#hsps 0
ok 303 - tile no_hsps.blastp hit 56 \#hsps 0
ok 304 - tile no_hsps.blastp hit 57 \#hsps 0
ok 305 - tile no_hsps.blastp hit 58 \#hsps 0
ok 306 - tile no_hsps.blastp hit 59 \#hsps 0
ok 307 - tile no_hsps.blastp hit 60 \#hsps 0
ok 308 - tile no_hsps.blastp hit 61 \#hsps 0
ok 309 - tile no_hsps.blastp hit 62 \#hsps 0
ok 310 - tile no_hsps.blastp hit 63 \#hsps 0
ok 311 - tile no_hsps.blastp hit 64 \#hsps 0
ok 312 - tile no_hsps.blastp hit 65 \#hsps 0
ok 313 - tile no_hsps.blastp hit 66 \#hsps 0
ok 314 - tile no_hsps.blastp hit 67 \#hsps 0
ok 315 - tile no_hsps.blastp hit 68 \#hsps 0
ok 316 - tile no_hsps.blastp hit 69 \#hsps 0
ok 317 - tile no_hsps.blastp hit 70 \#hsps 0
ok 318 - tile no_hsps.blastp hit 71 \#hsps 0
ok 319 - tile no_hsps.blastp hit 72 \#hsps 0
ok 320 - tile no_hsps.blastp hit 73 \#hsps 0
ok 321 - tile no_hsps.blastp hit 74 \#hsps 0
ok 322 - tile no_hsps.blastp hit 75 \#hsps 0
ok 323 - tile no_hsps.blastp hit 76 \#hsps 0
ok 324 - tile no_hsps.blastp hit 77 \#hsps 0
ok 325 - tile no_hsps.blastp hit 78 \#hsps 0
ok 326 - tile no_hsps.blastp hit 79 \#hsps 0
ok 327 - tile no_hsps.blastp hit 80 \#hsps 0
ok 328 - tile no_hsps.blastp hit 81 \#hsps 0
ok 329 - tile no_hsps.blastp hit 82 \#hsps 0
ok 330 - tile no_hsps.blastp hit 83 \#hsps 0
ok 331 - tile no_hsps.blastp hit 84 \#hsps 0
ok 332 - tile no_hsps.blastp hit 85 \#hsps 0
ok 333 - tile no_hsps.blastp hit 86 \#hsps 0
ok 334 - tile no_hsps.blastp hit 87 \#hsps 0
ok 335 - tile no_hsps.blastp hit 88 \#hsps 0
ok 336 - tile no_hsps.blastp hit 89 \#hsps 0
ok 337 - tile no_hsps.blastp hit 90 \#hsps 0
ok 338 - tile no_hsps.blastp hit 91 \#hsps 0
ok 339 - tile no_hsps.blastp hit 92 \#hsps 0
ok 340 - tile no_hsps.blastp hit 93 \#hsps 0
ok 341 - tile no_hsps.blastp hit 94 \#hsps 0
ok 342 - tile no_hsps.blastp hit 95 \#hsps 0
ok 343 - tile no_hsps.blastp hit 96 \#hsps 0
ok 344 - tile no_hsps.blastp hit 97 \#hsps 0
ok 345 - tile no_hsps.blastp hit 98 \#hsps 0
ok 346 - tile no_hsps.blastp hit 99 \#hsps 0
ok 347 - tile no_hsps.blastp hit 100 \#hsps 0
ok 348 - tile no_hsps.blastp hit 101 \#hsps 0
ok 349 - tile no_hsps.blastp hit 102 \#hsps 0
ok 350 - tile no_hsps.blastp hit 103 \#hsps 0
ok 351 - tile no_hsps.blastp hit 104 \#hsps 0
ok 352 - tile no_hsps.blastp hit 105 \#hsps 0
ok 353 - tile no_hsps.blastp hit 106 \#hsps 0
ok 354 - tile no_hsps.blastp hit 107 \#hsps 0
ok 355 - tile no_hsps.blastp hit 108 \#hsps 0
ok 356 - tile no_hsps.blastp hit 109 \#hsps 0
ok 357 - tile no_hsps.blastp hit 110 \#hsps 0
ok 358 - tile no_hsps.blastp hit 111 \#hsps 0
ok 359 - tile no_hsps.blastp hit 112 \#hsps 0
ok 360 - tile no_hsps.blastp hit 113 \#hsps 0
ok 361 - tile no_hsps.blastp hit 114 \#hsps 0
ok 362 - tile no_hsps.blastp hit 115 \#hsps 0
ok 363 - tile no_hsps.blastp hit 116 \#hsps 0
ok 364 - tile no_hsps.blastp hit 117 \#hsps 0
ok 365 - tile no_hsps.blastp hit 118 \#hsps 0
ok 366 - tile no_hsps.blastp hit 119 \#hsps 0
ok 367 - tile no_hsps.blastp hit 120 \#hsps 0
ok 368 - tile no_hsps.blastp hit 121 \#hsps 0
ok 369 - tile no_hsps.blastp hit 122 \#hsps 0
ok 370 - tile no_hsps.blastp hit 123 \#hsps 0
ok 371 - tile no_hsps.blastp hit 124 \#hsps 0
ok 372 - tile no_hsps.blastp hit 125 \#hsps 0
ok 373 - tile no_hsps.blastp hit 126 \#hsps 0
ok 374 - tile no_hsps.blastp hit 127 \#hsps 0
ok 375 - tile no_hsps.blastp hit 128 \#hsps 0
ok 376 - tile no_hsps.blastp hit 129 \#hsps 0
ok 377 - tile no_hsps.blastp hit 130 \#hsps 0
ok 378 - tile no_hsps.blastp hit 131 \#hsps 0
ok 379 - tile no_hsps.blastp hit 132 \#hsps 0
ok 380 - tile no_hsps.blastp hit 133 \#hsps 0
ok 381 - tile no_hsps.blastp hit 134 \#hsps 0
ok 382 - tile no_hsps.blastp hit 135 \#hsps 0
ok 383 - tile no_hsps.blastp hit 136 \#hsps 0
ok 384 - tile no_hsps.blastp hit 137 \#hsps 0
ok 385 - tile no_hsps.blastp hit 138 \#hsps 0
ok 386 - tile no_hsps.blastp hit 139 \#hsps 0
ok 387 - tile no_hsps.blastp hit 140 \#hsps 0
ok 388 - tile no_hsps.blastp hit 141 \#hsps 0
ok 389 - tile no_hsps.blastp hit 142 \#hsps 0
ok 390 - tile no_hsps.blastp hit 143 \#hsps 0
ok 391 - tile no_hsps.blastp hit 144 \#hsps 0
ok 392 - tile no_hsps.blastp hit 145 \#hsps 0
ok 393 - tile no_hsps.blastp hit 146 \#hsps 0
ok 394 - tile no_hsps.blastp hit 147 \#hsps 0
ok 395 - tile no_hsps.blastp hit 148 \#hsps 0
ok 396 - tile no_hsps.blastp hit 149 \#hsps 0
ok 397 - tile no_hsps.blastp hit 150 \#hsps 0
ok 398 - tile no_hsps.blastp hit 151 \#hsps 0
ok 399 - tile no_hsps.blastp hit 152 \#hsps 0
ok 400 - tile no_hsps.blastp hit 153 \#hsps 0
ok 401 - tile no_hsps.blastp hit 154 \#hsps 0
ok 402 - tile no_hsps.blastp hit 155 \#hsps 0
ok 403 - tile no_hsps.blastp hit 156 \#hsps 0
ok 404 - tile no_hsps.blastp hit 157 \#hsps 0
ok 405 - tile no_hsps.blastp hit 158 \#hsps 0
ok 406 - tile no_hsps.blastp hit 159 \#hsps 0
ok 407 - tile no_hsps.blastp hit 160 \#hsps 0
ok 408 - tile no_hsps.blastp hit 161 \#hsps 0
ok 409 - tile no_hsps.blastp hit 162 \#hsps 0
ok 410 - tile no_hsps.blastp hit 163 \#hsps 0
ok 411 - tile no_hsps.blastp hit 164 \#hsps 0
ok 412 - tile no_hsps.blastp hit 165 \#hsps 0
ok 413 - tile no_hsps.blastp hit 166 \#hsps 0
ok 414 - tile no_hsps.blastp hit 167 \#hsps 0
ok 415 - tile no_hsps.blastp hit 168 \#hsps 0
ok 416 - tile no_hsps.blastp hit 169 \#hsps 0
ok 417 - tile no_hsps.blastp hit 170 \#hsps 0
ok 418 - tile no_hsps.blastp hit 171 \#hsps 0
ok 419 - tile no_hsps.blastp hit 172 \#hsps 0
ok 420 - tile no_hsps.blastp hit 173 \#hsps 0
ok 421 - tile no_hsps.blastp hit 174 \#hsps 0
ok 422 - tile no_hsps.blastp hit 175 \#hsps 0
ok 423 - tile no_hsps.blastp hit 176 \#hsps 0
ok 424 - tile no_hsps.blastp hit 177 \#hsps 0
ok 425 - tile no_hsps.blastp hit 178 \#hsps 0
ok 426 - tile no_hsps.blastp hit 179 \#hsps 0
ok 427 - tile no_hsps.blastp hit 180 \#hsps 0
ok 428 - tile no_hsps.blastp hit 181 \#hsps 0
ok 429 - tile no_hsps.blastp hit 182 \#hsps 0
ok 430 - tile no_hsps.blastp hit 183 \#hsps 0
ok 431 - tile no_hsps.blastp hit 184 \#hsps 0
ok 432 - tile no_hsps.blastp hit 185 \#hsps 0
ok 433 - tile no_hsps.blastp hit 186 \#hsps 0
ok 434 - tile no_hsps.blastp hit 187 \#hsps 0
ok 435 - tile no_hsps.blastp hit 188 \#hsps 0
ok 436 - tile no_hsps.blastp hit 189 \#hsps 0
ok 437 - tile no_hsps.blastp hit 190 \#hsps 0
ok 438 - tile no_hsps.blastp hit 191 \#hsps 0
ok 439 - tile no_hsps.blastp hit 192 \#hsps 0
ok 440 - tile no_hsps.blastp hit 193 \#hsps 0
ok 441 - tile no_hsps.blastp hit 194 \#hsps 0
ok 442 - tile no_hsps.blastp hit 195 \#hsps 0
ok 443 - tile no_hsps.blastp hit 196 \#hsps 0
ok 444 - tile no_hsps.blastp hit 197 \#hsps 0
ok 445 - tile no_hsps.blastp hit 198 \#hsps 0
ok 446 - tile no_hsps.blastp hit 199 \#hsps 0
ok 447 - tile no_hsps.blastp hit 200 \#hsps 0
ok 448 - tile no_hsps.blastp hit 201 \#hsps 0
ok 449 - tile no_hsps.blastp hit 202 \#hsps 0
ok 450 - tile no_hsps.blastp hit 203 \#hsps 0
ok 451 - tile no_hsps.blastp hit 204 \#hsps 0
ok 452 - tile no_hsps.blastp hit 205 \#hsps 0
ok 453 - tile no_hsps.blastp hit 206 \#hsps 0
ok 454 - tile no_hsps.blastp hit 207 \#hsps 0
ok 455 - tile no_hsps.blastp hit 208 \#hsps 0
ok 456 - tile no_hsps.blastp hit 209 \#hsps 0
ok 457 - tile no_hsps.blastp hit 210 \#hsps 0
ok 458 - tile no_hsps.blastp hit 211 \#hsps 0
ok 459 - tile no_hsps.blastp hit 212 \#hsps 0
ok 460 - tile no_hsps.blastp hit 213 \#hsps 0
ok 461 - tile no_hsps.blastp hit 214 \#hsps 0
ok 462 - tile no_hsps.blastp hit 215 \#hsps 0
ok 463 - tile no_hsps.blastp hit 216 \#hsps 0
ok 464 - tile no_hsps.blastp hit 217 \#hsps 0
ok 465 - tile no_hsps.blastp hit 218 \#hsps 0
ok 466 - tile no_hsps.blastp hit 219 \#hsps 0
ok 467 - tile no_hsps.blastp hit 220 \#hsps 0
ok 468 - tile no_hsps.blastp hit 221 \#hsps 0
ok 469 - tile no_hsps.blastp hit 222 \#hsps 0
ok 470 - tile no_hsps.blastp hit 223 \#hsps 0
ok 471 - tile no_hsps.blastp hit 224 \#hsps 0
ok 472 - tile no_hsps.blastp hit 225 \#hsps 0
ok 473 - tile no_hsps.blastp hit 226 \#hsps 0
ok 474 - tile no_hsps.blastp hit 227 \#hsps 0
ok 475 - tile no_hsps.blastp hit 228 \#hsps 0
ok 476 - tile no_hsps.blastp hit 229 \#hsps 0
ok 477 - tile no_hsps.blastp hit 230 \#hsps 0
ok 478 - tile no_hsps.blastp hit 231 \#hsps 0
ok 479 - tile no_hsps.blastp hit 232 \#hsps 0
ok 480 - tile no_hsps.blastp hit 233 \#hsps 0
ok 481 - tile no_hsps.blastp hit 234 \#hsps 0
ok 482 - tile no_hsps.blastp hit 235 \#hsps 0
ok 483 - tile no_hsps.blastp hit 236 \#hsps 0
ok 484 - tile no_hsps.blastp hit 237 \#hsps 0
ok 485 - tile no_hsps.blastp hit 238 \#hsps 0
ok 486 - tile no_hsps.blastp hit 239 \#hsps 0
ok 487 - tile no_hsps.blastp hit 240 \#hsps 0
ok 488 - tile no_hsps.blastp hit 241 \#hsps 0
ok 489 - tile no_hsps.blastp hit 242 \#hsps 0
ok 490 - tile no_hsps.blastp hit 243 \#hsps 0
ok 491 - tile no_hsps.blastp hit 244 \#hsps 0
ok 492 - tile no_hsps.blastp hit 245 \#hsps 0
ok 493 - tile no_hsps.blastp hit 246 \#hsps 0
ok 494 - tile no_hsps.blastp hit 247 \#hsps 0
ok 495 - tile no_hsps.blastp hit 248 \#hsps 0
ok 496 - tile no_hsps.blastp hit 249 \#hsps 0
ok 497 - tile no_hsps.blastp hit 250 \#hsps 0
ok 498 - tile no_hsps.blastp hit 251 \#hsps 0
ok 499 - tile no_hsps.blastp hit 252 \#hsps 0
ok 500 - tile no_hsps.blastp hit 253 \#hsps 0
ok 501 - tile no_hsps.blastp hit 254 \#hsps 0
ok 502 - tile no_hsps.blastp hit 255 \#hsps 0
ok 503 - tile no_hsps.blastp hit 256 \#hsps 0
ok 504 - tile no_hsps.blastp hit 257 \#hsps 0
ok 505 - tile no_hsps.blastp hit 258 \#hsps 0
ok 506 - tile no_hsps.blastp hit 259 \#hsps 0
ok 507 - tile no_hsps.blastp hit 260 \#hsps 0
ok 508 - tile no_hsps.blastp hit 261 \#hsps 0
ok 509 - tile no_hsps.blastp hit 262 \#hsps 0
ok 510 - tile no_hsps.blastp hit 263 \#hsps 0
ok 511 - tile no_hsps.blastp hit 264 \#hsps 0
ok 512 - tile no_hsps.blastp hit 265 \#hsps 0
ok 513 - tile no_hsps.blastp hit 266 \#hsps 0
ok 514 - tile no_hsps.blastp hit 267 \#hsps 0
ok 515 - tile no_hsps.blastp hit 268 \#hsps 0
ok 516 - tile no_hsps.blastp hit 269 \#hsps 0
ok 517 - tile no_hsps.blastp hit 270 \#hsps 0
ok 518 - tile no_hsps.blastp hit 271 \#hsps 0
ok 519 - tile no_hsps.blastp hit 272 \#hsps 0
ok 520 - tile no_hsps.blastp hit 273 \#hsps 0
ok 521 - tile no_hsps.blastp hit 274 \#hsps 0
ok 522 - tile no_hsps.blastp hit 275 \#hsps 0
ok 523 - tile no_hsps.blastp hit 276 \#hsps 0
ok 524 - tile no_hsps.blastp hit 277 \#hsps 0
ok 525 - tile no_hsps.blastp hit 278 \#hsps 0
ok 526 - tile no_hsps.blastp hit 279 \#hsps 0
ok 527 - tile no_hsps.blastp hit 280 \#hsps 0
ok 528 - tile no_hsps.blastp hit 281 \#hsps 0
ok 529 - tile no_hsps.blastp hit 282 \#hsps 0
ok 530 - tile no_hsps.blastp hit 283 \#hsps 0
ok 531 - tile no_hsps.blastp hit 284 \#hsps 0
ok 532 - tile no_hsps.blastp hit 285 \#hsps 0
ok 533 - tile no_hsps.blastp hit 286 \#hsps 0
ok 534 - tile no_hsps.blastp hit 287 \#hsps 0
ok 535 - tile no_hsps.blastp hit 288 \#hsps 0
ok 536 - tile no_hsps.blastp hit 289 \#hsps 0
ok 537 - tile no_hsps.blastp hit 290 \#hsps 0
ok 538 - tile no_hsps.blastp hit 291 \#hsps 0
ok 539 - tile no_hsps.blastp hit 292 \#hsps 0
ok 540 - tile no_hsps.blastp hit 293 \#hsps 0
ok 541 - tile no_hsps.blastp hit 294 \#hsps 0
ok 542 - tile no_hsps.blastp hit 295 \#hsps 0
ok 543 - tile no_hsps.blastp hit 296 \#hsps 0
ok 544 - tile no_hsps.blastp hit 297 \#hsps 0
ok 545 - tile no_hsps.blastp hit 298 \#hsps 0
ok 546 - tile no_hsps.blastp hit 299 \#hsps 0
ok 547 - tile no_hsps.blastp hit 300 \#hsps 0
ok 548 - tile no_hsps.blastp hit 301 \#hsps 0
ok 549 - tile no_hsps.blastp hit 302 \#hsps 0
ok 550 - tile no_hsps.blastp hit 303 \#hsps 0
ok 551 - tile no_hsps.blastp hit 304 \#hsps 0
ok 552 - tile no_hsps.blastp hit 305 \#hsps 0
ok 553 - tile no_hsps.blastp hit 306 \#hsps 0
ok 554 - tile no_hsps.blastp hit 307 \#hsps 0
ok 555 - tile no_hsps.blastp hit 308 \#hsps 0
ok 556 - tile no_hsps.blastp hit 309 \#hsps 0
ok 557 - tile no_hsps.blastp hit 310 \#hsps 0
ok 558 - tile no_hsps.blastp hit 311 \#hsps 0
ok 559 - tile no_hsps.blastp hit 312 \#hsps 0
ok 560 - tile no_hsps.blastp hit 313 \#hsps 0
ok 561 - tile no_hsps.blastp hit 314 \#hsps 0
ok 562 - tile no_hsps.blastp hit 315 \#hsps 0
ok 563 - tile no_hsps.blastp hit 316 \#hsps 0
ok 564 - tile no_hsps.blastp hit 317 \#hsps 0
ok 565 - tile no_hsps.blastp hit 318 \#hsps 0
ok 566 - tile no_hsps.blastp hit 319 \#hsps 0
ok 567 - tile no_hsps.blastp hit 320 \#hsps 0
ok 568 - tile no_hsps.blastp hit 321 \#hsps 0
ok 569 - tile no_hsps.blastp hit 322 \#hsps 0
ok 570 - tile no_hsps.blastp hit 323 \#hsps 0
ok 571 - tile no_hsps.blastp hit 324 \#hsps 0
ok 572 - tile no_hsps.blastp hit 325 \#hsps 0
ok 573 - tile no_hsps.blastp hit 326 \#hsps 0
ok 574 - tile no_hsps.blastp hit 327 \#hsps 0
ok 575 - tile no_hsps.blastp hit 328 \#hsps 0
ok 576 - tile no_hsps.blastp hit 329 \#hsps 0
ok 577 - tile no_hsps.blastp hit 330 \#hsps 0
ok 578 - tile no_hsps.blastp hit 331 \#hsps 0
ok 579 - tile no_hsps.blastp hit 332 \#hsps 0
ok 580 - tile no_hsps.blastp hit 333 \#hsps 0
ok 581 - tile no_hsps.blastp hit 334 \#hsps 0
ok 582 - tile no_hsps.blastp hit 335 \#hsps 0
ok 583 - tile no_hsps.blastp hit 336 \#hsps 0
ok 584 - tile no_hsps.blastp hit 337 \#hsps 0
ok 585 - tile no_hsps.blastp hit 338 \#hsps 0
ok 586 - tile no_hsps.blastp hit 339 \#hsps 0
ok 587 - tile no_hsps.blastp hit 340 \#hsps 0
ok 588 - tile no_hsps.blastp hit 341 \#hsps 0
ok 589 - tile no_hsps.blastp hit 342 \#hsps 0
ok 590 - tile no_hsps.blastp hit 343 \#hsps 0
ok 591 - tile no_hsps.blastp hit 344 \#hsps 0
ok 592 - tile no_hsps.blastp hit 345 \#hsps 0
ok 593 - tile no_hsps.blastp hit 346 \#hsps 0
ok 594 - tile no_hsps.blastp hit 347 \#hsps 0
ok 595 - tile no_hsps.blastp hit 348 \#hsps 0
ok 596 - tile no_hsps.blastp hit 349 \#hsps 0
ok 597 - tile no_hsps.blastp hit 350 \#hsps 0
ok 598 - tile no_hsps.blastp hit 351 \#hsps 0
ok 599 - tile no_hsps.blastp hit 352 \#hsps 0
ok 600 - tile no_hsps.blastp hit 353 \#hsps 0
ok 601 - tile no_hsps.blastp hit 354 \#hsps 0
ok 602 - tile no_hsps.blastp hit 355 \#hsps 0
ok 603 - tile no_hsps.blastp hit 356 \#hsps 0
ok 604 - tile no_hsps.blastp hit 357 \#hsps 0
ok 605 - tile no_hsps.blastp hit 358 \#hsps 0
ok 606 - tile no_hsps.blastp hit 359 \#hsps 0
ok 607 - tile no_hsps.blastp hit 360 \#hsps 0
ok 608 - tile no_hsps.blastp hit 361 \#hsps 0
ok 609 - tile no_hsps.blastp hit 362 \#hsps 0
ok 610 - tile no_hsps.blastp hit 363 \#hsps 0
ok 611 - tile no_hsps.blastp hit 364 \#hsps 0
ok 612 - tile no_hsps.blastp hit 365 \#hsps 0
ok 613 - tile no_hsps.blastp hit 366 \#hsps 0
ok 614 - tile no_hsps.blastp hit 367 \#hsps 0
ok 615 - tile no_hsps.blastp hit 368 \#hsps 0
ok 616 - tile no_hsps.blastp hit 369 \#hsps 0
ok 617 - tile no_hsps.blastp hit 370 \#hsps 0
ok 618 - tile no_hsps.blastp hit 371 \#hsps 0
ok 619 - tile no_hsps.blastp hit 372 \#hsps 0
ok 620 - tile no_hsps.blastp hit 373 \#hsps 0
ok 621 - tile no_hsps.blastp hit 374 \#hsps 0
ok 622 - tile no_hsps.blastp hit 375 \#hsps 0
ok 623 - tile no_hsps.blastp hit 376 \#hsps 0
ok 624 - tile no_hsps.blastp hit 377 \#hsps 0
ok 625 - tile no_hsps.blastp hit 378 \#hsps 0
ok 626 - tile no_hsps.blastp hit 379 \#hsps 0
ok 627 - tile no_hsps.blastp hit 380 \#hsps 0
ok 628 - tile no_hsps.blastp hit 381 \#hsps 0
ok 629 - tile no_hsps.blastp hit 382 \#hsps 0
ok 630 - tile no_hsps.blastp hit 383 \#hsps 0
ok 631 - tile no_hsps.blastp hit 384 \#hsps 0
ok 632 - tile no_hsps.blastp hit 385 \#hsps 0
ok 633 - tile no_hsps.blastp hit 386 \#hsps 0
ok 634 - tile no_hsps.blastp hit 387 \#hsps 0
ok 635 - tile no_hsps.blastp hit 388 \#hsps 0
ok 636 - tile no_hsps.blastp hit 389 \#hsps 0
ok 637 - tile no_hsps.blastp hit 390 \#hsps 0
ok 638 - tile no_hsps.blastp hit 391 \#hsps 0
ok 639 - tile no_hsps.blastp hit 392 \#hsps 0
ok 640 - tile no_hsps.blastp hit 393 \#hsps 0
ok 641 - tile no_hsps.blastp hit 394 \#hsps 0
ok 642 - tile no_hsps.blastp hit 395 \#hsps 0
ok 643 - tile no_hsps.blastp hit 396 \#hsps 0
ok 644 - tile no_hsps.blastp hit 397 \#hsps 0
ok 645 - tile no_hsps.blastp hit 398 \#hsps 0
ok 646 - tile no_hsps.blastp hit 399 \#hsps 0
ok 647 - tile no_hsps.blastp hit 400 \#hsps 0
ok 648 - tile no_hsps.blastp hit 401 \#hsps 0
ok 649 - tile no_hsps.blastp hit 402 \#hsps 0
ok 650 - tile no_hsps.blastp hit 403 \#hsps 0
ok 651 - tile no_hsps.blastp hit 404 \#hsps 0
ok 652 - tile no_hsps.blastp hit 405 \#hsps 0
ok 653 - tile no_hsps.blastp hit 406 \#hsps 0
ok 654 - tile no_hsps.blastp hit 407 \#hsps 0
ok 655 - tile no_hsps.blastp hit 408 \#hsps 0
ok 656 - tile no_hsps.blastp hit 409 \#hsps 0
ok 657 - tile no_hsps.blastp hit 410 \#hsps 0
ok 658 - tile no_hsps.blastp hit 411 \#hsps 0
ok 659 - tile no_hsps.blastp hit 412 \#hsps 0
ok 660 - tile no_hsps.blastp hit 413 \#hsps 0
ok 661 - tile no_hsps.blastp hit 414 \#hsps 0
ok 662 - tile no_hsps.blastp hit 415 \#hsps 0
ok 663 - catalase-webblast.BLASTP
ok 664 - tile catalase-webblast.BLASTP hit 1 \#hsps 1
ok 665 - q id: est (1.00000) = fast (1.00000)
ok 666 - q cn: est (1.00000) = fast (1.00000)
ok 667 - h id: est (1.00000) = fast (1.00000)
ok 668 - h cn: est (1.00000) = fast (1.00000)
ok 669 - tile catalase-webblast.BLASTP hit 2 \#hsps 1
ok 670 - q id: est (0.80973) = fast (0.80973)
ok 671 - q cn: est (0.89006) = fast (0.89006)
ok 672 - h id: est (0.82543) = fast (0.82543)
ok 673 - h cn: est (0.90733) = fast (0.90733)
ok 674 - tile catalase-webblast.BLASTP hit 3 \#hsps 1
ok 675 - q id: est (0.71670) = fast (0.71670)
ok 676 - q cn: est (0.84144) = fast (0.84144)
ok 677 - h id: est (0.72747) = fast (0.72747)
ok 678 - h cn: est (0.85408) = fast (0.85408)
ok 679 - tile catalase-webblast.BLASTP hit 4 \#hsps 1
ok 680 - q id: est (0.58910) = fast (0.58910)
ok 681 - q cn: est (0.70860) = fast (0.70860)
ok 682 - h id: est (0.65654) = fast (0.65654)
ok 683 - h cn: est (0.78972) = fast (0.78972)
ok 684 - tile catalase-webblast.BLASTP hit 5 \#hsps 1
ok 685 - q id: est (0.49245) = fast (0.49245)
ok 686 - q cn: est (0.65257) = fast (0.65257)
ok 687 - h id: est (0.49544) = fast (0.49544)
ok 688 - h cn: est (0.65653) = fast (0.65653)
ok 689 - tile catalase-webblast.BLASTP hit 6 \#hsps 1
ok 690 - q id: est (0.44366) = fast (0.44366)
ok 691 - q cn: est (0.58920) = fast (0.58920)
ok 692 - h id: est (0.44787) = fast (0.44787)
ok 693 - h cn: est (0.59479) = fast (0.59479)
ok 694 - tile catalase-webblast.BLASTP hit 7 \#hsps 1
ok 695 - q id: est (0.42564) = fast (0.42564)
ok 696 - q cn: est (0.61282) = fast (0.61282)
ok 697 - h id: est (0.43229) = fast (0.43229)
ok 698 - h cn: est (0.62240) = fast (0.62240)
ok 699 - tile catalase-webblast.BLASTP hit 8 \#hsps 1
ok 700 - q id: est (0.48358) = fast (0.48358)
ok 701 - q cn: est (0.63881) = fast (0.63881)
ok 702 - h id: est (0.48943) = fast (0.48943)
ok 703 - h cn: est (0.64653) = fast (0.64653)
ok 704 - tile catalase-webblast.BLASTP hit 9 \#hsps 1
ok 705 - q id: est (0.42308) = fast (0.42308)
ok 706 - q cn: est (0.61282) = fast (0.61282)
ok 707 - h id: est (0.42969) = fast (0.42969)
ok 708 - h cn: est (0.62240) = fast (0.62240)
ok 709 - tile catalase-webblast.BLASTP hit 10 \#hsps 1
ok 710 - q id: est (0.39675) = fast (0.39675)
ok 711 - q cn: est (0.58933) = fast (0.58933)
ok 712 - h id: est (0.39767) = fast (0.39767)
ok 713 - h cn: est (0.59070) = fast (0.59070)
ok 714 - dcr1_sp.WUBLASTP
ok 715 - tile dcr1_sp.WUBLASTP hit 1 \#hsps 1
ok 716 - q id: est (1.00000) = fast (1.00000)
ok 717 - q cn: est (1.00000) = fast (1.00000)
ok 718 - h id: est (1.00000) = fast (1.00000)
ok 719 - h cn: est (1.00000) = fast (1.00000)
ok 720 - tile dcr1_sp.WUBLASTP hit 2 \#hsps 4
ok 721 - q id: exact (0.36876) ~ est (0.36973)
ok 722 - q id: exact (0.36876) <= max (0.37070)
ok 723 - q cn: exact (0.55022) ~ est (0.55041)
ok 724 - q cn: exact (0.55022) <= max (0.55105)
ok 725 - h id: exact (0.35111) ~ est (0.35111)
ok 726 - h id: exact (0.35111) <= max (0.35111)
ok 727 - h cn: exact (0.52305) ~ est (0.52305)
ok 728 - h cn: exact (0.52305) <= max (0.52305)
ok 729 - tile dcr1_sp.WUBLASTP hit 3 \#hsps 1
ok 730 - q id: est (0.38685) = fast (0.38685)
ok 731 - q cn: est (0.55397) = fast (0.55397)
ok 732 - h id: est (0.37613) = fast (0.37613)
ok 733 - h cn: est (0.53863) = fast (0.53863)
ok 734 - tile dcr1_sp.WUBLASTP hit 4 \#hsps 1
ok 735 - q id: est (0.38247) = fast (0.38247)
ok 736 - q cn: est (0.55068) = fast (0.55068)
ok 737 - h id: est (0.37306) = fast (0.37306)
ok 738 - h cn: est (0.53715) = fast (0.53715)
ok 739 - tile dcr1_sp.WUBLASTP hit 5 \#hsps 5
ok 740 - q id: exact (0.35010) ~ est (0.35010)
ok 741 - q id: exact (0.35010) <= max (0.35010)
ok 742 - q cn: exact (0.53183) ~ est (0.53183)
ok 743 - q cn: exact (0.53183) <= max (0.53183)
ok 744 - h id: exact (0.35082) ~ est (0.35082)
ok 745 - h id: exact (0.35082) <= max (0.35082)
ok 746 - h cn: exact (0.53292) ~ est (0.53292)
ok 747 - h cn: exact (0.53292) <= max (0.53292)
ok 748 - tile dcr1_sp.WUBLASTP hit 6 \#hsps 8
ok 749 - q id: exact (0.30547) ~ est (0.30659)
ok 750 - q id: exact (0.30547) <= max (0.30623)
ok 751 - q cn: exact (0.50076) ~ est (0.50205)
ok 752 - q cn: exact (0.50076) <= max (0.50076)
ok 753 - h id: exact (0.31390) ~ est (0.31179)
ok 754 - h id: exact (0.31390) <= max (0.31795)
ok 755 - h cn: exact (0.50531) ~ est (0.50557)
ok 756 - h cn: exact (0.50531) <= max (0.51091)
ok 757 - tile dcr1_sp.WUBLASTP hit 7 \#hsps 7
ok 758 - q id: exact (0.30136) ~ est (0.30184)
ok 759 - q id: exact (0.30136) <= max (0.30498)
ok 760 - q cn: exact (0.48688) ~ est (0.48742)
ok 761 - q cn: exact (0.48688) <= max (0.49140)
ok 762 - h id: exact (0.30944) ~ est (0.31034)
ok 763 - h id: exact (0.30944) <= max (0.30988)
ok 764 - h cn: exact (0.50178) ~ est (0.50277)
ok 765 - h cn: exact (0.50178) <= max (0.50223)
ok 766 - tile dcr1_sp.WUBLASTP hit 8 \#hsps 10
ok 767 - q id: exact (0.28918) ~ est (0.28961)
ok 768 - q id: exact (0.28918) <= max (0.28955)
ok 769 - q cn: exact (0.46418) ~ est (0.46247)
ok 770 - q cn: exact (0.46418) <= max (0.46866)
ok 771 - h id: exact (0.30166) ~ est (0.30299)
ok 772 - h id: exact (0.30166) <= max (0.30800)
ok 773 - h cn: exact (0.48179) ~ est (0.48439)
ok 774 - h cn: exact (0.48179) <= max (0.48535)
ok 775 - tile dcr1_sp.WUBLASTP hit 9 \#hsps 8
ok 776 - q id: exact (0.30289) ~ est (0.30238)
ok 777 - q id: exact (0.30289) <= max (0.30651)
ok 778 - q cn: exact (0.49955) ~ est (0.49787)
ok 779 - q cn: exact (0.49955) <= max (0.50362)
ok 780 - h id: exact (0.31395) ~ est (0.31347)
ok 781 - h id: exact (0.31395) <= max (0.31721)
ok 782 - h cn: exact (0.51535) ~ est (0.51578)
ok 783 - h cn: exact (0.51535) <= max (0.51814)
ok 784 - tile dcr1_sp.WUBLASTP hit 10 \#hsps 5
ok 785 - q id: exact (0.29334) ~ est (0.29534)
ok 786 - q id: exact (0.29334) <= max (0.29810)
ok 787 - q cn: exact (0.46617) ~ est (0.46719)
ok 788 - q cn: exact (0.46617) <= max (0.47040)
ok 789 - h id: exact (0.31176) ~ est (0.31176)
ok 790 - h id: exact (0.31176) <= max (0.31176)
ok 791 - h cn: exact (0.49299) ~ est (0.49299)
ok 792 - h cn: exact (0.49299) <= max (0.49299)
ok 793 - tile dcr1_sp.WUBLASTP hit 11 \#hsps 7
ok 794 - q id: exact (0.30456) ~ est (0.30514)
ok 795 - q id: exact (0.30456) <= max (0.30650)
ok 796 - q cn: exact (0.48739) ~ est (0.48879)
ok 797 - q cn: exact (0.48739) <= max (0.49370)
ok 798 - h id: exact (0.32062) ~ est (0.31987)
ok 799 - h id: exact (0.32062) <= max (0.32932)
ok 800 - h cn: exact (0.51071) ~ est (0.51306)
ok 801 - h cn: exact (0.51071) <= max (0.52410)
ok 802 - tile dcr1_sp.WUBLASTP hit 12 \#hsps 8
ok 803 - q id: exact (0.29615) ~ est (0.29879)
ok 804 - q id: exact (0.29615) <= max (0.30009)
ok 805 - q cn: exact (0.47419) ~ est (0.47394)
ok 806 - q cn: exact (0.47419) <= max (0.48119)
ok 807 - h id: exact (0.31611) ~ est (0.31482)
ok 808 - h id: exact (0.31611) <= max (0.32227)
ok 809 - h cn: exact (0.49779) ~ est (0.49788)
ok 810 - h cn: exact (0.49779) <= max (0.50616)
ok 811 - tile dcr1_sp.WUBLASTP hit 13 \#hsps 8
ok 812 - q id: exact (0.30390) ~ est (0.30440)
ok 813 - q id: exact (0.30390) <= max (0.30701)
ok 814 - q cn: exact (0.45874) ~ est (0.45993)
ok 815 - q cn: exact (0.45874) <= max (0.45963)
ok 816 - h id: exact (0.32282) ~ est (0.32324)
ok 817 - h id: exact (0.32282) <= max (0.32560)
ok 818 - h cn: exact (0.48052) ~ est (0.48136)
ok 819 - h cn: exact (0.48052) <= max (0.48330)
ok 820 - tile dcr1_sp.WUBLASTP hit 14 \#hsps 6
ok 821 - q id: exact (0.29769) ~ est (0.29851)
ok 822 - q id: exact (0.29769) <= max (0.29769)
ok 823 - q cn: exact (0.48480) ~ est (0.48628)
ok 824 - q cn: exact (0.48480) <= max (0.48637)
ok 825 - h id: exact (0.30704) ~ est (0.30810)
ok 826 - h id: exact (0.30704) <= max (0.30917)
ok 827 - h cn: exact (0.50107) ~ est (0.50292)
ok 828 - h cn: exact (0.50107) <= max (0.50320)
ok 829 - tile dcr1_sp.WUBLASTP hit 15 \#hsps 6
ok 830 - q id: exact (0.27854) ~ est (0.27854)
ok 831 - q id: exact (0.27854) <= max (0.27854)
ok 832 - q cn: exact (0.48174) ~ est (0.48174)
ok 833 - q cn: exact (0.48174) <= max (0.48174)
ok 834 - h id: exact (0.28514) ~ est (0.28623)
ok 835 - h id: exact (0.28514) <= max (0.28594)
ok 836 - h cn: exact (0.49197) ~ est (0.49154)
ok 837 - h cn: exact (0.49197) <= max (0.49237)
ok 838 - tile dcr1_sp.WUBLASTP hit 16 \#hsps 8
ok 839 - q id: exact (0.30362) ~ est (0.30824)
ok 840 - q id: exact (0.30362) <= max (0.30852)
ok 841 - q cn: exact (0.47111) ~ est (0.47587)
ok 842 - q cn: exact (0.47111) <= max (0.47405)
ok 843 - h id: exact (0.32347) ~ est (0.32392)
ok 844 - h id: exact (0.32347) <= max (0.32643)
ok 845 - h cn: exact (0.49310) ~ est (0.49360)
ok 846 - h cn: exact (0.49310) <= max (0.49606)
ok 847 - tile dcr1_sp.WUBLASTP hit 17 \#hsps 4
ok 848 - q id: exact (0.29174) ~ est (0.29174)
ok 849 - q id: exact (0.29174) <= max (0.29174)
ok 850 - q cn: exact (0.46230) ~ est (0.46230)
ok 851 - q cn: exact (0.46230) <= max (0.46230)
ok 852 - h id: exact (0.30204) ~ est (0.30204)
ok 853 - h id: exact (0.30204) <= max (0.30204)
ok 854 - h cn: exact (0.47862) ~ est (0.47862)
ok 855 - h cn: exact (0.47862) <= max (0.47862)
ok 856 - tile dcr1_sp.WUBLASTP hit 18 \#hsps 6
ok 857 - q id: exact (0.29064) ~ est (0.29089)
ok 858 - q id: exact (0.29064) <= max (0.29115)
ok 859 - q cn: exact (0.48765) ~ est (0.48670)
ok 860 - q cn: exact (0.48765) <= max (0.48868)
ok 861 - h id: exact (0.29848) ~ est (0.29887)
ok 862 - h id: exact (0.29848) <= max (0.29902)
ok 863 - h cn: exact (0.50108) ~ est (0.50116)
ok 864 - h cn: exact (0.50108) <= max (0.50163)
ok 865 - tile dcr1_sp.WUBLASTP hit 19 \#hsps 5
ok 866 - q id: exact (0.29510) ~ est (0.29505)
ok 867 - q id: exact (0.29510) <= max (0.29510)
ok 868 - q cn: exact (0.48982) ~ est (0.49039)
ok 869 - q cn: exact (0.48982) <= max (0.49029)
ok 870 - h id: exact (0.30019) ~ est (0.30019)
ok 871 - h id: exact (0.30019) <= max (0.30019)
ok 872 - h cn: exact (0.49906) ~ est (0.49906)
ok 873 - h cn: exact (0.49906) <= max (0.49906)
ok 874 - 503384.MEGABLAST.2
ok 875 - tile 503384.MEGABLAST.2 hit 1 \#hsps 5
ok 876 - q id: exact (0.91435) ~ est (0.91435)
ok 877 - q id: exact (0.91435) <= max (0.91435)
ok 878 - q cn: exact (0.91435) ~ est (0.91435)
ok 879 - q cn: exact (0.91435) <= max (0.91435)
ok 880 - h id: exact (0.91157) ~ est (0.91157)
ok 881 - h id: exact (0.91157) <= max (0.91157)
ok 882 - h cn: exact (0.91157) ~ est (0.91157)
ok 883 - h cn: exact (0.91157) <= max (0.91157)
ok 884 - tile 503384.MEGABLAST.2 hit 2 \#hsps 9
ok 885 - q id: exact (0.92895) ~ est (0.92895)
ok 886 - q id: exact (0.92895) <= max (0.92895)
ok 887 - q cn: exact (0.92895) ~ est (0.92895)
ok 888 - q cn: exact (0.92895) <= max (0.92895)
ok 889 - h id: exact (0.92854) ~ est (0.92854)
ok 890 - h id: exact (0.92854) <= max (0.92854)
ok 891 - h cn: exact (0.92854) ~ est (0.92854)
ok 892 - h cn: exact (0.92854) <= max (0.92854)
ok 893 - tile 503384.MEGABLAST.2 hit 3 \#hsps 3
ok 894 - q id: exact (0.93516) ~ est (0.93516)
ok 895 - q id: exact (0.93516) <= max (0.93516)
ok 896 - q cn: exact (0.93516) ~ est (0.93516)
ok 897 - q cn: exact (0.93516) <= max (0.93516)
ok 898 - h id: exact (0.93651) ~ est (0.93651)
ok 899 - h id: exact (0.93651) <= max (0.93651)
ok 900 - h cn: exact (0.93651) ~ est (0.93651)
ok 901 - h cn: exact (0.93651) <= max (0.93651)
ok 902 - tile 503384.MEGABLAST.2 hit 4 \#hsps 3
ok 903 - q id: exact (0.93064) ~ est (0.93064)
ok 904 - q id: exact (0.93064) <= max (0.93064)
ok 905 - q cn: exact (0.93064) ~ est (0.93064)
ok 906 - q cn: exact (0.93064) <= max (0.93064)
ok 907 - h id: exact (0.92885) ~ est (0.92885)
ok 908 - h id: exact (0.92885) <= max (0.92885)
ok 909 - h cn: exact (0.92885) ~ est (0.92885)
ok 910 - h cn: exact (0.92885) <= max (0.92885)
ok 911 - bl2seq.blastx.out
ok 912 - tile bl2seq.blastx.out hit 1 \#hsps 6
ok 913 - q id: est (0.35714) = fast (0.35714)
ok 914 - q cn: est (0.57143) = fast (0.57143)
ok 915 - q id: est (0.71429) = fast (0.71429)
ok 916 - q cn: est (1.00000) = fast (1.00000)
ok 917 - q id: exact (0.70536) ~ est (0.70495)
ok 918 - q id: exact (0.70536) <= max (0.94286)
ok 919 - q cn: exact (0.78810) ~ est (0.78803)
ok 920 - q cn: exact (0.78810) <= max (0.96429)
ok 921 - h id: exact (0.61923) ~ est (0.61955)
ok 922 - h id: exact (0.61923) <= max (0.64231)
ok 923 - h cn: exact (0.73077) ~ est (0.73077)
ok 924 - h cn: exact (0.73077) <= max (0.75000)
ok 925 - dnaEbsub_ecoli.wublastx
ok 926 - tile dnaEbsub_ecoli.wublastx hit 1 \#hsps 1
ok 927 - q id: est (0.36386) = fast (0.36386)
ok 928 - q cn: est (0.53735) = fast (0.53735)
ok 929 - h id: est (0.36562) = fast (0.36562)
ok 930 - h cn: est (0.53995) = fast (0.53995)
ok 931 - tblastn.out
ok 932 - tile tblastn.out hit 1 \#hsps 2
ok 933 - q id: exact (0.31250) ~ est (0.33325)
ok 934 - q id: exact (0.31250) <= max (0.33333)
ok 935 - q cn: exact (0.44792) ~ est (0.47055)
ok 936 - q cn: exact (0.44792) <= max (0.45833)
ok 937 - h id: exact (0.33333) ~ est (0.33333)
ok 938 - h id: exact (0.33333) <= max (0.33333)
ok 939 - h cn: exact (0.47059) ~ est (0.47059)
ok 940 - h cn: exact (0.47059) <= max (0.47059)
ok 941 - tile tblastn.out hit 2 \#hsps 2
ok 942 - q id: exact (0.68750) ~ est (0.68750)
ok 943 - q id: exact (0.68750) <= max (0.68750)
ok 944 - q cn: exact (0.81250) ~ est (0.81250)
ok 945 - q cn: exact (0.81250) <= max (0.81250)
ok 946 - h id: est (0.71429) = fast (0.71429)
ok 947 - h cn: est (0.85714) = fast (0.85714)
ok 948 - h id: est (0.66667) = fast (0.66667)
ok 949 - h cn: est (0.77778) = fast (0.77778)
ok 950 - dnaEbsub_ecoli.wutblastn
ok 951 - tile dnaEbsub_ecoli.wutblastn hit 1 \#hsps 1
ok 952 - q id: est (0.36386) = fast (0.36386)
ok 953 - q cn: est (0.53735) = fast (0.53735)
ok 954 - h id: est (0.36562) = fast (0.36562)
ok 955 - h cn: est (0.53995) = fast (0.53995)
ok 956 - HUMBETGLOA.tblastx
ok 957 - tile HUMBETGLOA.tblastx hit 1 \#hsps 1
ok 958 - q id: est (0.42308) = fast (0.42308)
ok 959 - q cn: est (0.61538) = fast (0.61538)
ok 960 - h id: est (0.42308) = fast (0.42308)
ok 961 - h cn: est (0.61538) = fast (0.61538)
ok 962 - tile HUMBETGLOA.tblastx hit 2 \#hsps 1
ok 963 - q id: est (0.47059) = fast (0.47059)
ok 964 - q cn: est (0.76471) = fast (0.76471)
ok 965 - h id: est (0.47059) = fast (0.47059)
ok 966 - h cn: est (0.76471) = fast (0.76471)
ok 967 - tile HUMBETGLOA.tblastx hit 3 \#hsps 1
ok 968 - q id: est (0.36000) = fast (0.36000)
ok 969 - q cn: est (0.56000) = fast (0.56000)
ok 970 - h id: est (0.36000) = fast (0.36000)
ok 971 - h cn: est (0.56000) = fast (0.56000)
ok 972 - tile HUMBETGLOA.tblastx hit 4 \#hsps 1
ok 973 - q id: est (0.29268) = fast (0.29268)
ok 974 - q cn: est (0.58537) = fast (0.58537)
ok 975 - h id: est (0.29268) = fast (0.29268)
ok 976 - h cn: est (0.58537) = fast (0.58537)
ok 977 - tile HUMBETGLOA.tblastx hit 5 \#hsps 1
ok 978 - q id: est (0.38889) = fast (0.38889)
ok 979 - q cn: est (0.55556) = fast (0.55556)
ok 980 - h id: est (0.38889) = fast (0.38889)
ok 981 - h cn: est (0.55556) = fast (0.55556)
ok 982 - tile HUMBETGLOA.tblastx hit 6 \#hsps 1
ok 983 - q id: est (0.43590) = fast (0.43590)
ok 984 - q cn: est (0.51282) = fast (0.51282)
ok 985 - h id: est (0.43590) = fast (0.43590)
ok 986 - h cn: est (0.51282) = fast (0.51282)
ok 987 - tile HUMBETGLOA.tblastx hit 7 \#hsps 1
ok 988 - q id: est (0.35714) = fast (0.35714)
ok 989 - q cn: est (0.42857) = fast (0.42857)
ok 990 - h id: est (0.35714) = fast (0.35714)
ok 991 - h cn: est (0.42857) = fast (0.42857)
ok 992 - tile HUMBETGLOA.tblastx hit 8 \#hsps 1
ok 993 - q id: est (0.33333) = fast (0.33333)
ok 994 - q cn: est (0.66667) = fast (0.66667)
ok 995 - h id: est (0.33333) = fast (0.33333)
ok 996 - h cn: est (0.66667) = fast (0.66667)
ok 997 - tile HUMBETGLOA.tblastx hit 9 \#hsps 2
ok 998 - q id: exact (0.40541) ~ est (0.40541)
ok 999 - q id: exact (0.40541) <= max (0.40541)
ok 1000 - q cn: exact (0.56757) ~ est (0.56757)
ok 1001 - q cn: exact (0.56757) <= max (0.56757)
ok 1002 - h id: est (0.36364) = fast (0.36364)
ok 1003 - h cn: est (0.63636) = fast (0.63636)
ok 1004 - h id: est (0.42308) = fast (0.42308)
ok 1005 - h cn: est (0.53846) = fast (0.53846)
ok 1006 - tile HUMBETGLOA.tblastx hit 10 \#hsps 1
ok 1007 - q id: est (0.29167) = fast (0.29167)
ok 1008 - q cn: est (0.39583) = fast (0.39583)
ok 1009 - h id: est (0.29167) = fast (0.29167)
ok 1010 - h cn: est (0.39583) = fast (0.39583)
ok 1011 - tile HUMBETGLOA.tblastx hit 11 \#hsps 1
ok 1012 - q id: est (0.60000) = fast (0.60000)
ok 1013 - q cn: est (0.65000) = fast (0.65000)
ok 1014 - h id: est (0.60000) = fast (0.60000)
ok 1015 - h cn: est (0.65000) = fast (0.65000)
ok 1016 - tile HUMBETGLOA.tblastx hit 12 \#hsps 1
ok 1017 - q id: est (0.50000) = fast (0.50000)
ok 1018 - q cn: est (0.68182) = fast (0.68182)
ok 1019 - h id: est (0.50000) = fast (0.50000)
ok 1020 - h cn: est (0.68182) = fast (0.68182)
ok 1021 - tile HUMBETGLOA.tblastx hit 13 \#hsps 1
ok 1022 - q id: est (0.29630) = fast (0.29630)
ok 1023 - q cn: est (0.48148) = fast (0.48148)
ok 1024 - h id: est (0.29630) = fast (0.29630)
ok 1025 - h cn: est (0.48148) = fast (0.48148)
ok 1026 - tile HUMBETGLOA.tblastx hit 14 \#hsps 1
ok 1027 - q id: est (0.47826) = fast (0.47826)
ok 1028 - q cn: est (0.52174) = fast (0.52174)
ok 1029 - h id: est (0.47826) = fast (0.47826)
ok 1030 - h cn: est (0.52174) = fast (0.52174)
ok 1031 - tile HUMBETGLOA.tblastx hit 15 \#hsps 1
ok 1032 - q id: est (0.47368) = fast (0.47368)
ok 1033 - q cn: est (0.63158) = fast (0.63158)
ok 1034 - h id: est (0.47368) = fast (0.47368)
ok 1035 - h cn: est (0.63158) = fast (0.63158)
ok 1036 - tile HUMBETGLOA.tblastx hit 16 \#hsps 1
ok 1037 - q id: est (0.44444) = fast (0.44444)
ok 1038 - q cn: est (0.55556) = fast (0.55556)
ok 1039 - h id: est (0.44444) = fast (0.44444)
ok 1040 - h cn: est (0.55556) = fast (0.55556)
ok 1041 - tile HUMBETGLOA.tblastx hit 17 \#hsps 1
ok 1042 - q id: est (0.47059) = fast (0.47059)
ok 1043 - q cn: est (0.70588) = fast (0.70588)
ok 1044 - h id: est (0.47059) = fast (0.47059)
ok 1045 - h cn: est (0.70588) = fast (0.70588)
ok 1046 - tile HUMBETGLOA.tblastx hit 18 \#hsps 1
ok 1047 - q id: est (0.38889) = fast (0.38889)
ok 1048 - q cn: est (0.66667) = fast (0.66667)
ok 1049 - h id: est (0.38889) = fast (0.38889)
ok 1050 - h cn: est (0.66667) = fast (0.66667)
ok 1051 - tile HUMBETGLOA.tblastx hit 19 \#hsps 1
ok 1052 - q id: est (0.27660) = fast (0.27660)
ok 1053 - q cn: est (0.48936) = fast (0.48936)
ok 1054 - h id: est (0.27660) = fast (0.27660)
ok 1055 - h cn: est (0.48936) = fast (0.48936)
ok 1056 - tile HUMBETGLOA.tblastx hit 20 \#hsps 1
ok 1057 - q id: est (0.40000) = fast (0.40000)
ok 1058 - q cn: est (0.60000) = fast (0.60000)
ok 1059 - h id: est (0.40000) = fast (0.40000)
ok 1060 - h cn: est (0.60000) = fast (0.60000)
ok 1061 - dnaEbsub_ecoli.wutblastx
ok 1062 - tile dnaEbsub_ecoli.wutblastx hit 1 \#hsps 12
ok 1063 - q id: exact (0.40224) ~ est (0.40912)
ok 1064 - q id: exact (0.40224) <= max (0.42628)
ok 1065 - q cn: exact (0.58494) ~ est (0.58968)
ok 1066 - q cn: exact (0.58494) <= max (0.62179)
ok 1067 - q id: est (0.25352) = fast (0.25352)
ok 1068 - q cn: est (0.47887) = fast (0.47887)
ok 1069 - q id: exact (0.44118) ~ est (0.44118)
ok 1070 - q id: exact (0.44118) <= max (0.44118)
ok 1071 - q cn: exact (0.54412) ~ est (0.54412)
ok 1072 - q cn: exact (0.54412) <= max (0.54412)
ok 1073 - q id: est (0.37500) = fast (0.37500)
ok 1074 - q cn: est (0.62500) = fast (0.62500)
ok 1075 - h id: exact (0.44118) ~ est (0.44118)
ok 1076 - h id: exact (0.44118) <= max (0.44118)
ok 1077 - h cn: exact (0.54412) ~ est (0.54412)
ok 1078 - h cn: exact (0.54412) <= max (0.54412)
ok 1079 - h id: exact (0.39848) ~ est (0.40304)
ok 1080 - h id: exact (0.39848) <= max (0.40355)
ok 1081 - h cn: exact (0.58376) ~ est (0.58889)
ok 1082 - h cn: exact (0.58376) <= max (0.58883)
ok 1083 - h id: est (0.25352) = fast (0.25352)
ok 1084 - h cn: est (0.47887) = fast (0.47887)
ok 1085 - tile dnaEbsub_ecoli.wutblastx hit 2 \#hsps 2
ok 1086 - q id: exact (0.41818) ~ est (0.41818)
ok 1087 - q id: exact (0.41818) <= max (0.41818)
ok 1088 - q cn: exact (0.52727) ~ est (0.52727)
ok 1089 - q cn: exact (0.52727) <= max (0.52727)
ok 1090 - h id: est (0.37500) = fast (0.37500)
ok 1091 - h cn: est (0.47500) = fast (0.47500)
ok 1092 - h id: est (0.53333) = fast (0.53333)
ok 1093 - h cn: est (0.66667) = fast (0.66667)
ok 1094 - bug2942: query m0: range correct
ok 1095 - bug2942: query m1: range correct
ok 1096 - bug2942: query m2: range correct
ok 1097 - bug2942: subject all : range correct
ok 1098 - get_tiled_alns
ok 1099 - got all alns
ok 1100
ok 1101 - aln and qfeat lengths correspond
ok 1102 - q length correct
ok 1103
ok 1104 - features on q and s correspond
ok 1105 - aln and hfeat lengths correspond
ok 1106 - s length correct
ok 1107
ok 1108 - aln and qfeat lengths correspond
ok 1109 - q length correct
ok 1110
ok 1111 - features on q and s correspond
ok 1112 - aln and hfeat lengths correspond
ok 1113 - s length correct
ok 1114
ok 1115 - aln and qfeat lengths correspond
ok 1116 - q length correct
ok 1117
ok 1118 - features on q and s correspond
ok 1119 - aln and hfeat lengths correspond
ok 1120 - s length correct
ok 1121
ok 1122 - aln and qfeat lengths correspond
ok 1123 - q length correct
ok 1124
ok 1125 - features on q and s correspond
ok 1126 - aln and hfeat lengths correspond
ok 1127 - s length correct
ok 1128
ok 1129 - aln and qfeat lengths correspond
ok 1130 - q length correct
ok 1131
ok 1132 - features on q and s correspond
ok 1133 - aln and hfeat lengths correspond
ok 1134 - s length correct
ok 1135
ok 1136 - aln and qfeat lengths correspond
ok 1137 - q length correct
ok 1138
ok 1139 - features on q and s correspond
ok 1140 - aln and hfeat lengths correspond
ok 1141 - s length correct
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/SearchIO/Writer/GbrowseGFF.t ............... 
1..4
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok 4
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/SearchIO/Writer/HSPTableWriter.t ........... 
1..8
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::SearchIO::Writer::HSPTableWriter;
ok 3 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI'
ok 4
ok 5
ok 6
ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 8
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/SearchIO/Writer/HTMLWriter.t ............... 
1..8
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::SearchIO::Writer::HTMLResultWriter;
ok 3 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI'
ok 4
ok 5
ok 6
ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 8
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/SearchIO/Writer/HitTableWriter.t ........... 
1..8
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::SearchIO::Writer::HitTableWriter;
ok 3 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI'
ok 4
ok 5
ok 6
ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 8
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/SearchIO/Writer/TextWriter.t ............... 
1..8
ok 1 - use Bio::SearchIO;
ok 2 - use Bio::SearchIO::Writer::TextResultWriter;
ok 3 - An object of class 'Bio::Search::Result::BlastResult' isa 'Bio::Search::Result::ResultI'
ok 4
ok 5
ok 6
ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 8
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/SearchIO/axt.t ............................. 
1..19
ok 1 - use Bio::SearchIO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29

Timeout (max run time is 300s)
C:\Perl64-5.18\bin\perl.exe exits with 37.