PATH=C:\mingw\bin;C:\cygwin\bin;C:\cpanfly-5.20\var\megalib\bin;C:\Perl-5.20\site\bin;C:\Perl-5.20\bin;C:\cygwin\bin;C:\Program Files\Perforce;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\instantclient_11_2;C:\cygwin\bin;C:\Program Files\Perforce;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\mysql\bin
Start 2014-09-28T20:45:32
ActivePerl-2000 CPAN-2.00
LIB=C:\PROGRA~1\MICROS~3\VC98\Lib\PSDK
PATH=C:/CPANFL~1.20/var/libs/bin;C:\mingw\bin;C:\cygwin\bin;C:\CPANFL~1.20\var\megalib\bin;C:\Perl-5.20\site\bin;C:\Perl-5.20\bin;C:\cygwin\bin;C:\PROGRA~1\Perforce;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WINDOW~2\v1.0;C:\WINDOWS\system32\WINDOW~2\v1.0;C:\INSTAN~1;C:\cygwin\bin;C:\PROGRA~1\Perforce;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WINDOW~2\v1.0;C:\WINDOWS\system32\WINDOW~2\v1.0;C:\mysql\bin
Reading 'C:\cpanfly-5.20\var\cpan\Metadata'
  Database was generated on Mon, 29 Sep 2014 00:17:02 GMT
Running make for C/CJ/CJFIELDS/BioPerl-1.6.923.tar.gz
Fetching with LWP:
http://cpan.nas1.activestate.com/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.923.tar.gz
Checksum for C:\cpanfly-5.20\var\cpan\sources\authors\id\C\CJ\CJFIELDS\BioPerl-1.6.923.tar.gz ok
BioPerl-1.6.923
BioPerl-1.6.923/.travis.yml
BioPerl-1.6.923/AUTHORS
BioPerl-1.6.923/BioPerl.pm
BioPerl-1.6.923/BUGS
BioPerl-1.6.923/Build.PL
BioPerl-1.6.923/Changes
BioPerl-1.6.923/DEPENDENCIES
BioPerl-1.6.923/DEPRECATED
BioPerl-1.6.923/INSTALL
BioPerl-1.6.923/INSTALL.SKIP
BioPerl-1.6.923/INSTALL.WIN
BioPerl-1.6.923/LICENSE
BioPerl-1.6.923/MANIFEST
BioPerl-1.6.923/META.json
BioPerl-1.6.923/META.yml
BioPerl-1.6.923/README
BioPerl-1.6.923/README.md
BioPerl-1.6.923/Bio
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BioPerl-1.6.923/Bio/Index/SwissPfam.pm
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BioPerl-1.6.923/Bio/TreeIO
BioPerl-1.6.923/Bio/TreeIO/cluster.pm
BioPerl-1.6.923/Bio/TreeIO/lintree.pm
BioPerl-1.6.923/Bio/TreeIO/newick.pm
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BioPerl-1.6.923/Bio/TreeIO/nexus.pm
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BioPerl-1.6.923/Bio/TreeIO/tabtree.pm
BioPerl-1.6.923/Bio/TreeIO/TreeEventBuilder.pm
BioPerl-1.6.923/Bio/Variation
BioPerl-1.6.923/Bio/Variation/AAChange.pm
BioPerl-1.6.923/Bio/Variation/AAReverseMutate.pm
BioPerl-1.6.923/Bio/Variation/Allele.pm
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BioPerl-1.6.923/Bio/Variation/IO.pm
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BioPerl-1.6.923/doc
BioPerl-1.6.923/doc/makedoc.PL
BioPerl-1.6.923/doc/README
BioPerl-1.6.923/doc/Deobfuscator
BioPerl-1.6.923/doc/Deobfuscator/Build.PL
BioPerl-1.6.923/doc/Deobfuscator/Changes
BioPerl-1.6.923/doc/Deobfuscator/excluded_modules.txt
BioPerl-1.6.923/doc/Deobfuscator/LICENSE
BioPerl-1.6.923/doc/Deobfuscator/Makefile.PL
BioPerl-1.6.923/doc/Deobfuscator/MANIFEST
BioPerl-1.6.923/doc/Deobfuscator/META.yml
BioPerl-1.6.923/doc/Deobfuscator/README
BioPerl-1.6.923/doc/Deobfuscator/bin
BioPerl-1.6.923/doc/Deobfuscator/bin/deob_index.pl
BioPerl-1.6.923/doc/Deobfuscator/bin/run-deobfuscator-update.pl
BioPerl-1.6.923/doc/Deobfuscator/cgi-bin
BioPerl-1.6.923/doc/Deobfuscator/cgi-bin/deob_detail.cgi
BioPerl-1.6.923/doc/Deobfuscator/cgi-bin/deob_flowchart.png
BioPerl-1.6.923/doc/Deobfuscator/cgi-bin/deob_help.html
BioPerl-1.6.923/doc/Deobfuscator/cgi-bin/deob_interface.cgi
BioPerl-1.6.923/doc/Deobfuscator/lib
BioPerl-1.6.923/doc/Deobfuscator/lib/Deobfuscator.pm
BioPerl-1.6.923/doc/Deobfuscator/t
BioPerl-1.6.923/doc/Deobfuscator/t/00.load.t
BioPerl-1.6.923/doc/Deobfuscator/t/pod.t
BioPerl-1.6.923/examples
BioPerl-1.6.923/examples/bioperl.pl
BioPerl-1.6.923/examples/generate_random_seq.pl
BioPerl-1.6.923/examples/longorf.pl
BioPerl-1.6.923/examples/make_primers.pl
BioPerl-1.6.923/examples/rev_and_trans.pl
BioPerl-1.6.923/examples/revcom_dir.pl
BioPerl-1.6.923/examples/subsequence.cgi
BioPerl-1.6.923/examples/align
BioPerl-1.6.923/examples/align/align_on_codons.pl
BioPerl-1.6.923/examples/align/aligntutorial.pl
BioPerl-1.6.923/examples/align/clustalw.pl
BioPerl-1.6.923/examples/align/FastAlign.pl
BioPerl-1.6.923/examples/align/simplealign.pl
BioPerl-1.6.923/examples/Bio-DB-GFF
BioPerl-1.6.923/examples/Bio-DB-GFF/load_ucsc.pl
BioPerl-1.6.923/examples/cluster
BioPerl-1.6.923/examples/cluster/dbsnp.pl
BioPerl-1.6.923/examples/contributed
BioPerl-1.6.923/examples/contributed/nmrpdb_parse.pl
BioPerl-1.6.923/examples/contributed/prosite2perl.pl
BioPerl-1.6.923/examples/contributed/rebase2list.pl
BioPerl-1.6.923/examples/db
BioPerl-1.6.923/examples/db/dbfetch
BioPerl-1.6.923/examples/db/est_tissue_query.pl
BioPerl-1.6.923/examples/db/gb2features.pl
BioPerl-1.6.923/examples/db/get_seqs.pl
BioPerl-1.6.923/examples/db/getGenBank.pl
BioPerl-1.6.923/examples/db/rfetch.pl
BioPerl-1.6.923/examples/db/use_registry.pl
BioPerl-1.6.923/examples/liveseq
BioPerl-1.6.923/examples/liveseq/change_gene.pl
BioPerl-1.6.923/examples/popgen
BioPerl-1.6.923/examples/popgen/parse_calc_stats.pl
BioPerl-1.6.923/examples/quality
BioPerl-1.6.923/examples/quality/svgtrace.pl
BioPerl-1.6.923/examples/root
BioPerl-1.6.923/examples/root/exceptions1.pl
BioPerl-1.6.923/examples/root/exceptions2.pl
BioPerl-1.6.923/examples/root/exceptions3.pl
BioPerl-1.6.923/examples/root/exceptions4.pl
BioPerl-1.6.923/examples/root/README
BioPerl-1.6.923/examples/root/lib
BioPerl-1.6.923/examples/root/lib/TestInterface.pm
BioPerl-1.6.923/examples/root/lib/TestObject.pm
BioPerl-1.6.923/examples/searchio
BioPerl-1.6.923/examples/searchio/blast_example.pl
BioPerl-1.6.923/examples/searchio/custom_writer.pl
BioPerl-1.6.923/examples/searchio/hitwriter.pl
BioPerl-1.6.923/examples/searchio/hspwriter.pl
BioPerl-1.6.923/examples/searchio/htmlwriter.pl
BioPerl-1.6.923/examples/searchio/psiblast_features.pl
BioPerl-1.6.923/examples/searchio/psiblast_iterations.pl
BioPerl-1.6.923/examples/searchio/rawwriter.pl
BioPerl-1.6.923/examples/searchio/resultwriter.pl
BioPerl-1.6.923/examples/searchio/waba2gff.pl
BioPerl-1.6.923/examples/searchio/waba2gff3.pl
BioPerl-1.6.923/examples/sirna
BioPerl-1.6.923/examples/sirna/rnai_finder.cgi
BioPerl-1.6.923/examples/sirna/TAG
BioPerl-1.6.923/examples/structure
BioPerl-1.6.923/examples/structure/structure-io.pl
BioPerl-1.6.923/examples/tk
BioPerl-1.6.923/examples/tk/gsequence.pl
BioPerl-1.6.923/examples/tk/hitdisplay.pl
BioPerl-1.6.923/examples/tools
BioPerl-1.6.923/examples/tools/extract_genes.pl
BioPerl-1.6.923/examples/tools/gb_to_gff.pl
BioPerl-1.6.923/examples/tools/gff2ps.pl
BioPerl-1.6.923/examples/tools/parse_codeml.pl
BioPerl-1.6.923/examples/tools/psw.pl
BioPerl-1.6.923/examples/tools/reverse-translate.pl
BioPerl-1.6.923/examples/tools/run_genscan.pl
BioPerl-1.6.923/examples/tools/run_primer3.pl
BioPerl-1.6.923/examples/tools/seq_pattern.pl
BioPerl-1.6.923/examples/tools/standaloneblast.pl
BioPerl-1.6.923/examples/tree
BioPerl-1.6.923/examples/tree/paup2phylip.pl
BioPerl-1.6.923/ide
BioPerl-1.6.923/ide/bioperl.komodo
BioPerl-1.6.923/ide/bioperl-mode
BioPerl-1.6.923/ide/bioperl-mode/README
BioPerl-1.6.923/ide/bioperl-mode/dist
BioPerl-1.6.923/ide/bioperl-mode/dist/bioperl-mode-xemacs.tar
BioPerl-1.6.923/ide/bioperl-mode/dist/bioperl-mode-xemacs.tar.md5
BioPerl-1.6.923/ide/bioperl-mode/dist/bioperl-mode.tar
BioPerl-1.6.923/ide/bioperl-mode/dist/bioperl-mode.tar.md5
BioPerl-1.6.923/ide/bioperl-mode/dist/Changes
BioPerl-1.6.923/ide/bioperl-mode/dist/package-me
BioPerl-1.6.923/ide/bioperl-mode/dist/SKIP
BioPerl-1.6.923/ide/bioperl-mode/etc
BioPerl-1.6.923/ide/bioperl-mode/etc/images
BioPerl-1.6.923/ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm
BioPerl-1.6.923/ide/bioperl-mode/etc/images/bpmode-tool.xpm
BioPerl-1.6.923/ide/bioperl-mode/site-lisp
BioPerl-1.6.923/ide/bioperl-mode/site-lisp/bioperl-init.el
BioPerl-1.6.923/ide/bioperl-mode/site-lisp/bioperl-mode.el
BioPerl-1.6.923/ide/bioperl-mode/site-lisp/bioperl-skel.el
BioPerl-1.6.923/ide/bioperl-mode/site-lisp/pod.el
BioPerl-1.6.923/maintenance
BioPerl-1.6.923/maintenance/authors.pl
BioPerl-1.6.923/maintenance/check_NAME.pl
BioPerl-1.6.923/maintenance/check_URLs.pl
BioPerl-1.6.923/maintenance/cvs2cl_by_file.pl
BioPerl-1.6.923/maintenance/dependencies.pl
BioPerl-1.6.923/maintenance/deprecated.pl
BioPerl-1.6.923/maintenance/find_mod_deps.pl
BioPerl-1.6.923/maintenance/module_usage.pl
BioPerl-1.6.923/maintenance/modules.pl
BioPerl-1.6.923/maintenance/ncbi_blast_switches.pl
BioPerl-1.6.923/maintenance/perltidy.conf
BioPerl-1.6.923/maintenance/pod.pl
BioPerl-1.6.923/maintenance/README
BioPerl-1.6.923/maintenance/symlink_script.pl
BioPerl-1.6.923/maintenance/version.pl
BioPerl-1.6.923/maintenance/big_split
BioPerl-1.6.923/maintenance/big_split/file_classification.csv
BioPerl-1.6.923/maintenance/big_split/rbuels_notes.txt
BioPerl-1.6.923/models
BioPerl-1.6.923/models/biblio.dia
BioPerl-1.6.923/models/bio_liveseq_variation.dia
BioPerl-1.6.923/models/bio_map.dia
BioPerl-1.6.923/models/bio_restriction.dia
BioPerl-1.6.923/models/bioperl.dia
BioPerl-1.6.923/models/coordinatemapper.dia
BioPerl-1.6.923/models/map_proposal.txt
BioPerl-1.6.923/models/maps_and_markers.dia
BioPerl-1.6.923/models/popgen.dia
BioPerl-1.6.923/models/population_proposal.txt
BioPerl-1.6.923/models/README
BioPerl-1.6.923/scripts
BioPerl-1.6.923/scripts/README
BioPerl-1.6.923/scripts/Bio-DB-GFF
BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_fast_load_gff.pl
BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_genbank2gff.pl
BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_genbank2gff3.pl
BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_generate_histogram.pl
BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_load_gff.pl
BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_meta_gff.pl
BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_process_gadfly.pl
BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_process_sgd.pl
BioPerl-1.6.923/scripts/Bio-DB-GFF/bp_process_wormbase.pl
BioPerl-1.6.923/scripts/Bio-DB-GFF/README
BioPerl-1.6.923/scripts/Bio-DB-SeqFeature-Store
BioPerl-1.6.923/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl
BioPerl-1.6.923/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl
BioPerl-1.6.923/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
BioPerl-1.6.923/scripts/das
BioPerl-1.6.923/scripts/das/bp_das_server.pl
BioPerl-1.6.923/scripts/das/README
BioPerl-1.6.923/scripts/das/TAG
BioPerl-1.6.923/scripts/DB
BioPerl-1.6.923/scripts/DB/bp_biofetch_genbank_proxy.pl
BioPerl-1.6.923/scripts/DB/bp_bioflat_index.pl
BioPerl-1.6.923/scripts/DB/bp_biogetseq.pl
BioPerl-1.6.923/scripts/DB/bp_flanks.pl
BioPerl-1.6.923/scripts/DB/TAG
BioPerl-1.6.923/scripts/DB-HIV
BioPerl-1.6.923/scripts/DB-HIV/bp_hivq.pl
BioPerl-1.6.923/scripts/index
BioPerl-1.6.923/scripts/index/bp_fetch.pl
BioPerl-1.6.923/scripts/index/bp_index.pl
BioPerl-1.6.923/scripts/index/bp_seqret.pl
BioPerl-1.6.923/scripts/index/TAG
BioPerl-1.6.923/scripts/popgen
BioPerl-1.6.923/scripts/popgen/bp_composite_LD.pl
BioPerl-1.6.923/scripts/popgen/bp_heterogeneity_test.pl
BioPerl-1.6.923/scripts/searchio
BioPerl-1.6.923/scripts/searchio/bp_fastam9_to_table.pl
BioPerl-1.6.923/scripts/searchio/bp_filter_search.pl
BioPerl-1.6.923/scripts/searchio/bp_hmmer_to_table.pl
BioPerl-1.6.923/scripts/searchio/bp_parse_hmmsearch.pl
BioPerl-1.6.923/scripts/searchio/bp_search2table.pl
BioPerl-1.6.923/scripts/searchio/README
BioPerl-1.6.923/scripts/searchio/TAG
BioPerl-1.6.923/scripts/seq
BioPerl-1.6.923/scripts/seq/bp_extract_feature_seq.pl
BioPerl-1.6.923/scripts/seq/bp_make_mrna_protein.pl
BioPerl-1.6.923/scripts/seq/bp_seqconvert.pl
BioPerl-1.6.923/scripts/seq/bp_seqcut.pl
BioPerl-1.6.923/scripts/seq/bp_seqpart.pl
BioPerl-1.6.923/scripts/seq/bp_seqretsplit.pl
BioPerl-1.6.923/scripts/seq/bp_split_seq.pl
BioPerl-1.6.923/scripts/seq/bp_translate_seq.pl
BioPerl-1.6.923/scripts/seq/bp_unflatten_seq.pl
BioPerl-1.6.923/scripts/seq/TAG
BioPerl-1.6.923/scripts/seqstats
BioPerl-1.6.923/scripts/seqstats/bp_aacomp.pl
BioPerl-1.6.923/scripts/seqstats/bp_chaos_plot.pl
BioPerl-1.6.923/scripts/seqstats/bp_gccalc.pl
BioPerl-1.6.923/scripts/seqstats/bp_oligo_count.pl
BioPerl-1.6.923/scripts/seqstats/TAG
BioPerl-1.6.923/scripts/taxa
BioPerl-1.6.923/scripts/taxa/bp_classify_hits_kingdom.pl
BioPerl-1.6.923/scripts/taxa/bp_local_taxonomydb_query.pl
BioPerl-1.6.923/scripts/taxa/bp_query_entrez_taxa.pl
BioPerl-1.6.923/scripts/taxa/bp_taxid4species.pl
BioPerl-1.6.923/scripts/taxa/bp_taxonomy2tree.pl
BioPerl-1.6.923/scripts/taxa/TAG
BioPerl-1.6.923/scripts/tree
BioPerl-1.6.923/scripts/tree/bp_blast2tree.pl
BioPerl-1.6.923/scripts/tree/bp_nexus2nh.pl
BioPerl-1.6.923/scripts/tree/bp_tree2pag.pl
BioPerl-1.6.923/scripts/tree/TAG
BioPerl-1.6.923/scripts/utilities
BioPerl-1.6.923/scripts/utilities/bp_dbsplit.pl
BioPerl-1.6.923/scripts/utilities/bp_download_query_genbank.pl
BioPerl-1.6.923/scripts/utilities/bp_mask_by_search.pl
BioPerl-1.6.923/scripts/utilities/bp_mrtrans.pl
BioPerl-1.6.923/scripts/utilities/bp_mutate.pl
BioPerl-1.6.923/scripts/utilities/bp_netinstall.pl
BioPerl-1.6.923/scripts/utilities/bp_nrdb.pl
BioPerl-1.6.923/scripts/utilities/bp_pairwise_kaks.pl
BioPerl-1.6.923/scripts/utilities/bp_remote_blast.pl
BioPerl-1.6.923/scripts/utilities/bp_revtrans-motif.pl
BioPerl-1.6.923/scripts/utilities/bp_search2alnblocks.pl
BioPerl-1.6.923/scripts/utilities/bp_search2BSML.pl
BioPerl-1.6.923/scripts/utilities/bp_search2gff.pl
BioPerl-1.6.923/scripts/utilities/bp_search2tribe.pl
BioPerl-1.6.923/scripts/utilities/bp_seq_length.pl
BioPerl-1.6.923/scripts/utilities/bp_sreformat.pl
BioPerl-1.6.923/scripts/utilities/README
BioPerl-1.6.923/scripts/utilities/TAG
BioPerl-1.6.923/t
BioPerl-1.6.923/t/Alphabet.t
BioPerl-1.6.923/t/nexml.t
BioPerl-1.6.923/t/Perl.t
BioPerl-1.6.923/t/PodSyntax.t
BioPerl-1.6.923/t/SearchDist.t
BioPerl-1.6.923/t/SeqEvolution.t
BioPerl-1.6.923/t/Species.t
BioPerl-1.6.923/t/Symbol.t
BioPerl-1.6.923/t/TaxonTree.t
BioPerl-1.6.923/t/Align
BioPerl-1.6.923/t/Align/AlignStats.t
BioPerl-1.6.923/t/Align/AlignUtil.t
BioPerl-1.6.923/t/Align/Graphics.t
BioPerl-1.6.923/t/Align/SimpleAlign.t
BioPerl-1.6.923/t/Align/TreeBuild.t
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BioPerl-1.6.923/t/AlignIO/nexus.t
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BioPerl-1.6.923/t/Annotation
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BioPerl-1.6.923/t/Annotation/AnnotationAdaptor.t
BioPerl-1.6.923/t/Assembly
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BioPerl-1.6.923/t/ClusterIO/unigene.t
BioPerl-1.6.923/t/Coordinate
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BioPerl-1.6.923/t/Coordinate/CoordinateGraph.t
BioPerl-1.6.923/t/Coordinate/CoordinateMapper.t
BioPerl-1.6.923/t/Coordinate/GeneCoordinateMapper.t
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BioPerl-1.6.923/t/Map
BioPerl-1.6.923/t/Map/Cyto.t
BioPerl-1.6.923/t/Map/Linkage.t
BioPerl-1.6.923/t/Map/Map.t
BioPerl-1.6.923/t/Map/MapIO.t
BioPerl-1.6.923/t/Map/MicrosatelliteMarker.t
BioPerl-1.6.923/t/Map/Physical.t
BioPerl-1.6.923/t/Matrix
BioPerl-1.6.923/t/Matrix/InstanceSite.t
BioPerl-1.6.923/t/Matrix/Matrix.t
BioPerl-1.6.923/t/Matrix/ProtMatrix.t
BioPerl-1.6.923/t/Matrix/ProtPsm.t
BioPerl-1.6.923/t/Matrix/SiteMatrix.t
BioPerl-1.6.923/t/Matrix/IO
BioPerl-1.6.923/t/Matrix/IO/masta.t
BioPerl-1.6.923/t/Matrix/IO/psm.t
BioPerl-1.6.923/t/Ontology
BioPerl-1.6.923/t/Ontology/GOterm.t
BioPerl-1.6.923/t/Ontology/GraphAdaptor.t
BioPerl-1.6.923/t/Ontology/Ontology.t
BioPerl-1.6.923/t/Ontology/OntologyEngine.t
BioPerl-1.6.923/t/Ontology/OntologyStore.t
BioPerl-1.6.923/t/Ontology/Relationship.t
BioPerl-1.6.923/t/Ontology/RelationshipType.t
BioPerl-1.6.923/t/Ontology/Term.t
BioPerl-1.6.923/t/Ontology/IO
BioPerl-1.6.923/t/Ontology/IO/go.t
BioPerl-1.6.923/t/Ontology/IO/interpro.t
BioPerl-1.6.923/t/Ontology/IO/obo.t
BioPerl-1.6.923/t/Phenotype
BioPerl-1.6.923/t/Phenotype/Correlate.t
BioPerl-1.6.923/t/Phenotype/Measure.t
BioPerl-1.6.923/t/Phenotype/MeSH.t
BioPerl-1.6.923/t/Phenotype/MiniMIMentry.t
BioPerl-1.6.923/t/Phenotype/OMIMentry.t
BioPerl-1.6.923/t/Phenotype/OMIMentryAllelicVariant.t
BioPerl-1.6.923/t/Phenotype/OMIMparser.t
BioPerl-1.6.923/t/Phenotype/Phenotype.t
BioPerl-1.6.923/t/PopGen
BioPerl-1.6.923/t/PopGen/Coalescent.t
BioPerl-1.6.923/t/PopGen/HtSNP.t
BioPerl-1.6.923/t/PopGen/MK.t
BioPerl-1.6.923/t/PopGen/PopGen.t
BioPerl-1.6.923/t/PopGen/PopGenSims.t
BioPerl-1.6.923/t/PopGen/TagHaplotype.t
BioPerl-1.6.923/t/RemoteDB
BioPerl-1.6.923/t/RemoteDB/BioFetch.t
BioPerl-1.6.923/t/RemoteDB/CUTG.t
BioPerl-1.6.923/t/RemoteDB/EMBL.t
BioPerl-1.6.923/t/RemoteDB/EntrezGene.t
BioPerl-1.6.923/t/RemoteDB/GenBank.t
BioPerl-1.6.923/t/RemoteDB/GenPept.t
BioPerl-1.6.923/t/RemoteDB/MeSH.t
BioPerl-1.6.923/t/RemoteDB/RefSeq.t
BioPerl-1.6.923/t/RemoteDB/SeqHound.t
BioPerl-1.6.923/t/RemoteDB/SeqRead_fail.t
BioPerl-1.6.923/t/RemoteDB/SeqVersion.t
BioPerl-1.6.923/t/RemoteDB/SwissProt.t
BioPerl-1.6.923/t/RemoteDB/Taxonomy.t
BioPerl-1.6.923/t/RemoteDB/HIV
BioPerl-1.6.923/t/RemoteDB/HIV/HIV.t
BioPerl-1.6.923/t/RemoteDB/HIV/HIVAnnotProcessor.t
BioPerl-1.6.923/t/RemoteDB/HIV/HIVQuery.t
BioPerl-1.6.923/t/RemoteDB/HIV/HIVQueryHelper.t
BioPerl-1.6.923/t/RemoteDB/Query
BioPerl-1.6.923/t/RemoteDB/Query/GenBank.t
BioPerl-1.6.923/t/Restriction
BioPerl-1.6.923/t/Restriction/Analysis-refac.t
BioPerl-1.6.923/t/Restriction/Analysis.t
BioPerl-1.6.923/t/Restriction/Gel.t
BioPerl-1.6.923/t/Restriction/IO.t
BioPerl-1.6.923/t/Root
BioPerl-1.6.923/t/Root/Exception.t
BioPerl-1.6.923/t/Root/HTTPget.t
BioPerl-1.6.923/t/Root/RootI.t
BioPerl-1.6.923/t/Root/RootIO.t
BioPerl-1.6.923/t/Root/Storable.t
BioPerl-1.6.923/t/Root/Tempfile.t
BioPerl-1.6.923/t/Root/Utilities.t
BioPerl-1.6.923/t/SearchIO
BioPerl-1.6.923/t/SearchIO/axt.t
BioPerl-1.6.923/t/SearchIO/blast.t
BioPerl-1.6.923/t/SearchIO/blast_pull.t
BioPerl-1.6.923/t/SearchIO/blasttable.t
BioPerl-1.6.923/t/SearchIO/blastxml.t
BioPerl-1.6.923/t/SearchIO/CigarString.t
BioPerl-1.6.923/t/SearchIO/cross_match.t
BioPerl-1.6.923/t/SearchIO/erpin.t
BioPerl-1.6.923/t/SearchIO/exonerate.t
BioPerl-1.6.923/t/SearchIO/fasta.t
BioPerl-1.6.923/t/SearchIO/gmap_f9.t
BioPerl-1.6.923/t/SearchIO/hmmer.t
BioPerl-1.6.923/t/SearchIO/hmmer_pull.t
BioPerl-1.6.923/t/SearchIO/infernal.t
BioPerl-1.6.923/t/SearchIO/megablast.t
BioPerl-1.6.923/t/SearchIO/psl.t
BioPerl-1.6.923/t/SearchIO/rnamotif.t
BioPerl-1.6.923/t/SearchIO/SearchIO.t
BioPerl-1.6.923/t/SearchIO/sim4.t
BioPerl-1.6.923/t/SearchIO/SimilarityPair.t
BioPerl-1.6.923/t/SearchIO/Tiling.t
BioPerl-1.6.923/t/SearchIO/waba.t
BioPerl-1.6.923/t/SearchIO/wise.t
BioPerl-1.6.923/t/SearchIO/Writer
BioPerl-1.6.923/t/SearchIO/Writer/GbrowseGFF.t
BioPerl-1.6.923/t/SearchIO/Writer/HitTableWriter.t
BioPerl-1.6.923/t/SearchIO/Writer/HSPTableWriter.t
BioPerl-1.6.923/t/SearchIO/Writer/HTMLWriter.t
BioPerl-1.6.923/t/SearchIO/Writer/TextWriter.t
BioPerl-1.6.923/t/Seq
BioPerl-1.6.923/t/Seq/DBLink.t
BioPerl-1.6.923/t/Seq/EncodedSeq.t
BioPerl-1.6.923/t/Seq/LargeLocatableSeq.t
BioPerl-1.6.923/t/Seq/LargePSeq.t
BioPerl-1.6.923/t/Seq/LocatableSeq.t
BioPerl-1.6.923/t/Seq/MetaSeq.t
BioPerl-1.6.923/t/Seq/PrimaryQual.t
BioPerl-1.6.923/t/Seq/PrimarySeq.t
BioPerl-1.6.923/t/Seq/PrimedSeq.t
BioPerl-1.6.923/t/Seq/Quality.t
BioPerl-1.6.923/t/Seq/Seq.t
BioPerl-1.6.923/t/Seq/SimulatedRead.t
BioPerl-1.6.923/t/Seq/WithQuality.t
BioPerl-1.6.923/t/SeqFeature
BioPerl-1.6.923/t/SeqFeature/Amplicon.t
BioPerl-1.6.923/t/SeqFeature/Clone.t
BioPerl-1.6.923/t/SeqFeature/Collection.t
BioPerl-1.6.923/t/SeqFeature/Computation.t
BioPerl-1.6.923/t/SeqFeature/FeaturePair.t
BioPerl-1.6.923/t/SeqFeature/Gene.t
BioPerl-1.6.923/t/SeqFeature/Generic.t
BioPerl-1.6.923/t/SeqFeature/Location.t
BioPerl-1.6.923/t/SeqFeature/LocationFactory.t
BioPerl-1.6.923/t/SeqFeature/Primer.t
BioPerl-1.6.923/t/SeqFeature/Range.t
BioPerl-1.6.923/t/SeqFeature/RangeI.t
BioPerl-1.6.923/t/SeqFeature/SeqAnalysisParser.t
BioPerl-1.6.923/t/SeqFeature/SubSeq.t
BioPerl-1.6.923/t/SeqFeature/Unflattener.t
BioPerl-1.6.923/t/SeqFeature/Unflattener2.t
BioPerl-1.6.923/t/SeqIO
BioPerl-1.6.923/t/SeqIO/abi.t
BioPerl-1.6.923/t/SeqIO/ace.t
BioPerl-1.6.923/t/SeqIO/agave.t
BioPerl-1.6.923/t/SeqIO/alf.t
BioPerl-1.6.923/t/SeqIO/asciitree.t
BioPerl-1.6.923/t/SeqIO/bsml.t
BioPerl-1.6.923/t/SeqIO/bsml_sax.t
BioPerl-1.6.923/t/SeqIO/chadoxml.t
BioPerl-1.6.923/t/SeqIO/chaos.t
BioPerl-1.6.923/t/SeqIO/chaosxml.t
BioPerl-1.6.923/t/SeqIO/ctf.t
BioPerl-1.6.923/t/SeqIO/embl.t
BioPerl-1.6.923/t/SeqIO/entrezgene.t
BioPerl-1.6.923/t/SeqIO/excel.t
BioPerl-1.6.923/t/SeqIO/exp.t
BioPerl-1.6.923/t/SeqIO/fasta.t
BioPerl-1.6.923/t/SeqIO/fastq.t
BioPerl-1.6.923/t/SeqIO/flybase_chadoxml.t
BioPerl-1.6.923/t/SeqIO/game.t
BioPerl-1.6.923/t/SeqIO/gbxml.t
BioPerl-1.6.923/t/SeqIO/gcg.t
BioPerl-1.6.923/t/SeqIO/genbank.t
BioPerl-1.6.923/t/SeqIO/Handler.t
BioPerl-1.6.923/t/SeqIO/interpro.t
BioPerl-1.6.923/t/SeqIO/kegg.t
BioPerl-1.6.923/t/SeqIO/largefasta.t
BioPerl-1.6.923/t/SeqIO/lasergene.t
BioPerl-1.6.923/t/SeqIO/locuslink.t
BioPerl-1.6.923/t/SeqIO/mbsout.t
BioPerl-1.6.923/t/SeqIO/metafasta.t
BioPerl-1.6.923/t/SeqIO/msout.t
BioPerl-1.6.923/t/SeqIO/MultiFile.t
BioPerl-1.6.923/t/SeqIO/Multiple_fasta.t
BioPerl-1.6.923/t/SeqIO/nexml.t
BioPerl-1.6.923/t/SeqIO/phd.t
BioPerl-1.6.923/t/SeqIO/pir.t
BioPerl-1.6.923/t/SeqIO/pln.t
BioPerl-1.6.923/t/SeqIO/qual.t
BioPerl-1.6.923/t/SeqIO/raw.t
BioPerl-1.6.923/t/SeqIO/scf.t
BioPerl-1.6.923/t/SeqIO/SeqBuilder.t
BioPerl-1.6.923/t/SeqIO/SeqIO.t
BioPerl-1.6.923/t/SeqIO/seqxml.t
BioPerl-1.6.923/t/SeqIO/Splicedseq.t
BioPerl-1.6.923/t/SeqIO/strider.t
BioPerl-1.6.923/t/SeqIO/swiss.t
BioPerl-1.6.923/t/SeqIO/tab.t
BioPerl-1.6.923/t/SeqIO/table.t
BioPerl-1.6.923/t/SeqIO/tigr.t
BioPerl-1.6.923/t/SeqIO/tigrxml.t
BioPerl-1.6.923/t/SeqIO/tinyseq.t
BioPerl-1.6.923/t/SeqIO/ztr.t
BioPerl-1.6.923/t/SeqTools
BioPerl-1.6.923/t/SeqTools/Backtranslate.t
BioPerl-1.6.923/t/SeqTools/CodonTable.t
BioPerl-1.6.923/t/SeqTools/ECnumber.t
BioPerl-1.6.923/t/SeqTools/GuessSeqFormat.t
BioPerl-1.6.923/t/SeqTools/OddCodes.t
BioPerl-1.6.923/t/SeqTools/SeqPattern.t
BioPerl-1.6.923/t/SeqTools/SeqStats.t
BioPerl-1.6.923/t/SeqTools/SeqUtils.t
BioPerl-1.6.923/t/SeqTools/SeqWords.t
BioPerl-1.6.923/t/Structure
BioPerl-1.6.923/t/Structure/IO.t
BioPerl-1.6.923/t/Structure/Structure.t
BioPerl-1.6.923/t/Tools
BioPerl-1.6.923/t/Tools/AmpliconSearch.t
BioPerl-1.6.923/t/Tools/ePCR.t
BioPerl-1.6.923/t/Tools/Est2Genome.t
BioPerl-1.6.923/t/Tools/FootPrinter.t
BioPerl-1.6.923/t/Tools/Geneid.t
BioPerl-1.6.923/t/Tools/Genewise.t
BioPerl-1.6.923/t/Tools/Genomewise.t
BioPerl-1.6.923/t/Tools/Genpred.t
BioPerl-1.6.923/t/Tools/GFF.t
BioPerl-1.6.923/t/Tools/GuessSeqFormat.t
BioPerl-1.6.923/t/Tools/Hmmer.t
BioPerl-1.6.923/t/Tools/IUPAC.t
BioPerl-1.6.923/t/Tools/Lucy.t
BioPerl-1.6.923/t/Tools/Match.t
BioPerl-1.6.923/t/Tools/pICalculator.t
BioPerl-1.6.923/t/Tools/Primer3.t
BioPerl-1.6.923/t/Tools/Promoterwise.t
BioPerl-1.6.923/t/Tools/Pseudowise.t
BioPerl-1.6.923/t/Tools/QRNA.t
BioPerl-1.6.923/t/Tools/RandDistFunctions.t
BioPerl-1.6.923/t/Tools/RepeatMasker.t
BioPerl-1.6.923/t/Tools/rnamotif.t
BioPerl-1.6.923/t/Tools/Seg.t
BioPerl-1.6.923/t/Tools/Sigcleave.t
BioPerl-1.6.923/t/Tools/Signalp.t
BioPerl-1.6.923/t/Tools/Sim4.t
BioPerl-1.6.923/t/Tools/SiRNA.t
BioPerl-1.6.923/t/Tools/TandemRepeatsFinder.t
BioPerl-1.6.923/t/Tools/TargetP.t
BioPerl-1.6.923/t/Tools/Tmhmm.t
BioPerl-1.6.923/t/Tools/tRNAscanSE.t
BioPerl-1.6.923/t/Tools/Alignment
BioPerl-1.6.923/t/Tools/Alignment/Consed.t
BioPerl-1.6.923/t/Tools/Analysis
BioPerl-1.6.923/t/Tools/Analysis/DNA
BioPerl-1.6.923/t/Tools/Analysis/DNA/ESEfinder.t
BioPerl-1.6.923/t/Tools/Analysis/Protein
BioPerl-1.6.923/t/Tools/Analysis/Protein/Domcut.t
BioPerl-1.6.923/t/Tools/Analysis/Protein/ELM.t
BioPerl-1.6.923/t/Tools/Analysis/Protein/GOR4.t
BioPerl-1.6.923/t/Tools/Analysis/Protein/HNN.t
BioPerl-1.6.923/t/Tools/Analysis/Protein/Mitoprot.t
BioPerl-1.6.923/t/Tools/Analysis/Protein/NetPhos.t
BioPerl-1.6.923/t/Tools/Analysis/Protein/Scansite.t
BioPerl-1.6.923/t/Tools/Analysis/Protein/Sopma.t
BioPerl-1.6.923/t/Tools/EMBOSS
BioPerl-1.6.923/t/Tools/EMBOSS/Palindrome.t
BioPerl-1.6.923/t/Tools/Phylo
BioPerl-1.6.923/t/Tools/Phylo/Gerp.t
BioPerl-1.6.923/t/Tools/Phylo/Molphy.t
BioPerl-1.6.923/t/Tools/Phylo/PAML.t
BioPerl-1.6.923/t/Tools/Phylo/Phylip
BioPerl-1.6.923/t/Tools/Phylo/Phylip/ProtDist.t
BioPerl-1.6.923/t/Tools/Run
BioPerl-1.6.923/t/Tools/Run/Dummy.pm
BioPerl-1.6.923/t/Tools/Run/RemoteBlast.t
BioPerl-1.6.923/t/Tools/Run/RemoteBlast_rpsblast.t
BioPerl-1.6.923/t/Tools/Run/StandAloneBlast.t
BioPerl-1.6.923/t/Tools/Run/WBCommandExts.t
BioPerl-1.6.923/t/Tools/Run/WrapperBase.t
BioPerl-1.6.923/t/Tools/Run/Dummy
BioPerl-1.6.923/t/Tools/Run/Dummy/Config.pm
BioPerl-1.6.923/t/Tools/Signalp
BioPerl-1.6.923/t/Tools/Signalp/ExtendedSignalp.t
BioPerl-1.6.923/t/Tools/Spidey
BioPerl-1.6.923/t/Tools/Spidey/Spidey.t
BioPerl-1.6.923/t/Tree
BioPerl-1.6.923/t/Tree/Compatible.t
BioPerl-1.6.923/t/Tree/Node.t
BioPerl-1.6.923/t/Tree/RandomTreeFactory.t
BioPerl-1.6.923/t/Tree/Tree.t
BioPerl-1.6.923/t/Tree/TreeIO.t
BioPerl-1.6.923/t/Tree/TreeStatistics.t
BioPerl-1.6.923/t/Tree/PhyloNetwork
BioPerl-1.6.923/t/Tree/PhyloNetwork/Factory.t
BioPerl-1.6.923/t/Tree/PhyloNetwork/GraphViz.t
BioPerl-1.6.923/t/Tree/PhyloNetwork/MuVector.t
BioPerl-1.6.923/t/Tree/PhyloNetwork/PhyloNetwork.t
BioPerl-1.6.923/t/Tree/PhyloNetwork/RandomFactory.t
BioPerl-1.6.923/t/Tree/PhyloNetwork/TreeFactory.t
BioPerl-1.6.923/t/Tree/TreeIO
BioPerl-1.6.923/t/Tree/TreeIO/lintree.t
BioPerl-1.6.923/t/Tree/TreeIO/newick.t
BioPerl-1.6.923/t/Tree/TreeIO/nexml.t
BioPerl-1.6.923/t/Tree/TreeIO/nexus.t
BioPerl-1.6.923/t/Tree/TreeIO/nhx.t
BioPerl-1.6.923/t/Tree/TreeIO/phyloxml.t
BioPerl-1.6.923/t/Tree/TreeIO/svggraph.t
BioPerl-1.6.923/t/Tree/TreeIO/tabtree.t
BioPerl-1.6.923/t/Variation
BioPerl-1.6.923/t/Variation/AAChange.t
BioPerl-1.6.923/t/Variation/AAReverseMutate.t
BioPerl-1.6.923/t/Variation/Allele.t
BioPerl-1.6.923/t/Variation/DNAMutation.t
BioPerl-1.6.923/t/Variation/RNAChange.t
BioPerl-1.6.923/t/Variation/SeqDiff.t
BioPerl-1.6.923/t/Variation/SNP.t
BioPerl-1.6.923/t/Variation/Variation_IO.t
BioPerl-1.6.923/travis_scripts
BioPerl-1.6.923/travis_scripts/dependency_installs

  CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-1.6.923.tar.gz

>>> C:\Perl-5.20\bin\perl.exe Build.PL
could not find ParserDetails.ini in C:/cpanfly-5.20/var/megalib/XML/SAX
Checking prerequisites...
  requires:
    !  DB_File is not installed
  recommends:
    *  Algorithm::Munkres is not installed
    *  Convert::Binary::C is not installed
    *  GraphViz is not installed
    *  PostScript::TextBlock is not installed
    *  SOAP::Lite is not installed
    *  YAML 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

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

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

Do you want to run tests that require connection to servers across the internet
(likely to cause some failures)? y/n [n]   - will not run internet-requiring tests
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'BioPerl' version '1.006923'
---- Unsatisfied dependencies detected during ----
----      CJFIELDS/BioPerl-1.6.923.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-5.20\etc\distroprefs\DB_File.yml' doc 0
  PMQS/DB_File-1.831.tar.gz
  [disabled] -- NA Disabled via prefs file 'C:\cpanfly-5.20\etc\distroprefs\DB_File.yml' doc 0
Running Build for C/CJ/CJFIELDS/BioPerl-1.6.923.tar.gz
  Has already been unwrapped into directory C:\cpanfly-5.20\var\cpan\build\BioPerl-1.6.923-R3lMxB

  CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-1.6.923.tar.gz

Warning: Prerequisite 'DB_File => 0' for 'CJFIELDS/BioPerl-1.6.923.tar.gz' failed when processing 'PMQS/DB_File-1.831.tar.gz' with 'unwrapped => NO Disabled via prefs file 'C:\cpanfly-5.20\etc\distroprefs\DB_File.yml' doc 0'. Continuing, but chances to succeed are limited.
>>> C:\Perl-5.20\bin\perl.exe ./Build
Building BioPerl
  CJFIELDS/BioPerl-1.6.923.tar.gz
  C:\Perl-5.20\bin\perl.exe ./Build -- OK
Running Build test
>>> C:\Perl-5.20\bin\perl.exe ./Build test verbose=1
t/Align/AlignStats.t ................... 
1..45
ok 1 - use Bio::Align::DNAStatistics;
ok 2 - use Bio::Align::ProteinStatistics;
ok 3 - use Bio::AlignIO;
ok 4 - 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
t/Align/AlignUtil.t .................... 
1..47
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 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok
t/Align/Graphics.t ..................... 
1..41
ok 1 - use Bio::Align::Graphics;
ok 2 - require Bio::Align::Graphics;
ok 3 - Bio::Align::Graphics->can(...)
ok 4 - input is defined
ok 5 - AlignIO object is defined
ok 6 - 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
t/Align/SimpleAlign.t .................. 
1..206
ok 1 - use Bio::SimpleAlign;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::SeqFeature::Generic;
ok 4 - use Bio::Location::Simple;
ok 5 - use Bio::Location::Split;
ok 6 - 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 - select_noncont_by_name
ok 18 - select_noncont_by_name
ok 19 - select_noncont_by_name
ok 20 - select_noncont_by_name
ok 21 - each_seq
ok 22 - get_nse
ok 23 - id
ok 24 - num_gaps
ok 25 - each_alphabetically
ok 26 - column_from_residue_number
ok 27 - display_name get/set
ok 28 - display_name get
ok 29 - consensus_string
ok 30 - consensus_string
ok 31 - consensus_string
ok 32
ok 33 - each_seq_with_id
ok 34 - is_flush
ok 35 - id get/set
ok 36 - length
ok 37 - num_residues
ok 38 - num_sequences
ok 39 - overall_percentage_identity
ok 40 - overall_percentage_identity (align)
ok 41 - overall_percentage_identity (short)
ok 42 - overall_percentage_identity (long)
ok 43 - average_percentage_identity
ok 44
ok 45 - set_displayname_count
ok 46
ok 47 - set_displayname_flat
ok 48
ok 49 - set_displayname_normal
ok 50
ok 51
ok 52 - uppercase, map_chars
ok 53 - match_line
ok 54 - remove_seqs
ok 55 - remove_seqs
ok 56 - add_seq
ok 57 - add_seq
ok 58 - get_seq_by_pos
ok 59 - get_seq_by_pos
ok 60
ok 61
ok 62
ok 63 - purge
ok 64 - purge
ok 65 - IO::String consensus_iupac
ok 66 - IO::String write_aln normal
ok 67 - IO::String write_aln slice
ok 68 - IO::String write_aln slice
ok 69 - IO::String write_aln slice
ok 70 - IO::String write_aln slice
ok 71 - IO::String write_aln slice
ok 72
ok 73 - remove_columns by position
ok 74 - remove_columns by position (wrong order)
ok 75 - cigar_line
ok 76 - cigar_line
ok 77 - cigar_line
ok 78 - cigar_line
ok 79 - sort_alphabetically - before
ok 80
ok 81 - sort_alphabetically - after
ok 82 - remove_gaps
ok 83 - remove_gaps all_gaps_only
ok 84 - set_new_reference
ok 85 - set_new_reference
ok 86 - uniq_seq
ok 87 - bug 2099
ok 88 - bug 2099
ok 89 - bug 2793
ok 90 - bug 2793
ok 91 - bug 2793
ok 92 - bug 2793
ok 93 - Bad sequence, bad!
ok 94 - An object of class 'Bio::SimpleAlign' isa 'Bio::AnnotatableI'
ok 95 - added 3 seqs
ok 96 - first 2 features added
ok 97 - 3rd feature added
ok 98
ok 99 - slice 1 len
ok 100 - correct masked seq
ok 101 - correct masked seq
ok 102 - correct masked seq
ok 103
ok 104 - slice 2 len
ok 105 - correct masked seq
ok 106 - correct masked seq
ok 107 - correct masked seq
ok 108
ok 109 - slice 3 len
ok 110 - correct masked seq
ok 111 - correct masked seq
ok 112 - correct masked seq
ok 113
ok 114 - slice 4 len
ok 115 - correct masked seq
ok 116 - correct masked seq
ok 117 - correct masked seq
ok 118 - initial display id ok
ok 119 - safe display id ok
ok 120 - restored display id ok
ok 121 - sort by list ok
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128 - BIC:GGATCCATT[C/C]CTACT
ok 129 - BIC:GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT
ok 130 - BIC:G[G/C]ATCCATT[C/G]CTACT
ok 131 - BIC:GGATCCATT[C/G]CTACT
ok 132 - BIC:GGATCCATT[C/G]CTAC[T/A]
ok 133 - BIC:GGATCCATT[C/G]CTA[C/G][T/A]
ok 134 - BIC:GGATCCATT[C/G]CTACT
ok 135 - BIC:GGATCCATT{C.C}CTACT
ok 136 - BIC:GGAT{C.-}{C.-}ATT{C.C}CT{A.C}CT
ok 137 - BIC:G{G.C}ATCCATT{C.G}CTACT
ok 138 - BIC:GGATCCATT{C.G}CTACT
ok 139 - BIC:GGATCCATT{C.G}CTAC{T.A}
ok 140 - BIC:GGATCCATT{C.G}CTA{C.G}{T.A}
ok 141 - BIC:GGATCCATT{C.G}CTACT
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok 176
ok 177
ok 178
ok 179
ok 180
ok 181
ok 182
ok 183
ok 184
ok 185
ok 186
ok 187
ok 188
ok 189
ok 190
ok 191
ok 192
ok 193
ok 194
ok 195
ok 196
ok 197
ok 198
ok 199 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 200 - consensus string looks ok
ok 201 - conservation length
ok 202 - conservation scores
ok 203 - looks like correct unmasked alignment (from clustalw)
ok 204 - looks like correct masked alignment (from clustalw)
ok 205
ok 206 - align after looks ok
ok
t/Align/TreeBuild.t .................... 
1..13
ok 1 - use Bio::Align::DNAStatistics;
ok 2 - use Bio::Align::ProteinStatistics;
ok 3 - use Bio::Align::Utilities;
ok 4 - use Bio::AlignIO;
ok 5 - use Bio::Tree::DistanceFactory;
ok 6 - use Bio::TreeIO;
ok 7 - 'SimpleAlign object parsed out' isa 'Bio::SimpleAlign'
ok 8 - 'Protein distance matrix retrieved' isa 'Bio::Matrix::MatrixI'
ok 9 - 'Tree object gotten back' isa 'Bio::Tree::TreeI'
ok 10 - NJ calculated Branch length
ok 11 - NJ calculated Branch length
ok 12 - Make sure two nodes are sister
ok 13 - 10 replicates formulated
ok
t/Align/Utilities.t .................... 
1..13
ok 1 - use Bio::Align::Utilities;
ok 2 - use Bio::SimpleAlign;
ok 3 - use Bio::PrimarySeq;
ok 4 - use Bio::LocatableSeq;
ok 5 - use Bio::AlignIO;
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok
t/AlignIO/AlignIO.t .................... 
1..29
ok 1 - use Bio::AlignIO;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::AnnotatableI'
ok 3 - input filehandle method test : psi
ok 4 - input filehandle method test : selex
ok 5 - input filehandle method test : phylip
ok 6 - input filehandle method test : clustalw
ok 7 - input filehandle method test : po
ok 8 - input filehandle method test : arp
ok 9 - input filehandle method test : xmfa
ok 10 - input filehandle method test : nexus
ok 11 - input filehandle method test : prodom
ok 12 - input filehandle method test : msf
ok 13 - input filehandle method test : metafasta
ok 14 - input filehandle method test : fasta
ok 15 - input filehandle method test : pfam
ok 16 - input filehandle method test : stockholm
ok 17 - input filehandle method test : mase
ok 18 - filehandle output test : psi
ok 19 - filehandle output test : selex
ok 20 - filehandle output test : phylip
ok 21 - filehandle output test : clustalw
ok 22 - filehandle output test : po
ok 23 - filehandle output test : xmfa
ok 24 - filehandle output test : nexus
ok 25 - filehandle output test : msf
ok 26 - filehandle output test : metafasta
ok 27 - filehandle output test : fasta
ok 28 - filehandle output test : pfam
ok 29 - filehandle output test : stockholm
ok
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
t/AlignIO/bl2seq.t ..................... 
1..7
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 4 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 5
ok 6
ok 7
ok
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
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
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
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
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
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
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
t/AlignIO/meme.t ....................... 
1..20
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 15 - An object of class 'Bio::AlignIO::meme' isa 'Bio::AlignIO'
ok 16 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 17
ok 18
ok 19
ok 20
ok
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
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
# 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
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
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
t/AlignIO/phylip.t ..................... 
1..17
ok 1 - use Bio::AlignIO::phylip;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3
ok 4 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 5
ok 6
ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 8
ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 10
ok 11 - phylip output test
ok 12
ok 13
ok 14
not ok 15 # TODO problems with default strand, length?

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

#   Failed (TODO) test at t/AlignIO/phylip.t line 82.
#          got: '50'
#     expected: '47'
ok 17 - newline between header and sequences is parsed correctly
ok
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
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
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
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
t/AlignIO/stockholm.t .................. 
1..87
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 85
ok 86
ok 87
ok
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
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
t/Annotation/Annotation.t .............. 
1..152
ok 1 - use Bio::Annotation::Collection;
ok 2 - use Bio::Annotation::DBLink;
ok 3 - use Bio::Annotation::Comment;
ok 4 - use Bio::Annotation::Reference;
ok 5 - use Bio::Annotation::SimpleValue;
ok 6 - use Bio::Annotation::Target;
ok 7 - use Bio::Annotation::AnnotationFactory;
ok 8 - use Bio::Annotation::StructuredValue;
ok 9 - use Bio::Annotation::TagTree;
ok 10 - use Bio::Annotation::Tree;
ok 11 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::AnnotationI'
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18 - An object of class 'Bio::Annotation::DBLink' isa 'Bio::AnnotationI'
ok 19
ok 20
ok 21
ok 22 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI'
ok 23
ok 24
ok 25 - An object of class 'Bio::Annotation::Target' isa 'Bio::AnnotationI'
ok 26
ok 27 - An object of class 'Bio::Annotation::Reference' isa 'Bio::AnnotationI'
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50 - An object of class 'Bio::Annotation::StructuredValue' isa 'Bio::AnnotationI'
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI'
ok 66
ok 67
ok 68
ok 69
ok 70 - An object of class 'Bio::Annotation::StructuredValue' isa 'Bio::Annotation::StructuredValue'
ok 71
ok 72
ok 73
ok 74
ok 75 - use Bio::Annotation::OntologyTerm;
ok 76 - An object of class 'Bio::Ontology::Term' isa 'Bio::Ontology::Term'
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82 # skip The optional module Bio::SeqFeature::Annotated (or dependencies thereof) was not installed
ok 83 # skip The optional module Bio::SeqFeature::Annotated (or dependencies thereof) was not installed
ok 84 # skip The optional module Bio::SeqFeature::Annotated (or dependencies thereof) was not installed
ok 85 # skip The optional module Bio::SeqFeature::Annotated (or dependencies thereof) was not installed
ok 86 - An object of class 'Bio::Annotation::AnnotationFactory' isa 'Bio::Factory::ObjectFactoryI'
ok 87 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue'
ok 88
ok 89 - An object of class 'Bio::Annotation::OntologyTerm' isa 'Bio::Annotation::OntologyTerm'
ok 90 - Bio::Annotation::Comment
ok 91 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment'
ok 92
ok 93 - Bio::Annotation::Comment
ok 94 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment'
ok 95 - Bio::Annotation::Comment
ok 96 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment'
ok 97
ok 98 - An object of class 'Bio::Annotation::Target' isa 'Bio::Annotation::Target'
ok 99
ok 100
ok 101 - An object of class 'Bio::Annotation::Tree' isa 'Bio::AnnotationI'
ok 102 - tree_id()
ok 103 - tagname()
ok 104
ok 105 - add tree to AlignI
ok 106 - get seq from node id
ok 107
ok 108 - An object of class 'Bio::Annotation::Tree' isa 'Bio::Annotation::Tree'
ok 109 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI'
ok 110 - default itext
ok 111 - roundtrip
ok 112 - itext
ok 113 - spxr
ok 114 - indent
ok 115 - xml
ok 116 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI'
ok 117
ok 118 - child changes
ok 119 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI'
ok 120
ok 121 - child changes
ok 122 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI'
ok 123
ok 124 - child changes
ok 125 - child changes in parent node
ok 126 - no tags
ok 127 - before Stag node
ok 128 - after Stag node
ok 129 - both stag nodes
ok 130 - different instances
ok 131 - before TagTree
ok 132 - after TagTree
ok 133 - both stag nodes
ok 134 - different instances
ok 135 - before TagTree
ok 136 - after TagTree
ok 137 - stag nodes
ok 138 - same instance
ok 139 - before TagTree
ok 140 - after TagTree
ok 141 - stag nodes
ok 142 - different instance
ok 143 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI'
ok 144 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI'
ok 145 - child changes
ok 146 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI'
ok 147 - child changes
ok 148 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI'
ok 149 - child changes
ok 150
ok 151
ok 152 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::Annotation::TagTree'
ok
t/Annotation/AnnotationAdaptor.t ....... 
1..23
ok 1 - use Bio::SeqFeature::Generic;
ok 2 - use Bio::SeqFeature::AnnotationAdaptor;
ok 3 - use Bio::Annotation::DBLink;
ok 4 - use Bio::Annotation::Comment;
ok 5 - use Bio::Annotation::SimpleValue;
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok
Bio::Assembly::IO: could not load tigr - for more details on supported formats please see the Assembly::IO docs
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::Assembly::IO::tigr. Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: . C:\cpanfly-5.20\var\cpan\build\BioPerl-1.6.923-R3lMxB\blib\lib C:\cpanfly-5.20\var\cpan\build\BioPerl-1.6.923-R3lMxB\blib\arch C:/cpanfly-5.20/var/cpan/build/BioPerl-1.6.923-R3lMxB C:\cpanfly-5.20\var\cpan\build\BioPerl-1.6.923-R3lMxB C:\cpanfly-5.20\var\megalib C:/cpanfly-5.20/var/megalib C:/Perl-5.20/site/lib C:/Perl-5.20/lib) at Bio/SeqFeature/Collection.pm line 146.
BEGIN failed--compilation aborted at Bio/SeqFeature/Collection.pm line 146.
Compilation failed in require at Bio/Assembly/Singlet.pm line 91.
BEGIN failed--compilation aborted at Bio/Assembly/Singlet.pm line 91.
Compilation failed in require at Bio\Assembly\IO\tigr.pm line 237.
BEGIN failed--compilation aborted at Bio\Assembly\IO\tigr.pm line 237.
Compilation failed in require at Bio/Root/Root.pm line 558.

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


#   Failed test 'undef isa 'Bio::Assembly::IO''
#   at t/Assembly/ContigSpectrum.t line 17.
#     undef isn't defined
Can't call method "next_assembly" on an undefined value at t/Assembly/ContigSpectrum.t line 18.
# Looks like you planned 239 tests but ran 3.
# Looks like you failed 1 test of 3 run.
# Looks like your test exited with 2 just after 3.
t/Assembly/ContigSpectrum.t ............ 
1..239
ok 1 - use Bio::Assembly::IO;
ok 2 - use Bio::Assembly::Tools::ContigSpectrum;
not ok 3 - undef isa 'Bio::Assembly::IO'
Dubious, test returned 2 (wstat 512, 0x200)
Failed 237/239 subtests 
t/Assembly/IO/bowtie.t ................. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Assembly/IO/sam.t .................... skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Assembly/core.t ...................... skipped: The optional module DB_File (or dependencies thereof) was not installed
t/Cluster/UniGene.t .................... 
1..2
ok 1 - use Bio::Cluster::UniGene;
ok 2 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::AnnotatableI'
ok
t/ClusterIO/ClusterIO.t ................ 
1..12
ok 1 - use Bio::ClusterIO;
ok 2 - use Bio::Cluster::ClusterFactory;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11 - 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
t/ClusterIO/SequenceFamily.t ........... 
1..17
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::Cluster::SequenceFamily;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok
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
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
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ok 152 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
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ok 154 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
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ok 164 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
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t/Coordinate/CoordinateGraph.t ......... 
1..7
ok 1 - use Bio::Coordinate::Graph;
ok 2
ok 3
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ok
t/Coordinate/CoordinateMapper.t ........ 
1..175
ok 1 - use Bio::Location::Simple;
ok 2 - use Bio::Coordinate::Pair;
ok 3 - use Bio::Coordinate::Result::Match;
ok 4 - use Bio::Coordinate::Result::Gap;
ok 5 - use Bio::Coordinate::Chain;
ok 6 - use Bio::Coordinate::Collection;
ok 7
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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
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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'
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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
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ok 106 - An object of class 'Bio::Coordinate::Result::Match' isa 'Bio::Coordinate::Result::Match'
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ok 138 - Match: |314696| Test: 314696|
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ok 142 - Match: |341| Test: 341|
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ok 146 - Match: |315843| Test: 315843|
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ok 152 - Match: |627011| Test: 627011|
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ok 156 - Match: |chr1| Test: chr1|
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ok
t/Coordinate/GeneCoordinateMapper.t .... 
1..116
ok 1 - use Bio::Location::Simple;
ok 2 - use Bio::Coordinate::Pair;
ok 3 - use Bio::Coordinate::ExtrapolatingPair;
ok 4 - use Bio::Coordinate::GeneMapper;
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
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ok 13
ok 14 - An object of class 'Bio::Coordinate::Result::Match' isa 'Bio::Location::Simple'
ok 15
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ok 75 - An object of class 'Bio::Coordinate::Result::Match' isa 'Bio::Location::Simple'
ok 76
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ok
t/Draw/Pictogram.t ..................... 
1..6
ok 1 - use Bio::Draw::Pictogram;
ok 2 - use Bio::SeqIO;
ok 3 - use Bio::Matrix::PSM::IO;
ok 4 - 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
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ok
t/LiveSeq/LiveSeq.t .................... 
1..48
ok 1 - use Bio::LiveSeq::IO::BioPerl;
ok 2
ok 3
ok 4 - Bio::LiveSeq::Gene
ok 5
ok 6
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ok
t/LiveSeq/Mutation.t ................... 
1..19
ok 1 - use Bio::LiveSeq::Mutation;
ok 2
ok 3
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ok
t/LiveSeq/Mutator.t .................... 
1..24
ok 1 - use Bio::LiveSeq::Mutator;
ok 2 - use Bio::LiveSeq::IO::BioPerl;
ok 3 - use Bio::Variation::IO;
ok 4
ok 5
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ok

Timeout (max run time is 300s)
C:\Perl-5.20\bin\perl.exe exits with 37.