PATH=/usr/bin:/bin:/data/fly2200/cpanfly-5.22/var/megalib/bin
Start 2016-11-08T02:14:14
ActivePerl-2200 CPAN-2.10
Reading '/data/fly2200/cpanfly-5.22/var/cpan/Metadata'
  Database was generated on Mon, 07 Nov 2016 02:29:02 GMT
Checksum for /data/fly2200/cpanfly-5.22/var/cpan/sources/authors/id/C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz ok
BioPerl-1.007001
BioPerl-1.007001/.travis.yml
BioPerl-1.007001/AUTHORS
BioPerl-1.007001/BioPerl.pm
BioPerl-1.007001/BUGS
BioPerl-1.007001/Build.PL
BioPerl-1.007001/Changes
BioPerl-1.007001/DEPENDENCIES
BioPerl-1.007001/DEPRECATED
BioPerl-1.007001/INSTALL-WIN.md
BioPerl-1.007001/INSTALL.md
BioPerl-1.007001/INSTALL.SKIP
BioPerl-1.007001/LICENSE
BioPerl-1.007001/MANIFEST
BioPerl-1.007001/META.json
BioPerl-1.007001/META.yml
BioPerl-1.007001/README.md
BioPerl-1.007001/Bio
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BioPerl-1.007001/Bio/Tools/isPcr.pm
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BioPerl-1.007001/Bio/Tools/Lucy.pm
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BioPerl-1.007001/Bio/Tools/Prediction
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BioPerl-1.007001/Bio/Tools/Primer
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BioPerl-1.007001/Bio/Tools/SeqPattern
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BioPerl-1.007001/Bio/Tools/Signalp
BioPerl-1.007001/Bio/Tools/Signalp/ExtendedSignalp.pm
BioPerl-1.007001/Bio/Tools/Sim4
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BioPerl-1.007001/Bio/Tools/SiRNA/Ruleset
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BioPerl-1.007001/Bio/Tools/SiRNA/Ruleset/tuschl.pm
BioPerl-1.007001/Bio/Tools/Spidey
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BioPerl-1.007001/Bio/Tree
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BioPerl-1.007001/Bio/Tree/AnnotatableNode.pm
BioPerl-1.007001/Bio/Tree/Compatible.pm
BioPerl-1.007001/Bio/Tree/DistanceFactory.pm
BioPerl-1.007001/Bio/Tree/Node.pm
BioPerl-1.007001/Bio/Tree/NodeI.pm
BioPerl-1.007001/Bio/Tree/NodeNHX.pm
BioPerl-1.007001/Bio/Tree/RandomFactory.pm
BioPerl-1.007001/Bio/Tree/Statistics.pm
BioPerl-1.007001/Bio/Tree/Tree.pm
BioPerl-1.007001/Bio/Tree/TreeFunctionsI.pm
BioPerl-1.007001/Bio/Tree/TreeI.pm
BioPerl-1.007001/Bio/Tree/Draw
BioPerl-1.007001/Bio/Tree/Draw/Cladogram.pm
BioPerl-1.007001/Bio/TreeIO
BioPerl-1.007001/Bio/TreeIO/cluster.pm
BioPerl-1.007001/Bio/TreeIO/lintree.pm
BioPerl-1.007001/Bio/TreeIO/newick.pm
BioPerl-1.007001/Bio/TreeIO/NewickParser.pm
BioPerl-1.007001/Bio/TreeIO/nexml.pm
BioPerl-1.007001/Bio/TreeIO/nexus.pm
BioPerl-1.007001/Bio/TreeIO/nhx.pm
BioPerl-1.007001/Bio/TreeIO/pag.pm
BioPerl-1.007001/Bio/TreeIO/phyloxml.pm
BioPerl-1.007001/Bio/TreeIO/svggraph.pm
BioPerl-1.007001/Bio/TreeIO/tabtree.pm
BioPerl-1.007001/Bio/TreeIO/TreeEventBuilder.pm
BioPerl-1.007001/Bio/Variation
BioPerl-1.007001/Bio/Variation/AAChange.pm
BioPerl-1.007001/Bio/Variation/AAReverseMutate.pm
BioPerl-1.007001/Bio/Variation/Allele.pm
BioPerl-1.007001/Bio/Variation/DNAMutation.pm
BioPerl-1.007001/Bio/Variation/IO.pm
BioPerl-1.007001/Bio/Variation/README
BioPerl-1.007001/Bio/Variation/RNAChange.pm
BioPerl-1.007001/Bio/Variation/SeqDiff.pm
BioPerl-1.007001/Bio/Variation/SNP.pm
BioPerl-1.007001/Bio/Variation/VariantI.pm
BioPerl-1.007001/Bio/Variation/IO
BioPerl-1.007001/Bio/Variation/IO/flat.pm
BioPerl-1.007001/Bio/Variation/IO/xml.pm
BioPerl-1.007001/deobfuscator
BioPerl-1.007001/deobfuscator/makedoc.PL
BioPerl-1.007001/deobfuscator/Deobfuscator
BioPerl-1.007001/deobfuscator/Deobfuscator/Build.PL
BioPerl-1.007001/deobfuscator/Deobfuscator/Changes
BioPerl-1.007001/deobfuscator/Deobfuscator/excluded_modules.txt
BioPerl-1.007001/deobfuscator/Deobfuscator/LICENSE
BioPerl-1.007001/deobfuscator/Deobfuscator/Makefile.PL
BioPerl-1.007001/deobfuscator/Deobfuscator/MANIFEST
BioPerl-1.007001/deobfuscator/Deobfuscator/META.yml
BioPerl-1.007001/deobfuscator/Deobfuscator/README
BioPerl-1.007001/deobfuscator/Deobfuscator/bin
BioPerl-1.007001/deobfuscator/Deobfuscator/bin/deob_index.pl
BioPerl-1.007001/deobfuscator/Deobfuscator/bin/run-deobfuscator-update.pl
BioPerl-1.007001/deobfuscator/Deobfuscator/cgi-bin
BioPerl-1.007001/deobfuscator/Deobfuscator/cgi-bin/deob_detail.cgi
BioPerl-1.007001/deobfuscator/Deobfuscator/cgi-bin/deob_flowchart.png
BioPerl-1.007001/deobfuscator/Deobfuscator/cgi-bin/deob_help.html
BioPerl-1.007001/deobfuscator/Deobfuscator/cgi-bin/deob_interface.cgi
BioPerl-1.007001/deobfuscator/Deobfuscator/lib
BioPerl-1.007001/deobfuscator/Deobfuscator/lib/Deobfuscator.pm
BioPerl-1.007001/deobfuscator/Deobfuscator/t
BioPerl-1.007001/deobfuscator/Deobfuscator/t/00.load.t
BioPerl-1.007001/deobfuscator/Deobfuscator/t/pod.t
BioPerl-1.007001/examples
BioPerl-1.007001/examples/bioperl.pl
BioPerl-1.007001/examples/generate_random_seq.pl
BioPerl-1.007001/examples/longorf.pl
BioPerl-1.007001/examples/make_primers.pl
BioPerl-1.007001/examples/rev_and_trans.pl
BioPerl-1.007001/examples/revcom_dir.pl
BioPerl-1.007001/examples/subsequence.cgi
BioPerl-1.007001/examples/align
BioPerl-1.007001/examples/align/align_on_codons.pl
BioPerl-1.007001/examples/align/aligntutorial.pl
BioPerl-1.007001/examples/align/clustalw.pl
BioPerl-1.007001/examples/align/FastAlign.pl
BioPerl-1.007001/examples/align/simplealign.pl
BioPerl-1.007001/examples/Bio-DB-GFF
BioPerl-1.007001/examples/Bio-DB-GFF/load_ucsc.pl
BioPerl-1.007001/examples/cluster
BioPerl-1.007001/examples/cluster/dbsnp.pl
BioPerl-1.007001/examples/contributed
BioPerl-1.007001/examples/contributed/nmrpdb_parse.pl
BioPerl-1.007001/examples/contributed/prosite2perl.pl
BioPerl-1.007001/examples/contributed/rebase2list.pl
BioPerl-1.007001/examples/db
BioPerl-1.007001/examples/db/dbfetch
BioPerl-1.007001/examples/db/est_tissue_query.pl
BioPerl-1.007001/examples/db/gb2features.pl
BioPerl-1.007001/examples/db/get_seqs.pl
BioPerl-1.007001/examples/db/getGenBank.pl
BioPerl-1.007001/examples/db/rfetch.pl
BioPerl-1.007001/examples/db/use_registry.pl
BioPerl-1.007001/examples/liveseq
BioPerl-1.007001/examples/liveseq/change_gene.pl
BioPerl-1.007001/examples/popgen
BioPerl-1.007001/examples/popgen/parse_calc_stats.pl
BioPerl-1.007001/examples/quality
BioPerl-1.007001/examples/quality/svgtrace.pl
BioPerl-1.007001/examples/root
BioPerl-1.007001/examples/root/exceptions1.pl
BioPerl-1.007001/examples/root/exceptions2.pl
BioPerl-1.007001/examples/root/exceptions3.pl
BioPerl-1.007001/examples/root/exceptions4.pl
BioPerl-1.007001/examples/root/README
BioPerl-1.007001/examples/searchio
BioPerl-1.007001/examples/searchio/blast_example.pl
BioPerl-1.007001/examples/searchio/custom_writer.pl
BioPerl-1.007001/examples/searchio/hitwriter.pl
BioPerl-1.007001/examples/searchio/hspwriter.pl
BioPerl-1.007001/examples/searchio/htmlwriter.pl
BioPerl-1.007001/examples/searchio/psiblast_features.pl
BioPerl-1.007001/examples/searchio/psiblast_iterations.pl
BioPerl-1.007001/examples/searchio/rawwriter.pl
BioPerl-1.007001/examples/searchio/resultwriter.pl
BioPerl-1.007001/examples/searchio/waba2gff.pl
BioPerl-1.007001/examples/searchio/waba2gff3.pl
BioPerl-1.007001/examples/sirna
BioPerl-1.007001/examples/sirna/rnai_finder.cgi
BioPerl-1.007001/examples/sirna/TAG
BioPerl-1.007001/examples/structure
BioPerl-1.007001/examples/structure/structure-io.pl
BioPerl-1.007001/examples/tk
BioPerl-1.007001/examples/tk/gsequence.pl
BioPerl-1.007001/examples/tk/hitdisplay.pl
BioPerl-1.007001/examples/tools
BioPerl-1.007001/examples/tools/extract_genes.pl
BioPerl-1.007001/examples/tools/gb_to_gff.pl
BioPerl-1.007001/examples/tools/gff2ps.pl
BioPerl-1.007001/examples/tools/parse_codeml.pl
BioPerl-1.007001/examples/tools/psw.pl
BioPerl-1.007001/examples/tools/reverse-translate.pl
BioPerl-1.007001/examples/tools/run_genscan.pl
BioPerl-1.007001/examples/tools/run_primer3.pl
BioPerl-1.007001/examples/tools/seq_pattern.pl
BioPerl-1.007001/examples/tools/standaloneblast.pl
BioPerl-1.007001/examples/tree
BioPerl-1.007001/examples/tree/paup2phylip.pl
BioPerl-1.007001/ide
BioPerl-1.007001/ide/bioperl.komodo
BioPerl-1.007001/ide/bioperl-mode
BioPerl-1.007001/ide/bioperl-mode/README
BioPerl-1.007001/ide/bioperl-mode/dist
BioPerl-1.007001/ide/bioperl-mode/dist/bioperl-mode-xemacs.tar
BioPerl-1.007001/ide/bioperl-mode/dist/bioperl-mode-xemacs.tar.md5
BioPerl-1.007001/ide/bioperl-mode/dist/bioperl-mode.tar
BioPerl-1.007001/ide/bioperl-mode/dist/bioperl-mode.tar.md5
BioPerl-1.007001/ide/bioperl-mode/dist/Changes
BioPerl-1.007001/ide/bioperl-mode/dist/package-me
BioPerl-1.007001/ide/bioperl-mode/dist/SKIP
BioPerl-1.007001/ide/bioperl-mode/etc
BioPerl-1.007001/ide/bioperl-mode/etc/images
BioPerl-1.007001/ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm
BioPerl-1.007001/ide/bioperl-mode/etc/images/bpmode-tool.xpm
BioPerl-1.007001/ide/bioperl-mode/site-lisp
BioPerl-1.007001/ide/bioperl-mode/site-lisp/bioperl-init.el
BioPerl-1.007001/ide/bioperl-mode/site-lisp/bioperl-mode.el
BioPerl-1.007001/ide/bioperl-mode/site-lisp/bioperl-skel.el
BioPerl-1.007001/ide/bioperl-mode/site-lisp/pod.el
BioPerl-1.007001/maintenance
BioPerl-1.007001/maintenance/authors.pl
BioPerl-1.007001/maintenance/check_NAME.pl
BioPerl-1.007001/maintenance/check_URLs.pl
BioPerl-1.007001/maintenance/cvs2cl_by_file.pl
BioPerl-1.007001/maintenance/dependencies.pl
BioPerl-1.007001/maintenance/deprecated.pl
BioPerl-1.007001/maintenance/find_mod_deps.pl
BioPerl-1.007001/maintenance/module_usage.pl
BioPerl-1.007001/maintenance/modules.pl
BioPerl-1.007001/maintenance/ncbi_blast_switches.pl
BioPerl-1.007001/maintenance/perltidy.conf
BioPerl-1.007001/maintenance/pod.pl
BioPerl-1.007001/maintenance/README
BioPerl-1.007001/maintenance/symlink_script.pl
BioPerl-1.007001/maintenance/version.pl
BioPerl-1.007001/maintenance/big_split
BioPerl-1.007001/maintenance/big_split/file_classification.csv
BioPerl-1.007001/maintenance/big_split/rbuels_notes.txt
BioPerl-1.007001/models
BioPerl-1.007001/models/biblio.dia
BioPerl-1.007001/models/bio_liveseq_variation.dia
BioPerl-1.007001/models/bio_map.dia
BioPerl-1.007001/models/bio_restriction.dia
BioPerl-1.007001/models/bioperl.dia
BioPerl-1.007001/models/coordinatemapper.dia
BioPerl-1.007001/models/map_proposal.txt
BioPerl-1.007001/models/maps_and_markers.dia
BioPerl-1.007001/models/popgen.dia
BioPerl-1.007001/models/population_proposal.txt
BioPerl-1.007001/models/README
BioPerl-1.007001/scripts
BioPerl-1.007001/scripts/README
BioPerl-1.007001/scripts/Bio-DB-GFF
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_fast_load_gff.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_genbank2gff.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_genbank2gff3.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_generate_histogram.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_load_gff.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_meta_gff.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_process_gadfly.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_process_sgd.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/bp_process_wormbase.pl
BioPerl-1.007001/scripts/Bio-DB-GFF/README
BioPerl-1.007001/scripts/Bio-DB-SeqFeature-Store
BioPerl-1.007001/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl
BioPerl-1.007001/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl
BioPerl-1.007001/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
BioPerl-1.007001/scripts/das
BioPerl-1.007001/scripts/das/bp_das_server.pl
BioPerl-1.007001/scripts/das/README
BioPerl-1.007001/scripts/das/TAG
BioPerl-1.007001/scripts/DB
BioPerl-1.007001/scripts/DB/bp_biofetch_genbank_proxy.pl
BioPerl-1.007001/scripts/DB/bp_bioflat_index.pl
BioPerl-1.007001/scripts/DB/bp_biogetseq.pl
BioPerl-1.007001/scripts/DB/bp_flanks.pl
BioPerl-1.007001/scripts/DB/TAG
BioPerl-1.007001/scripts/DB-HIV
BioPerl-1.007001/scripts/DB-HIV/bp_hivq.pl
BioPerl-1.007001/scripts/index
BioPerl-1.007001/scripts/index/bp_fetch.pl
BioPerl-1.007001/scripts/index/bp_index.pl
BioPerl-1.007001/scripts/index/bp_seqret.pl
BioPerl-1.007001/scripts/index/TAG
BioPerl-1.007001/scripts/popgen
BioPerl-1.007001/scripts/popgen/bp_composite_LD.pl
BioPerl-1.007001/scripts/popgen/bp_heterogeneity_test.pl
BioPerl-1.007001/scripts/searchio
BioPerl-1.007001/scripts/searchio/bp_fastam9_to_table.pl
BioPerl-1.007001/scripts/searchio/bp_filter_search.pl
BioPerl-1.007001/scripts/searchio/bp_hmmer_to_table.pl
BioPerl-1.007001/scripts/searchio/bp_parse_hmmsearch.pl
BioPerl-1.007001/scripts/searchio/bp_search2table.pl
BioPerl-1.007001/scripts/searchio/README
BioPerl-1.007001/scripts/searchio/TAG
BioPerl-1.007001/scripts/seq
BioPerl-1.007001/scripts/seq/bp_extract_feature_seq.pl
BioPerl-1.007001/scripts/seq/bp_make_mrna_protein.pl
BioPerl-1.007001/scripts/seq/bp_seqconvert.pl
BioPerl-1.007001/scripts/seq/bp_seqcut.pl
BioPerl-1.007001/scripts/seq/bp_seqpart.pl
BioPerl-1.007001/scripts/seq/bp_seqretsplit.pl
BioPerl-1.007001/scripts/seq/bp_split_seq.pl
BioPerl-1.007001/scripts/seq/bp_translate_seq.pl
BioPerl-1.007001/scripts/seq/bp_unflatten_seq.pl
BioPerl-1.007001/scripts/seq/TAG
BioPerl-1.007001/scripts/seqstats
BioPerl-1.007001/scripts/seqstats/bp_aacomp.pl
BioPerl-1.007001/scripts/seqstats/bp_chaos_plot.pl
BioPerl-1.007001/scripts/seqstats/bp_gccalc.pl
BioPerl-1.007001/scripts/seqstats/bp_oligo_count.pl
BioPerl-1.007001/scripts/seqstats/TAG
BioPerl-1.007001/scripts/taxa
BioPerl-1.007001/scripts/taxa/bp_classify_hits_kingdom.pl
BioPerl-1.007001/scripts/taxa/bp_local_taxonomydb_query.pl
BioPerl-1.007001/scripts/taxa/bp_query_entrez_taxa.pl
BioPerl-1.007001/scripts/taxa/bp_taxid4species.pl
BioPerl-1.007001/scripts/taxa/bp_taxonomy2tree.pl
BioPerl-1.007001/scripts/taxa/TAG
BioPerl-1.007001/scripts/tree
BioPerl-1.007001/scripts/tree/bp_blast2tree.pl
BioPerl-1.007001/scripts/tree/bp_nexus2nh.pl
BioPerl-1.007001/scripts/tree/bp_tree2pag.pl
BioPerl-1.007001/scripts/tree/TAG
BioPerl-1.007001/scripts/utilities
BioPerl-1.007001/scripts/utilities/bp_dbsplit.pl
BioPerl-1.007001/scripts/utilities/bp_download_query_genbank.pl
BioPerl-1.007001/scripts/utilities/bp_find-blast-matches.pl
BioPerl-1.007001/scripts/utilities/bp_mask_by_search.pl
BioPerl-1.007001/scripts/utilities/bp_mrtrans.pl
BioPerl-1.007001/scripts/utilities/bp_mutate.pl
BioPerl-1.007001/scripts/utilities/bp_netinstall.pl
BioPerl-1.007001/scripts/utilities/bp_nrdb.pl
BioPerl-1.007001/scripts/utilities/bp_pairwise_kaks.pl
BioPerl-1.007001/scripts/utilities/bp_remote_blast.pl
BioPerl-1.007001/scripts/utilities/bp_revtrans-motif.pl
BioPerl-1.007001/scripts/utilities/bp_search2alnblocks.pl
BioPerl-1.007001/scripts/utilities/bp_search2gff.pl
BioPerl-1.007001/scripts/utilities/bp_search2tribe.pl
BioPerl-1.007001/scripts/utilities/bp_seq_length.pl
BioPerl-1.007001/scripts/utilities/bp_sreformat.pl
BioPerl-1.007001/scripts/utilities/README
BioPerl-1.007001/scripts/utilities/TAG
BioPerl-1.007001/t
BioPerl-1.007001/t/Alphabet.t
BioPerl-1.007001/t/nexml.t
BioPerl-1.007001/t/Perl.t
BioPerl-1.007001/t/PodSyntax.t
BioPerl-1.007001/t/SearchDist.t
BioPerl-1.007001/t/SeqEvolution.t
BioPerl-1.007001/t/Species.t
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BioPerl-1.007001/t/Tools/Phylo/Gerp.t
BioPerl-1.007001/t/Tools/Phylo/Molphy.t
BioPerl-1.007001/t/Tools/Phylo/PAML.t
BioPerl-1.007001/t/Tools/Phylo/Phylip
BioPerl-1.007001/t/Tools/Phylo/Phylip/ProtDist.t
BioPerl-1.007001/t/Tools/Run
BioPerl-1.007001/t/Tools/Run/RemoteBlast.t
BioPerl-1.007001/t/Tools/Run/RemoteBlast_rpsblast.t
BioPerl-1.007001/t/Tools/Signalp
BioPerl-1.007001/t/Tools/Signalp/ExtendedSignalp.t
BioPerl-1.007001/t/Tools/Spidey
BioPerl-1.007001/t/Tools/Spidey/Spidey.t
BioPerl-1.007001/t/Tree
BioPerl-1.007001/t/Tree/Compatible.t
BioPerl-1.007001/t/Tree/Node.t
BioPerl-1.007001/t/Tree/RandomTreeFactory.t
BioPerl-1.007001/t/Tree/Tree.t
BioPerl-1.007001/t/Tree/TreeIO.t
BioPerl-1.007001/t/Tree/TreeStatistics.t
BioPerl-1.007001/t/Tree/PhyloNetwork
BioPerl-1.007001/t/Tree/PhyloNetwork/Factory.t
BioPerl-1.007001/t/Tree/PhyloNetwork/GraphViz.t
BioPerl-1.007001/t/Tree/PhyloNetwork/MuVector.t
BioPerl-1.007001/t/Tree/PhyloNetwork/PhyloNetwork.t
BioPerl-1.007001/t/Tree/PhyloNetwork/RandomFactory.t
BioPerl-1.007001/t/Tree/PhyloNetwork/TreeFactory.t
BioPerl-1.007001/t/Tree/TreeIO
BioPerl-1.007001/t/Tree/TreeIO/lintree.t
BioPerl-1.007001/t/Tree/TreeIO/newick.t
BioPerl-1.007001/t/Tree/TreeIO/nexml.t
BioPerl-1.007001/t/Tree/TreeIO/nexus.t
BioPerl-1.007001/t/Tree/TreeIO/nhx.t
BioPerl-1.007001/t/Tree/TreeIO/phyloxml.t
BioPerl-1.007001/t/Tree/TreeIO/svggraph.t
BioPerl-1.007001/t/Tree/TreeIO/tabtree.t
BioPerl-1.007001/t/Variation
BioPerl-1.007001/t/Variation/AAChange.t
BioPerl-1.007001/t/Variation/AAReverseMutate.t
BioPerl-1.007001/t/Variation/Allele.t
BioPerl-1.007001/t/Variation/DNAMutation.t
BioPerl-1.007001/t/Variation/RNAChange.t
BioPerl-1.007001/t/Variation/SeqDiff.t
BioPerl-1.007001/t/Variation/SNP.t
BioPerl-1.007001/t/Variation/Variation_IO.t
BioPerl-1.007001/travis_scripts
BioPerl-1.007001/travis_scripts/dependency_installs
BioPerl-1.007001/travis_scripts/trigger-dockerhub.sh
Configuring C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz with Build.PL
>>> /data/fly2200/ap2200-299134/bin/perl-static Build.PL
could not find ParserDetails.ini in /data/fly2200/cpanfly-5.22/var/megalib/XML/SAX
Checking prerequisites...
  recommends:
    *  GraphViz 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 '1.007001'
  CJFIELDS/BioPerl-1.007001.tar.gz
  /data/fly2200/ap2200-299134/bin/perl-static Build.PL -- OK
Running Build for C/CJ/CJFIELDS/BioPerl-1.007001.tar.gz
>>> ./Build
Building BioPerl
  CJFIELDS/BioPerl-1.007001.tar.gz
  ./Build -- OK
Running Build test
>>> ./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..14
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 14
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 : selex
ok 4 - input filehandle method test : stockholm
ok 5 - input filehandle method test : xmfa
ok 6 - input filehandle method test : mase
ok 7 - input filehandle method test : phylip
ok 8 - input filehandle method test : po
ok 9 - input filehandle method test : msf
ok 10 - input filehandle method test : fasta
ok 11 - input filehandle method test : clustalw
ok 12 - input filehandle method test : nexus
ok 13 - input filehandle method test : arp
ok 14 - input filehandle method test : pfam
ok 15 - input filehandle method test : psi
ok 16 - input filehandle method test : prodom
ok 17 - input filehandle method test : metafasta
ok 18 - filehandle output test : selex
ok 19 - filehandle output test : stockholm
ok 20 - filehandle output test : xmfa
ok 21 - filehandle output test : phylip
ok 22 - filehandle output test : po
ok 23 - filehandle output test : msf
ok 24 - filehandle output test : fasta
ok 25 - filehandle output test : clustalw
ok 26 - filehandle output test : nexus
ok 27 - filehandle output test : pfam
ok 28 - filehandle output test : psi
ok 29 - filehandle output test : metafasta
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 output test
ok 5 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 6 - clustalw 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..12
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 
ok 5 - fasta input test for description
ok 6 - fasta input test for id
ok 7 - fasta input test, captures formatted start/end
ok 8 - fasta input test for end
ok 9 - fasta input test for description
ok 10 - fasta output test
ok 11 - filehandle input test  
ok 12 - 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..20
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
ok 15
not ok 16 # TODO problems with default strand

#   Failed (TODO) test at t/AlignIO/phylip.t line 78.
#          got: undef
#     expected: '0'
ok 17 - newline between header and sequences is parsed correctly
ok 18 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 19 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 20
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 - 'isa SeqFeatureI' isa 'Bio::SeqFeatureI'
ok 83 - 'isa AnnotatableI' isa 'Bio::AnnotatableI'
ok 84 - 'isa SeqFeatureI' isa 'Bio::SeqFeatureI'
ok 85 - 'isa AnnotatableI' isa 'Bio::AnnotatableI'
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
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/function(\s+)([a-z0-9_]+)(\s*){{ <-- HERE (.*?)}}/ at /data/fly2200/cpanfly-5.22/var/megalib/Inline/SMITH.pm line 63.
t/Assembly/ContigSpectrum.t ............ 
1..239
ok 1 - use Bio::Assembly::IO;
ok 2 - use Bio::Assembly::Tools::ContigSpectrum;
ok 3 - An object of class 'Bio::Assembly::IO::tigr' isa 'Bio::Assembly::IO'
ok 4 - An object of class 'Bio::Assembly::Scaffold' isa 'Bio::Assembly::Scaffold'
ok 5 - get/set methods
ok 6 - An object of class 'Bio::Assembly::Tools::ContigSpectrum' isa 'Bio::Assembly::Tools::ContigSpectrum'
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 - simple spectrum
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 - contig spectrum score
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57 - mixed contig spectrum
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 - dissolved contig spectrum
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 - cross-contig spectrum
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139 - cross-contig spectrum
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151 - cross-contig spectrum
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160 - contig spectrum sum
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 - average contig spectrum
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 - drop assembly
ok 190
ok 191 - An object of class 'Bio::Assembly::IO::ace' isa 'Bio::Assembly::IO'
ok 192 - An object of class 'Bio::Assembly::Scaffold' isa 'Bio::Assembly::Scaffold'
ok 193 - large contig spectrum
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 - 74.7485808732225
ok 207 - 74.7485808732225
ok 208 - large cross-contig spectrum
ok 209
ok 210 - 88.8076923076923
ok 211 - 88.8076923076923
ok 212
ok 213
ok 214
ok 215
ok 216
ok 217
ok 218
ok 219
ok 220
ok 221
ok 222 - one contig at a time
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
t/Assembly/IO/bowtie.t ................. skipped: The optional module Bio::Tools::Run::Samtools (or dependencies thereof) was not installed
t/Assembly/IO/sam.t .................... skipped: The optional module Bio::Tools::Run::Samtools (or dependencies thereof) was not installed
t/Assembly/core.t ...................... 
1..892
ok 1 - use Bio::Seq;
ok 2 - use Bio::LocatableSeq;
ok 3 - use Bio::Seq::Quality;
ok 4 - use Bio::Assembly::IO;
ok 5 - use Bio::Assembly::Singlet;
ok 6 - singlet from Bio::PrimarySeq
ok 7 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 8 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Singlet'
ok 9
ok 10
ok 11 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq'
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 - singlet from Bio::Seq::Quality
ok 25
ok 26
ok 27 - An object of class 'Bio::Seq::PrimaryQual' isa 'Bio::Seq::QualI'
ok 28
ok 29 - singlet from LocatableSeq
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38 - singlet from LocatableSeq with set coordinates
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48 - consed
ok 49
ok 50
ok 51
ok 52
ok 53 - An object of class 'Bio::Assembly::IO::phrap' isa 'Bio::Assembly::IO'
ok 54 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 55 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 56 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 57 - An object of class 'Bio::Assembly::IO::phrap' isa 'Bio::Assembly::IO'
not ok 58 # TODO phrap parser doesn't include the sequence string in the sequence objects.

#   Failed (TODO) test at t/Assembly/core.t line 128.
ok 59
ok 60 - An object of class 'Bio::Assembly::Scaffold' isa 'Bio::Assembly::Scaffold'
ok 61
ok 62
ok 63 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI'
ok 64 - no annotations in Annotation collection?
ok 65
ok 66
ok 67 - get_nof_singlets
ok 68 - get_contig_seq_ids
ok 69 - get_contig_ids
ok 70 - get_singlet_ids
ok 71 - 'the contig is a Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 72 - 'the singlet is a Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 73 - 'the singlet is a Bio::Assembly::Singlet' isa 'Bio::Assembly::Singlet'
ok 74 - get_contig_seq_ids
ok 75
ok 76
ok 77
ok 78 - get_contig_ids
ok 79
ok 80
ok 81 - get_singlet_ids
ok 82
ok 83
ok 84
ok 85 - get_all_seq_ids
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92 - contig features
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99 - get_nof_singlets
ok 100 - get_contig_seq_ids
ok 101 - get_contig_ids
ok 102 - get_singlet_ids
ok 103 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 104 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 105 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 106 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 107 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 108 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 109 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 110 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 111 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 112 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 113 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 114 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 115 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 116 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 117 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 118 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 119 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 120 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 121 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 122 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 123 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 124 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 125 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 126 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 127 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 128 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 129 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 130 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 131 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 132 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 133 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 134 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 135 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 136 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 137 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 138 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 139
ok 140 - 'the contig is a Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146 - get_nof_singlets
ok 147 - 'the singlet is a Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 148 - 'the singlet is a Bio::Assembly::Singlet' isa 'Bio::Assembly::Singlet'
ok 149 - get_contig_seq_ids
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157 - get_contig_ids
ok 158
ok 159
ok 160
ok 161
ok 162 - get_singlet_ids
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 - get_all_seq_ids
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 - 454 ACE variant coordinates check
ok 240
ok 241 - 454 ACE variant consensus check
ok 242
ok 243
ok 244
ok 245
ok 246 - writing in the ACE format
ok 247
ok 248
ok 249
ok 250
ok 251
ok 252 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 253 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 254 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 255 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 256 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 257 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 258 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 259 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 260 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 261 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 262 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 263 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 264 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 265 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 266 - An object of class 'Bio::Assembly::Scaffold' isa 'Bio::Assembly::Scaffold'
ok 267
ok 268
ok 269
ok 270
ok 271
ok 272
ok 273
ok 274 - An object of class 'Bio::LocatableSeq' isa 'Bio::LocatableSeq'
ok 275 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 276
ok 277
ok 278
ok 279 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI'
ok 280 - no annotations in Annotation collection?
ok 281 - writing in the TIGR format
ok 282 - init maq IO object
ok 283 - get maq assy
ok 284 - got all contigs
ok 285 - read test file as text
ok 286 - recorded all maq reads
ok 287 - no singlets
ok 288
ok 289 - An object of class 'Bio::Assembly::IO::maq' isa 'Bio::Assembly::IO'
ok 290 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 291 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 292 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 293 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 294 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 295 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 296 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 297 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 298 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 299 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 300 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 301
ok 302 - get maq assy
ok 303 - An object of class 'Bio::Assembly::IO::maq' isa 'Bio::Assembly::IO'
ok 304 - get_contig_seq_ids
ok 305
ok 306
ok 307
ok 308
ok 309
ok 310
ok 311
ok 312
ok 313
ok 314
ok 315
ok 316
ok 317
ok 318
ok 319
ok 320
ok 321
ok 322
ok 323
ok 324
ok 325
ok 326
ok 327
ok 328
ok 329
ok 330
ok 331
ok 332
ok 333
ok 334
ok 335
ok 336
ok 337
ok 338
ok 339
ok 340
ok 341
ok 342
ok 343
ok 344
ok 345
ok 346
ok 347
ok 348
ok 349
ok 350
ok 351
ok 352
ok 353
ok 354
ok 355
ok 356
ok 357
ok 358
ok 359
ok 360
ok 361
ok 362
ok 363
ok 364
ok 365
ok 366
ok 367
ok 368
ok 369
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ok 371
ok 372
ok 373
ok 374
ok 375
ok 376
ok 377
ok 378
ok 379
ok 380
ok 381
ok 382
ok 383
ok 384
ok 385
ok 386
ok 387
ok 388
ok 389
ok 390
ok 391
ok 392
ok 393
ok 394
ok 395
ok 396
ok 397
ok 398
ok 399
ok 400
ok 401
ok 402
ok 403
ok 404
ok 405
ok 406
ok 407
ok 408
ok 409
ok 410
ok 411
ok 412
ok 413
ok 414
ok 415
ok 416
ok 417
ok 418
ok 419
ok 420
ok 421
ok 422
ok 423
ok 424
ok 425
ok 426
ok 427
ok 428
ok 429
ok 430
ok 431
ok 432
ok 433
ok 434
ok 435
ok 436
ok 437
ok 438
ok 439
ok 440
ok 441
ok 442
ok 443
ok 444
ok 445
ok 446
ok 447
ok 448
ok 449
ok 450
ok 451
ok 452
ok 453
ok 454
ok 455
ok 456
ok 457
ok 458
ok 459
ok 460
ok 461
ok 462
ok 463
ok 464
ok 465
ok 466
ok 467
ok 468
ok 469
ok 470
ok 471
ok 472
ok 473
ok 474
ok 475
ok 476
ok 477
ok 478
ok 479
ok 480
ok 481
ok 482
ok 483
ok 484
ok 485
ok 486
ok 487
ok 488
ok 489
ok 490
ok 491
ok 492
ok 493
ok 494
ok 495
ok 496
ok 497
ok 498
ok 499
ok 500
ok 501
ok 502
ok 503
ok 504
ok 505
ok 506
ok 507
ok 508
ok 509
ok 510
ok 511
ok 512
ok 513
ok 514
ok 515
ok 516
ok 517
ok 518
ok 519
ok 520
ok 521
ok 522
ok 523
ok 524
ok 525
ok 526
ok 527
ok 528
ok 529
ok 530
ok 531
ok 532
ok 533
ok 534
ok 535
ok 536
ok 537
ok 538
ok 539
ok 540
ok 541
ok 542
ok 543
ok 544
ok 545
ok 546
ok 547
ok 548
ok 549
ok 550
ok 551
ok 552 - get_contig_ids
ok 553
ok 554
ok 555
ok 556
ok 557
ok 558
ok 559
ok 560
ok 561
ok 562
ok 563
ok 564
ok 565
ok 566
ok 567
ok 568
ok 569
ok 570
ok 571
ok 572
ok 573
ok 574
ok 575
ok 576
ok 577
ok 578
ok 579
ok 580
ok 581
ok 582
ok 583
ok 584
ok 585
ok 586
ok 587
ok 588
ok 589
ok 590
ok 591 - get_singlet_ids
ok 592
ok 593
ok 594
ok 595
ok 596
ok 597 - get_all_seq_ids
ok 598
ok 599
ok 600
ok 601
ok 602
ok 603
ok 604
ok 605
ok 606
ok 607
ok 608
ok 609
ok 610
ok 611
ok 612
ok 613
ok 614
ok 615
ok 616
ok 617
ok 618
ok 619
ok 620
ok 621
ok 622
ok 623
ok 624
ok 625
ok 626
ok 627
ok 628
ok 629
ok 630
ok 631
ok 632
ok 633
ok 634
ok 635
ok 636
ok 637
ok 638
ok 639
ok 640
ok 641
ok 642
ok 643
ok 644
ok 645
ok 646
ok 647
ok 648
ok 649
ok 650
ok 651
ok 652
ok 653
ok 654
ok 655
ok 656
ok 657
ok 658
ok 659
ok 660
ok 661
ok 662
ok 663
ok 664
ok 665
ok 666
ok 667
ok 668
ok 669
ok 670
ok 671
ok 672
ok 673
ok 674
ok 675
ok 676
ok 677
ok 678
ok 679
ok 680
ok 681
ok 682
ok 683
ok 684
ok 685
ok 686
ok 687
ok 688
ok 689
ok 690
ok 691
ok 692
ok 693
ok 694
ok 695
ok 696
ok 697
ok 698
ok 699
ok 700
ok 701
ok 702
ok 703
ok 704
ok 705
ok 706
ok 707
ok 708
ok 709
ok 710
ok 711
ok 712
ok 713
ok 714
ok 715
ok 716
ok 717
ok 718
ok 719
ok 720
ok 721
ok 722
ok 723
ok 724
ok 725
ok 726
ok 727
ok 728
ok 729
ok 730
ok 731
ok 732
ok 733
ok 734
ok 735
ok 736
ok 737
ok 738
ok 739
ok 740
ok 741
ok 742
ok 743
ok 744
ok 745
ok 746
ok 747
ok 748
ok 749
ok 750
ok 751
ok 752
ok 753
ok 754
ok 755
ok 756
ok 757
ok 758
ok 759
ok 760
ok 761
ok 762
ok 763
ok 764
ok 765
ok 766
ok 767
ok 768
ok 769
ok 770
ok 771
ok 772
ok 773
ok 774
ok 775
ok 776
ok 777
ok 778
ok 779
ok 780
ok 781
ok 782
ok 783
ok 784
ok 785
ok 786
ok 787
ok 788
ok 789
ok 790
ok 791
ok 792
ok 793
ok 794
ok 795
ok 796
ok 797
ok 798
ok 799
ok 800
ok 801
ok 802
ok 803
ok 804
ok 805
ok 806
ok 807
ok 808
ok 809
ok 810
ok 811
ok 812
ok 813
ok 814
ok 815
ok 816
ok 817
ok 818
ok 819
ok 820
ok 821
ok 822
ok 823
ok 824
ok 825
ok 826
ok 827
ok 828
ok 829
ok 830
ok 831
ok 832
ok 833
ok 834
ok 835
ok 836
ok 837
ok 838
ok 839
ok 840
ok 841
ok 842
ok 843
ok 844
ok 845
ok 846
ok 847
ok 848
ok 849
ok 850 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 851 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 852 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 853 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 854 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 855 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 856 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 857 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 858 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 859 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 860 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 861 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 862 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 863 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 864 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 865 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 866 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 867 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 868 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 869 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 870 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 871 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 872 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 873 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 874 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 875 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 876 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 877 - An object of class 'Bio::Assembly::Singlet' isa 'Bio::Assembly::Contig'
ok 878 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 879 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 880 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 881 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 882 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 883 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 884 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 885 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 886 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 887 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 888 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 889 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 890 - An object of class 'Bio::Assembly::Contig' isa 'Bio::Assembly::Contig'
ok 891
ok 892
ok
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/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
t/LiveSeq/LiveSeq.t .................... 
1..48
ok 1 - use Bio::LiveSeq::IO::BioPerl;
ok 2
ok 3
ok 4 - Bio::LiveSeq::Gene
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok
t/LiveSeq/Mutation.t ................... 
1..19
ok 1 - use Bio::LiveSeq::Mutation;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok
t/LiveSeq/Mutator.t .................... 
1..24
ok 1 - use Bio::LiveSeq::Mutator;
ok 2 - use Bio::LiveSeq::IO::BioPerl;
ok 3 - use Bio::Variation::IO;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok

You are loading a Bio::DB::GFF database with GFF3 formatted data.
While this will likely work fine, the Bio::DB::GFF schema does not
always faithfully capture the complexity represented in GFF3 files.
Unless you have a specific reason for using Bio::DB::GFF, we suggest
that you use a Bio::DB::SeqFeature::Store database and its corresponding
loader, bp_seqfeature_load.pl.

t/LocalDB/BioDBGFF.t ................... 
1..275
ok 1 - use Bio::DB::GFF;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101 # skip fetch_feature_by_gid() not implemented by this adaptor
ok 102 # skip fetch_feature_by_gid() not implemented by this adaptor
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 # skip delete_groups() not implemented by this adaptor
ok 133 # skip delete_groups() not implemented by this adaptor
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
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 # skip fetch_feature_by_gid() not implemented by this adaptor
ok 239 # skip fetch_feature_by_gid() not implemented by this adaptor
ok 240
ok 241
ok 242
ok 243
ok 244
ok 245
ok 246 # skip preferred groups are not supported by gff3
ok 247 # skip preferred groups are not supported by gff3
ok 248 # skip preferred groups are not supported by gff3
ok 249
ok 250
ok 251
ok 252
ok 253
ok 254
ok 255
ok 256
ok 257
ok 258
ok 259
ok 260
ok 261
ok 262
ok 263
ok 264
ok 265
ok 266
ok 267
ok 268
ok 269 # skip delete_groups() not implemented by this adaptor
ok 270 # skip delete_groups() not implemented by this adaptor
ok 271
ok 272
ok 273
ok 274
ok 275
ok
Subroutine dl_load_flags redefined at (eval 74) line 8.
Subroutine Bio::DB::IndexedBase::_strip_crnl redefined at (eval 74) line 9.
t/LocalDB/Fasta.t ...................... 
1..109
ok 1 - Index a directory
ok 2
ok 3 - An object of class 'Bio::DB::Fasta' isa 'Bio::DB::Fasta'
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeq::Fasta'
ok 29 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeqI'
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - bug 3126
ok 38
ok 39
ok 40 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeq::Fasta'
ok 41 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeqI'
ok 42
ok 43
ok 44
ok 45 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeq::Fasta'
ok 46 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeqI'
ok 47
ok 48
ok 49 - use Class::Unload;
ok 50 - Re-open an existing index
ok 51
ok 52 - Tied hash access
ok 53
ok 54
ok 55
ok 56
ok 57 - Writing with SeqIO
ok 58
ok 59
ok 60 - Index a single file
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72 - An object of class 'Bio::DB::Indexed::Stream' isa 'Bio::DB::Indexed::Stream'
ok 73
ok 74 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeq::Fasta'
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 - Make single ID
ok 91
ok 92
ok 93 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeqI'
ok 94 - Make multiple IDs, bug \#3389
ok 95
ok 96
ok 97 - An object of class 'Bio::PrimarySeq::Fasta' isa 'Bio::PrimarySeqI'
ok 98 - Index a set of files
ok 99
ok 100
ok 101
ok 102
ok 103 - threw Regexp ((?^:FASTA header doesn't match))
ok 104 - threw Regexp ((?^:Blank lines can only precede header lines))
ok 105
ok 106 - length is correct in sequences past spaces
ok 107
ok 108 - subseq is correct
ok 109 - subseq is correct
ok
t/LocalDB/Flat.t ....................... 
1..25
ok 1 - use Bio::DB::Flat;
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
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
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 ................ 
1..73
ok 1 - use Bio::Index::Fasta;
ok 2 - use Bio::Index::Qual;
ok 3 - use Bio::Index::SwissPfam;
ok 4 - use Bio::Index::EMBL;
ok 5 - use Bio::Index::GenBank;
ok 6 - use Bio::Index::Stockholm;
ok 7 - use Bio::Index::Swissprot;
ok 8 - use Bio::Index::Hmmer;
ok 9 - use Bio::DB::InMemoryCache;
ok 10 - use Bio::DB::InMemoryCache;
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19 - An object of class 'Bio::Seq' isa 'Bio::PrimarySeqI'
ok 20
ok 21
ok 22
ok 23 - An object of class 'Bio::Seq' isa 'Bio::SeqI'
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 - An object of class 'Bio::Index::Stockholm' isa 'Bio::Index::Stockholm'
ok 69
ok 70 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 71 - An object of class 'Bio::Index::Hmmer' isa 'Bio::Index::Hmmer'
ok 72
ok 73
ok
t/LocalDB/Qual.t ....................... 
1..56
ok 1 - use Bio::Root::IO;
ok 2 - use File::Copy;
ok 3
ok 4
ok 5 - An object of class 'Bio::DB::Qual' isa 'Bio::DB::Qual'
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual::Qual'
ok 23 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::QualI'
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual::Qual'
ok 38 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::QualI'
ok 39
ok 40
ok 41
ok 42 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual::Qual'
ok 43 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual'
ok 44
ok 45
ok 46
ok 47
ok 48 - An object of class 'Bio::DB::Indexed::Stream' isa 'Bio::DB::Indexed::Stream'
ok 49
ok 50 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual'
ok 51
ok 52 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual'
ok 53
ok 54
ok 55
ok 56
ok
t/LocalDB/Registry.t ................... 
1..14
ok 1 - use Bio::DB::Registry;
ok 2 - use Bio::DB::Flat;
ok 3
ok 4
ok 5
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
t/LocalDB/SeqFeature.t ................. 
1..116
ok 1 - use Bio::SeqFeature::Generic;
ok 2 - use Bio::DB::SeqFeature::Store;
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
ok 8
ok 9
ok 10 - adding a feature
ok 11
ok 12
ok 13
ok 14 - adding a feature with no primary_id
ok 15
ok 16 - searching for a feature that shouldnt exist
ok 17 - simple type
ok 18 - base type with colon
ok 19 - base type alone
ok 20 - queried types are not interpolated
ok 21
ok 22
ok 23 - An object of class 'Bio::DB::GFF::Typename' isa 'Bio::DB::GFF::Typename'
ok 24 - feature deletion
ok 25
ok 26
ok 27 - adding subfeatures
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 - feature names should be case insensitive
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 - base type
ok 65 - base:source type
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73 - An object of class 'Bio::Location::Split' isa 'Bio::Location::Split'
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 - keyword search; 1 term
ok 103 - keyword search; 2 terms
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 112 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 113 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 114 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 115 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok 116 # skip Namespaces only supported for DBI::mysql and DBI::Pg adaptors
ok
t/LocalDB/Taxonomy/greengenes.t ........ 
1..38
ok 1 - use Bio::DB::Taxonomy;
ok 2 - use Bio::Tree::Tree;
ok 3
ok 4 - An object of class 'Bio::DB::Taxonomy::greengenes' isa 'Bio::DB::Taxonomy::greengenes'
ok 5 - An object of class 'Bio::DB::Taxonomy::greengenes' isa 'Bio::DB::Taxonomy::list'
ok 6 - An object of class 'Bio::DB::Taxonomy::greengenes' isa 'Bio::DB::Taxonomy'
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok
t/LocalDB/Taxonomy/silva.t ............. 
1..42
ok 1 - use Bio::DB::Taxonomy;
ok 2 - use Bio::Tree::Tree;
ok 3
ok 4 - An object of class 'Bio::DB::Taxonomy::silva' isa 'Bio::DB::Taxonomy::silva'
ok 5 - An object of class 'Bio::DB::Taxonomy::silva' isa 'Bio::DB::Taxonomy::list'
ok 6 - An object of class 'Bio::DB::Taxonomy::silva' isa 'Bio::DB::Taxonomy'
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok
t/LocalDB/Taxonomy/sqlite.t ............ 
ok 1 - use Bio::DB::Taxonomy;
ok 2 - use Bio::Tree::Tree;
ok 3
ok 4 - An object of class 'Bio::DB::Taxonomy::sqlite' isa 'Bio::DB::Taxonomy::sqlite'
ok 5 - An object of class 'Bio::DB::Taxonomy::sqlite' isa 'Bio::DB::Taxonomy'
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 - Bio::DB::Taxonomy::sqlite: common names
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 # skip Network tests have not been requested
ok 56 # skip Network tests have not been requested
ok 57 # skip Network tests have not been requested
ok 58 # skip Network tests have not been requested
ok 59 # skip Network tests have not been requested
ok 60 # skip Network tests have not been requested
ok 61 # skip Network tests have not been requested
ok 62 # skip Network tests have not been requested
ok 63 # skip Network tests have not been requested
ok 64
ok 65
ok 66
ok 67
1..67
ok
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;
ok 4
ok 5
ok 6
ok 7
ok 8 - An object of class 'Bio::Annotation::Reference' isa 'Bio::Annotation::Reference'
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 - An object of class 'Bio::Seq' isa 'Bio::Seq'
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 - An object of class 'Bio::Matrix::PSM::SiteMatrix' isa 'Bio::Matrix::PSM::SiteMatrix'
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
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 - An object of class 'Bio::Seq' isa 'Bio::SeqI'
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107 - An object of class 'Bio::Map::TranscriptionFactor' isa 'Bio::Map::TranscriptionFactor'
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok
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
t/Map/Linkage.t ........................ 
1..18
ok 1 - use Bio::Map::LinkagePosition;
ok 2 - use Bio::Map::Microsatellite;
ok 3 - use Bio::Map::LinkageMap;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok
t/Map/Map.t ............................ 
1..267
ok 1 - use Bio::Map::SimpleMap;
ok 2 - use Bio::Map::Marker;
ok 3 - use Bio::Map::Position;
ok 4 - use Bio::Map::Relative;
ok 5 - use Bio::Map::Mappable;
ok 6
ok 7
ok 8
ok 9
ok 10 - Length is 0
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
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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
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ok 163
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ok 247
ok 248
ok 249 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 250 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 251 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 252 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 253 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 254 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 255 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 256 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 257 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 258 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 259 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 260 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 261 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 262 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 263 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 264 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 265 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 266 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 267 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok
t/Map/MapIO.t .......................... 
1..51
ok 1 - use Bio::MapIO;
ok 2
ok 3 - 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
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ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok
t/Map/MicrosatelliteMarker.t ........... 
1..8
ok 1 - use Bio::Map::SimpleMap;
ok 2 - use Bio::Map::Position;
ok 3 - use Bio::Map::Microsatellite;
ok 4
ok 5
ok 6
ok 7
ok 8
ok
t/Map/Physical.t ....................... 
1..40
ok 1 - use Bio::Map::Physical;
ok 2 - use Bio::MapIO;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12 - code holds and returns a string, definition requires a boolean
ok 13 - code holds and returns a string, definition requires a boolean
ok 14
ok 15
ok 16
ok 17
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ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok
t/Matrix/IO/masta.t .................... 
1..16
ok 1 - use Bio::Matrix::PSM::IO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok
t/Matrix/IO/psm.t ...................... 
1..63
ok 1 - use Bio::Matrix::PSM::IO;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
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ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok
t/Matrix/InstanceSite.t ................ 
1..6
ok 1 - use Bio::Matrix::PSM::InstanceSite;
ok 2
ok 3
ok 4
ok 5
ok 6
ok
t/Matrix/Matrix.t ...................... 
1..77
ok 1 - use Bio::Matrix::Generic;
ok 2 - use Bio::Matrix::IO;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30 - 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
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ok 69
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ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok
t/Matrix/ProtMatrix.t .................. 
1..14
ok 1 - use Bio::Matrix::PSM::ProtMatrix;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok
t/Matrix/ProtPsm.t ..................... 
1..14
ok 1 - use Bio::Matrix::PSM::IO;
ok 2
ok 3
ok 4
ok 5 # skip TODO: Module incomplete
ok 6 # skip TODO: Module incomplete
ok 7 # skip TODO: Module incomplete
ok 8 # skip TODO: Module incomplete
ok 9 # skip TODO: Module incomplete
ok 10 # skip TODO: Module incomplete
ok 11 # skip TODO: Module incomplete
ok 12 # skip TODO: Module incomplete
ok 13 # skip TODO: Module incomplete
ok 14 # skip TODO: Module incomplete
ok
t/Matrix/SiteMatrix.t .................. 
1..14
ok 1 - use Bio::Matrix::PSM::SiteMatrix;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok
t/Ontology/GOterm.t .................... 
1..62
ok 1 - use Bio::Ontology::GOterm;
ok 2 - use Bio::Ontology::Ontology;
ok 3 - use Bio::Annotation::DBLink;
ok 4 - 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
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ok 15
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ok 18
ok 19
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ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok
t/Ontology/GraphAdaptor.t .............. 
1..28
ok 1 - use Bio::Ontology::SimpleGOEngine::GraphAdaptor;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok
t/Ontology/IO/go.t ..................... 
1..102
ok 1 - use Bio::OntologyIO;
ok 2
ok 3 - 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
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ok 91
ok 92
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ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok
t/Ontology/IO/interpro.t ............... 
1..69
ok 1 - use Bio::OntologyIO;
ok 2 - 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 Helix-turn-helix, AraC type  in ontology InterPro
ok 21 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 22 - term post-translational modification in ontology InterPro
ok 23 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 24 - term Kringle in ontology InterPro
ok 25 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 26 - term Conserved Site in ontology InterPro
ok 27 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 28 - term Region in ontology InterPro
ok 29 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 30 - term Cdc20/Fizzy in ontology InterPro
ok 31 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 32 - term Binding Site in ontology InterPro
ok 33 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 34 - term Active Site in ontology InterPro
ok 35 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 36 - term Integrins alpha chain in ontology InterPro
ok 37 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
ok 38 - term Repeat 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 - Helix-turn-helix, AraC type  term has one parent
ok 62 - Helix-turn-helix, AraC type  term has one ancestor
ok 63 - Kringle term has one parent
ok 64 - Kringle term has one ancestor
ok 65 - Cdc20/Fizzy term has one parent
ok 66 - Cdc20/Fizzy 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
t/Ontology/IO/obo.t .................... 
1..92
ok 1 - use Bio::OntologyIO;
ok 2 - use Bio::Ontology::RelationshipType;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46 - 'got a ontology IO handler' isa 'Bio::OntologyIO'
ok 47 - 'got ontology parser2' isa 'Bio::Ontology::Ontology'
ok 48 - 'got OBO engine object' isa 'Bio::Ontology::OBOEngine'
ok 49 - 'got ontology parser2' isa 'Bio::Ontology::Ontology'
ok 50 - 'got OBO engine object' isa 'Bio::Ontology::OBOEngine'
ok 51 - 'got ontology parser2' isa 'Bio::Ontology::Ontology'
ok 52 - 'got OBO engine object' isa 'Bio::Ontology::OBOEngine'
ok 53 - Gene ontology
ok 54 - biological process
ok 55 - molecular function
ok 56 - Got root
ok 57 - Got root
ok 58 - Got regulates
# 	 from gene_ontology
ok 59 - Got
# 	 positively regulates from gene_ontology
ok 60 - Got
# 	  regulates from biological_process
ok 61 - Got
# 	 positively regulates from biological_process
ok 62 - Got predicates for gene_ontology
ok 63 - Got predicates for biological_process
ok 64 - Got regulates predicate
ok 65 - Got positively regulates predicate
ok 66 - Got relationships for biological_process
ok 67 - Got relationships for molecular_function
ok 68 - Got is a relationship from
# 	 molecular_function
ok 69 - 'Got term object' isa 'Bio::Ontology::Term'
ok 70 - Got term id
ok 71 - Got term name
ok 72 - 'Got regulated object' isa 'Bio::Ontology::Term'
ok 73 - Got regulated term1 id
ok 74 - 'Got term1 object' isa 'Bio::Ontology::Term'
ok 75 - Got back the child
ok 76 - 'Got term object' isa 'Bio::Ontology::Term'
ok 77 - Got term id
ok 78 - Got term name
ok 79 - 'Got regulated object' isa 'Bio::Ontology::Term'
ok 80 - Got regulated term1 id
ok 81 - Got identical regulation
ok 82 - 'Got term1 object' isa 'Bio::Ontology::Term'
ok 83 - Got back the child
ok 84 - 'got a ontology IO handler' isa 'Bio::OntologyIO'
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok
t/Ontology/Ontology.t .................. 
1..55
ok 1 - use Bio::OntologyIO;
ok 2 - use Bio::Ontology::RelationshipType;
ok 3 - 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
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
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
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
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
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
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
t/Phenotype/MeSH.t ..................... 
1..24
ok 1 - use Bio::Phenotype::MeSH::Term;
ok 2 - use Bio::Phenotype::MeSH::Twig;
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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'
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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'
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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'
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ok 79 - operator overloading in AnnotationI is deprecated
ok 80 - operator overloading in AnnotationI is deprecated
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ok 84 - operator overloading in AnnotationI is deprecated
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ok 136 - operator overloading in AnnotationI is deprecated
ok 137 - operator overloading in AnnotationI is deprecated
ok 138
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ok 140 - operator overloading in AnnotationI is deprecated
ok 141 - operator overloading in AnnotationI is deprecated
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ok
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'
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ok
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
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ok 16
ok 17
ok 18
ok 19 - An object of class 'Bio::Phenotype::OMIM::MiniMIMentry' isa 'Bio::Phenotype::OMIM::MiniMIMentry'
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ok 89 - An object of class 'Bio::Phenotype::OMIM::OMIMentry' isa 'Bio::Phenotype::OMIM::OMIMentry'
ok 90
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ok 105 - An object of class 'Bio::Phenotype::OMIM::MiniMIMentry' isa 'Bio::Phenotype::OMIM::MiniMIMentry'
ok 106
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ok 175 - missing linebreak caught
ok
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
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ok 21
ok 22
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ok 24
ok 25
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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
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ok 86
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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
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ok 109
ok 110
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ok
t/PodSyntax.t .......................... 
1..927
ok 1 - POD test for Bio/SimpleAnalysisI.pm
ok 2 - POD test for Bio/AnalysisI.pm
ok 3 - POD test for Bio/ClusterI.pm
ok 4 - POD test for Bio/ClusterIO.pm
ok 5 - POD test for Bio/Taxon.pm
ok 6 - POD test for Bio/SeqIO.pm
ok 7 - POD test for Bio/ParameterBaseI.pm
ok 8 - POD test for Bio/NexmlIO.pm
ok 9 - POD test for Bio/SeqAnalysisParserI.pm
ok 10 - POD test for Bio/AnnotationCollectionI.pm
ok 11 - POD test for Bio/Seq.pm
ok 12 - POD test for Bio/Taxonomy.pm
ok 13 - POD test for Bio/AnnotationI.pm
ok 14 - POD test for Bio/LocatableSeq.pm
ok 15 - POD test for Bio/PhyloNetwork.pm
ok 16 - POD test for Bio/SimpleAlign.pm
ok 17 - POD test for Bio/FeatureHolderI.pm
ok 18 - POD test for Bio/DasI.pm
ok 19 - POD test for Bio/OntologyIO.pm
ok 20 - POD test for Bio/DescribableI.pm
ok 21 - POD test for Bio/Species.pm
ok 22 - POD test for Bio/PullParserI.pm
ok 23 - POD test for Bio/IdCollectionI.pm
ok 24 - POD test for Bio/MapIO.pm
ok 25 - POD test for Bio/AlignIO.pm
ok 26 - POD test for Bio/AnalysisResultI.pm
ok 27 - POD test for Bio/PrimarySeqI.pm
ok 28 - POD test for Bio/IdentifiableI.pm
ok 29 - POD test for Bio/HandlerBaseI.pm
ok 30 - POD test for Bio/UpdateableSeqI.pm
ok 31 - POD test for Bio/SeqI.pm
ok 32 - POD test for Bio/SearchDist.pm
ok 33 - POD test for Bio/LocationI.pm
ok 34 - POD test for Bio/DBLinkContainerI.pm
ok 35 - POD test for Bio/WebAgent.pm
ok 36 - POD test for Bio/Range.pm
ok 37 - POD test for Bio/Perl.pm
ok 38 - POD test for Bio/RangeI.pm
ok 39 - POD test for Bio/SeqFeatureI.pm
ok 40 - POD test for Bio/SeqUtils.pm
ok 41 - POD test for Bio/PrimarySeq.pm
ok 42 - POD test for Bio/TreeIO.pm
ok 43 - POD test for Bio/SearchIO.pm
ok 44 - POD test for Bio/AnalysisParserI.pm
ok 45 - POD test for Bio/AnnotatableI.pm
ok 46 - POD test for Bio/Taxonomy/Node.pm
ok 47 - POD test for Bio/Taxonomy/Taxon.pm
ok 48 - POD test for Bio/Taxonomy/FactoryI.pm
ok 49 - POD test for Bio/Taxonomy/Tree.pm
ok 50 - POD test for Bio/MolEvol/CodonModel.pm
ok 51 - POD test for Bio/Index/Swissprot.pm
ok 52 - POD test for Bio/Index/Fasta.pm
ok 53 - POD test for Bio/Index/Qual.pm
ok 54 - POD test for Bio/Index/Stockholm.pm
ok 55 - POD test for Bio/Index/EMBL.pm
ok 56 - POD test for Bio/Index/GenBank.pm
ok 57 - POD test for Bio/Index/SwissPfam.pm
ok 58 - POD test for Bio/Index/AbstractSeq.pm
ok 59 - POD test for Bio/Index/Blast.pm
ok 60 - POD test for Bio/Index/Abstract.pm
ok 61 - POD test for Bio/Index/Hmmer.pm
ok 62 - POD test for Bio/Index/BlastTable.pm
ok 63 - POD test for Bio/Index/Fastq.pm
ok 64 - POD test for Bio/Phenotype/Phenotype.pm
ok 65 - POD test for Bio/Phenotype/Measure.pm
ok 66 - POD test for Bio/Phenotype/Correlate.pm
ok 67 - POD test for Bio/Phenotype/PhenotypeI.pm
ok 68 - POD test for Bio/Phenotype/MeSH/Twig.pm
ok 69 - POD test for Bio/Phenotype/MeSH/Term.pm
ok 70 - POD test for Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm
ok 71 - POD test for Bio/Phenotype/OMIM/MiniMIMentry.pm
ok 72 - POD test for Bio/Phenotype/OMIM/OMIMparser.pm
ok 73 - POD test for Bio/Phenotype/OMIM/OMIMentry.pm
ok 74 - POD test for Bio/MapIO/mapmaker.pm
ok 75 - POD test for Bio/MapIO/fpc.pm
ok 76 - POD test for Bio/Factory/AnalysisI.pm
ok 77 - POD test for Bio/Factory/SequenceFactoryI.pm
ok 78 - POD test for Bio/Factory/TreeFactoryI.pm
ok 79 - POD test for Bio/Factory/SequenceProcessorI.pm
ok 80 - POD test for Bio/Factory/DriverFactory.pm
ok 81 - POD test for Bio/Factory/ApplicationFactoryI.pm
ok 82 - POD test for Bio/Factory/ObjectFactoryI.pm
ok 83 - POD test for Bio/Factory/LocationFactoryI.pm
ok 84 - POD test for Bio/Factory/MapFactoryI.pm
ok 85 - POD test for Bio/Factory/SeqAnalysisParserFactory.pm
ok 86 - POD test for Bio/Factory/ObjectBuilderI.pm
ok 87 - POD test for Bio/Factory/ObjectFactory.pm
ok 88 - POD test for Bio/Factory/SequenceStreamI.pm
ok 89 - POD test for Bio/Factory/SeqAnalysisParserFactoryI.pm
ok 90 - POD test for Bio/Factory/FTLocationFactory.pm
ok 91 - POD test for Bio/CodonUsage/IO.pm
ok 92 - POD test for Bio/CodonUsage/Table.pm
ok 93 - POD test for Bio/Ontology/PathI.pm
ok 94 - POD test for Bio/Ontology/TermFactory.pm
ok 95 - POD test for Bio/Ontology/RelationshipType.pm
ok 96 - POD test for Bio/Ontology/OBOterm.pm
ok 97 - POD test for Bio/Ontology/OntologyEngineI.pm
ok 98 - POD test for Bio/Ontology/OntologyI.pm
ok 99 - POD test for Bio/Ontology/Path.pm
ok 100 - POD test for Bio/Ontology/SimpleOntologyEngine.pm
ok 101 - POD test for Bio/Ontology/OntologyStore.pm
ok 102 - POD test for Bio/Ontology/DocumentRegistry.pm
ok 103 - POD test for Bio/Ontology/OBOEngine.pm
ok 104 - POD test for Bio/Ontology/Ontology.pm
ok 105 - POD test for Bio/Ontology/InterProTerm.pm
ok 106 - POD test for Bio/Ontology/RelationshipFactory.pm
ok 107 - POD test for Bio/Ontology/RelationshipI.pm
ok 108 - POD test for Bio/Ontology/GOterm.pm
ok 109 - POD test for Bio/Ontology/TermI.pm
ok 110 - POD test for Bio/Ontology/Relationship.pm
ok 111 - POD test for Bio/Ontology/Term.pm
ok 112 - POD test for Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm
ok 113 - POD test for Bio/Nexml/Factory.pm
ok 114 - POD test for Bio/Das/SegmentI.pm
ok 115 - POD test for Bio/Das/FeatureTypeI.pm
ok 116 - POD test for Bio/Variation/IO.pm
ok 117 - POD test for Bio/Variation/SeqDiff.pm
ok 118 - POD test for Bio/Variation/AAReverseMutate.pm
ok 119 - POD test for Bio/Variation/AAChange.pm
ok 120 - POD test for Bio/Variation/DNAMutation.pm
ok 121 - POD test for Bio/Variation/Allele.pm
ok 122 - POD test for Bio/Variation/RNAChange.pm
ok 123 - POD test for Bio/Variation/VariantI.pm
ok 124 - POD test for Bio/Variation/SNP.pm
ok 125 - POD test for Bio/Variation/IO/flat.pm
ok 126 - POD test for Bio/Variation/IO/xml.pm
ok 127 - POD test for Bio/Cluster/FamilyI.pm
ok 128 - POD test for Bio/Cluster/UniGeneI.pm
ok 129 - POD test for Bio/Cluster/UniGene.pm
ok 130 - POD test for Bio/Cluster/ClusterFactory.pm
ok 131 - POD test for Bio/Cluster/SequenceFamily.pm
ok 132 - POD test for Bio/SeqFeature/TypedSeqFeatureI.pm
ok 133 - POD test for Bio/SeqFeature/CollectionI.pm
ok 134 - POD test for Bio/SeqFeature/Computation.pm
ok 135 - POD test for Bio/SeqFeature/Amplicon.pm
ok 136 - POD test for Bio/SeqFeature/Generic.pm
ok 137 - POD test for Bio/SeqFeature/SubSeq.pm
ok 138 - POD test for Bio/SeqFeature/AnnotationAdaptor.pm
ok 139 - POD test for Bio/SeqFeature/Similarity.pm
ok 140 - POD test for Bio/SeqFeature/SimilarityPair.pm
ok 141 - POD test for Bio/SeqFeature/PositionProxy.pm
ok 142 - POD test for Bio/SeqFeature/Collection.pm
ok 143 - POD test for Bio/SeqFeature/FeaturePair.pm
ok 144 - POD test for Bio/SeqFeature/Primer.pm
ok 145 - POD test for Bio/SeqFeature/Lite.pm
ok 146 - POD test for Bio/SeqFeature/SiRNA/Oligo.pm
ok 147 - POD test for Bio/SeqFeature/SiRNA/Pair.pm
ok 148 - POD test for Bio/SeqFeature/Gene/TranscriptI.pm
ok 149 - POD test for Bio/SeqFeature/Gene/GeneStructureI.pm
ok 150 - POD test for Bio/SeqFeature/Gene/Transcript.pm
ok 151 - POD test for Bio/SeqFeature/Gene/NC_Feature.pm
ok 152 - POD test for Bio/SeqFeature/Gene/ExonI.pm
ok 153 - POD test for Bio/SeqFeature/Gene/GeneStructure.pm
ok 154 - POD test for Bio/SeqFeature/Gene/Promoter.pm
ok 155 - POD test for Bio/SeqFeature/Gene/Intron.pm
ok 156 - POD test for Bio/SeqFeature/Gene/Poly_A_site.pm
ok 157 - POD test for Bio/SeqFeature/Gene/Exon.pm
ok 158 - POD test for Bio/SeqFeature/Gene/UTR.pm
ok 159 - POD test for Bio/SeqFeature/Tools/IDHandler.pm
ok 160 - POD test for Bio/SeqFeature/Tools/Unflattener.pm
ok 161 - POD test for Bio/SeqFeature/Tools/TypeMapper.pm
ok 162 - POD test for Bio/SeqFeature/Tools/FeatureNamer.pm
ok 163 - POD test for Bio/Map/OrderedPosition.pm
ok 164 - POD test for Bio/Map/LinkagePosition.pm
ok 165 - POD test for Bio/Map/PositionHandler.pm
ok 166 - POD test for Bio/Map/GeneMap.pm
ok 167 - POD test for Bio/Map/Contig.pm
ok 168 - POD test for Bio/Map/LinkageMap.pm
ok 169 - POD test for Bio/Map/CytoMap.pm
ok 170 - POD test for Bio/Map/OrderedPositionWithDistance.pm
ok 171 - POD test for Bio/Map/PositionHandlerI.pm
ok 172 - POD test for Bio/Map/CytoPosition.pm
ok 173 - POD test for Bio/Map/Clone.pm
ok 174 - POD test for Bio/Map/PositionI.pm
ok 175 - POD test for Bio/Map/Prediction.pm
ok 176 - POD test for Bio/Map/EntityI.pm
ok 177 - POD test for Bio/Map/Marker.pm
ok 178 - POD test for Bio/Map/CytoMarker.pm
ok 179 - POD test for Bio/Map/Gene.pm
ok 180 - POD test for Bio/Map/RelativeI.pm
ok 181 - POD test for Bio/Map/FPCMarker.pm
ok 182 - POD test for Bio/Map/MarkerI.pm
ok 183 - POD test for Bio/Map/TranscriptionFactor.pm
ok 184 - POD test for Bio/Map/Mappable.pm
ok 185 - POD test for Bio/Map/Microsatellite.pm
ok 186 - POD test for Bio/Map/PositionWithSequence.pm
ok 187 - POD test for Bio/Map/MappableI.pm
ok 188 - POD test for Bio/Map/SimpleMap.pm
ok 189 - POD test for Bio/Map/Relative.pm
ok 190 - POD test for Bio/Map/MapI.pm
ok 191 - POD test for Bio/Map/Position.pm
ok 192 - POD test for Bio/Map/GenePosition.pm
ok 193 - POD test for Bio/Map/GeneRelative.pm
ok 194 - POD test for Bio/Map/Physical.pm
ok 195 - POD test for Bio/OntologyIO/obo.pm
ok 196 - POD test for Bio/OntologyIO/dagflat.pm
ok 197 - POD test for Bio/OntologyIO/simplehierarchy.pm
ok 198 - POD test for Bio/OntologyIO/InterProParser.pm
ok 199 - POD test for Bio/OntologyIO/soflat.pm
ok 200 - POD test for Bio/OntologyIO/goflat.pm
ok 201 - POD test for Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
ok 202 - POD test for Bio/OntologyIO/Handlers/BaseSAXHandler.pm
ok 203 - POD test for Bio/OntologyIO/Handlers/InterProHandler.pm
ok 204 - POD test for Bio/Event/EventHandlerI.pm
ok 205 - POD test for Bio/Event/EventGeneratorI.pm
ok 206 - POD test for Bio/Root/Exception.pm
ok 207 - POD test for Bio/Root/IO.pm
ok 208 - POD test for Bio/Root/Utilities.pm
ok 209 - POD test for Bio/Root/Test.pm
ok 210 - POD test for Bio/Root/Root.pm
ok 211 - POD test for Bio/Root/HTTPget.pm
ok 212 - POD test for Bio/Root/TestObject.pm
ok 213 - POD test for Bio/Root/Version.pm
ok 214 - POD test for Bio/Root/RootI.pm
ok 215 - POD test for Bio/Root/Storable.pm
ok 216 - POD test for Bio/Root/Build.pm
ok 217 - POD test for Bio/Restriction/Analysis.pm
ok 218 - POD test for Bio/Restriction/IO.pm
ok 219 - POD test for Bio/Restriction/EnzymeI.pm
ok 220 - POD test for Bio/Restriction/EnzymeCollection.pm
ok 221 - POD test for Bio/Restriction/Enzyme.pm
ok 222 - POD test for Bio/Restriction/IO/base.pm
ok 223 - POD test for Bio/Restriction/IO/itype2.pm
ok 224 - POD test for Bio/Restriction/IO/prototype.pm
ok 225 - POD test for Bio/Restriction/IO/withrefm.pm
ok 226 - POD test for Bio/Restriction/IO/bairoch.pm
ok 227 - POD test for Bio/Restriction/Enzyme/MultiCut.pm
ok 228 - POD test for Bio/Restriction/Enzyme/MultiSite.pm
ok 229 - POD test for Bio/Location/Atomic.pm
ok 230 - POD test for Bio/Location/Simple.pm
ok 231 - POD test for Bio/Location/CoordinatePolicyI.pm
ok 232 - POD test for Bio/Location/NarrowestCoordPolicy.pm
ok 233 - POD test for Bio/Location/AvWithinCoordPolicy.pm
ok 234 - POD test for Bio/Location/Split.pm
ok 235 - POD test for Bio/Location/FuzzyLocationI.pm
ok 236 - POD test for Bio/Location/WidestCoordPolicy.pm
ok 237 - POD test for Bio/Location/SplitLocationI.pm
ok 238 - POD test for Bio/Location/Fuzzy.pm
ok 239 - POD test for Bio/Seq/LargeSeq.pm
ok 240 - POD test for Bio/Seq/Quality.pm
ok 241 - POD test for Bio/Seq/SimulatedRead.pm
ok 242 - POD test for Bio/Seq/RichSeqI.pm
ok 243 - POD test for Bio/Seq/SeqFastaSpeedFactory.pm
ok 244 - POD test for Bio/Seq/SequenceTrace.pm
ok 245 - POD test for Bio/Seq/RichSeq.pm
ok 246 - POD test for Bio/Seq/MetaI.pm
ok 247 - POD test for Bio/Seq/SeqWithQuality.pm
ok 248 - POD test for Bio/Seq/EncodedSeq.pm
ok 249 - POD test for Bio/Seq/LargeLocatableSeq.pm
ok 250 - POD test for Bio/Seq/SeqBuilder.pm
ok 251 - POD test for Bio/Seq/LargePrimarySeq.pm
ok 252 - POD test for Bio/Seq/SeqFactory.pm
ok 253 - POD test for Bio/Seq/TraceI.pm
ok 254 - POD test for Bio/Seq/LargeSeqI.pm
ok 255 - POD test for Bio/Seq/QualI.pm
ok 256 - POD test for Bio/Seq/Meta.pm
ok 257 - POD test for Bio/Seq/PrimaryQual.pm
ok 258 - POD test for Bio/Seq/PrimedSeq.pm
ok 259 - POD test for Bio/Seq/BaseSeqProcessor.pm
ok 260 - POD test for Bio/Seq/Meta/Array.pm
ok 261 - POD test for Bio/Structure/Residue.pm
ok 262 - POD test for Bio/Structure/IO.pm
ok 263 - POD test for Bio/Structure/Atom.pm
ok 264 - POD test for Bio/Structure/Entry.pm
ok 265 - POD test for Bio/Structure/Chain.pm
ok 266 - POD test for Bio/Structure/StructureI.pm
ok 267 - POD test for Bio/Structure/Model.pm
ok 268 - POD test for Bio/Structure/SecStr/DSSP/Res.pm
ok 269 - POD test for Bio/Structure/SecStr/STRIDE/Res.pm
ok 270 - POD test for Bio/Structure/IO/pdb.pm
ok 271 - POD test for Bio/TreeIO/pag.pm
ok 272 - POD test for Bio/TreeIO/lintree.pm
ok 273 - POD test for Bio/TreeIO/NewickParser.pm
ok 274 - POD test for Bio/TreeIO/newick.pm
ok 275 - POD test for Bio/TreeIO/nhx.pm
ok 276 - POD test for Bio/TreeIO/svggraph.pm
ok 277 - POD test for Bio/TreeIO/cluster.pm
ok 278 - POD test for Bio/TreeIO/nexus.pm
ok 279 - POD test for Bio/TreeIO/phyloxml.pm
ok 280 - POD test for Bio/TreeIO/tabtree.pm
ok 281 - POD test for Bio/TreeIO/nexml.pm
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ok 561 - POD test for Bio/Tools/Genewise.pm
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ok 688 - POD test for Bio/SearchIO/Writer/HSPTableWriter.pm
ok 689 - POD test for Bio/SearchIO/Writer/HTMLResultWriter.pm
ok 690 - POD test for Bio/ClusterIO/unigene.pm
ok 691 - POD test for Bio/ClusterIO/dbsnp.pm
ok 692 - POD test for Bio/SeqIO/abi.pm
ok 693 - POD test for Bio/SeqIO/ctf.pm
ok 694 - POD test for Bio/SeqIO/MultiFile.pm
ok 695 - POD test for Bio/SeqIO/gcg.pm
ok 696 - POD test for Bio/SeqIO/strider.pm
ok 697 - POD test for Bio/SeqIO/fasta.pm
ok 698 - POD test for Bio/SeqIO/fastq.pm
ok 699 - POD test for Bio/SeqIO/alf.pm
ok 700 - POD test for Bio/SeqIO/tigrxml.pm
ok 701 - POD test for Bio/SeqIO/ztr.pm
ok 702 - POD test for Bio/SeqIO/mbsout.pm
ok 703 - POD test for Bio/SeqIO/metafasta.pm
ok 704 - POD test for Bio/SeqIO/bsml.pm
ok 705 - POD test for Bio/SeqIO/excel.pm
ok 706 - POD test for Bio/SeqIO/seqxml.pm
ok 707 - POD test for Bio/SeqIO/ace.pm
ok 708 - POD test for Bio/SeqIO/tab.pm
ok 709 - POD test for Bio/SeqIO/largefasta.pm
ok 710 - POD test for Bio/SeqIO/game.pm
ok 711 - POD test for Bio/SeqIO/scf.pm
ok 712 - POD test for Bio/SeqIO/raw.pm
ok 713 - POD test for Bio/SeqIO/locuslink.pm
ok 714 - POD test for Bio/SeqIO/qual.pm
ok 715 - POD test for Bio/SeqIO/gbdriver.pm
ok 716 - POD test for Bio/SeqIO/swiss.pm
ok 717 - POD test for Bio/SeqIO/msout.pm
ok 718 - POD test for Bio/SeqIO/kegg.pm
ok 719 - POD test for Bio/SeqIO/embl.pm
ok 720 - POD test for Bio/SeqIO/chaosxml.pm
ok 721 - POD test for Bio/SeqIO/interpro.pm
ok 722 - POD test for Bio/SeqIO/chaos.pm
ok 723 - POD test for Bio/SeqIO/exp.pm
ok 724 - POD test for Bio/SeqIO/tigr.pm
ok 725 - POD test for Bio/SeqIO/genbank.pm
ok 726 - POD test for Bio/SeqIO/embldriver.pm
ok 727 - POD test for Bio/SeqIO/chadoxml.pm
ok 728 - POD test for Bio/SeqIO/gbxml.pm
ok 729 - POD test for Bio/SeqIO/pir.pm
ok 730 - POD test for Bio/SeqIO/agave.pm
ok 731 - POD test for Bio/SeqIO/FTHelper.pm
ok 732 - POD test for Bio/SeqIO/bsml_sax.pm
ok 733 - POD test for Bio/SeqIO/table.pm
ok 734 - POD test for Bio/SeqIO/entrezgene.pm
ok 735 - POD test for Bio/SeqIO/swissdriver.pm
ok 736 - POD test for Bio/SeqIO/lasergene.pm
ok 737 - POD test for Bio/SeqIO/asciitree.pm
ok 738 - POD test for Bio/SeqIO/pln.pm
ok 739 - POD test for Bio/SeqIO/phd.pm
ok 740 - POD test for Bio/SeqIO/flybase_chadoxml.pm
ok 741 - POD test for Bio/SeqIO/nexml.pm
ok 742 - POD test for Bio/SeqIO/tinyseq.pm
ok 743 - POD test for Bio/SeqIO/game/gameHandler.pm
ok 744 - POD test for Bio/SeqIO/game/seqHandler.pm
ok 745 - POD test for Bio/SeqIO/game/gameWriter.pm
ok 746 - POD test for Bio/SeqIO/game/gameSubs.pm
ok 747 - POD test for Bio/SeqIO/game/featHandler.pm
ok 748 - POD test for Bio/SeqIO/Handler/GenericRichSeqHandler.pm
ok 749 - POD test for Bio/SeqIO/tinyseq/tinyseqHandler.pm
ok 750 - POD test for Bio/Draw/Pictogram.pm
ok 751 - POD test for Bio/LiveSeq/Repeat_Unit.pm
ok 752 - POD test for Bio/LiveSeq/Mutator.pm
ok 753 - POD test for Bio/LiveSeq/Transcript.pm
ok 754 - POD test for Bio/LiveSeq/DNA.pm
ok 755 - POD test for Bio/LiveSeq/Repeat_Region.pm
ok 756 - POD test for Bio/LiveSeq/Mutation.pm
ok 757 - POD test for Bio/LiveSeq/ChainI.pm
ok 758 - POD test for Bio/LiveSeq/AARange.pm
ok 759 - POD test for Bio/LiveSeq/Chain.pm
ok 760 - POD test for Bio/LiveSeq/Gene.pm
ok 761 - POD test for Bio/LiveSeq/Translation.pm
ok 762 - POD test for Bio/LiveSeq/SeqI.pm
ok 763 - POD test for Bio/LiveSeq/Intron.pm
ok 764 - POD test for Bio/LiveSeq/Range.pm
ok 765 - POD test for Bio/LiveSeq/Prim_Transcript.pm
ok 766 - POD test for Bio/LiveSeq/Exon.pm
ok 767 - POD test for Bio/LiveSeq/IO/BioPerl.pm
ok 768 - POD test for Bio/LiveSeq/IO/Loader.pm
ok 769 - POD test for Bio/PopGen/IO.pm
ok 770 - POD test for Bio/PopGen/Population.pm
ok 771 - POD test for Bio/PopGen/Individual.pm
ok 772 - POD test for Bio/PopGen/TagHaplotype.pm
ok 773 - POD test for Bio/PopGen/Utilities.pm
ok 774 - POD test for Bio/PopGen/GenotypeI.pm
ok 775 - POD test for Bio/PopGen/Marker.pm
ok 776 - POD test for Bio/PopGen/MarkerI.pm
ok 777 - POD test for Bio/PopGen/HtSNP.pm
ok 778 - POD test for Bio/PopGen/PopulationI.pm
ok 779 - POD test for Bio/PopGen/Genotype.pm
ok 780 - POD test for Bio/PopGen/Statistics.pm
ok 781 - POD test for Bio/PopGen/IndividualI.pm
ok 782 - POD test for Bio/PopGen/PopStats.pm
ok 783 - POD test for Bio/PopGen/Simulation/Coalescent.pm
ok 784 - POD test for Bio/PopGen/Simulation/GeneticDrift.pm
ok 785 - POD test for Bio/PopGen/IO/prettybase.pm
ok 786 - POD test for Bio/PopGen/IO/phase.pm
ok 787 - POD test for Bio/PopGen/IO/csv.pm
ok 788 - POD test for Bio/PopGen/IO/hapmap.pm
ok 789 - POD test for Bio/SeqEvolution/EvolutionI.pm
ok 790 - POD test for Bio/SeqEvolution/Factory.pm
ok 791 - POD test for Bio/SeqEvolution/DNAPoint.pm
ok 792 - POD test for scripts/utilities/bp_seq_length.pl
ok 793 - POD test for scripts/utilities/bp_nrdb.pl
ok 794 - POD test for scripts/utilities/bp_find-blast-matches.pl
ok 795 - POD test for scripts/utilities/bp_pairwise_kaks.pl
ok 796 - POD test for scripts/utilities/bp_download_query_genbank.pl
ok 797 - POD test for scripts/utilities/bp_search2alnblocks.pl
ok 798 - POD test for scripts/utilities/bp_mutate.pl
ok 799 - POD test for scripts/utilities/bp_search2gff.pl
ok 800 - POD test for scripts/utilities/bp_mrtrans.pl
ok 801 - POD test for scripts/utilities/bp_dbsplit.pl
ok 802 - POD test for scripts/utilities/bp_revtrans-motif.pl
ok 803 - POD test for scripts/utilities/bp_mask_by_search.pl
ok 804 - POD test for scripts/utilities/bp_remote_blast.pl
ok 805 - POD test for scripts/utilities/bp_search2tribe.pl
ok 806 - POD test for scripts/utilities/bp_netinstall.pl
ok 807 - POD test for scripts/utilities/bp_sreformat.pl
ok 808 - POD test for scripts/index/bp_seqret.pl
ok 809 - POD test for scripts/index/bp_fetch.pl
ok 810 - POD test for scripts/index/bp_index.pl
ok 811 - POD test for scripts/popgen/bp_heterogeneity_test.pl
ok 812 - POD test for scripts/popgen/bp_composite_LD.pl
ok 813 - POD test for scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl (no pod)
ok 814 - POD test for scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl (no pod)
ok 815 - POD test for scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
ok 816 - POD test for scripts/DB-HIV/bp_hivq.pl
ok 817 - POD test for scripts/taxa/bp_query_entrez_taxa.pl
ok 818 - POD test for scripts/taxa/bp_taxonomy2tree.pl
ok 819 - POD test for scripts/taxa/bp_local_taxonomydb_query.pl
ok 820 - POD test for scripts/taxa/bp_classify_hits_kingdom.pl
ok 821 - POD test for scripts/taxa/bp_taxid4species.pl
ok 822 - POD test for scripts/Bio-DB-GFF/bp_process_gadfly.pl
ok 823 - POD test for scripts/Bio-DB-GFF/bp_process_wormbase.pl
ok 824 - POD test for scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
ok 825 - POD test for scripts/Bio-DB-GFF/bp_genbank2gff3.pl
ok 826 - POD test for scripts/Bio-DB-GFF/bp_process_sgd.pl
ok 827 - POD test for scripts/Bio-DB-GFF/bp_genbank2gff.pl
ok 828 - POD test for scripts/Bio-DB-GFF/bp_meta_gff.pl
ok 829 - POD test for scripts/Bio-DB-GFF/bp_load_gff.pl
ok 830 - POD test for scripts/Bio-DB-GFF/bp_generate_histogram.pl
ok 831 - POD test for scripts/Bio-DB-GFF/bp_fast_load_gff.pl
ok 832 - POD test for scripts/DB/bp_flanks.pl
ok 833 - POD test for scripts/DB/bp_biofetch_genbank_proxy.pl
ok 834 - POD test for scripts/DB/bp_biogetseq.pl
ok 835 - POD test for scripts/DB/bp_bioflat_index.pl
ok 836 - POD test for scripts/seqstats/bp_chaos_plot.pl
ok 837 - POD test for scripts/seqstats/bp_oligo_count.pl
ok 838 - POD test for scripts/seqstats/bp_gccalc.pl
ok 839 - POD test for scripts/seqstats/bp_aacomp.pl
ok 840 - POD test for scripts/das/bp_das_server.pl (no pod)
ok 841 - POD test for scripts/searchio/bp_filter_search.pl
ok 842 - POD test for scripts/searchio/bp_search2table.pl
ok 843 - POD test for scripts/searchio/bp_hmmer_to_table.pl
ok 844 - POD test for scripts/searchio/bp_fastam9_to_table.pl
ok 845 - POD test for scripts/searchio/bp_parse_hmmsearch.pl
ok 846 - POD test for scripts/tree/bp_tree2pag.pl
ok 847 - POD test for scripts/tree/bp_nexus2nh.pl
ok 848 - POD test for scripts/tree/bp_blast2tree.pl
ok 849 - POD test for scripts/seq/bp_seqconvert.pl
ok 850 - POD test for scripts/seq/bp_translate_seq.pl
ok 851 - POD test for scripts/seq/bp_seqpart.pl
ok 852 - POD test for scripts/seq/bp_extract_feature_seq.pl
ok 853 - POD test for scripts/seq/bp_make_mrna_protein.pl
ok 854 - POD test for scripts/seq/bp_split_seq.pl
ok 855 - POD test for scripts/seq/bp_seqretsplit.pl
ok 856 - POD test for scripts/seq/bp_seqcut.pl
ok 857 - POD test for scripts/seq/bp_unflatten_seq.pl
ok 858 - POD test for examples/generate_random_seq.pl (no pod)
ok 859 - POD test for examples/make_primers.pl (no pod)
ok 860 - POD test for examples/rev_and_trans.pl (no pod)
ok 861 - POD test for examples/bioperl.pl (no pod)
ok 862 - POD test for examples/longorf.pl
ok 863 - POD test for examples/subsequence.cgi (no pod)
ok 864 - POD test for examples/revcom_dir.pl (no pod)
ok 865 - POD test for examples/db/use_registry.pl (no pod)
ok 866 - POD test for examples/db/getGenBank.pl (no pod)
ok 867 - POD test for examples/db/get_seqs.pl (no pod)
ok 868 - POD test for examples/db/dbfetch
ok 869 - POD test for examples/db/gb2features.pl (no pod)
ok 870 - POD test for examples/db/est_tissue_query.pl (no pod)
ok 871 - POD test for examples/db/rfetch.pl (no pod)
ok 872 - POD test for examples/liveseq/change_gene.pl (no pod)
ok 873 - POD test for examples/cluster/dbsnp.pl (no pod)
ok 874 - POD test for examples/popgen/parse_calc_stats.pl (no pod)
ok 875 - POD test for examples/tools/parse_codeml.pl (no pod)
ok 876 - POD test for examples/tools/run_primer3.pl
ok 877 - POD test for examples/tools/gff2ps.pl
ok 878 - POD test for examples/tools/extract_genes.pl
ok 879 - POD test for examples/tools/gb_to_gff.pl (no pod)
ok 880 - POD test for examples/tools/psw.pl (no pod)
ok 881 - POD test for examples/tools/standaloneblast.pl (no pod)
ok 882 - POD test for examples/tools/seq_pattern.pl (no pod)
ok 883 - POD test for examples/tools/reverse-translate.pl
ok 884 - POD test for examples/tools/run_genscan.pl (no pod)
ok 885 - POD test for examples/contributed/prosite2perl.pl (no pod)
ok 886 - POD test for examples/contributed/rebase2list.pl (no pod)
ok 887 - POD test for examples/contributed/nmrpdb_parse.pl (no pod)
ok 888 - POD test for examples/sirna/rnai_finder.cgi
ok 889 - POD test for examples/Bio-DB-GFF/load_ucsc.pl (no pod)
ok 890 - POD test for examples/tk/gsequence.pl (no pod)
ok 891 - POD test for examples/tk/hitdisplay.pl (no pod)
ok 892 - POD test for examples/structure/structure-io.pl (no pod)
ok 893 - POD test for examples/align/align_on_codons.pl (no pod)
ok 894 - POD test for examples/align/clustalw.pl (no pod)
ok 895 - POD test for examples/align/FastAlign.pl
ok 896 - POD test for examples/align/simplealign.pl (no pod)
ok 897 - POD test for examples/align/aligntutorial.pl (no pod)
ok 898 - POD test for examples/quality/svgtrace.pl (no pod)
ok 899 - POD test for examples/searchio/psiblast_iterations.pl (no pod)
ok 900 - POD test for examples/searchio/waba2gff3.pl
ok 901 - POD test for examples/searchio/custom_writer.pl (no pod)
ok 902 - POD test for examples/searchio/psiblast_features.pl (no pod)
ok 903 - POD test for examples/searchio/hspwriter.pl (no pod)
ok 904 - POD test for examples/searchio/waba2gff.pl (no pod)
ok 905 - POD test for examples/searchio/resultwriter.pl (no pod)
ok 906 - POD test for examples/searchio/rawwriter.pl (no pod)
ok 907 - POD test for examples/searchio/blast_example.pl (no pod)
ok 908 - POD test for examples/searchio/hitwriter.pl (no pod)
ok 909 - POD test for examples/searchio/htmlwriter.pl (no pod)
ok 910 - POD test for examples/root/exceptions3.pl (no pod)
ok 911 - POD test for examples/root/exceptions2.pl (no pod)
ok 912 - POD test for examples/root/exceptions1.pl (no pod)
ok 913 - POD test for examples/root/exceptions4.pl (no pod)
ok 914 - POD test for examples/tree/paup2phylip.pl (no pod)
ok 915 - POD test for maintenance/cvs2cl_by_file.pl
ok 916 - POD test for maintenance/version.pl
ok 917 - POD test for maintenance/find_mod_deps.pl
ok 918 - POD test for maintenance/ncbi_blast_switches.pl (no pod)
ok 919 - POD test for maintenance/modules.pl
ok 920 - POD test for maintenance/check_NAME.pl
ok 921 - POD test for maintenance/pod.pl
ok 922 - POD test for maintenance/module_usage.pl (no pod)
ok 923 - POD test for maintenance/dependencies.pl
ok 924 - POD test for maintenance/symlink_script.pl
ok 925 - POD test for maintenance/deprecated.pl
ok 926 - POD test for maintenance/authors.pl
ok 927 - POD test for maintenance/check_URLs.pl
ok
t/PopGen/Coalescent.t .................. 
1..13
ok 1 - use Bio::PopGen::Simulation::Coalescent;
ok 2 - use Bio::PopGen::Statistics;
ok 3 - use Bio::TreeIO;
ok 4
ok 5
ok 6 - pi
ok 7 - theta
ok 8 - tajimaD
ok 9 - all the mutations should be polymorphic (by definition)
ok 10 - fu and li D
ok 11 - fu and li D*
ok 12 - fu and li F
ok 13 - fu and li F
ok
t/PopGen/HtSNP.t ....................... 
1..8
ok 1 - use Bio::PopGen::HtSNP;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok
t/PopGen/MK.t .......................... 
1..46
ok 1 - use Bio::AlignIO;
ok 2 - use Bio::PopGen::Statistics;
ok 3 - use Bio::PopGen::Utilities;
ok 4 - 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
t/PopGen/PopGen.t ...................... 
1..105
ok 1 - use IO::String;
ok 2 - use Bio::PopGen::Individual;
ok 3 - use Bio::PopGen::Genotype;
ok 4 - use Bio::PopGen::Population;
ok 5 - use Bio::PopGen::IO;
ok 6 - use Bio::PopGen::PopStats;
ok 7 - use Bio::AlignIO;
ok 8 - use Bio::PopGen::Statistics;
ok 9 - use Bio::PopGen::Utilities;
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40 - mrsa,mssa aflp1
ok 41 - all pops, aflp1
ok 42 - mrsa,envpop aflp1,aflp2
ok 43
ok 44
ok 45
ok 46 - mssa,mrsa all_bands
ok 47 - env,mssa mkr1
ok 48 - env,mssa,mrsa all bands
ok 49 - env,mssa,mrsa mkr2
ok 50 - mrsa,nc all_bands
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104 - Pi on 3-allele data
ok 105 - Theta on 3-allele data
ok
t/PopGen/PopGenSims.t .................. 
1..23
ok 1 - use Bio::PopGen::Simulation::GeneticDrift;
ok 2 - Allele freqs should sum to 1
ok 3 - Allele freqs should sum to 1
ok 4 - Allele freqs should sum to 1
ok 5 - Allele freqs should sum to 1
ok 6 - Allele freqs should sum to 1
ok 7 - Allele freqs should sum to 1
ok 8 - Allele freqs should sum to 1
ok 9 - Allele freqs should sum to 1
ok 10 - Allele freqs should sum to 1
ok 11 - Allele freqs should sum to 1
ok 12
ok 13 - All frequencies should be <= 1
ok 14 - Allele freqs should sum to 1
ok 15 - Allele freqs should sum to 1
ok 16 - Allele freqs should sum to 1
ok 17 - Allele freqs should sum to 1
ok 18 - Allele freqs should sum to 1
ok 19 - Allele freqs should sum to 1
ok 20 - Allele freqs should sum to 1
ok 21 - Allele freqs should sum to 1
ok 22 - Allele freqs should sum to 1
ok 23 - Allele freqs should sum to 1
ok
t/PopGen/TagHaplotype.t ................ 
1..3
ok 1 - use Bio::PopGen::TagHaplotype;
ok 2
ok 3
ok
t/RemoteDB/BioFetch.t .................. skipped: Network tests have not been requested
t/RemoteDB/CUTG.t ...................... 
1..37
ok 1 - use Bio::DB::CUTG;
ok 2 - use Bio::CodonUsage::Table;
ok 3 - use Bio::CodonUsage::IO;
ok 4 - use Bio::SeqIO;
ok 5 - use Bio::Tools::SeqStats;
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24 # skip Network tests have not been requested
ok 25 # skip Network tests have not been requested
ok 26 # skip Network tests have not been requested
ok 27 # skip Network tests have not been requested
ok 28 # skip Network tests have not been requested
ok 29 # skip Network tests have not been requested
ok 30 # skip Network tests have not been requested
ok 31 # skip Network tests have not been requested
ok 32 # skip Network tests have not been requested
ok 33 # skip Network tests have not been requested
ok 34 # skip Network tests have not been requested
ok 35 # skip Network tests have not been requested
ok 36 # skip Network tests have not been requested
ok 37 # skip Network tests have not been requested
ok
t/RemoteDB/EMBL.t ...................... skipped: Network tests have not been requested
t/RemoteDB/EntrezGene.t ................ skipped: Network tests have not been requested
t/RemoteDB/GenBank.t ................... skipped: Network tests have not been requested
t/RemoteDB/GenPept.t ................... skipped: Network tests have not been requested
t/RemoteDB/HIV/HIV.t ................... 
1..30
ok 1 - use Bio::DB::HIV;
ok 2 - use Bio::DB::WebDBSeqI;
ok 3 - use Bio::DB::HIV::HIVAnnotProcessor;
ok 4 - 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
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
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
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

Timeout (max run time is 300s)
/data/fly2200/ap2200-299134/bin/perl-static killed by signal 15.