PATH=C:\mingw\bin;C:\cygwin\bin;C:\cpanfly-5.18\var\megalib\bin;C:\Perl-5.18\site\bin;C:\Perl-5.18\bin;C:\cygwin\bin;C:\Program Files\Perforce;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\instantclient_11_2;C:\cygwin\bin;C:\Program Files\Perforce;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\WINDOWS\system32\WindowsPowerShell\v1.0
Start 2014-03-04T00:22:50
ActivePerl-1800 CPAN-2.00
LIB=C:\PROGRA~1\MICROS~3\VC98\Lib\PSDK
PATH=C:/CPANFL~1.18/var/libs/bin;C:\mingw\bin;C:\cygwin\bin;C:\CPANFL~1.18\var\megalib\bin;C:\Perl-5.18\site\bin;C:\Perl-5.18\bin;C:\cygwin\bin;C:\PROGRA~1\Perforce;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WINDOW~2\v1.0;C:\WINDOWS\system32\WINDOW~2\v1.0;C:\INSTAN~1;C:\cygwin\bin;C:\PROGRA~1\Perforce;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WINDOW~2\v1.0;C:\WINDOWS\system32\WINDOW~2\v1.0
Reading 'C:\cpanfly-5.18\var\cpan\Metadata'
  Database was generated on Tue, 04 Mar 2014 06:41:02 GMT
Running make for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
Fetching with LWP:
http://cpan.nas1.activestate.com/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
Checksum for C:\cpanfly-5.18\var\cpan\sources\authors\id\C\CJ\CJFIELDS\BioPerl-1.6.1.tar.gz ok
BioPerl-1.6.1
BioPerl-1.6.1/AUTHORS
BioPerl-1.6.1/BioPerl.pm
BioPerl-1.6.1/BUGS
BioPerl-1.6.1/Build.PL
BioPerl-1.6.1/Changes
BioPerl-1.6.1/DEPENDENCIES
BioPerl-1.6.1/DEPRECATED
BioPerl-1.6.1/INSTALL
BioPerl-1.6.1/INSTALL.SKIP
BioPerl-1.6.1/INSTALL.WIN
BioPerl-1.6.1/LICENSE
BioPerl-1.6.1/Makefile.PL
BioPerl-1.6.1/MANIFEST
BioPerl-1.6.1/MANIFEST.SKIP
BioPerl-1.6.1/META.yml
BioPerl-1.6.1/README
BioPerl-1.6.1/Bio
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BioPerl-1.6.1/Bio/Biblio
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BioPerl-1.6.1/Bio/Biblio/IO/medline2ref.pm
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BioPerl-1.6.1/Bio/DB/SeqVersion.pm
BioPerl-1.6.1/Bio/DB/SwissProt.pm
BioPerl-1.6.1/Bio/DB/Taxonomy.pm
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BioPerl-1.6.1/examples
BioPerl-1.6.1/examples/bioperl.pl
BioPerl-1.6.1/examples/generate_random_seq.pl
BioPerl-1.6.1/examples/longorf.pl
BioPerl-1.6.1/examples/make_primers.pl
BioPerl-1.6.1/examples/rev_and_trans.pl
BioPerl-1.6.1/examples/revcom_dir.pl
BioPerl-1.6.1/examples/subsequence.cgi
BioPerl-1.6.1/examples/align
BioPerl-1.6.1/examples/align/align_on_codons.pl
BioPerl-1.6.1/examples/align/aligntutorial.pl
BioPerl-1.6.1/examples/align/clustalw.pl
BioPerl-1.6.1/examples/align/simplealign.pl
BioPerl-1.6.1/examples/biblio
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BioPerl-1.6.1/examples/biblio/biblio-soap-example.pl
BioPerl-1.6.1/examples/biblio/biblio_soap.pl
BioPerl-1.6.1/examples/Bio-DB-GFF
BioPerl-1.6.1/examples/Bio-DB-GFF/load_ucsc.pl
BioPerl-1.6.1/examples/cluster
BioPerl-1.6.1/examples/cluster/dbsnp.pl
BioPerl-1.6.1/examples/contributed
BioPerl-1.6.1/examples/contributed/nmrpdb_parse.pl
BioPerl-1.6.1/examples/contributed/prosite2perl.pl
BioPerl-1.6.1/examples/contributed/rebase2list.pl
BioPerl-1.6.1/examples/db
BioPerl-1.6.1/examples/db/dbfetch
BioPerl-1.6.1/examples/db/est_tissue_query.pl
BioPerl-1.6.1/examples/db/gb2features.pl
BioPerl-1.6.1/examples/db/get_seqs.pl
BioPerl-1.6.1/examples/db/getGenBank.pl
BioPerl-1.6.1/examples/db/rfetch.pl
BioPerl-1.6.1/examples/db/use_registry.pl
BioPerl-1.6.1/examples/liveseq
BioPerl-1.6.1/examples/liveseq/change_gene.pl
BioPerl-1.6.1/examples/popgen
BioPerl-1.6.1/examples/popgen/parse_calc_stats.pl
BioPerl-1.6.1/examples/quality
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BioPerl-1.6.1/examples/root
BioPerl-1.6.1/examples/root/exceptions1.pl
BioPerl-1.6.1/examples/root/exceptions2.pl
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BioPerl-1.6.1/examples/root/lib/TestObject.pm
BioPerl-1.6.1/examples/root/lib/Bio
BioPerl-1.6.1/examples/root/lib/Bio/PrimarySeq.pm
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BioPerl-1.6.1/examples/root/lib/Bio/SeqI.pm
BioPerl-1.6.1/examples/searchio
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BioPerl-1.6.1/examples/searchio/custom_writer.pl
BioPerl-1.6.1/examples/searchio/hitwriter.pl
BioPerl-1.6.1/examples/searchio/hspwriter.pl
BioPerl-1.6.1/examples/searchio/htmlwriter.pl
BioPerl-1.6.1/examples/searchio/psiblast_features.pl
BioPerl-1.6.1/examples/searchio/psiblast_iterations.pl
BioPerl-1.6.1/examples/searchio/rawwriter.pl
BioPerl-1.6.1/examples/searchio/resultwriter.pl
BioPerl-1.6.1/examples/searchio/waba2gff.pl
BioPerl-1.6.1/examples/searchio/waba2gff3.pl
BioPerl-1.6.1/examples/sirna
BioPerl-1.6.1/examples/sirna/rnai_finder.cgi
BioPerl-1.6.1/examples/sirna/TAG
BioPerl-1.6.1/examples/structure
BioPerl-1.6.1/examples/structure/structure-io.pl
BioPerl-1.6.1/examples/tk
BioPerl-1.6.1/examples/tk/gsequence.pl
BioPerl-1.6.1/examples/tk/hitdisplay.pl
BioPerl-1.6.1/examples/tools
BioPerl-1.6.1/examples/tools/extract_genes.pl
BioPerl-1.6.1/examples/tools/gb_to_gff.pl
BioPerl-1.6.1/examples/tools/gff2ps.pl
BioPerl-1.6.1/examples/tools/parse_codeml.pl
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BioPerl-1.6.1/examples/tools/reverse-translate.pl
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BioPerl-1.6.1/scripts/Bio-DB-GFF
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BioPerl-1.6.1/scripts/Bio-DB-GFF/fast_load_gff.PLS
BioPerl-1.6.1/scripts/Bio-DB-GFF/genbank2gff.PLS
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BioPerl-1.6.1/scripts/Bio-DB-GFF/meta_gff.PLS
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BioPerl-1.6.1/scripts/Bio-DB-GFF/process_wormbase.PLS
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BioPerl-1.6.1/scripts/Bio-SeqFeature-Store
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BioPerl-1.6.1/scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
BioPerl-1.6.1/scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
BioPerl-1.6.1/scripts/das
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BioPerl-1.6.1/scripts/das/TAG
BioPerl-1.6.1/scripts/DB
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BioPerl-1.6.1/scripts/DB/bioflat_index.PLS
BioPerl-1.6.1/scripts/DB/biogetseq.PLS
BioPerl-1.6.1/scripts/DB/flanks.PLS
BioPerl-1.6.1/scripts/DB/TAG
BioPerl-1.6.1/scripts/DB-HIV
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BioPerl-1.6.1/scripts/index
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BioPerl-1.6.1/scripts/index/bp_index.PLS
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BioPerl-1.6.1/scripts/popgen
BioPerl-1.6.1/scripts/popgen/composite_LD.PLS
BioPerl-1.6.1/scripts/popgen/heterogeneity_test.PLS
BioPerl-1.6.1/scripts/searchio
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BioPerl-1.6.1/scripts/searchio/filter_search.PLS
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BioPerl-1.6.1/scripts/searchio/parse_hmmsearch.PLS
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BioPerl-1.6.1/scripts/seq
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BioPerl-1.6.1/scripts/seq/seqretsplit.PLS
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BioPerl-1.6.1/scripts/seqstats
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BioPerl-1.6.1/t/SeqFeature/LocationFactory.t
BioPerl-1.6.1/t/SeqFeature/Primer.t
BioPerl-1.6.1/t/SeqFeature/Range.t
BioPerl-1.6.1/t/SeqFeature/RangeI.t
BioPerl-1.6.1/t/SeqFeature/SeqAnalysisParser.t
BioPerl-1.6.1/t/SeqFeature/SeqFeatAnnotated.t
BioPerl-1.6.1/t/SeqFeature/SeqFeatCollection.t
BioPerl-1.6.1/t/SeqFeature/SeqFeature.t
BioPerl-1.6.1/t/SeqFeature/SeqFeaturePrimer.t
BioPerl-1.6.1/t/SeqFeature/Unflattener.t
BioPerl-1.6.1/t/SeqFeature/Unflattener2.t
BioPerl-1.6.1/t/SeqIO
BioPerl-1.6.1/t/SeqIO/abi.t
BioPerl-1.6.1/t/SeqIO/ace.t
BioPerl-1.6.1/t/SeqIO/agave.t
BioPerl-1.6.1/t/SeqIO/alf.t
BioPerl-1.6.1/t/SeqIO/asciitree.t
BioPerl-1.6.1/t/SeqIO/bsml.t
BioPerl-1.6.1/t/SeqIO/bsml_sax.t
BioPerl-1.6.1/t/SeqIO/chadoxml.t
BioPerl-1.6.1/t/SeqIO/chaos.t
BioPerl-1.6.1/t/SeqIO/chaosxml.t
BioPerl-1.6.1/t/SeqIO/ctf.t
BioPerl-1.6.1/t/SeqIO/embl.t
BioPerl-1.6.1/t/SeqIO/entrezgene.t
BioPerl-1.6.1/t/SeqIO/excel.t
BioPerl-1.6.1/t/SeqIO/exp.t
BioPerl-1.6.1/t/SeqIO/fasta.t
BioPerl-1.6.1/t/SeqIO/fastq.t
BioPerl-1.6.1/t/SeqIO/flybase_chadoxml.t
BioPerl-1.6.1/t/SeqIO/game.t
BioPerl-1.6.1/t/SeqIO/gcg.t
BioPerl-1.6.1/t/SeqIO/genbank.t
BioPerl-1.6.1/t/SeqIO/Handler.t
BioPerl-1.6.1/t/SeqIO/interpro.t
BioPerl-1.6.1/t/SeqIO/kegg.t
BioPerl-1.6.1/t/SeqIO/largefasta.t
BioPerl-1.6.1/t/SeqIO/lasergene.t
BioPerl-1.6.1/t/SeqIO/locuslink.t
BioPerl-1.6.1/t/SeqIO/metafasta.t
BioPerl-1.6.1/t/SeqIO/MultiFile.t
BioPerl-1.6.1/t/SeqIO/Multiple_fasta.t
BioPerl-1.6.1/t/SeqIO/phd.t
BioPerl-1.6.1/t/SeqIO/pir.t
BioPerl-1.6.1/t/SeqIO/pln.t
BioPerl-1.6.1/t/SeqIO/qual.t
BioPerl-1.6.1/t/SeqIO/raw.t
BioPerl-1.6.1/t/SeqIO/scf.t
BioPerl-1.6.1/t/SeqIO/SeqBuilder.t
BioPerl-1.6.1/t/SeqIO/Splicedseq.t
BioPerl-1.6.1/t/SeqIO/strider.t
BioPerl-1.6.1/t/SeqIO/swiss.t
BioPerl-1.6.1/t/SeqIO/tab.t
BioPerl-1.6.1/t/SeqIO/table.t
BioPerl-1.6.1/t/SeqIO/tigr.t
BioPerl-1.6.1/t/SeqIO/tigrxml.t
BioPerl-1.6.1/t/SeqIO/tinyseq.t
BioPerl-1.6.1/t/SeqIO/ztr.t
BioPerl-1.6.1/t/SeqTools
BioPerl-1.6.1/t/SeqTools/Backtranslate.t
BioPerl-1.6.1/t/SeqTools/CodonTable.t
BioPerl-1.6.1/t/SeqTools/ECnumber.t
BioPerl-1.6.1/t/SeqTools/GuessSeqFormat.t
BioPerl-1.6.1/t/SeqTools/OddCodes.t
BioPerl-1.6.1/t/SeqTools/SeqPattern.t
BioPerl-1.6.1/t/SeqTools/SeqStats.t
BioPerl-1.6.1/t/SeqTools/SeqUtils.t
BioPerl-1.6.1/t/SeqTools/SeqWords.t
BioPerl-1.6.1/t/Structure
BioPerl-1.6.1/t/Structure/IO.t
BioPerl-1.6.1/t/Structure/Structure.t
BioPerl-1.6.1/t/Tools
BioPerl-1.6.1/t/Tools/ePCR.t
BioPerl-1.6.1/t/Tools/Est2Genome.t
BioPerl-1.6.1/t/Tools/FootPrinter.t
BioPerl-1.6.1/t/Tools/Geneid.t
BioPerl-1.6.1/t/Tools/Genewise.t
BioPerl-1.6.1/t/Tools/Genomewise.t
BioPerl-1.6.1/t/Tools/Genpred.t
BioPerl-1.6.1/t/Tools/GFF.t
BioPerl-1.6.1/t/Tools/Hmmer.t
BioPerl-1.6.1/t/Tools/IUPAC.t
BioPerl-1.6.1/t/Tools/Lucy.t
BioPerl-1.6.1/t/Tools/Match.t
BioPerl-1.6.1/t/Tools/pICalculator.t
BioPerl-1.6.1/t/Tools/Primer3.t
BioPerl-1.6.1/t/Tools/Promoterwise.t
BioPerl-1.6.1/t/Tools/Pseudowise.t
BioPerl-1.6.1/t/Tools/QRNA.t
BioPerl-1.6.1/t/Tools/RandDistFunctions.t
BioPerl-1.6.1/t/Tools/RepeatMasker.t
BioPerl-1.6.1/t/Tools/rnamotif.t
BioPerl-1.6.1/t/Tools/Seg.t
BioPerl-1.6.1/t/Tools/Sigcleave.t
BioPerl-1.6.1/t/Tools/Signalp.t
BioPerl-1.6.1/t/Tools/Sim4.t
BioPerl-1.6.1/t/Tools/SiRNA.t
BioPerl-1.6.1/t/Tools/TandemRepeatsFinder.t
BioPerl-1.6.1/t/Tools/TargetP.t
BioPerl-1.6.1/t/Tools/Tmhmm.t
BioPerl-1.6.1/t/Tools/tRNAscanSE.t
BioPerl-1.6.1/t/Tools/Alignment
BioPerl-1.6.1/t/Tools/Alignment/Consed.t
BioPerl-1.6.1/t/Tools/Analysis
BioPerl-1.6.1/t/Tools/Analysis/DNA
BioPerl-1.6.1/t/Tools/Analysis/DNA/ESEfinder.t
BioPerl-1.6.1/t/Tools/Analysis/Protein
BioPerl-1.6.1/t/Tools/Analysis/Protein/Domcut.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/ELM.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/GOR4.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/HNN.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/Mitoprot.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/NetPhos.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/Scansite.t
BioPerl-1.6.1/t/Tools/Analysis/Protein/Sopma.t
BioPerl-1.6.1/t/Tools/EMBOSS
BioPerl-1.6.1/t/Tools/EMBOSS/Palindrome.t
BioPerl-1.6.1/t/Tools/EUtilities
BioPerl-1.6.1/t/Tools/EUtilities/egquery.t
BioPerl-1.6.1/t/Tools/EUtilities/einfo.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_acheck.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_lcheck.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_llinks.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_ncheck.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_neighbor.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_neighbor_history.t
BioPerl-1.6.1/t/Tools/EUtilities/elink_scores.t
BioPerl-1.6.1/t/Tools/EUtilities/epost.t
BioPerl-1.6.1/t/Tools/EUtilities/esearch.t
BioPerl-1.6.1/t/Tools/EUtilities/espell.t
BioPerl-1.6.1/t/Tools/EUtilities/esummary.t
BioPerl-1.6.1/t/Tools/EUtilities/EUtilParameters.t
BioPerl-1.6.1/t/Tools/Phylo
BioPerl-1.6.1/t/Tools/Phylo/Gerp.t
BioPerl-1.6.1/t/Tools/Phylo/Molphy.t
BioPerl-1.6.1/t/Tools/Phylo/PAML.t
BioPerl-1.6.1/t/Tools/Phylo/Phylip
BioPerl-1.6.1/t/Tools/Phylo/Phylip/ProtDist.t
BioPerl-1.6.1/t/Tools/Run
BioPerl-1.6.1/t/Tools/Run/RemoteBlast.t
BioPerl-1.6.1/t/Tools/Run/RemoteBlast_rpsblast.t
BioPerl-1.6.1/t/Tools/Run/StandAloneBlast.t
BioPerl-1.6.1/t/Tools/Run/WrapperBase.t
BioPerl-1.6.1/t/Tools/Signalp
BioPerl-1.6.1/t/Tools/Signalp/ExtendedSignalp.t
BioPerl-1.6.1/t/Tools/Spidey
BioPerl-1.6.1/t/Tools/Spidey/Spidey.t
BioPerl-1.6.1/t/Tree
BioPerl-1.6.1/t/Tree/Compatible.t
BioPerl-1.6.1/t/Tree/Node.t
BioPerl-1.6.1/t/Tree/RandomTreeFactory.t
BioPerl-1.6.1/t/Tree/Tree.t
BioPerl-1.6.1/t/Tree/TreeIO.t
BioPerl-1.6.1/t/Tree/TreeStatistics.t
BioPerl-1.6.1/t/Tree/PhyloNetwork
BioPerl-1.6.1/t/Tree/PhyloNetwork/Factory.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/GraphViz.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/MuVector.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/PhyloNetwork.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/RandomFactory.t
BioPerl-1.6.1/t/Tree/PhyloNetwork/TreeFactory.t
BioPerl-1.6.1/t/Tree/TreeIO
BioPerl-1.6.1/t/Tree/TreeIO/lintree.t
BioPerl-1.6.1/t/Tree/TreeIO/newick.t
BioPerl-1.6.1/t/Tree/TreeIO/nexus.t
BioPerl-1.6.1/t/Tree/TreeIO/nhx.t
BioPerl-1.6.1/t/Tree/TreeIO/phyloxml.t
BioPerl-1.6.1/t/Tree/TreeIO/svggraph.t
BioPerl-1.6.1/t/Tree/TreeIO/tabtree.t
BioPerl-1.6.1/t/Variation
BioPerl-1.6.1/t/Variation/AAChange.t
BioPerl-1.6.1/t/Variation/AAReverseMutate.t
BioPerl-1.6.1/t/Variation/Allele.t
BioPerl-1.6.1/t/Variation/DNAMutation.t
BioPerl-1.6.1/t/Variation/RNAChange.t
BioPerl-1.6.1/t/Variation/SeqDiff.t
BioPerl-1.6.1/t/Variation/SNP.t
BioPerl-1.6.1/t/Variation/Variation_IO.t

  CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz

>>> C:\Perl-5.18\bin\perl.exe Makefile.PL
# running Build.PL 
 - ERROR: DB_File is not installed

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

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

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

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

Do you want to run tests that require connection to servers across the internet
(likely to cause some failures)? y/n [n] Encountered CODE ref, using dummy placeholder at C:/cpanfly-5.18/var/megalib/Data/Dumper.pm line 222.
Could not get valid metadata. Error is: Invalid metadata structure. Errors: 'Bio::FeatureIO::interpro' for 'URI::Escape' is not a valid version. (prereqs -> runtime -> recommends -> URI::Escape) [Validation: 2], 'Bio::DB::Biblio::eutils' for 'URI::Escape' is not a valid version. (prereqs -> runtime -> recommends -> URI::Escape) [Validation: 2], 'Bio::DB::EUtilParameters' for 'URI::Escape' is not a valid version. (prereqs -> runtime -> recommends -> URI::Escape) [Validation: 2], 'Bio::DB::Query::GenBank' for 'URI::Escape' is not a valid version. (prereqs -> runtime -> recommends -> URI::Escape) [Validation: 2], 'Bio::DB::NCBIHelper' for 'URI::Escape' is not a valid version. (prereqs -> runtime -> recommends -> URI::Escape) [Validation: 2], 'Bio::SeqFeature::Annotated' for 'URI::Escape' is not a valid version. (prereqs -> runtime -> recommends -> URI::Escape) [Validation: 2], 'Bio::SeqFeature::Collection' for 'Storable' is not a valid version. (prereqs -> runtime -> recommends -> Storable) [Validation: 2], 'Bio::PopGen::HtSNP' for 'Storable' is not a valid version. (prereqs -> runtime -> recommends -> Storable) [Validation: 2], 'Bio::PopGen::TagHaplotype' for 'Storable' is not a valid version. (prereqs -> runtime -> recommends -> Storable) [Validation: 2], 'Bio::DB::GFF::Adaptor::berkeleydb' for 'Storable' is not a valid version. (prereqs -> runtime -> recommends -> Storable) [Validation: 2], 'Bio::Microarray::Tools::ReseqChip' for 'Spreadsheet::ParseExcel' is not a valid version. (prereqs -> runtime -> recommends -> Spreadsheet::ParseExcel) [Validation: 2], 'Bio::Tools::SeqPattern::BackTranslate' for 'List::MoreUtils' is not a valid version. (prereqs -> runtime -> recommends -> List::MoreUtils) [Validation: 2], 'Bio::SeqIO::game::gameSubs' for 'XML::Parser::PerlSAX' is not a valid version. (prereqs -> runtime -> recommends -> XML::Parser::PerlSAX) [Validation: 2], 'Bio::OntologyIO::InterProParser' for 'XML::Parser::PerlSAX' is not a valid version. (prereqs -> runtime -> recommends -> XML::Parser::PerlSAX) [Validation: 2], 'Bio::ClusterIO::dbsnp' for 'XML::Parser::PerlSAX' is not a valid version. (prereqs -> runtime -> recommends -> XML::Parser::PerlSAX) [Validation: 2], 'Bio::SeqIO::game::gameWriter' for 'XML::Writer' is not a valid version. (prereqs -> runtime -> recommends -> XML::Writer) [Validation: 2], 'Bio::SeqIO::chadoxml' for 'XML::Writer' is not a valid version. (prereqs -> runtime -> recommends -> XML::Writer) [Validation: 2], 'Bio::SeqIO::tinyseq' for 'XML::Writer' is not a valid version. (prereqs -> runtime -> recommends -> XML::Writer) [Validation: 2], 'Bio::Variation::IO::xml' for 'XML::Writer' is not a valid version. (prereqs -> runtime -> recommends -> XML::Writer) [Validation: 2], 'Bio::SearchIO::Writer::BSMLResultWriter' for 'XML::Writer' is not a valid version. (prereqs -> runtime -> recommends -> XML::Writer) [Validation: 2], 'Bio::DB::HIV' for 'XML::Simple' is not a valid version. (prereqs -> runtime -> recommends -> XML::Simple) [Validation: 2], 'Bio::DB::Query::HIVQuery' for 'XML::Simple' is not a valid version. (prereqs -> runtime -> recommends -> XML::Simple) [Validation: 2], 'Bio::DB::GFF::Adaptor::ace' for 'Ace' is not a valid version. (prereqs -> runtime -> recommends -> Ace) [Validation: 2], ' remote http Blast jobs/Bio::DB::*' for 'HTTP::Request::Common' is not a valid version. (prereqs -> runtime -> recommends -> HTTP::Request::Common) [Validation: 2], 'Bio::Tools::Run::RemoteBlast' for 'HTTP::Request::Common' is not a valid version. (prereqs -> runtime -> recommends -> HTTP::Request::Common) [Validation: 2], 'Bio::Tools::Analysis::Protein*' for 'HTTP::Request::Common' is not a valid version. (prereqs -> runtime -> recommends -> HTTP::Request::Common) [Validation: 2], 'Bio::Tools::Analysis::DNA*' for 'HTTP::Request::Common' is not a valid version. (prereqs -> runtime -> recommends -> HTTP::Request::Common) [Validation: 2], 'Bio::Tools::Run::RemoteBlast' for 'LWP::UserAgent' is not a valid version. (prereqs -> runtime -> recommends -> LWP::UserAgent) [Validation: 2], 'Bio::WebAgent' for 'LWP::UserAgent' is not a valid version. (prereqs -> runtime -> recommends -> LWP::UserAgent) [Validation: 2], 'Bio::SeqIO::tigrxml' for 'XML::SAX' is not a valid version. (prereqs -> runtime -> recommends -> XML::SAX) [Validation: 2], 'Bio::SeqIO::bsml_sax' for 'XML::SAX' is not a valid version. (prereqs -> runtime -> recommends -> XML::SAX) [Validation: 2], 'Bio::DB::Taxonomy::entrez' for 'XML::Twig' is not a valid version. (prereqs -> runtime -> recommends -> XML::Twig) [Validation: 2], 'Bio::DB::Biblio::eutils' for 'XML::Twig' is not a valid version. (prereqs -> runtime -> recommends -> XML::Twig) [Validation: 2]
 at C:/cpanfly-5.18/var/megalib/Module/Build/Base.pm line 4555.

Could not create MYMETA files
  - will not run internet-requiring tests
Creating new 'Build' script for 'BioPerl' version '1.006001'
Could not read metadata file. Falling back to other methods to determine prerequisites
---- Unsatisfied dependencies detected during ----
----       CJFIELDS/BioPerl-1.6.1.tar.gz      ----
    DB_File [requires]
Running make test
  Delayed until after prerequisites
Running test for module 'DB_File'

______________________ D i s t r o P r e f s ______________________
                           DB_File.yml[0]                           
Running make for P/PM/PMQS/DB_File-1.831.tar.gz
Disabled via prefs file 'C:\cpanfly-5.18\etc\distroprefs\DB_File.yml' doc 0
  PMQS/DB_File-1.831.tar.gz
  [disabled] -- NA Disabled via prefs file 'C:\cpanfly-5.18\etc\distroprefs\DB_File.yml' doc 0
Running make for C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
  Has already been unwrapped into directory C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.1-LkNiOT

  CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz

Warning: Prerequisite 'DB_File => 0' for 'CJFIELDS/BioPerl-1.6.1.tar.gz' failed when processing 'PMQS/DB_File-1.831.tar.gz' with 'unwrapped => NO Disabled via prefs file 'C:\cpanfly-5.18\etc\distroprefs\DB_File.yml' doc 0'. Continuing, but chances to succeed are limited.
>>> dmake
C:\Perl-5.18\bin\perl.exe Build --makefile_env_macros 1
Encountered CODE ref, using dummy placeholder at C:\cpanfly-5.18\var\megalib/Data/Dumper.pm line 222.
Building BioPerl
blib\script\biofetch_genbank_proxy.PLS -> blib\script\bp_biofetch_genbank_proxy.pl
blib\script\genbank2gff.PLS -> blib\script\bp_genbank2gff.pl
blib\script\extract_feature_seq.PLS -> blib\script\bp_extract_feature_seq.pl
blib\script\taxonomy2tree.PLS -> blib\script\bp_taxonomy2tree.pl
blib\script\make_mrna_protein.PLS -> blib\script\bp_make_mrna_protein.pl
blib\script\filter_search.PLS -> blib\script\bp_filter_search.pl
blib\script\seqconvert.PLS -> blib\script\bp_seqconvert.pl
blib\script\generate_histogram.PLS -> blib\script\bp_generate_histogram.pl
blib\script\bulk_load_gff.PLS -> blib\script\bp_bulk_load_gff.pl
blib\script\load_gff.PLS -> blib\script\bp_load_gff.pl
blib\script\heterogeneity_test.PLS -> blib\script\bp_heterogeneity_test.pl
blib\script\process_wormbase.PLS -> blib\script\bp_process_wormbase.pl
blib\script\process_sgd.PLS -> blib\script\bp_process_sgd.pl
blib\script\parse_hmmsearch.PLS -> blib\script\bp_parse_hmmsearch.pl
blib\script\aacomp.PLS -> blib\script\bp_aacomp.pl
blib\script\fast_load_gff.PLS -> blib\script\bp_fast_load_gff.pl
blib\script\biogetseq.PLS -> blib\script\bp_biogetseq.pl
blib\script\mutate.PLS -> blib\script\bp_mutate.pl
blib\script\process_gadfly.PLS -> blib\script\bp_process_gadfly.pl
blib\script\taxid4species.PLS -> blib\script\bp_taxid4species.pl
blib\script\local_taxonomydb_query.PLS -> blib\script\bp_local_taxonomydb_query.pl
blib\script\search2alnblocks.PLS -> blib\script\bp_search2alnblocks.pl
blib\script\hmmer_to_table.PLS -> blib\script\bp_hmmer_to_table.pl
blib\script\search2BSML.PLS -> blib\script\bp_search2BSML.pl
blib\script\genbank2gff3.PLS -> blib\script\bp_genbank2gff3.pl
blib\script\bp_seqret.PLS -> blib\script\bp_seqret.pl
blib\script\bp_mrtrans.PLS -> blib\script\bp_mrtrans.pl
blib\script\blast2tree.PLS -> blib\script\bp_blast2tree.pl
blib\script\bp_seqfeature_gff3.PLS -> blib\script\bp_seqfeature_gff3.pl
blib\script\fastam9_to_table.PLS -> blib\script\bp_fastam9_to_table.pl
blib\script\classify_hits_kingdom.PLS -> blib\script\bp_classify_hits_kingdom.pl
blib\script\search2tribe.PLS -> blib\script\bp_search2tribe.pl
blib\script\gccalc.PLS -> blib\script\bp_gccalc.pl
blib\script\download_query_genbank.PLS -> blib\script\bp_download_query_genbank.pl
blib\script\bp_sreformat.PLS -> blib\script\bp_sreformat.pl
blib\script\flanks.PLS -> blib\script\bp_flanks.pl
blib\script\bp_index.PLS -> blib\script\bp_index.pl
blib\script\seq_length.PLS -> blib\script\bp_seq_length.pl
blib\script\oligo_count.PLS -> blib\script\bp_oligo_count.pl
blib\script\nexus2nh.PLS -> blib\script\bp_nexus2nh.pl
blib\script\mask_by_search.PLS -> blib\script\bp_mask_by_search.pl
blib\script\translate_seq.PLS -> blib\script\bp_translate_seq.pl
blib\script\bp_seqfeature_load.PLS -> blib\script\bp_seqfeature_load.pl
blib\script\remote_blast.PLS -> blib\script\bp_remote_blast.pl
blib\script\meta_gff.PLS -> blib\script\bp_meta_gff.pl
blib\script\bp_nrdb.PLS -> blib\script\bp_nrdb.pl
blib\script\bp_fetch.PLS -> blib\script\bp_fetch.pl
blib\script\bioflat_index.PLS -> blib\script\bp_bioflat_index.pl
blib\script\revtrans-motif.PLS -> blib\script\bp_revtrans-motif.pl
blib\script\unflatten_seq.PLS -> blib\script\bp_unflatten_seq.pl
blib\script\composite_LD.PLS -> blib\script\bp_composite_LD.pl
blib\script\biblio.PLS -> blib\script\bp_biblio.pl
blib\script\hivq.PLS -> blib\script\bp_hivq.pl
blib\script\chaos_plot.PLS -> blib\script\bp_chaos_plot.pl
blib\script\dbsplit.PLS -> blib\script\bp_dbsplit.pl
blib\script\search2gff.PLS -> blib\script\bp_search2gff.pl
blib\script\pairwise_kaks.PLS -> blib\script\bp_pairwise_kaks.pl
blib\script\search2table.PLS -> blib\script\bp_search2table.pl
blib\script\bp_seqfeature_delete.PLS -> blib\script\bp_seqfeature_delete.pl
blib\script\split_seq.PLS -> blib\script\bp_split_seq.pl
blib\script\query_entrez_taxa.PLS -> blib\script\bp_query_entrez_taxa.pl
blib\script\tree2pag.PLS -> blib\script\bp_tree2pag.pl
blib\script\seqretsplit.PLS -> blib\script\bp_seqretsplit.pl
blib\script\einfo.PLS -> blib\script\bp_einfo.pl
  CJFIELDS/BioPerl-1.6.1.tar.gz
  dmake -- OK
Running make test
>>> dmake test TEST_VERBOSE=1
C:\Perl-5.18\bin\perl.exe Build --makefile_env_macros 1 test
Copying scripts\Bio-SeqFeature-Store\bp_seqfeature_load.PLS -> blib\script\bp_seqfeature_load.PLS
Changing sharpbang in blib\script\bp_seqfeature_load.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\bp_seqfeature_load.PLS.bak
blib\script\bp_seqfeature_load.PLS -> blib\script\bp_seqfeature_load.pl
Copying scripts\tree\tree2pag.PLS -> blib\script\tree2pag.PLS
Changing sharpbang in blib\script\tree2pag.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\tree2pag.PLS.bak
blib\script\tree2pag.PLS -> blib\script\bp_tree2pag.pl
Copying scripts\utilities\search2BSML.PLS -> blib\script\search2BSML.PLS
Changing sharpbang in blib\script\search2BSML.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\search2BSML.PLS.bak
blib\script\search2BSML.PLS -> blib\script\bp_search2BSML.pl
Copying scripts\Bio-DB-GFF\generate_histogram.PLS -> blib\script\generate_histogram.PLS
Changing sharpbang in blib\script\generate_histogram.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\generate_histogram.PLS.bak
blib\script\generate_histogram.PLS -> blib\script\bp_generate_histogram.pl
Copying scripts\seqstats\aacomp.PLS -> blib\script\aacomp.PLS
Changing sharpbang in blib\script\aacomp.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\aacomp.PLS.bak
blib\script\aacomp.PLS -> blib\script\bp_aacomp.pl
Copying scripts\DB\flanks.PLS -> blib\script\flanks.PLS
Changing sharpbang in blib\script\flanks.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\flanks.PLS.bak
blib\script\flanks.PLS -> blib\script\bp_flanks.pl
Copying scripts\utilities\bp_nrdb.PLS -> blib\script\bp_nrdb.PLS
Changing sharpbang in blib\script\bp_nrdb.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\bp_nrdb.PLS.bak
blib\script\bp_nrdb.PLS -> blib\script\bp_nrdb.pl
Copying scripts\Bio-DB-GFF\process_wormbase.PLS -> blib\script\process_wormbase.PLS
Changing sharpbang in blib\script\process_wormbase.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\process_wormbase.PLS.bak
blib\script\process_wormbase.PLS -> blib\script\bp_process_wormbase.pl
Copying scripts\Bio-DB-GFF\process_gadfly.PLS -> blib\script\process_gadfly.PLS
Changing sharpbang in blib\script\process_gadfly.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\process_gadfly.PLS.bak
blib\script\process_gadfly.PLS -> blib\script\bp_process_gadfly.pl
Copying scripts\seq\unflatten_seq.PLS -> blib\script\unflatten_seq.PLS
Changing sharpbang in blib\script\unflatten_seq.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\unflatten_seq.PLS.bak
blib\script\unflatten_seq.PLS -> blib\script\bp_unflatten_seq.pl
Copying scripts\searchio\fastam9_to_table.PLS -> blib\script\fastam9_to_table.PLS
Changing sharpbang in blib\script\fastam9_to_table.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\fastam9_to_table.PLS.bak
blib\script\fastam9_to_table.PLS -> blib\script\bp_fastam9_to_table.pl
Copying scripts\seq\translate_seq.PLS -> blib\script\translate_seq.PLS
Changing sharpbang in blib\script\translate_seq.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\translate_seq.PLS.bak
blib\script\translate_seq.PLS -> blib\script\bp_translate_seq.pl
Copying scripts\searchio\filter_search.PLS -> blib\script\filter_search.PLS
Changing sharpbang in blib\script\filter_search.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\filter_search.PLS.bak
blib\script\filter_search.PLS -> blib\script\bp_filter_search.pl
Copying scripts\searchio\search2table.PLS -> blib\script\search2table.PLS
Changing sharpbang in blib\script\search2table.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\search2table.PLS.bak
blib\script\search2table.PLS -> blib\script\bp_search2table.pl
Copying scripts\utilities\bp_sreformat.PLS -> blib\script\bp_sreformat.PLS
Changing sharpbang in blib\script\bp_sreformat.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\bp_sreformat.PLS.bak
blib\script\bp_sreformat.PLS -> blib\script\bp_sreformat.pl
Copying scripts\Bio-DB-GFF\load_gff.PLS -> blib\script\load_gff.PLS
Changing sharpbang in blib\script\load_gff.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\load_gff.PLS.bak
blib\script\load_gff.PLS -> blib\script\bp_load_gff.pl
Copying scripts\tree\blast2tree.PLS -> blib\script\blast2tree.PLS
Changing sharpbang in blib\script\blast2tree.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\blast2tree.PLS.bak
blib\script\blast2tree.PLS -> blib\script\bp_blast2tree.pl
Copying scripts\taxa\taxid4species.PLS -> blib\script\taxid4species.PLS
Changing sharpbang in blib\script\taxid4species.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\taxid4species.PLS.bak
blib\script\taxid4species.PLS -> blib\script\bp_taxid4species.pl
Copying scripts\searchio\hmmer_to_table.PLS -> blib\script\hmmer_to_table.PLS
Changing sharpbang in blib\script\hmmer_to_table.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\hmmer_to_table.PLS.bak
blib\script\hmmer_to_table.PLS -> blib\script\bp_hmmer_to_table.pl
Copying scripts\Bio-DB-GFF\fast_load_gff.PLS -> blib\script\fast_load_gff.PLS
Changing sharpbang in blib\script\fast_load_gff.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\fast_load_gff.PLS.bak
blib\script\fast_load_gff.PLS -> blib\script\bp_fast_load_gff.pl
Copying scripts\seqstats\oligo_count.PLS -> blib\script\oligo_count.PLS
Changing sharpbang in blib\script\oligo_count.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\oligo_count.PLS.bak
blib\script\oligo_count.PLS -> blib\script\bp_oligo_count.pl
Copying scripts\seq\extract_feature_seq.PLS -> blib\script\extract_feature_seq.PLS
Changing sharpbang in blib\script\extract_feature_seq.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\extract_feature_seq.PLS.bak
blib\script\extract_feature_seq.PLS -> blib\script\bp_extract_feature_seq.pl
Copying scripts\DB-HIV\hivq.PLS -> blib\script\hivq.PLS
Changing sharpbang in blib\script\hivq.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\hivq.PLS.bak
blib\script\hivq.PLS -> blib\script\bp_hivq.pl
Copying scripts\utilities\dbsplit.PLS -> blib\script\dbsplit.PLS
Changing sharpbang in blib\script\dbsplit.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\dbsplit.PLS.bak
blib\script\dbsplit.PLS -> blib\script\bp_dbsplit.pl
Copying scripts\index\bp_seqret.PLS -> blib\script\bp_seqret.PLS
Changing sharpbang in blib\script\bp_seqret.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\bp_seqret.PLS.bak
blib\script\bp_seqret.PLS -> blib\script\bp_seqret.pl
Copying scripts\Bio-DB-GFF\genbank2gff.PLS -> blib\script\genbank2gff.PLS
Changing sharpbang in blib\script\genbank2gff.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\genbank2gff.PLS.bak
blib\script\genbank2gff.PLS -> blib\script\bp_genbank2gff.pl
Copying scripts\utilities\bp_mrtrans.PLS -> blib\script\bp_mrtrans.PLS
Changing sharpbang in blib\script\bp_mrtrans.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\bp_mrtrans.PLS.bak
blib\script\bp_mrtrans.PLS -> blib\script\bp_mrtrans.pl
Copying scripts\Bio-DB-GFF\process_sgd.PLS -> blib\script\process_sgd.PLS
Changing sharpbang in blib\script\process_sgd.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\process_sgd.PLS.bak
blib\script\process_sgd.PLS -> blib\script\bp_process_sgd.pl
Copying scripts\seqstats\chaos_plot.PLS -> blib\script\chaos_plot.PLS
Changing sharpbang in blib\script\chaos_plot.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\chaos_plot.PLS.bak
blib\script\chaos_plot.PLS -> blib\script\bp_chaos_plot.pl
Copying scripts\utilities\mutate.PLS -> blib\script\mutate.PLS
Changing sharpbang in blib\script\mutate.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\mutate.PLS.bak
blib\script\mutate.PLS -> blib\script\bp_mutate.pl
Copying scripts\seq\split_seq.PLS -> blib\script\split_seq.PLS
Changing sharpbang in blib\script\split_seq.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\split_seq.PLS.bak
blib\script\split_seq.PLS -> blib\script\bp_split_seq.pl
Copying scripts\biblio\biblio.PLS -> blib\script\biblio.PLS
Changing sharpbang in blib\script\biblio.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\biblio.PLS.bak
blib\script\biblio.PLS -> blib\script\bp_biblio.pl
Copying scripts\Bio-SeqFeature-Store\bp_seqfeature_delete.PLS -> blib\script\bp_seqfeature_delete.PLS
Changing sharpbang in blib\script\bp_seqfeature_delete.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\bp_seqfeature_delete.PLS.bak
blib\script\bp_seqfeature_delete.PLS -> blib\script\bp_seqfeature_delete.pl
Copying scripts\Bio-DB-GFF\genbank2gff3.PLS -> blib\script\genbank2gff3.PLS
Changing sharpbang in blib\script\genbank2gff3.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\genbank2gff3.PLS.bak
blib\script\genbank2gff3.PLS -> blib\script\bp_genbank2gff3.pl
Copying scripts\DB\bioflat_index.PLS -> blib\script\bioflat_index.PLS
Changing sharpbang in blib\script\bioflat_index.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\bioflat_index.PLS.bak
blib\script\bioflat_index.PLS -> blib\script\bp_bioflat_index.pl
Copying scripts\index\bp_fetch.PLS -> blib\script\bp_fetch.PLS
Changing sharpbang in blib\script\bp_fetch.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\bp_fetch.PLS.bak
blib\script\bp_fetch.PLS -> blib\script\bp_fetch.pl
Copying scripts\utilities\seq_length.PLS -> blib\script\seq_length.PLS
Changing sharpbang in blib\script\seq_length.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\seq_length.PLS.bak
blib\script\seq_length.PLS -> blib\script\bp_seq_length.pl
Copying scripts\utilities\mask_by_search.PLS -> blib\script\mask_by_search.PLS
Changing sharpbang in blib\script\mask_by_search.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\mask_by_search.PLS.bak
blib\script\mask_by_search.PLS -> blib\script\bp_mask_by_search.pl
Copying scripts\taxa\query_entrez_taxa.PLS -> blib\script\query_entrez_taxa.PLS
Changing sharpbang in blib\script\query_entrez_taxa.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\query_entrez_taxa.PLS.bak
blib\script\query_entrez_taxa.PLS -> blib\script\bp_query_entrez_taxa.pl
Copying scripts\taxa\classify_hits_kingdom.PLS -> blib\script\classify_hits_kingdom.PLS
Changing sharpbang in blib\script\classify_hits_kingdom.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\classify_hits_kingdom.PLS.bak
blib\script\classify_hits_kingdom.PLS -> blib\script\bp_classify_hits_kingdom.pl
Copying scripts\utilities\search2tribe.PLS -> blib\script\search2tribe.PLS
Changing sharpbang in blib\script\search2tribe.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\search2tribe.PLS.bak
blib\script\search2tribe.PLS -> blib\script\bp_search2tribe.pl
Copying scripts\taxa\local_taxonomydb_query.PLS -> blib\script\local_taxonomydb_query.PLS
Changing sharpbang in blib\script\local_taxonomydb_query.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\local_taxonomydb_query.PLS.bak
blib\script\local_taxonomydb_query.PLS -> blib\script\bp_local_taxonomydb_query.pl
Copying scripts\tree\nexus2nh.PLS -> blib\script\nexus2nh.PLS
Changing sharpbang in blib\script\nexus2nh.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\nexus2nh.PLS.bak
blib\script\nexus2nh.PLS -> blib\script\bp_nexus2nh.pl
Copying scripts\Bio-DB-GFF\meta_gff.PLS -> blib\script\meta_gff.PLS
Changing sharpbang in blib\script\meta_gff.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\meta_gff.PLS.bak
blib\script\meta_gff.PLS -> blib\script\bp_meta_gff.pl
Copying scripts\utilities\search2gff.PLS -> blib\script\search2gff.PLS
Changing sharpbang in blib\script\search2gff.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\search2gff.PLS.bak
blib\script\search2gff.PLS -> blib\script\bp_search2gff.pl
Copying scripts\DB\biogetseq.PLS -> blib\script\biogetseq.PLS
Changing sharpbang in blib\script\biogetseq.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\biogetseq.PLS.bak
blib\script\biogetseq.PLS -> blib\script\bp_biogetseq.pl
Copying scripts\index\bp_index.PLS -> blib\script\bp_index.PLS
Changing sharpbang in blib\script\bp_index.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\bp_index.PLS.bak
blib\script\bp_index.PLS -> blib\script\bp_index.pl
Copying scripts\popgen\heterogeneity_test.PLS -> blib\script\heterogeneity_test.PLS
Changing sharpbang in blib\script\heterogeneity_test.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\heterogeneity_test.PLS.bak
blib\script\heterogeneity_test.PLS -> blib\script\bp_heterogeneity_test.pl
Copying scripts\Bio-SeqFeature-Store\bp_seqfeature_gff3.PLS -> blib\script\bp_seqfeature_gff3.PLS
blib\script\bp_seqfeature_gff3.PLS -> blib\script\bp_seqfeature_gff3.pl
Copying scripts\popgen\composite_LD.PLS -> blib\script\composite_LD.PLS
Changing sharpbang in blib\script\composite_LD.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\composite_LD.PLS.bak
blib\script\composite_LD.PLS -> blib\script\bp_composite_LD.pl
Copying scripts\searchio\parse_hmmsearch.PLS -> blib\script\parse_hmmsearch.PLS
Changing sharpbang in blib\script\parse_hmmsearch.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\parse_hmmsearch.PLS.bak
blib\script\parse_hmmsearch.PLS -> blib\script\bp_parse_hmmsearch.pl
Copying scripts\Bio-DB-GFF\bulk_load_gff.PLS -> blib\script\bulk_load_gff.PLS
Changing sharpbang in blib\script\bulk_load_gff.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\bulk_load_gff.PLS.bak
blib\script\bulk_load_gff.PLS -> blib\script\bp_bulk_load_gff.pl
Copying scripts\utilities\revtrans-motif.PLS -> blib\script\revtrans-motif.PLS
Changing sharpbang in blib\script\revtrans-motif.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\revtrans-motif.PLS.bak
blib\script\revtrans-motif.PLS -> blib\script\bp_revtrans-motif.pl
Copying scripts\utilities\remote_blast.PLS -> blib\script\remote_blast.PLS
Changing sharpbang in blib\script\remote_blast.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\remote_blast.PLS.bak
blib\script\remote_blast.PLS -> blib\script\bp_remote_blast.pl
Copying scripts\seq\seqconvert.PLS -> blib\script\seqconvert.PLS
Changing sharpbang in blib\script\seqconvert.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\seqconvert.PLS.bak
blib\script\seqconvert.PLS -> blib\script\bp_seqconvert.pl
Copying scripts\seq\make_mrna_protein.PLS -> blib\script\make_mrna_protein.PLS
Changing sharpbang in blib\script\make_mrna_protein.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\make_mrna_protein.PLS.bak
blib\script\make_mrna_protein.PLS -> blib\script\bp_make_mrna_protein.pl
Copying scripts\utilities\search2alnblocks.PLS -> blib\script\search2alnblocks.PLS
Changing sharpbang in blib\script\search2alnblocks.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\search2alnblocks.PLS.bak
blib\script\search2alnblocks.PLS -> blib\script\bp_search2alnblocks.pl
Copying scripts\seqstats\gccalc.PLS -> blib\script\gccalc.PLS
Changing sharpbang in blib\script\gccalc.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\gccalc.PLS.bak
blib\script\gccalc.PLS -> blib\script\bp_gccalc.pl
Copying scripts\utilities\pairwise_kaks.PLS -> blib\script\pairwise_kaks.PLS
Changing sharpbang in blib\script\pairwise_kaks.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\pairwise_kaks.PLS.bak
blib\script\pairwise_kaks.PLS -> blib\script\bp_pairwise_kaks.pl
Copying scripts\utilities\download_query_genbank.PLS -> blib\script\download_query_genbank.PLS
Changing sharpbang in blib\script\download_query_genbank.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\download_query_genbank.PLS.bak
blib\script\download_query_genbank.PLS -> blib\script\bp_download_query_genbank.pl
Copying scripts\taxa\taxonomy2tree.PLS -> blib\script\taxonomy2tree.PLS
Changing sharpbang in blib\script\taxonomy2tree.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\taxonomy2tree.PLS.bak
blib\script\taxonomy2tree.PLS -> blib\script\bp_taxonomy2tree.pl
Copying scripts\Bio-DB-EUtilities\einfo.PLS -> blib\script\einfo.PLS
Changing sharpbang in blib\script\einfo.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\einfo.PLS.bak
blib\script\einfo.PLS -> blib\script\bp_einfo.pl
Copying scripts\DB\biofetch_genbank_proxy.PLS -> blib\script\biofetch_genbank_proxy.PLS
Changing sharpbang in blib\script\biofetch_genbank_proxy.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\biofetch_genbank_proxy.PLS.bak
blib\script\biofetch_genbank_proxy.PLS -> blib\script\bp_biofetch_genbank_proxy.pl
Copying scripts\seq\seqretsplit.PLS -> blib\script\seqretsplit.PLS
Changing sharpbang in blib\script\seqretsplit.PLS to C:\Perl-5.18\bin\perl.exe
Deleting blib\script\seqretsplit.PLS.bak
blib\script\seqretsplit.PLS -> blib\script\bp_seqretsplit.pl
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Align/AlignStats.t ......................... 
1..43
ok 1 - use Bio::Align::DNAStatistics;
ok 2 - use Bio::Align::ProteinStatistics;
ok 3 - use Bio::AlignIO;
ok 4 - 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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Align/AlignUtil.t .......................... 
1..33
ok 1 - use Bio::Align::Utilities;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::SeqIO;
ok 4 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Align/SimpleAlign.t ........................ 
1..179
ok 1 - use Bio::SimpleAlign;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::SeqFeature::Generic;
ok 4 - use Bio::Location::Simple;
ok 5 - use Bio::Location::Split;
ok 6 - An object of class 'Bio::AlignIO::pfam' isa 'Bio::AlignIO'
ok 7 - pfam input test
ok 8 - match_line
ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 10 - num_sequences
ok 11 - num_sequences
ok 12 - select_noncont
ok 13 - select_noncont
ok 14 - num_sequences
ok 15 - select_noncont
ok 16 - select_noncont
ok 17 - each_seq
ok 18 - get_nse
ok 19 - id
ok 20 - num_gaps
ok 21 - each_alphabetically
ok 22 - column_from_residue_number
ok 23 - display_name get/set
ok 24 - display_name get
ok 25 - consensus_string
ok 26 - consensus_string
ok 27 - consensus_string
ok 28
ok 29 - each_seq_with_id
ok 30 - is_flush
ok 31 - id get/set
ok 32 - length
ok 33 - num_residues
ok 34 - num_sequences
ok 35 - overall_percentage_identity
ok 36 - overall_percentage_identity
ok 37 - overall_percentage_identity
ok 38 - overall_percentage_identity
ok 39 - average_percentage_identity
ok 40
ok 41 - set_displayname_count
ok 42
ok 43 - set_displayname_flat
ok 44
ok 45 - set_displayname_normal
ok 46
ok 47
ok 48 - uppercase, map_chars
ok 49 - match_line
ok 50 - remove_seqs
ok 51 - remove_seqs
ok 52 - add_seq
ok 53 - add_seq
ok 54 - get_seq_by_pos
ok 55 - get_seq_by_pos
ok 56
ok 57
ok 58
ok 59 - purge
ok 60 - purge
ok 61 - IO::String consensus_iupac
ok 62 - IO::String write_aln normal
ok 63 - IO::String write_aln slice
ok 64 - IO::String write_aln slice
ok 65 - IO::String write_aln slice
ok 66 - IO::String write_aln slice
ok 67 - IO::String write_aln slice
ok 68
ok 69 - remove_columns by position
ok 70 - remove_columns by position (wrong order)
ok 71 - cigar_line
ok 72 - cigar_line
ok 73 - cigar_line
ok 74 - cigar_line
ok 75 - sort_alphabetically - before
ok 76
ok 77 - sort_alphabetically - after
ok 78 - remove_gaps
ok 79 - remove_gaps all_gaps_only
ok 80 - set_new_reference
ok 81 - set_new_reference
ok 82 - uniq_seq
ok 83 - bug 2099
ok 84 - bug 2099
ok 85 - bug 2793
ok 86 - bug 2793
ok 87 - bug 2793
ok 88 - bug 2793
ok 89 - Bad sequence, bad!
ok 90 - added 3 seqs
ok 91 - first 2 features added
ok 92 - 3rd feature added
not ok 93 # TODO This should pass but dies; see bug 2842

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

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

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

#   Failed (TODO) test at t/Align/SimpleAlign.t line 421.
# died: Bio::Root::Exception (
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: In sequence one residue count gives end value 6.  
# Overriding value [4] with value 6 for Bio::LocatableSeq::end().
# ??
# STACK: Error::throw
# STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:181
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:196
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1143
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421
# STACK: t/Align/SimpleAlign.t:421
# -----------------------------------------------------------
# )
ok 109 - slice 4 len
ok 110 - correct masked seq
ok 111 - correct masked seq
ok 112 - correct masked seq
ok 113 - initial display id ok
ok 114 - safe display id ok
ok 115 - restored display id ok
ok 116 - sort by list ok
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123 - BIC:GGATCCATT[C/C]CTACT
ok 124 - BIC:GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT
ok 125 - BIC:G[G/C]ATCCATT[C/G]CTACT
ok 126 - BIC:GGATCCATT[C/G]CTACT
ok 127 - BIC:GGATCCATT[C/G]CTAC[T/A]
ok 128 - BIC:GGATCCATT[C/G]CTA[C/G][T/A]
ok 129 - BIC:GGATCCATT[C/G]CTACT
ok 130 - BIC:GGATCCATT{C.C}CTACT
ok 131 - BIC:GGAT{C.-}{C.-}ATT{C.C}CT{A.C}CT
ok 132 - BIC:G{G.C}ATCCATT{C.G}CTACT
ok 133 - BIC:GGATCCATT{C.G}CTACT
ok 134 - BIC:GGATCCATT{C.G}CTAC{T.A}
ok 135 - BIC:GGATCCATT{C.G}CTA{C.G}{T.A}
ok 136 - BIC:GGATCCATT{C.G}CTACT
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign'
ok 175 - consensus string looks ok
ok 176 - looks like correct unmasked alignment (from clustalw)
ok 177 - looks like correct masked alignment (from clustalw)
ok 178
ok 179 - align after looks ok
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Align/TreeBuild.t .......................... 
1..13
ok 1 - use Bio::Align::DNAStatistics;
ok 2 - use Bio::Align::ProteinStatistics;
ok 3 - use Bio::Align::Utilities;
ok 4 - use Bio::AlignIO;
ok 5 - use Bio::Tree::DistanceFactory;
ok 6 - use Bio::TreeIO;
ok 7 - 'SimpleAlign object parsed out' isa 'Bio::SimpleAlign'
ok 8 - 'Protein distance matrix retrieved' isa 'Bio::Matrix::MatrixI'
ok 9 - 'Tree object gotten back' isa 'Bio::Tree::TreeI'
ok 10 - NJ calculated Branch length
ok 11 - NJ calculated Branch length
ok 12 - Make sure two nodes are sister
ok 13 - 10 replicates formulated
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Align/Utilities.t .......................... 
1..13
ok 1 - use Bio::Align::Utilities;
ok 2 - use Bio::SimpleAlign;
ok 3 - use Bio::PrimarySeq;
ok 4 - use Bio::LocatableSeq;
ok 5 - use Bio::AlignIO;
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/AlignIO.t .......................... 
1..28
ok 1 - use Bio::AlignIO;
ok 2 - input filehandle method test : po
ok 3 - input filehandle method test : clustalw
ok 4 - input filehandle method test : msf
ok 5 - input filehandle method test : nexus
ok 6 - input filehandle method test : phylip
ok 7 - input filehandle method test : prodom
ok 8 - input filehandle method test : metafasta
ok 9 - input filehandle method test : mase
ok 10 - input filehandle method test : arp
ok 11 - input filehandle method test : psi
ok 12 - input filehandle method test : stockholm
ok 13 - input filehandle method test : fasta
ok 14 - input filehandle method test : pfam
ok 15 - input filehandle method test : xmfa
ok 16 - input filehandle method test : selex
ok 17 - filehandle output test : po
ok 18 - filehandle output test : clustalw
ok 19 - filehandle output test : msf
ok 20 - filehandle output test : nexus
ok 21 - filehandle output test : phylip
ok 22 - filehandle output test : metafasta
ok 23 - filehandle output test : psi
ok 24 - filehandle output test : stockholm
ok 25 - filehandle output test : fasta
ok 26 - filehandle output test : pfam
ok 27 - filehandle output test : xmfa
ok 28 - filehandle output test : selex
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/arp.t .............................. 
1..48
ok 1 - use Bio::AlignIO::arp;
ok 2 - An object of class 'Bio::AlignIO::arp' isa 'Bio::AlignIO'
ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 4 - ARP get_nse()
ok 5
ok 6 - ARP num_sequences()
ok 7 - ARP id()
ok 8 - ARP description()
ok 9 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI'
ok 10 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI'
ok 11
ok 12
ok 13
ok 14
ok 15 - An object of class 'Bio::AlignIO::arp' isa 'Bio::AlignIO'
ok 16 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 17 - ARP get_nse()
ok 18 - ARP num_sequences()
ok 19 - ARP id()
ok 20 - ARP description()
ok 21 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI'
ok 22 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI'
ok 23
ok 24
ok 25
ok 26
ok 27 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 28 - ARP get_nse()
ok 29 - ARP num_sequences()
ok 30 - ARP id()
ok 31 - ARP description()
ok 32 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI'
ok 33 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI'
ok 34
ok 35
ok 36
ok 37
ok 38 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 39 - ARP get_nse()
ok 40 - ARP num_sequences()
ok 41 - ARP id()
ok 42 - ARP description()
ok 43 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI'
ok 44 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI'
ok 45
ok 46
ok 47
ok 48
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/bl2seq.t ........................... 
1..3
ok 1 - use Bio::AlignIO::bl2seq;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3 - BLAST bl2seq format test
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/clustalw.t ......................... 
1..6
ok 1 - use Bio::AlignIO::clustalw;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3 - clustalw consensus_string test
ok 4 - clustalw (.aln) output test
ok 5 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 6 - clustalw (.aln) input test
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/emboss.t ........................... 
1..37
ok 1 - use Bio::AlignIO::emboss;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 11
ok 12
ok 13
ok 14 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 15
ok 16
ok 17
ok 18 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 19
ok 20
ok 21 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 33
ok 34
ok 35
ok 36
ok 37
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/fasta.t ............................ 
1..10
ok 1 - use Bio::AlignIO::fasta;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3 - fasta input test 
ok 4 - fasta input test for description
ok 5 - fasta input test for id
ok 6 - fasta input test for end
ok 7 - fasta input test for description
ok 8 - fasta output test
ok 9 - filehandle input test  
ok 10 - filehandle output test
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/largemultifasta.t .................. 
1..7
ok 1 - use Bio::AlignIO::largemultifasta;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3 - fasta input test 
ok 4 - fasta input test for description
ok 5 - fasta input test for id
ok 6 - fasta input test for description
ok 7 - fasta output test
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/maf.t .............................. 
1..11
ok 1 - use Bio::AlignIO::maf;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3 - maf input test
ok 4
ok 5 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 6 - maf input test
ok 7
ok 8 - maf input test
ok 9
ok 10 - maf input test
ok 11
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/mase.t ............................. 
1..3
ok 1 - use Bio::AlignIO::mase;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3 - mase input test 
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/mega.t ............................. 
1..6
ok 1 - use Bio::AlignIO::mega;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3
ok 4
ok 5
ok 6 - mega output test
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/meme.t ............................. 
1..14
ok 1 - use Bio::AlignIO::meme;
ok 2 - An object of class 'Bio::AlignIO::meme' isa 'Bio::AlignIO'
ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 4
ok 5
ok 6
ok 7
ok 8 - An object of class 'Bio::AlignIO::meme' isa 'Bio::AlignIO'
ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 10
ok 11
ok 12
ok 13
ok 14
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/metafasta.t ........................ 
1..4
ok 1 - use Bio::AlignIO::metafasta;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3 - consensus_string on metafasta
ok 4 - symbol_chars() using metafasta
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/msf.t .............................. 
1..4
ok 1 - use Bio::AlignIO::msf;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3 - msf input test
ok 4 - msf output test
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/nexus.t ............................ 
1..43
ok 1 - use Bio::AlignIO::nexus;
ok 2 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 4
ok 5 - nexus output test
ok 6 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 8 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 10 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 11 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 12 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 13 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 14 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 15 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 16 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 17 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 18 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 19 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 20 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 21 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 22 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 23 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 24 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 25 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 26 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 27 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 28 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 29 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 30 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 31 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 32 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 33 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 34 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 35 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 36 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 37 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 38 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 39 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 40 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 41 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 42 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO'
ok 43 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/pfam.t ............................. 
1..5
ok 1 - use Bio::AlignIO::pfam;
ok 2 - An object of class 'Bio::AlignIO::pfam' isa 'Bio::AlignIO'
ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 4
ok 5 -  pfam output test
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/phylip.t ........................... 
1..11
ok 1 - use Bio::AlignIO::phylip;
ok 2 - An object of class 'Bio::AlignIO::phylip' isa 'Bio::AlignIO'
ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 4
ok 5 - phylip output test
ok 6 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 7
ok 8 - An object of class 'Bio::AlignIO::phylip' isa 'Bio::AlignIO'
ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 10
ok 11
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/po.t ............................... 
1..11
ok 1 - use Bio::AlignIO::po;
ok 2 - An object of class 'Bio::AlignIO::po' isa 'Bio::AlignIO'
ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 4
ok 5 - An object of class 'Bio::AlignIO::clustalw' isa 'Bio::AlignIO'
ok 6 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 7 - po output test
ok 8 - An object of class 'Bio::AlignIO::po' isa 'Bio::AlignIO'
ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 10
ok 11
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/prodom.t ........................... 
1..3
ok 1 - use Bio::AlignIO::prodom;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3 - prodom input test 
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/psi.t .............................. 
1..5
ok 1 - use Bio::AlignIO::psi;
ok 2 - An object of class 'Bio::AlignIO::psi' isa 'Bio::AlignIO'
ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 4
ok 5
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/selex.t ............................ 
1..4
ok 1 - use Bio::AlignIO::selex;
ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 3 - selex format test 
ok 4 - selex output test
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/stockholm.t ........................ 
1..83
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 - An object of class 'Bio::Seq::Meta' isa 'Bio::Seq::MetaI'
ok 35 - Rfam meta data
ok 36 - Rfam meta data
ok 37 - An object of class 'Bio::AlignIO::stockholm' isa 'Bio::AlignIO'
ok 38
ok 39 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 40
ok 41
ok 42
ok 43
ok 44 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue'
ok 45 - Pfam annotation
ok 46
ok 47 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 48
ok 49
ok 50
ok 51
ok 52 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58 - An object of class 'Bio::Seq::Meta' isa 'Bio::Seq::MetaI'
ok 59 - Pfam aln meta data
ok 60 - Pfam aln meta data
ok 61 - Pfam aln meta data
ok 62 - Pfam aln meta data
ok 63 - Pfam aln meta data
ok 64 - Pfam aln meta data
ok 65 - Pfam seq meta data
ok 66 - Pfam seq meta data
ok 67 - Pfam seq meta data
ok 68 - Pfam seq meta data
ok 69
ok 70 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeatureI'
ok 71 - An object of class 'Bio::Seq::Meta' isa 'Bio::Seq::Meta'
ok 72 - An object of class 'Bio::Annotation::Target' isa 'Bio::AnnotationI'
ok 73 - An object of class 'Bio::Annotation::Target' isa 'Bio::Annotation::DBLink'
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/AlignIO/xmfa.t ............................. 
1..16
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 description
ok 5 - xmfa input test for id
ok 6 - xmfa input test for end
ok 7 - xmfa input test for end
ok 8 - xmfa alignment score
ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI'
ok 10 - xmfa input test 
ok 11 - xmfa input test for description
ok 12 - xmfa input test for id
ok 13 - xmfa input test for end
ok 14 - xmfa input test for end
ok 15 - xmfa alignment score
ok 16 - xmfa output test
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Alphabet.t ................................. 
1..100
ok 1 - use Bio::Symbol::Alphabet;
ok 2 - use Bio::Symbol::Symbol;
ok 3 - use Bio::Symbol::DNAAlphabet;
ok 4 - use Bio::Symbol::ProteinAlphabet;
ok 5 - An object of class 'Bio::Symbol::Alphabet' isa 'Bio::Symbol::Alphabet'
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11 - An object of class 'Bio::Symbol::DNAAlphabet' isa 'Bio::Symbol::AlphabetI'
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46 - An object of class 'Bio::Symbol::ProteinAlphabet' isa 'Bio::Symbol::AlphabetI'
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Annotation/Annotation.t .................... 
1..158
ok 1 - use Bio::Annotation::Collection;
ok 2 - use Bio::Annotation::DBLink;
ok 3 - use Bio::Annotation::Comment;
ok 4 - use Bio::Annotation::Reference;
ok 5 - use Bio::Annotation::SimpleValue;
ok 6 - use Bio::Annotation::Target;
ok 7 - use Bio::Annotation::AnnotationFactory;
ok 8 - use Bio::Annotation::StructuredValue;
ok 9 - use Bio::Annotation::TagTree;
ok 10 - use Bio::Annotation::Tree;
ok 11 - use Bio::Seq;
ok 12 - use Bio::SimpleAlign;
ok 13 - use Bio::Cluster::UniGene;
ok 14 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::AnnotationI'
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21 - An object of class 'Bio::Annotation::DBLink' isa 'Bio::AnnotationI'
ok 22
ok 23
ok 24
ok 25 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI'
ok 26
ok 27
ok 28 - An object of class 'Bio::Annotation::Target' isa 'Bio::AnnotationI'
ok 29
ok 30 - An object of class 'Bio::Annotation::Reference' isa 'Bio::AnnotationI'
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53 - An object of class 'Bio::Annotation::StructuredValue' isa 'Bio::AnnotationI'
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI'
ok 69
ok 70
ok 71
ok 72
ok 73 - An object of class 'Bio::Annotation::StructuredValue' isa 'Bio::Annotation::StructuredValue'
ok 74
ok 75
ok 76
ok 77
ok 78 - use Bio::Annotation::OntologyTerm;
ok 79 - An object of class 'Bio::Ontology::Term' isa 'Bio::Ontology::Term'
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85 - An object of class 'Bio::Seq' isa 'Bio::AnnotatableI'
ok 86 - 'isa SeqFeatureI' isa 'Bio::SeqFeatureI'
ok 87 - 'isa AnnotatableI' isa 'Bio::AnnotatableI'
ok 88 - 'isa SeqFeatureI' isa 'Bio::SeqFeatureI'
ok 89 - 'isa AnnotatableI' isa 'Bio::AnnotatableI'
ok 90 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::AnnotatableI'
ok 91 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::AnnotatableI'
ok 92 - An object of class 'Bio::Annotation::AnnotationFactory' isa 'Bio::Factory::ObjectFactoryI'
ok 93 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue'
ok 94
ok 95 - An object of class 'Bio::Annotation::OntologyTerm' isa 'Bio::Annotation::OntologyTerm'
ok 96 - Bio::Annotation::Comment
ok 97 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment'
ok 98
ok 99 - Bio::Annotation::Comment
ok 100 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment'
ok 101 - Bio::Annotation::Comment
ok 102 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment'
ok 103
ok 104 - An object of class 'Bio::Annotation::Target' isa 'Bio::Annotation::Target'
ok 105
ok 106
ok 107 - An object of class 'Bio::Annotation::Tree' isa 'Bio::AnnotationI'
ok 108 - tree_id()
ok 109 - tagname()
ok 110 - An object of class 'Bio::SimpleAlign' isa 'Bio::AnnotatableI'
ok 111 - add tree to AlignI
ok 112 - get seq from node id
ok 113
ok 114 - An object of class 'Bio::Annotation::Tree' isa 'Bio::Annotation::Tree'
ok 115 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI'
ok 116 - default itext
ok 117 - roundtrip
ok 118 - itext
ok 119 - spxr
ok 120 - indent
ok 121 - xml
ok 122 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI'
ok 123
ok 124 - child changes
ok 125 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI'
ok 126
ok 127 - child changes
ok 128 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI'
ok 129
ok 130 - child changes
ok 131 - child changes in parent node
ok 132 - no tags
ok 133 - before Stag node
ok 134 - after Stag node
ok 135 - both stag nodes
ok 136 - different instances
ok 137 - before TagTree
ok 138 - after TagTree
ok 139 - both stag nodes
ok 140 - different instances
ok 141 - before TagTree
ok 142 - after TagTree
ok 143 - stag nodes
ok 144 - same instance
ok 145 - before TagTree
ok 146 - after TagTree
ok 147 - stag nodes
ok 148 - different instance
ok 149 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI'
ok 150 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI'
ok 151 - child changes
ok 152 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI'
ok 153 - child changes
ok 154 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI'
ok 155 - child changes
ok 156
ok 157
ok 158 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::Annotation::TagTree'
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Annotation/AnnotationAdaptor.t ............. 
1..23
ok 1 - use Bio::SeqFeature::Generic;
ok 2 - use Bio::SeqFeature::AnnotationAdaptor;
ok 3 - use Bio::Annotation::DBLink;
ok 4 - use Bio::Annotation::Comment;
ok 5 - use Bio::Annotation::SimpleValue;
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok
t/Assembly/Assembly.t ........................ skipped: The optional module DB_File (or dependencies thereof) was not installed
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
Bio::Assembly::IO: could not load tigr - for more details on supported formats please see the Assembly::IO docs
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::Assembly::IO::tigr. Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: . C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.1-LkNiOT\blib\lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.1-LkNiOT\blib\arch C:/cpanfly-5.18/var/cpan/build/BioPerl-1.6.1-LkNiOT C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.1-LkNiOT C:\cpanfly-5.18\var\megalib C:\Perl-5.18\site\lib C:\Perl-5.18\lib C:/cpanfly-5.18/var/megalib C:/Perl-5.18/site/lib C:/Perl-5.18/lib) at Bio/SeqFeature/Collection.pm line 147.
BEGIN failed--compilation aborted at Bio/SeqFeature/Collection.pm line 147.
Compilation failed in require at Bio/Assembly/Contig.pm line 223.
BEGIN failed--compilation aborted at Bio/Assembly/Contig.pm line 223.
Compilation failed in require at Bio\Assembly\IO\tigr.pm line 236.
BEGIN failed--compilation aborted at Bio\Assembly\IO\tigr.pm line 236.
Compilation failed in require at Bio/Root/Root.pm line 439.

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


#   Failed test 'undef isa 'Bio::Assembly::IO''
#   at t/Assembly/ContigSpectrum.t line 15.
#     undef isn't defined
Can't call method "next_assembly" on an undefined value at t/Assembly/ContigSpectrum.t line 16.
# Looks like you planned 134 tests but ran 3.
# Looks like you failed 1 test of 3 run.
# Looks like your test exited with 2 just after 3.
t/Assembly/ContigSpectrum.t .................. 
1..134
ok 1 - use Bio::Assembly::IO;
ok 2 - use Bio::Assembly::Tools::ContigSpectrum;
not ok 3 - undef isa 'Bio::Assembly::IO'
Dubious, test returned 2 (wstat 512, 0x200)
Failed 132/134 subtests 
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Biblio/Biblio.t ............................ 
1..24
ok 1 - use Bio::Biblio;
ok 2 - use Bio::Biblio::IO;
ok 3 # skip The optional module SOAP::Lite (or dependencies thereof) was not installed
ok 4
ok 5 - citation 1
ok 6 - citation 2
ok 7 - citation 3
ok 8 - in callback
ok 9 - in callback
ok 10 - in callback
ok 11 - calling callback
ok 12 - citation 1
ok 13 - citation 2
ok 14 - citation 1
ok 15 - citation 2
ok 16
ok 17 - citation 1
ok 18 - citation 2
ok 19 - citation 3
ok 20 - citation 4
ok 21 - filehandle test
ok 22 - filehandle test
ok 23 - filehandle test
ok 24 - filehandle test
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Biblio/References.t ........................ 
1..537
ok 1 - use Bio::Biblio::Article;
ok 2 - use Bio::Biblio::Book;
ok 3 - use Bio::Biblio::BookArticle;
ok 4 - use Bio::Biblio::Journal;
ok 5 - use Bio::Biblio::JournalArticle;
ok 6 - use Bio::Biblio::MedlineArticle;
ok 7 - use Bio::Biblio::MedlineBook;
ok 8 - use Bio::Biblio::MedlineBookArticle;
ok 9 - use Bio::Biblio::MedlineJournal;
ok 10 - use Bio::Biblio::MedlineJournalArticle;
ok 11 - use Bio::Biblio::Organisation;
ok 12 - use Bio::Biblio::Patent;
ok 13 - use Bio::Biblio::Person;
ok 14 - use Bio::Biblio::Proceeding;
ok 15 - use Bio::Biblio::Provider;
ok 16 - use Bio::Biblio::Ref;
ok 17 - use Bio::Biblio::Service;
ok 18 - use Bio::Biblio::TechReport;
ok 19 - use Bio::Biblio::Thesis;
ok 20 - use Bio::Biblio::WebResource;
ok 21 - use Bio::Biblio::PubmedArticle;
ok 22 - use Bio::Biblio::PubmedBookArticle;
ok 23 - use Bio::Biblio::PubmedJournalArticle;
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47 - set 'abstract'
ok 48 - get 'abstract'
ok 49 - set 'abstract_language'
ok 50 - get 'abstract_language'
ok 51 - set 'abstract_type'
ok 52 - get 'abstract_type'
ok 53 - set 'author_list_complete'
ok 54 - get 'author_list_complete'
ok 55 - set 'cross_references_list_complete'
ok 56 - get 'cross_references_list_complete'
ok 57 - set 'date'
ok 58 - get 'date'
ok 59 - set 'date_completed'
ok 60 - get 'date_completed'
ok 61 - set 'date_created'
ok 62 - get 'date_created'
ok 63 - set 'date_revised'
ok 64 - get 'date_revised'
ok 65 - set 'format'
ok 66 - get 'format'
ok 67 - set 'identifier'
ok 68 - get 'identifier'
ok 69 - set 'language'
ok 70 - get 'language'
ok 71 - set 'last_modified_date'
ok 72 - get 'last_modified_date'
ok 73 - set 'repository_subset'
ok 74 - get 'repository_subset'
ok 75 - set 'rights'
ok 76 - get 'rights'
ok 77 - set 'spatial_location'
ok 78 - get 'spatial_location'
ok 79 - set 'subject_headings_source'
ok 80 - get 'subject_headings_source'
ok 81 - set 'temporal_period'
ok 82 - get 'temporal_period'
ok 83 - set 'title'
ok 84 - get 'title'
ok 85 - set 'toc'
ok 86 - get 'toc'
ok 87 - set 'toc_type'
ok 88 - get 'toc_type'
ok 89 - set 'type'
ok 90 - get 'type'
ok 91 - set 'first_page'
ok 92 - get 'first_page'
ok 93 - set 'last_page'
ok 94 - get 'last_page'
ok 95 - set 'issue'
ok 96 - get 'issue'
ok 97 - set 'issue_supplement'
ok 98 - get 'issue_supplement'
ok 99 - set 'volume'
ok 100 - get 'volume'
ok 101 - set 'affiliation'
ok 102 - get 'affiliation'
ok 103 - set 'citation_owner'
ok 104 - get 'citation_owner'
ok 105 - set 'date_of_electronic_publication'
ok 106 - get 'date_of_electronic_publication'
ok 107 - set 'gene_symbols'
ok 108 - get 'gene_symbols'
ok 109 - set 'grant_list_complete'
ok 110 - get 'grant_list_complete'
ok 111 - set 'medline_date'
ok 112 - get 'medline_date'
ok 113 - set 'medline_id'
ok 114 - get 'medline_id'
ok 115 - set 'medline_page'
ok 116 - get 'medline_page'
ok 117 - set 'number_of_references'
ok 118 - get 'number_of_references'
ok 119 - set 'other_languages'
ok 120 - get 'other_languages'
ok 121 - set 'pmid'
ok 122 - get 'pmid'
ok 123 - set 'season'
ok 124 - get 'season'
ok 125 - set 'status'
ok 126 - get 'status'
ok 127 - set 'vernacular_title'
ok 128 - get 'vernacular_title'
ok 129
ok 130 - abstract
ok 131 - abstract_language
ok 132 - abstract_type
ok 133 - author_list_complete
ok 134 - cross_references_list_complete
ok 135 - date
ok 136 - date_completed
ok 137 - date_created
ok 138 - date_revised
ok 139 - format
ok 140 - identifier
ok 141 - language
ok 142 - last_modified_date
ok 143 - repository_subset
ok 144 - rights
ok 145 - spatial_location
ok 146 - subject_headings_source
ok 147 - temporal_period
ok 148 - title
ok 149 - toc
ok 150 - toc_type
ok 151 - type
ok 152 - first_page
ok 153 - last_page
ok 154 - issue
ok 155 - issue_supplement
ok 156 - volume
ok 157 - affiliation
ok 158 - citation_owner
ok 159 - date_of_electronic_publication
ok 160 - gene_symbols
ok 161 - grant_list_complete
ok 162 - medline_date
ok 163 - medline_id
ok 164 - medline_page
ok 165 - number_of_references
ok 166 - other_languages
ok 167 - pmid
ok 168 - season
ok 169 - status
ok 170 - vernacular_title
ok 171 - get 'authors'
ok 172 - get 'cross_references'
ok 173 - get 'codes'
ok 174 - get 'contributors'
ok 175 - get 'keywords'
ok 176 - get 'publisher'
ok 177 - get 'subject_headings'
ok 178 - get 'journal'
ok 179 - get 'chemicals'
ok 180 - get 'comment_ins'
ok 181 - get 'comment_ons'
ok 182 - get 'erratum_fors'
ok 183 - get 'erratum_ins'
ok 184 - get 'general_notes'
ok 185 - get 'grants'
ok 186 - get 'mesh_headings'
ok 187 - get 'original_report_ins'
ok 188 - get 'other_abstracts'
ok 189 - get 'other_ids'
ok 190 - get 'republished_froms'
ok 191 - get 'republished_ins'
ok 192 - get 'retraction_ins'
ok 193 - get 'retraction_ofs'
ok 194 - get 'summary_for_patients_ins'
ok 195 - get 'update_ins'
ok 196 - get 'update_ofs'
ok 197 - get 'journal'
ok 198 - add_author 1
ok 199 - add_author 2
ok 200 - get authors
ok 201 - add_contributor 1
ok 202 - add_contributor 2
ok 203 - get contributors
ok 204 - add_cross_reference 1
ok 205 - add_cross_reference 2
ok 206 - get cross_references
ok 207 - get cross_references
ok 208 - set 'abstract'
ok 209 - get 'abstract'
ok 210 - set 'abstract_language'
ok 211 - get 'abstract_language'
ok 212 - set 'abstract_type'
ok 213 - get 'abstract_type'
ok 214 - set 'author_list_complete'
ok 215 - get 'author_list_complete'
ok 216 - set 'cross_references_list_complete'
ok 217 - get 'cross_references_list_complete'
ok 218 - set 'date'
ok 219 - get 'date'
ok 220 - set 'date_completed'
ok 221 - get 'date_completed'
ok 222 - set 'date_created'
ok 223 - get 'date_created'
ok 224 - set 'date_revised'
ok 225 - get 'date_revised'
ok 226 - set 'format'
ok 227 - get 'format'
ok 228 - set 'identifier'
ok 229 - get 'identifier'
ok 230 - set 'language'
ok 231 - get 'language'
ok 232 - set 'last_modified_date'
ok 233 - get 'last_modified_date'
ok 234 - set 'repository_subset'
ok 235 - get 'repository_subset'
ok 236 - set 'rights'
ok 237 - get 'rights'
ok 238 - set 'spatial_location'
ok 239 - get 'spatial_location'
ok 240 - set 'subject_headings_source'
ok 241 - get 'subject_headings_source'
ok 242 - set 'temporal_period'
ok 243 - get 'temporal_period'
ok 244 - set 'title'
ok 245 - get 'title'
ok 246 - set 'toc'
ok 247 - get 'toc'
ok 248 - set 'toc_type'
ok 249 - get 'toc_type'
ok 250 - set 'type'
ok 251 - get 'type'
ok 252 - set 'first_page'
ok 253 - get 'first_page'
ok 254 - set 'last_page'
ok 255 - get 'last_page'
ok 256 - set 'affiliation'
ok 257 - get 'affiliation'
ok 258 - set 'citation_owner'
ok 259 - get 'citation_owner'
ok 260 - set 'date_of_electronic_publication'
ok 261 - get 'date_of_electronic_publication'
ok 262 - set 'gene_symbols'
ok 263 - get 'gene_symbols'
ok 264 - set 'grant_list_complete'
ok 265 - get 'grant_list_complete'
ok 266 - set 'medline_date'
ok 267 - get 'medline_date'
ok 268 - set 'medline_id'
ok 269 - get 'medline_id'
ok 270 - set 'medline_page'
ok 271 - get 'medline_page'
ok 272 - set 'number_of_references'
ok 273 - get 'number_of_references'
ok 274 - set 'other_languages'
ok 275 - get 'other_languages'
ok 276 - set 'pmid'
ok 277 - get 'pmid'
ok 278 - set 'season'
ok 279 - get 'season'
ok 280 - set 'status'
ok 281 - get 'status'
ok 282 - set 'vernacular_title'
ok 283 - get 'vernacular_title'
ok 284
ok 285 - abstract
ok 286 - abstract_language
ok 287 - abstract_type
ok 288 - author_list_complete
ok 289 - cross_references_list_complete
ok 290 - date
ok 291 - date_completed
ok 292 - date_created
ok 293 - date_revised
ok 294 - format
ok 295 - identifier
ok 296 - language
ok 297 - last_modified_date
ok 298 - repository_subset
ok 299 - rights
ok 300 - spatial_location
ok 301 - subject_headings_source
ok 302 - temporal_period
ok 303 - title
ok 304 - toc
ok 305 - toc_type
ok 306 - type
ok 307 - first_page
ok 308 - last_page
ok 309 - affiliation
ok 310 - citation_owner
ok 311 - date_of_electronic_publication
ok 312 - gene_symbols
ok 313 - grant_list_complete
ok 314 - medline_date
ok 315 - medline_id
ok 316 - medline_page
ok 317 - number_of_references
ok 318 - other_languages
ok 319 - pmid
ok 320 - season
ok 321 - status
ok 322 - vernacular_title
ok 323 - get 'authors'
ok 324 - get 'cross_references'
ok 325 - get 'codes'
ok 326 - get 'contributors'
ok 327 - get 'keywords'
ok 328 - get 'publisher'
ok 329 - get 'subject_headings'
ok 330 - get 'book'
ok 331 - get 'chemicals'
ok 332 - get 'comment_ins'
ok 333 - get 'comment_ons'
ok 334 - get 'erratum_fors'
ok 335 - get 'erratum_ins'
ok 336 - get 'general_notes'
ok 337 - get 'grants'
ok 338 - get 'mesh_headings'
ok 339 - get 'original_report_ins'
ok 340 - get 'other_abstracts'
ok 341 - get 'other_ids'
ok 342 - get 'republished_froms'
ok 343 - get 'republished_ins'
ok 344 - get 'retraction_ins'
ok 345 - get 'retraction_ofs'
ok 346 - get 'summary_for_patients_ins'
ok 347 - get 'update_ins'
ok 348 - get 'update_ofs'
ok 349 - get 'book'
ok 350 - set 'abstract'
ok 351 - get 'abstract'
ok 352 - set 'abstract_language'
ok 353 - get 'abstract_language'
ok 354 - set 'abstract_type'
ok 355 - get 'abstract_type'
ok 356 - set 'author_list_complete'
ok 357 - get 'author_list_complete'
ok 358 - set 'cross_references_list_complete'
ok 359 - get 'cross_references_list_complete'
ok 360 - set 'date'
ok 361 - get 'date'
ok 362 - set 'date_completed'
ok 363 - get 'date_completed'
ok 364 - set 'date_created'
ok 365 - get 'date_created'
ok 366 - set 'date_revised'
ok 367 - get 'date_revised'
ok 368 - set 'format'
ok 369 - get 'format'
ok 370 - set 'identifier'
ok 371 - get 'identifier'
ok 372 - set 'language'
ok 373 - get 'language'
ok 374 - set 'last_modified_date'
ok 375 - get 'last_modified_date'
ok 376 - set 'repository_subset'
ok 377 - get 'repository_subset'
ok 378 - set 'rights'
ok 379 - get 'rights'
ok 380 - set 'spatial_location'
ok 381 - get 'spatial_location'
ok 382 - set 'subject_headings_source'
ok 383 - get 'subject_headings_source'
ok 384 - set 'temporal_period'
ok 385 - get 'temporal_period'
ok 386 - set 'title'
ok 387 - get 'title'
ok 388 - set 'toc'
ok 389 - get 'toc'
ok 390 - set 'toc_type'
ok 391 - get 'toc_type'
ok 392 - set 'type'
ok 393 - get 'type'
ok 394 - set 'edition'
ok 395 - get 'edition'
ok 396 - set 'isbn'
ok 397 - get 'isbn'
ok 398 - set 'series'
ok 399 - get 'series'
ok 400 - set 'volume'
ok 401 - get 'volume'
ok 402
ok 403 - abstract
ok 404 - abstract_language
ok 405 - abstract_type
ok 406 - author_list_complete
ok 407 - cross_references_list_complete
ok 408 - date
ok 409 - date_completed
ok 410 - date_created
ok 411 - date_revised
ok 412 - format
ok 413 - identifier
ok 414 - language
ok 415 - last_modified_date
ok 416 - repository_subset
ok 417 - rights
ok 418 - spatial_location
ok 419 - subject_headings_source
ok 420 - temporal_period
ok 421 - title
ok 422 - toc
ok 423 - toc_type
ok 424 - type
ok 425 - edition
ok 426 - isbn
ok 427 - series
ok 428 - volume
ok 429 - get 'authors'
ok 430 - get 'cross_references'
ok 431 - get 'codes'
ok 432 - get 'contributors'
ok 433 - get 'keywords'
ok 434 - get 'publisher'
ok 435 - get 'subject_headings'
ok 436 - get 'editor'
ok 437 - set 'abbreviation'
ok 438 - get 'abbreviation'
ok 439 - set 'issn'
ok 440 - get 'issn'
ok 441 - set 'name'
ok 442 - get 'name'
ok 443 - set 'coden'
ok 444 - get 'coden'
ok 445 - set 'country'
ok 446 - get 'country'
ok 447 - set 'medline_code'
ok 448 - get 'medline_code'
ok 449 - set 'medline_ta'
ok 450 - get 'medline_ta'
ok 451 - set 'nlm_unique_id'
ok 452 - get 'nlm_unique_id'
ok 453
ok 454 - abbreviation
ok 455 - issn
ok 456 - name
ok 457 - coden
ok 458 - country
ok 459 - medline_code
ok 460 - medline_ta
ok 461 - nlm_unique_id
ok 462 - set 'doc_number'
ok 463 - get 'doc_number'
ok 464 - set 'doc_office'
ok 465 - get 'doc_office'
ok 466 - set 'doc_type'
ok 467 - get 'doc_type'
ok 468
ok 469 - doc_number
ok 470 - doc_office
ok 471 - doc_type
ok 472 - get 'applicants'
ok 473 - set 'url'
ok 474 - get 'url'
ok 475 - set 'estimated_size'
ok 476 - get 'estimated_size'
ok 477 - set 'cost'
ok 478 - get 'cost'
ok 479
ok 480 - url
ok 481 - estimated_size
ok 482 - cost
ok 483 - set 'type'
ok 484 - get 'type'
ok 485 - set 'affiliation'
ok 486 - get 'affiliation'
ok 487 - set 'email'
ok 488 - get 'email'
ok 489 - set 'firstname'
ok 490 - get 'firstname'
ok 491 - set 'forename'
ok 492 - get 'forename'
ok 493 - set 'initials'
ok 494 - get 'initials'
ok 495 - set 'lastname'
ok 496 - get 'lastname'
ok 497 - set 'middlename'
ok 498 - get 'middlename'
ok 499 - set 'postal_address'
ok 500 - get 'postal_address'
ok 501 - set 'suffix'
ok 502 - get 'suffix'
ok 503
ok 504 - type
ok 505 - affiliation
ok 506 - email
ok 507 - firstname
ok 508 - forename
ok 509 - initials
ok 510 - lastname
ok 511 - middlename
ok 512 - postal_address
ok 513 - suffix
ok 514 - set 'type'
ok 515 - get 'type'
ok 516 - set 'name'
ok 517 - get 'name'
ok 518
ok 519 - type
ok 520 - name
ok 521 - set 'type'
ok 522 - get 'type'
ok 523 - set 'name'
ok 524 - get 'name'
ok 525
ok 526 - type
ok 527 - name
ok 528 - set 'pubmed_status'
ok 529 - get 'pubmed_status'
ok 530 - set 'pubmed_provider_id'
ok 531 - get 'pubmed_provider_id'
ok 532
ok 533 - pubmed_status
ok 534 - pubmed_provider_id
ok 535 - get 'pubmed_history_list'
ok 536 - get 'pubmed_article_id_list'
ok 537 - get 'pubmed_url_list'
ok
t/Biblio/biofetch.t .......................... skipped: Network tests have not been requested
t/Biblio/eutils.t ............................ skipped: Network tests have not been requested
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/ClusterIO/ClusterIO.t ...................... 
1..12
ok 1 - use Bio::ClusterIO;
ok 2 - use Bio::Cluster::ClusterFactory;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::Cluster::UniGeneI'
ok 12 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::Cluster::UniGeneI'
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/ClusterIO/SequenceFamily.t ................. 
1..19
ok 1 - use Bio::SeqIO;
ok 2 - use Bio::Cluster::SequenceFamily;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/ClusterIO/unigene.t ........................ 
1..73
ok 1 - use Bio::ClusterIO;
ok 2 - new Bio::ClusterIO object defined
ok 3
ok 4 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::Cluster::UniGeneI'
ok 5 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::ClusterI'
ok 6 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::IdentifiableI'
ok 7 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::DescribableI'
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::PrimarySeqI'
ok 49
ok 50
ok 51 - annotation object defined
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::PrimarySeqI'
ok 67
ok 68 - next cluster
ok 69
ok 70
ok 71
ok 72
ok 73
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Coordinate/CoordinateGraph.t ............... 
1..7
ok 1 - use Bio::Coordinate::Graph;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Coordinate/CoordinateMapper.t .............. 
1..175
ok 1 - use Bio::Location::Simple;
ok 2 - use Bio::Coordinate::Pair;
ok 3 - use Bio::Coordinate::Result::Match;
ok 4 - use Bio::Coordinate::Result::Gap;
ok 5 - use Bio::Coordinate::Chain;
ok 6 - use Bio::Coordinate::Collection;
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result'
ok 15 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Location::SplitLocationI'
ok 16
ok 17
ok 18
ok 19 - An object of class 'Bio::Coordinate::Result::Match' isa 'Bio::LocationI'
ok 20 - An object of class 'Bio::Coordinate::Result::Match' isa 'Bio::Coordinate::Result::Match'
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - An object of class 'Bio::Coordinate::Result::Gap' isa 'Bio::Coordinate::Result::Gap'
ok 38 - An object of class 'Bio::Coordinate::Result::Gap' isa 'Bio::LocationI'
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106 - An object of class 'Bio::Coordinate::Result::Match' isa 'Bio::Coordinate::Result::Match'
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138 - Match: |314696| Test: 314696|
ok 139
ok 140
ok 141
ok 142 - Match: |341| Test: 341|
ok 143
ok 144
ok 145
ok 146 - Match: |315843| Test: 315843|
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152 - Match: |627011| Test: 627011|
ok 153
ok 154
ok 155
ok 156 - Match: |chr1| Test: chr1|
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Coordinate/GeneCoordinateMapper.t .......... 
1..116
ok 1 - use Bio::Location::Simple;
ok 2 - use Bio::Coordinate::Pair;
ok 3 - use Bio::Coordinate::ExtrapolatingPair;
ok 4 - use Bio::Coordinate::GeneMapper;
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14 - An object of class 'Bio::Coordinate::Result::Match' isa 'Bio::Location::Simple'
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75 - An object of class 'Bio::Coordinate::Result::Match' isa 'Bio::Location::Simple'
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok
t/LiveSeq/Chain.t ............................ 
1..45
ok 1 - use Bio::LiveSeq::Chain;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/LiveSeq/LiveSeq.t .......................... 
1..48
ok 1 - use Bio::LiveSeq::IO::BioPerl;
ok 2
ok 3
ok 4 - Bio::LiveSeq::Gene
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/LiveSeq/Mutation.t ......................... 
1..19
ok 1 - use Bio::LiveSeq::Mutation;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/LocalDB/BioDBGFF.t ......................... 
1..279
ok 1 - use Bio::DB::GFF;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103 # skip fetch_feature_by_gid() not implemented by this adaptor
ok 104 # skip fetch_feature_by_gid() not implemented by this adaptor
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134 # skip delete_groups() not implemented by this adaptor
ok 135 # skip delete_groups() not implemented by this adaptor
ok 136 # skip Not compatible with your Operating System
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok 154
ok 155
ok 156
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok 176
ok 177
ok 178
ok 179
ok 180
ok 181
ok 182
ok 183
ok 184
ok 185
ok 186
ok 187
ok 188
ok 189
ok 190
ok 191
ok 192
ok 193
ok 194
ok 195
ok 196
ok 197
ok 198
ok 199
ok 200
ok 201
ok 202
ok 203
ok 204
ok 205
ok 206
ok 207
ok 208
ok 209
ok 210
ok 211
ok 212
ok 213
ok 214
ok 215
ok 216
ok 217
ok 218
ok 219
ok 220
ok 221
ok 222
ok 223
ok 224
ok 225
ok 226
ok 227
ok 228
ok 229
ok 230
ok 231
ok 232
ok 233
ok 234
ok 235
ok 236
ok 237
ok 238
ok 239
ok 240
ok 241
ok 242 # skip fetch_feature_by_gid() not implemented by this adaptor
ok 243 # skip fetch_feature_by_gid() not implemented by this adaptor
ok 244
ok 245
ok 246
ok 247
ok 248
ok 249
ok 250 # skip preferred groups are not supported by gff3
ok 251 # skip preferred groups are not supported by gff3
ok 252 # skip preferred groups are not supported by gff3
ok 253
ok 254
ok 255
ok 256
ok 257
ok 258
ok 259
ok 260
ok 261
ok 262
ok 263
ok 264
ok 265
ok 266
ok 267
ok 268
ok 269
ok 270
ok 271
ok 272
ok 273 # skip delete_groups() not implemented by this adaptor
ok 274 # skip delete_groups() not implemented by this adaptor
ok 275 # skip Not compatible with your Operating System
ok 276
ok 277
ok 278
ok 279
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/LocalDB/BlastIndex.t ....................... 
1..26
ok 1 - use Cwd;
ok 2 - use Bio::SearchIO;
ok 3 - use Bio::Index::Blast;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/LocalDB/DBFasta.t .......................... 
1..15
ok 1 - use Bio::Root::IO;
ok 2 - use File::Copy;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/LocalDB/DBQual.t ........................... 
1..38
ok 1 - use Bio::Root::IO;
ok 2 - use File::Copy;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual'
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual'
ok 26
ok 27
ok 28 - An object of class 'Bio::Seq::PrimaryQual' isa 'Bio::Seq::PrimaryQual'
ok 29
ok 30
ok 31
ok 32 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual'
ok 33
ok 34 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual'
ok 35
ok 36
ok 37
ok 38
ok
t/LocalDB/Flat.t ............................. skipped: The optional module DB_File (or dependencies thereof) was not installed
t/LocalDB/Index.t ............................ skipped: The optional module DB_File (or dependencies thereof) was not installed
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/LocalDB/Registry.t ......................... 
1..14
ok 1 - use Bio::DB::Registry;
ok 2 - use Bio::DB::Flat;
ok 3
ok 4 # skip The optional module DB_File (or dependencies thereof) was not installed
ok 5 # skip The optional module DB_File (or dependencies thereof) was not installed
ok 6 # skip Network tests have not been requested
ok 7 # skip Network tests have not been requested
ok 8 # skip Network tests have not been requested
ok 9 # skip Network tests have not been requested
ok 10 # skip Network tests have not been requested
ok 11 # skip Network tests have not been requested
ok 12 # skip Network tests have not been requested
ok 13 # skip Network tests have not been requested
ok 14 # skip Network tests have not been requested
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29

#   Failed test 'use Bio::DB::SeqFeature::Store::GFF3Loader;'
#   at t/LocalDB/SeqFeature.t line 17.
#     Tried to use 'Bio::DB::SeqFeature::Store::GFF3Loader'.
#     Error:  Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: . /home/lstein/projects/bioperl-live C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.1-LkNiOT\blib\lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.1-LkNiOT\blib\arch C:/cpanfly-5.18/var/cpan/build/BioPerl-1.6.1-LkNiOT C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.1-LkNiOT C:\cpanfly-5.18\var\megalib C:\Perl-5.18\site\lib C:\Perl-5.18\lib C:/cpanfly-5.18/var/megalib C:/Perl-5.18/site/lib C:/Perl-5.18/lib) at Bio/DB/SeqFeature/Store/LoadHelper.pm line 39.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/LoadHelper.pm line 39.
# Compilation failed in require at Bio/DB/SeqFeature/Store/GFF3Loader.pm line 73.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/GFF3Loader.pm line 73.
# Compilation failed in require at t/LocalDB/SeqFeature.t line 17.
# BEGIN failed--compilation aborted at t/LocalDB/SeqFeature.t line 17.
# Looks like you failed 1 test of 69.
t/LocalDB/SeqFeature.t ....................... 
1..69
ok 1 - use Bio::DB::SeqFeature::Store;
not ok 2 - use Bio::DB::SeqFeature::Store::GFF3Loader;
ok 3 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 4 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 5 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 6 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 7 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 8 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 9 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 10 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 11 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 12 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 13 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 14 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 15 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 16 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 17 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 18 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 19 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 20 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 21 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 22 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 23 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 24 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 25 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 26 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 27 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 28 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 29 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 30 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 31 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 32 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 33 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 34 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 35 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 36 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 37 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 38 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 39 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 40 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 41 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 42 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 43 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 44 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 45 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 46 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 47 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 48 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 49 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 50 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 51 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 52 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 53 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 54 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 55 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 56 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 57 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 58 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 59 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 60 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 61 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 62 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 63 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 64 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 65 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 66 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 67 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 68 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
ok 69 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted.
# Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 126.
# BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 126.
# Compilation failed in require at (eval 88) line 2.
#  at t/LocalDB/SeqFeature.t line 28.
# 
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/69 subtests 
	(less 67 skipped subtests: 1 okay)
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: . C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.1-LkNiOT\blib\lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.1-LkNiOT\blib\arch C:/cpanfly-5.18/var/cpan/build/BioPerl-1.6.1-LkNiOT C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.1-LkNiOT C:\cpanfly-5.18\var\megalib C:\Perl-5.18\site\lib C:\Perl-5.18\lib C:/cpanfly-5.18/var/megalib C:/Perl-5.18/site/lib C:/Perl-5.18/lib) at Bio\DB\Taxonomy\flatfile.pm line 90.
BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 90.
Compilation failed in require at Bio/Root/Root.pm line 439.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441
STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:264
STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:115
STACK: t/LocalDB/transfac_pro.t:18
-----------------------------------------------------------
Bio::DB::Taxonomy: flatfile cannot be found
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: . C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.1-LkNiOT\blib\lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.1-LkNiOT\blib\arch C:/cpanfly-5.18/var/cpan/build/BioPerl-1.6.1-LkNiOT C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.1-LkNiOT C:\cpanfly-5.18\var\megalib C:\Perl-5.18\site\lib C:\Perl-5.18\lib C:/cpanfly-5.18/var/megalib C:/Perl-5.18/site/lib C:/Perl-5.18/lib) at Bio\DB\Taxonomy\flatfile.pm line 90.
BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 90.
Compilation failed in require at Bio/Root/Root.pm line 439.

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

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

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::TFBS::transfac_pro. syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 346, near "$let qw(probA probC probG probT)"
Global symbol "$self" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 357.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 358, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 394, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 412, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 429, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 446, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 464, near "}"
Can't use global @_ in "my" at Bio/Matrix/PSM/SiteMatrix.pm line 479, near "= @_"
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 480.
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 483.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 491, near "}"
Bio/Matrix/PSM/SiteMatrix.pm has too many errors.
Compilation failed in require at Bio\DB\TFBS\transfac_pro.pm line 112.
BEGIN failed--compilation aborted at Bio\DB\TFBS\transfac_pro.pm line 112.
Compilation failed in require at Bio/Root/Root.pm line 439.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441
STACK: Bio::DB::TFBS::_load_tax_module Bio/DB/TFBS.pm:151
STACK: Bio::DB::TFBS::new Bio/DB/TFBS.pm:130
STACK: t/LocalDB/transfac_pro.t:25
-----------------------------------------------------------
Bio::DB::TFBS: transfac_pro cannot be found
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::TFBS::transfac_pro. syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 346, near "$let qw(probA probC probG probT)"
Global symbol "$self" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 357.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 358, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 394, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 412, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 429, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 446, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 464, near "}"
Can't use global @_ in "my" at Bio/Matrix/PSM/SiteMatrix.pm line 479, near "= @_"
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 480.
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 483.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 491, near "}"
Bio/Matrix/PSM/SiteMatrix.pm has too many errors.
Compilation failed in require at Bio\DB\TFBS\transfac_pro.pm line 112.
BEGIN failed--compilation aborted at Bio\DB\TFBS\transfac_pro.pm line 112.
Compilation failed in require at Bio/Root/Root.pm line 439.

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

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

#   Failed test at t/LocalDB/transfac_pro.t line 25.
Can't call method "get_reference_ids" on an undefined value at t/LocalDB/transfac_pro.t line 33.
# Looks like you planned 115 tests but ran 4.
# Looks like you failed 1 test of 4 run.
# Looks like your test exited with 255 just after 4.
t/LocalDB/transfac_pro.t ..................... 
1..115
ok 1 - use Bio::Matrix::PSM::IO;
ok 2 - use Bio::DB::TFBS;
ok 3 - use Bio::DB::Taxonomy;
not ok 4
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 112/115 subtests 
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Map/Cyto.t ................................. 
1..110
ok 1 - use Bio::Map::CytoMap;
ok 2 - use Bio::Map::CytoPosition;
ok 3 - use Bio::Map::CytoMarker;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14 - An object of class 'Bio::Map::CytoPosition' isa 'Bio::Map::CytoPosition'
ok 15
ok 16
ok 17
ok 18 - An object of class 'Bio::Range' isa 'Bio::Range'
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Map/Linkage.t .............................. 
1..18
ok 1 - use Bio::Map::LinkagePosition;
ok 2 - use Bio::Map::Microsatellite;
ok 3 - use Bio::Map::LinkageMap;
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Map/Map.t .................................. 
1..267
ok 1 - use Bio::Map::SimpleMap;
ok 2 - use Bio::Map::Marker;
ok 3 - use Bio::Map::Position;
ok 4 - use Bio::Map::Relative;
ok 5 - use Bio::Map::Mappable;
ok 6
ok 7
ok 8
ok 9
ok 10 - Length is 0
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136
ok 137
ok 138
ok 139
ok 140
ok 141
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151 - use Bio::Map::Gene;
ok 152 - use Bio::Map::GeneMap;
ok 153 - use Bio::Map::TranscriptionFactor;
ok 154 - use Bio::Map::GeneRelative;
ok 155 - use Bio::Map::GenePosition;
ok 156 - use Bio::Map::Prediction;
ok 157
ok 158
ok 159
ok 160
ok 161
ok 162
ok 163
ok 164
ok 165
ok 166
ok 167
ok 168
ok 169
ok 170
ok 171
ok 172
ok 173
ok 174
ok 175
ok 176
ok 177
ok 178
ok 179
ok 180
ok 181
ok 182
ok 183
ok 184
ok 185
ok 186
ok 187
ok 188
ok 189
ok 190
ok 191
ok 192
ok 193
ok 194
ok 195
ok 196
ok 197
ok 198
ok 199
ok 200
ok 201
ok 202
ok 203
ok 204
ok 205
ok 206
ok 207
ok 208
ok 209
ok 210
ok 211
ok 212
ok 213
ok 214
ok 215
ok 216
ok 217
ok 218
ok 219
ok 220
ok 221
ok 222
ok 223
ok 224
ok 225
ok 226
ok 227
ok 228
ok 229
ok 230
ok 231
ok 232
ok 233
ok 234
ok 235
ok 236
ok 237
ok 238
ok 239
ok 240
ok 241
ok 242
ok 243
ok 244
ok 245
ok 246
ok 247
ok 248
ok 249 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 250 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 251 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 252 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 253 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 254 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 255 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 256 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 257 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 258 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 259 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 260 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 261 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 262 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 263 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 264 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 265 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 266 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok 267 # skip The optional module Bio::Tools::Run::Ensembl (or dependencies thereof) was not installed
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Map/MapIO.t ................................ 
1..51
ok 1 - use Bio::MapIO;
ok 2
ok 3 - An object of class 'Bio::Map::SimpleMap' isa 'Bio::Map::MapI'
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Map/MicrosatelliteMarker.t ................. 
1..8
ok 1 - use Bio::Map::SimpleMap;
ok 2 - use Bio::Map::Position;
ok 3 - use Bio::Map::Microsatellite;
ok 4
ok 5
ok 6
ok 7
ok 8
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29

#   Failed test at t/Map/Physical.t line 96.
#          got: '1248'
#     expected: '1249'
# Looks like you failed 1 test of 39.
t/Map/Physical.t ............................. 
1..39
ok 1 - use Bio::Map::Physical;
ok 2 - use Bio::MapIO;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12 - code holds and returns a string, definition requires a boolean
ok 13 - code holds and returns a string, definition requires a boolean
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
not ok 39
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/39 subtests 
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
Bio::Matrix::PSM::IO: masta cannot be found
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::Matrix::PSM::IO::masta. syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 346, near "$let qw(probA probC probG probT)"
Global symbol "$self" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 357.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 358, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 394, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 412, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 429, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 446, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 464, near "}"
Can't use global @_ in "my" at Bio/Matrix/PSM/SiteMatrix.pm line 479, near "= @_"
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 480.
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 483.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 491, near "}"
Bio/Matrix/PSM/SiteMatrix.pm has too many errors.
Compilation failed in require at Bio\Matrix\PSM\IO\masta.pm line 79.
BEGIN failed--compilation aborted at Bio\Matrix\PSM\IO\masta.pm line 79.
Compilation failed in require at Bio/Root/Root.pm line 439.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441
STACK: Bio::Matrix::PSM::IO::_load_format_module Bio/Matrix/PSM/IO.pm:195
STACK: Bio::Matrix::PSM::IO::new Bio/Matrix/PSM/IO.pm:155
STACK: t/Matrix/IO/masta.t:16
-----------------------------------------------------------

For more information about the Matrix::PSM::IO system please see the
Matrix::PSM::IO docs.  This includes ways of checking for formats at
compile time, not run time
Bio::Matrix::PSM::IO: masta cannot be found
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::Matrix::PSM::IO::masta. Attempt to reload Bio\Matrix\PSM\IO\masta.pm aborted.
Compilation failed in require at Bio/Root/Root.pm line 439.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441
STACK: Bio::Matrix::PSM::IO::_load_format_module Bio/Matrix/PSM/IO.pm:195
STACK: Bio::Matrix::PSM::IO::new Bio/Matrix/PSM/IO.pm:155
STACK: t/Matrix/IO/masta.t:19
-----------------------------------------------------------

For more information about the Matrix::PSM::IO system please see the
Matrix::PSM::IO docs.  This includes ways of checking for formats at
compile time, not run time
Can't call method "_flush_on_write" on an undefined value at t/Matrix/IO/masta.t line 21.
# Looks like you planned 16 tests but ran 1.
# Looks like your test exited with 25 just after 1.
t/Matrix/IO/masta.t .......................... 
1..16
ok 1 - use Bio::Matrix::PSM::IO;
Dubious, test returned 25 (wstat 6400, 0x1900)
Failed 15/16 subtests 
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
Bio::Matrix::PSM::IO: meme cannot be found
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::Matrix::PSM::IO::meme. syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 346, near "$let qw(probA probC probG probT)"
Global symbol "$self" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 357.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 358, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 394, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 412, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 429, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 446, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 464, near "}"
Can't use global @_ in "my" at Bio/Matrix/PSM/SiteMatrix.pm line 479, near "= @_"
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 480.
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 483.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 491, near "}"
Bio/Matrix/PSM/SiteMatrix.pm has too many errors.
Compilation failed in require at Bio\Matrix\PSM\IO\meme.pm line 59.
BEGIN failed--compilation aborted at Bio\Matrix\PSM\IO\meme.pm line 59.
Compilation failed in require at Bio/Root/Root.pm line 439.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441
STACK: Bio::Matrix::PSM::IO::_load_format_module Bio/Matrix/PSM/IO.pm:195
STACK: Bio::Matrix::PSM::IO::new Bio/Matrix/PSM/IO.pm:155
STACK: t/Matrix/IO/psm.t:35
-----------------------------------------------------------

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

#   Failed test at t/Matrix/IO/psm.t line 37.
Can't call method "unstructured" on an undefined value at t/Matrix/IO/psm.t line 39.
# Looks like you planned 63 tests but ran 2.
# Looks like you failed 1 test of 2 run.
# Looks like your test exited with 255 just after 2.
t/Matrix/IO/psm.t ............................ 
1..63
ok 1 - use Bio::Matrix::PSM::IO;
not ok 2
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 62/63 subtests 
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Matrix/InstanceSite.t ...................... 
1..6
ok 1 - use Bio::Matrix::PSM::InstanceSite;
ok 2
ok 3
ok 4
ok 5
ok 6
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Matrix/Matrix.t ............................ 
1..77
ok 1 - use Bio::Matrix::Generic;
ok 2 - use Bio::Matrix::IO;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30 - An object of class 'Bio::Matrix::Scoring' isa 'Bio::Matrix::Scoring'
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42 - An object of class 'Bio::Matrix::Scoring' isa 'Bio::Matrix::Scoring'
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Matrix/ProtMatrix.t ........................ 
1..14
ok 1 - use Bio::Matrix::PSM::ProtMatrix;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
Bio::Matrix::PSM::IO: psiblast cannot be found
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::Matrix::PSM::IO::psiblast. syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 346, near "$let qw(probA probC probG probT)"
Global symbol "$self" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 357.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 358, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 394, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 412, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 429, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 446, near "}"
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 464, near "}"
Can't use global @_ in "my" at Bio/Matrix/PSM/SiteMatrix.pm line 479, near "= @_"
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 480.
Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 483.
syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 491, near "}"
Bio/Matrix/PSM/SiteMatrix.pm has too many errors.
Compilation failed in require at (eval 66) line 2.
	...propagated at C:\cpanfly-5.18\var\megalib/base.pm line 84.
BEGIN failed--compilation aborted at Bio/Matrix/PSM/Psm.pm line 131.
Compilation failed in require at Bio\Matrix\PSM\IO\psiblast.pm line 58.
BEGIN failed--compilation aborted at Bio\Matrix\PSM\IO\psiblast.pm line 58.
Compilation failed in require at Bio/Root/Root.pm line 439.

STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:441
STACK: Bio::Matrix::PSM::IO::_load_format_module Bio/Matrix/PSM/IO.pm:195
STACK: Bio::Matrix::PSM::IO::new Bio/Matrix/PSM/IO.pm:155
STACK: t/Matrix/ProtPsm.t:17
-----------------------------------------------------------

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

#   Failed test at t/Matrix/ProtPsm.t line 19.
Can't call method "next_psm" on an undefined value at t/Matrix/ProtPsm.t line 21.
# Looks like you planned 14 tests but ran 2.
# Looks like you failed 1 test of 2 run.
# Looks like your test exited with 255 just after 2.
t/Matrix/ProtPsm.t ........................... 
1..14
ok 1 - use Bio::Matrix::PSM::IO;
not ok 2
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 13/14 subtests 
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29

#   Failed test 'use Bio::Matrix::PSM::SiteMatrix;'
#   at t/Matrix/SiteMatrix.t line 13.
#     Tried to use 'Bio::Matrix::PSM::SiteMatrix'.
#     Error:  syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 346, near "$let qw(probA probC probG probT)"
# Global symbol "$self" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 357.
# syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 358, near "}"
# syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 394, near "}"
# syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 412, near "}"
# syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 429, near "}"
# syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 446, near "}"
# syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 464, near "}"
# Can't use global @_ in "my" at Bio/Matrix/PSM/SiteMatrix.pm line 479, near "= @_"
# Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 480.
# Global symbol "$thresh" requires explicit package name at Bio/Matrix/PSM/SiteMatrix.pm line 483.
# syntax error at Bio/Matrix/PSM/SiteMatrix.pm line 491, near "}"
# Bio/Matrix/PSM/SiteMatrix.pm has too many errors.
# Compilation failed in require at t/Matrix/SiteMatrix.t line 13.
# BEGIN failed--compilation aborted at t/Matrix/SiteMatrix.t line 13.
Undefined subroutine &Bio::Matrix::PSM::SiteMatrix::_to_IUPAC called at Bio/Matrix/PSM/SiteMatrix.pm line 321.
# Looks like you planned 14 tests but ran 1.
# Looks like you failed 1 test of 1 run.
# Looks like your test exited with 255 just after 1.
t/Matrix/SiteMatrix.t ........................ 
1..14
not ok 1 - use Bio::Matrix::PSM::SiteMatrix;
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 14/14 subtests 
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Ontology/GOterm.t .......................... 
1..62
ok 1 - use Bio::Ontology::GOterm;
ok 2 - use Bio::Ontology::Ontology;
ok 3 - use Bio::Annotation::DBLink;
ok 4 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::GOterm'
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Ontology/GraphAdaptor.t .................... 
1..28
ok 1 - use Bio::Ontology::SimpleGOEngine::GraphAdaptor;
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Ontology/IO/go.t ........................... 
1..102
ok 1 - use Bio::OntologyIO;
ok 2
ok 3 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::OntologyI'
ok 4
ok 5 - An object of class 'Bio::Ontology::OBOEngine' isa 'Bio::Ontology::OntologyEngineI'
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Ontology/IO/interpro.t ..................... 
1..47
ok 1 - use Bio::OntologyIO;
ok 2
ok 3
ok 4
ok 5
ok 6 - term Helix-turn-helix, AraC type  in ontology InterPro
ok 7
ok 8 - term Binding Site in ontology InterPro
ok 9
ok 10 - term Cdc20/Fizzy in ontology InterPro
ok 11
ok 12 - term post-translational modification in ontology InterPro
ok 13
ok 14 - term Repeat in ontology InterPro
ok 15
ok 16 - term Active Site in ontology InterPro
ok 17
ok 18 - term Kringle in ontology InterPro
ok 19
ok 20 - term Integrins alpha chain in ontology InterPro
ok 21
ok 22 - term Active Site in ontology InterPro
ok 23
ok 24 - term Binding Site in ontology InterPro
ok 25
ok 26 - term Domain in ontology InterPro
ok 27
ok 28 - term Family in ontology InterPro
ok 29
ok 30 - term Repeat in ontology InterPro
ok 31
ok 32 - term post-translational modification in ontology InterPro
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29

#   Failed test at t/Ontology/IO/obo.t line 47.
#          got: '9'
#     expected: '5'

#   Failed test at t/Ontology/IO/obo.t line 49.

#   Failed test at t/Ontology/IO/obo.t line 51.

#   Failed test at t/Ontology/IO/obo.t line 53.

#   Failed test at t/Ontology/IO/obo.t line 55.

#   Failed test at t/Ontology/IO/obo.t line 57.

#   Failed test at t/Ontology/IO/obo.t line 61.
#          got: '9'
#     expected: '2'

#   Failed test 'Got positively regulates predicate'
#   at t/Ontology/IO/obo.t line 182.
#          got: 'REGULATES'
#     expected: 'POSITIVELY_REGULATES'
# Looks like you failed 8 tests of 83.
t/Ontology/IO/obo.t .......................... 
1..83
ok 1 - use Bio::OntologyIO;
ok 2 - use Bio::Ontology::RelationshipType;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
not ok 14
not ok 15
not ok 16
not ok 17
not ok 18
not ok 19
not 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
not 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
Dubious, test returned 8 (wstat 2048, 0x800)
Failed 8/83 subtests 
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Ontology/Ontology.t ........................ 
1..52
ok 1 - use Bio::OntologyIO;
ok 2 - use Bio::Ontology::RelationshipType;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Ontology/OntologyEngine.t .................. 
1..27
ok 1 - use Bio::Ontology::Term;
ok 2 - use Bio::Ontology::Relationship;
ok 3 - use Bio::Ontology::RelationshipType;
ok 4 - use Bio::Ontology::SimpleOntologyEngine;
ok 5 - use Bio::Ontology::Ontology;
ok 6 - An object of class 'Bio::Ontology::SimpleOntologyEngine' isa 'Bio::Ontology::OntologyEngineI'
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok
t/Ontology/OntologyStore.t ................... skipped: Network tests have not been requested
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Ontology/Relationship.t .................... 
1..12
ok 1 - use Bio::Ontology::Relationship;
ok 2 - use Bio::Ontology::GOterm;
ok 3 - use Bio::Ontology::RelationshipType;
ok 4 - An object of class 'Bio::Ontology::RelationshipType' isa 'Bio::Ontology::RelationshipType'
ok 5 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::GOterm'
ok 6 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::GOterm'
ok 7 - An object of class 'Bio::Ontology::Relationship' isa 'Bio::Ontology::Relationship'
ok 8
ok 9
ok 10
ok 11
ok 12
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Ontology/RelationshipType.t ................ 
1..23
ok 1 - use Bio::Ontology::RelationshipType;
ok 2 - use Bio::Ontology::Ontology;
ok 3 - An object of class 'Bio::Ontology::RelationshipType' isa 'Bio::Ontology::RelationshipType'
ok 4 - An object of class 'Bio::Ontology::RelationshipType' isa 'Bio::Ontology::TermI'
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Ontology/Term.t ............................ 
1..54
ok 1 - use Bio::Ontology::Term;
ok 2 - use Bio::Ontology::TermFactory;
ok 3 - use Bio::Annotation::DBLink;
ok 4 - An object of class 'Bio::Ontology::Term' isa 'Bio::Ontology::TermI'
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44 - An object of class 'Bio::Ontology::Term' isa 'Bio::Ontology::TermI'
ok 45
ok 46 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::TermI'
ok 47 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::GOterm'
ok 48
ok 49
ok 50 - An object of class 'Bio::Annotation::OntologyTerm' isa 'Bio::Ontology::TermI'
ok 51 - An object of class 'Bio::Annotation::OntologyTerm' isa 'Bio::AnnotationI'
ok 52
ok 53
ok 54
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Perl.t ..................................... 
1..29
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
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Phenotype/Correlate.t ...................... 
1..17
ok 1 - use Bio::Phenotype::Correlate;
ok 2 - use Bio::Species;
ok 3 - An object of class 'Bio::Phenotype::Correlate' isa 'Bio::Phenotype::Correlate'
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Phenotype/MeSH.t ........................... 
1..24
ok 1 - use Bio::Phenotype::MeSH::Term;
ok 2 - use Bio::Phenotype::MeSH::Twig;
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Phenotype/Measure.t ........................ 
1..21
ok 1 - use Bio::Phenotype::Measure;
ok 2 - An object of class 'Bio::Phenotype::Measure' isa 'Bio::Phenotype::Measure'
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Phenotype/MiniMIMentry.t ................... 
1..15
ok 1 - use Bio::Phenotype::OMIM::MiniMIMentry;
ok 2 - An object of class 'Bio::Phenotype::OMIM::MiniMIMentry' isa 'Bio::Phenotype::OMIM::MiniMIMentry'
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Phenotype/OMIMentry.t ...................... 
1..153
ok 1 - use Bio::Phenotype::OMIM::OMIMentry;
ok 2 - use Bio::Phenotype::OMIM::MiniMIMentry;
ok 3 - use Bio::Species;
ok 4 - use Bio::Annotation::Reference;
ok 5 - use Bio::Map::CytoPosition;
ok 6 - use Bio::Phenotype::Correlate;
ok 7 - use Bio::Phenotype::Measure;
ok 8 - use Bio::Annotation::DBLink;
ok 9 - An object of class 'Bio::Phenotype::OMIM::OMIMentry' isa 'Bio::Phenotype::OMIM::OMIMentry'
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79 - operator overloading in AnnotationI is deprecated
ok 80 - operator overloading in AnnotationI is deprecated
ok 81
ok 82
ok 83 - operator overloading in AnnotationI is deprecated
ok 84 - operator overloading in AnnotationI is deprecated
ok 85
ok 86
ok 87
ok 88
ok 89
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
ok 131
ok 132
ok 133
ok 134
ok 135
ok 136 - operator overloading in AnnotationI is deprecated
ok 137 - operator overloading in AnnotationI is deprecated
ok 138
ok 139
ok 140 - operator overloading in AnnotationI is deprecated
ok 141 - operator overloading in AnnotationI is deprecated
ok 142
ok 143
ok 144
ok 145
ok 146
ok 147
ok 148
ok 149
ok 150
ok 151
ok 152
ok 153
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
t/Phenotype/OMIMentryAllelicVariant.t ........ 
1..27
ok 1 - use Bio::Phenotype::OMIM::OMIMentryAllelicVariant;
ok 2 - An object of class 'Bio::Phenotype::OMIM::OMIMentryAllelicVariant' isa 'Bio::Phenotype::OMIM::OMIMentryAllelicVariant'
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
t/Phenotype/OMIMparser.t ..................... 
1..175
ok 1 - use Bio::Phenotype::OMIM::OMIMparser;
ok 2 - An object of class 'Bio::Phenotype::OMIM::OMIMparser' isa 'Bio::Phenotype::OMIM::OMIMparser'
ok 3 - An object of class 'Bio::Phenotype::OMIM::OMIMentry' isa 'Bio::Phenotype::OMIM::OMIMentry'
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19 - An object of class 'Bio::Phenotype::OMIM::MiniMIMentry' isa 'Bio::Phenotype::OMIM::MiniMIMentry'
ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
ok 45
ok 46
ok 47
ok 48
ok 49
ok 50
ok 51
ok 52
ok 53
ok 54
ok 55
ok 56
ok 57
ok 58
ok 59
ok 60
ok 61
ok 62
ok 63
ok 64
ok 65
ok 66
ok 67
ok 68
ok 69
ok 70
ok 71
ok 72
ok 73
ok 74
ok 75
ok 76
ok 77
ok 78
ok 79
ok 80
ok 81
ok 82
ok 83
ok 84
ok 85
ok 86
ok 87
ok 88
ok 89 - An object of class 'Bio::Phenotype::OMIM::OMIMentry' isa 'Bio::Phenotype::OMIM::OMIMentry'
ok 90
ok 91
ok 92
ok 93
ok 94
ok 95
ok 96
ok 97
ok 98
ok 99
ok 100
ok 101
ok 102
ok 103
ok 104
ok 105 - An object of class 'Bio::Phenotype::OMIM::MiniMIMentry' isa 'Bio::Phenotype::OMIM::MiniMIMentry'
ok 106
ok 107
ok 108
ok 109
ok 110
ok 111
ok 112
ok 113
ok 114
ok 115
ok 116
ok 117
ok 118
ok 119
ok 120
ok 121
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128
ok 129
ok 130
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ok 175 - missing linebreak caught
ok
# Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29
UNIVERSAL->import is deprecated and will be removed in a future perl at Bio/Tree/TreeFunctionsI.pm line 94.
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
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ok 42 - operator overloading in AnnotationI is deprecated
ok 43 - operator overloading in AnnotationI is deprecated
ok 44
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ok 99 - operator overloading in AnnotationI is deprecated
ok 100 - operator overloading in AnnotationI is deprecated
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ok 104 - operator overloading in AnnotationI is deprecated
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ok

#   Failed test 'POD test for Bio/Tools/Geneid.pm'
#   at C:\cpanfly-5.18\var\megalib/Test/Pod.pm line 186.
# Bio/Tools/Geneid.pm (38): Non-ASCII character seen before =encoding in 'Guigó'. Assuming ISO8859-1

#   Failed test 'POD test for Bio/Tools/GuessSeqFormat.pm'
#   at C:\cpanfly-5.18\var\megalib/Test/Pod.pm line 186.
# Bio/Tools/GuessSeqFormat.pm (226): Non-ASCII character seen before =encoding in 'Kähäri,'. Assuming ISO8859-1

#   Failed test 'POD test for Bio/Tools/Run/WrapperBase.pm'
#   at C:\cpanfly-5.18\var\megalib/Test/Pod.pm line 186.
# Bio/Tools/Run/WrapperBase.pm (182): Non-ASCII character seen before =encoding in 'NB:ÊThis'. Assuming ISO8859-1

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