FAIL bioperl-1.4 OpenBSD.i386-openbsd-thread-multi-64int 4.2

Front page | perl.cpan.testers | Postings from July 2008
FAIL bioperl-1.4 OpenBSD.i386-openbsd-thread-multi-64int 4.2

Thread Next
From:
chris
Date:
July 28, 2008 02:36
Subject:
FAIL bioperl-1.4 OpenBSD.i386-openbsd-thread-multi-64int 4.2
This distribution has been tested as part of the cpan-testers
effort to test as many new uploads to CPAN as possible.  See
http://testers.cpan.org/


--

Dear Ewan Birney,
    
This is a computer-generated error report created automatically by
CPANPLUS, version 0.84. Testers personal comments may appear 
at the end of this report.


Thank you for uploading your work to CPAN.  However, it appears that
there were some problems testing your distribution.

TEST RESULTS:

Below is the error stack from stage 'make test':

[MSG] [Mon Jul 28 10:18:21 2008] Trying to get 'ftp://ftp.funet.fi/pub/CPAN/authors/id/P/PE/PETDANCE/CHECKSUMS'
[MSG] [Mon Jul 28 10:18:23 2008] Checksum matches for 'HTML-Tagset-3.20.tar.gz'
[MSG] [Mon Jul 28 10:18:25 2008] Extracted 'HTML-Tagset-3.20/'
[MSG] [Mon Jul 28 10:18:25 2008] Extracted 'HTML-Tagset-3.20/Tagset.pm'
[MSG] [Mon Jul 28 10:18:25 2008] Extracted 'HTML-Tagset-3.20/Makefile.PL'
[MSG] [Mon Jul 28 10:18:25 2008] Extracted 'HTML-Tagset-3.20/META.yml'
[MSG] [Mon Jul 28 10:18:25 2008] Extracted 'HTML-Tagset-3.20/MANIFEST.SKIP'
[MSG] [Mon Jul 28 10:18:25 2008] Extracted 'HTML-Tagset-3.20/MANIFEST'
[MSG] [Mon Jul 28 10:18:25 2008] Extracted 'HTML-Tagset-3.20/README'
[MSG] [Mon Jul 28 10:18:25 2008] Extracted 'HTML-Tagset-3.20/t/'
[MSG] [Mon Jul 28 10:18:26 2008] Extracted 'HTML-Tagset-3.20/t/01_old_junk.t'
[MSG] [Mon Jul 28 10:18:26 2008] Extracted 'HTML-Tagset-3.20/t/pod.t'
[MSG] [Mon Jul 28 10:18:26 2008] Extracted 'HTML-Tagset-3.20/t/00_about_verbose.t'
[MSG] [Mon Jul 28 10:18:26 2008] Extracted 'HTML-Tagset-3.20/Changes'
[MSG] [Mon Jul 28 10:18:26 2008] Extracted 'HTML::Tagset' to '/home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20'
[MSG] [Mon Jul 28 10:18:29 2008] Writing Makefile for HTML::Tagset

[MSG] [Mon Jul 28 10:18:29 2008] DEFAULT 'filter_prereqs' HANDLER RETURNING 'sub return value'
[MSG] [Mon Jul 28 10:18:29 2008] Checking for previous PASS result for "HTML-Tagset-3.20"
[MSG] [Mon Jul 28 10:18:29 2008] Found previous PASS result for "HTML-Tagset-3.20" skipping tests.
[MSG] [Mon Jul 28 10:18:32 2008] Manifying blib/man3/HTML::Tagset.3

[MSG] [Mon Jul 28 10:18:33 2008] Sending test report for 'HTML-Tagset-3.20'
[MSG] [Mon Jul 28 10:18:34 2008] Ok, not sending test report
[MSG] [Mon Jul 28 10:18:53 2008] cc -c    -pthread -fno-strict-aliasing -fno-delete-null-pointer-checks -pipe -I/usr/local/include -O2     -DVERSION=\"3.56\"  -DXS_VERSION=\"3.56\" -DPIC -fPIC "-I/home/cpan/perl588/lib/5.8.8/OpenBSD.i386-openbsd-thread-multi-64int/CORE"  -DMARKED_SECTION Parser.c
Running Mkbootstrap for HTML::Parser ()
chmod 644 Parser.bs
rm -f blib/arch/auto/HTML/Parser/Parser.so
cc  -shared -fPIC  -L/usr/local/lib Parser.o  -o blib/arch/auto/HTML/Parser/Parser.so 	    	 
chmod 755 blib/arch/auto/HTML/Parser/Parser.so
cp Parser.bs blib/arch/auto/HTML/Parser/Parser.bs
chmod 644 blib/arch/auto/HTML/Parser/Parser.bs
Manifying blib/man3/HTML::PullParser.3
Manifying blib/man3/HTML::Entities.3
Manifying blib/man3/HTML::Parser.3
Manifying blib/man3/HTML::LinkExtor.3
Manifying blib/man3/HTML::TokeParser.3
Manifying blib/man3/HTML::HeadParser.3
Manifying blib/man3/HTML::Filter.3

[MSG] [Mon Jul 28 10:18:53 2008] Sending test report for 'HTML-Parser-3.56'
[MSG] [Mon Jul 28 10:18:54 2008] Ok, not sending test report
[MSG] [Mon Jul 28 10:18:54 2008] Trying to get 'ftp://ftp.funet.fi/pub/CPAN/authors/id/D/DS/DSKOLL/CHECKSUMS'
[MSG] [Mon Jul 28 10:18:56 2008] Checksum matches for 'IO-stringy-2.110.tar.gz'
[MSG] [Mon Jul 28 10:18:58 2008] Extracted 'IO-stringy-2.110/'
[MSG] [Mon Jul 28 10:18:58 2008] Extracted 'IO-stringy-2.110/examples/'
[MSG] [Mon Jul 28 10:18:58 2008] Extracted 'IO-stringy-2.110/examples/IO_Scalar_synopsis'
[MSG] [Mon Jul 28 10:18:58 2008] Extracted 'IO-stringy-2.110/lib/'
[MSG] [Mon Jul 28 10:18:59 2008] Extracted 'IO-stringy-2.110/lib/IO/'
[MSG] [Mon Jul 28 10:18:59 2008] Extracted 'IO-stringy-2.110/lib/IO/Stringy.pm'
[MSG] [Mon Jul 28 10:18:59 2008] Extracted 'IO-stringy-2.110/lib/IO/AtomicFile.pm'
[MSG] [Mon Jul 28 10:18:59 2008] Extracted 'IO-stringy-2.110/lib/IO/Scalar.pm'
[MSG] [Mon Jul 28 10:18:59 2008] Extracted 'IO-stringy-2.110/lib/IO/WrapTie.pm'
[MSG] [Mon Jul 28 10:18:59 2008] Extracted 'IO-stringy-2.110/lib/IO/Lines.pm'
[MSG] [Mon Jul 28 10:18:59 2008] Extracted 'IO-stringy-2.110/lib/IO/ScalarArray.pm'
[MSG] [Mon Jul 28 10:18:59 2008] Extracted 'IO-stringy-2.110/lib/IO/Wrap.pm'
[MSG] [Mon Jul 28 10:18:59 2008] Extracted 'IO-stringy-2.110/lib/IO/InnerFile.pm'
[MSG] [Mon Jul 28 10:18:59 2008] Extracted 'IO-stringy-2.110/t/'
[MSG] [Mon Jul 28 10:18:59 2008] Extracted 'IO-stringy-2.110/t/two.t'
[MSG] [Mon Jul 28 10:18:59 2008] Extracted 'IO-stringy-2.110/t/IO_ScalarArray.t'
[MSG] [Mon Jul 28 10:19:00 2008] Extracted 'IO-stringy-2.110/t/simple.t'
[MSG] [Mon Jul 28 10:19:00 2008] Extracted 'IO-stringy-2.110/t/ExtUtils/'
[MSG] [Mon Jul 28 10:19:00 2008] Extracted 'IO-stringy-2.110/t/ExtUtils/TBone.pm'
[MSG] [Mon Jul 28 10:19:00 2008] Extracted 'IO-stringy-2.110/t/Common.pm'
[MSG] [Mon Jul 28 10:19:00 2008] Extracted 'IO-stringy-2.110/t/IO_Scalar.t'
[MSG] [Mon Jul 28 10:19:00 2008] Extracted 'IO-stringy-2.110/t/IO_Lines.t'
[MSG] [Mon Jul 28 10:19:00 2008] Extracted 'IO-stringy-2.110/t/IO_WrapTie.t'
[MSG] [Mon Jul 28 10:19:00 2008] Extracted 'IO-stringy-2.110/COPYING'
[MSG] [Mon Jul 28 10:19:00 2008] Extracted 'IO-stringy-2.110/contrib/'
[MSG] [Mon Jul 28 10:19:00 2008] Extracted 'IO-stringy-2.110/contrib/Clever.pm'
[MSG] [Mon Jul 28 10:19:00 2008] Extracted 'IO-stringy-2.110/MANIFEST'
[MSG] [Mon Jul 28 10:19:00 2008] Extracted 'IO-stringy-2.110/META.yml'
[MSG] [Mon Jul 28 10:19:00 2008] Extracted 'IO-stringy-2.110/README'
[MSG] [Mon Jul 28 10:19:01 2008] Extracted 'IO-stringy-2.110/Makefile.PL'
[MSG] [Mon Jul 28 10:19:01 2008] Extracted 'IO::Scalar' to '/home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110'
[MSG] [Mon Jul 28 10:19:04 2008] Writing Makefile for IO::Stringy

[MSG] [Mon Jul 28 10:19:04 2008] DEFAULT 'filter_prereqs' HANDLER RETURNING 'sub return value'
[MSG] [Mon Jul 28 10:19:04 2008] Checking for previous PASS result for "IO-stringy-2.110"
[MSG] [Mon Jul 28 10:19:04 2008] Found previous PASS result for "IO-stringy-2.110" skipping tests.
[MSG] [Mon Jul 28 10:19:09 2008] Manifying blib/man3/IO::Lines.3
Manifying blib/man3/IO::ScalarArray.3
Manifying blib/man3/IO::Stringy.3
Manifying blib/man3/IO::Wrap.3
Manifying blib/man3/IO::AtomicFile.3
Manifying blib/man3/IO::Scalar.3
Manifying blib/man3/IO::InnerFile.3
Manifying blib/man3/IO::WrapTie.3

[MSG] [Mon Jul 28 10:19:09 2008] Sending test report for 'IO-stringy-2.110'
[MSG] [Mon Jul 28 10:19:10 2008] Ok, not sending test report
[MSG] [Mon Jul 28 10:19:10 2008] Trying to get 'ftp://ftp.funet.fi/pub/CPAN/authors/id/G/GA/GAAS/CHECKSUMS'
[MSG] [Mon Jul 28 10:19:12 2008] Checksum matches for 'IO-String-1.08.tar.gz'
[MSG] [Mon Jul 28 10:19:13 2008] Extracted 'IO-String-1.08/'
[MSG] [Mon Jul 28 10:19:13 2008] Extracted 'IO-String-1.08/META.yml'
[MSG] [Mon Jul 28 10:19:14 2008] Extracted 'IO-String-1.08/t/'
[MSG] [Mon Jul 28 10:19:14 2008] Extracted 'IO-String-1.08/t/truncate.t'
[MSG] [Mon Jul 28 10:19:14 2008] Extracted 'IO-String-1.08/t/read.t'
[MSG] [Mon Jul 28 10:19:14 2008] Extracted 'IO-String-1.08/t/close.t'
[MSG] [Mon Jul 28 10:19:14 2008] Extracted 'IO-String-1.08/t/write.t'
[MSG] [Mon Jul 28 10:19:14 2008] Extracted 'IO-String-1.08/t/para.t'
[MSG] [Mon Jul 28 10:19:14 2008] Extracted 'IO-String-1.08/t/seek.t'
[MSG] [Mon Jul 28 10:19:14 2008] Extracted 'IO-String-1.08/String.pm'
[MSG] [Mon Jul 28 10:19:14 2008] Extracted 'IO-String-1.08/Changes'
[MSG] [Mon Jul 28 10:19:14 2008] Extracted 'IO-String-1.08/MANIFEST'
[MSG] [Mon Jul 28 10:19:14 2008] Extracted 'IO-String-1.08/Makefile.PL'
[MSG] [Mon Jul 28 10:19:14 2008] Extracted 'IO-String-1.08/README'
[MSG] [Mon Jul 28 10:19:15 2008] Extracted 'IO::String' to '/home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08'
[MSG] [Mon Jul 28 10:19:18 2008] Writing Makefile for IO::String

[MSG] [Mon Jul 28 10:19:18 2008] DEFAULT 'filter_prereqs' HANDLER RETURNING 'sub return value'
[MSG] [Mon Jul 28 10:19:18 2008] Checking for previous PASS result for "IO-String-1.08"
[MSG] [Mon Jul 28 10:19:18 2008] Found previous PASS result for "IO-String-1.08" skipping tests.
[MSG] [Mon Jul 28 10:19:20 2008] Manifying blib/man3/IO::String.3

[MSG] [Mon Jul 28 10:19:21 2008] Sending test report for 'IO-String-1.08'
[MSG] [Mon Jul 28 10:19:22 2008] Ok, not sending test report
[MSG] [Mon Jul 28 10:21:29 2008] cp Bio/PopGen/MarkerI.pm blib/lib/Bio/PopGen/MarkerI.pm
cp Bio/Matrix/PSM/Psm.pm blib/lib/Bio/Matrix/PSM/Psm.pm
cp Bio/Tools/Blast/CHANGES blib/lib/Bio/Tools/Blast/CHANGES
cp Bio/WebAgent.pm blib/lib/Bio/WebAgent.pm
cp Bio/LiveSeq/ChainI.pm blib/lib/Bio/LiveSeq/ChainI.pm
cp Bio/LiveSeq/Mutation.pm blib/lib/Bio/LiveSeq/Mutation.pm
cp Bio/AlignIO/mega.pm blib/lib/Bio/AlignIO/mega.pm
cp Bio/Tools/HMMER/Set.pm blib/lib/Bio/Tools/HMMER/Set.pm
cp Bio/Factory/ObjectFactory.pm blib/lib/Bio/Factory/ObjectFactory.pm
cp Bio/SearchIO/megablast.pm blib/lib/Bio/SearchIO/megablast.pm
cp Bio/Factory/SeqAnalysisParserFactoryI.pm blib/lib/Bio/Factory/SeqAnalysisParserFactoryI.pm
cp Bio/DB/GFF/Aggregator/ucsc_unigene.pm blib/lib/Bio/DB/GFF/Aggregator/ucsc_unigene.pm
cp Bio/TreeIO.pm blib/lib/Bio/TreeIO.pm
cp Bio/Search/HSP/PSLHSP.pm blib/lib/Bio/Search/HSP/PSLHSP.pm
cp Bio/DB/GFF/Aggregator/ucsc_acembly.pm blib/lib/Bio/DB/GFF/Aggregator/ucsc_acembly.pm
cp Bio/Cluster/UniGeneI.pm blib/lib/Bio/Cluster/UniGeneI.pm
cp Bio/Tools/GuessSeqFormat.pm blib/lib/Bio/Tools/GuessSeqFormat.pm
cp Bio/Biblio/PubmedBookArticle.pm blib/lib/Bio/Biblio/PubmedBookArticle.pm
cp Bio/Search/HSP/WABAHSP.pm blib/lib/Bio/Search/HSP/WABAHSP.pm
cp Bio/Align/Utilities.pm blib/lib/Bio/Align/Utilities.pm
cp Bio/Tools/Run/README blib/lib/Bio/Tools/Run/README
cp Bio/DB/Flat.pm blib/lib/Bio/DB/Flat.pm
cp Bio/SearchIO/fasta.pm blib/lib/Bio/SearchIO/fasta.pm
cp Bio/DB/SwissProt.pm blib/lib/Bio/DB/SwissProt.pm
cp Bio/TreeIO/nexus.pm blib/lib/Bio/TreeIO/nexus.pm
cp Bio/Biblio/Provider.pm blib/lib/Bio/Biblio/Provider.pm
cp Bio/Coordinate/Graph.pm blib/lib/Bio/Coordinate/Graph.pm
cp Bio/DB/GFF/Aggregator/ucsc_sanger22.pm blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm
cp Bio/Root/RootI.pm blib/lib/Bio/Root/RootI.pm
cp Bio/LocationI.pm blib/lib/Bio/LocationI.pm
cp Bio/Taxonomy.pm blib/lib/Bio/Taxonomy.pm
cp Bio/TreeIO/TreeEventBuilder.pm blib/lib/Bio/TreeIO/TreeEventBuilder.pm
cp Bio/Matrix/PSM/PsmI.pm blib/lib/Bio/Matrix/PSM/PsmI.pm
cp Bio/DBLinkContainerI.pm blib/lib/Bio/DBLinkContainerI.pm
cp Bio/Location/Fuzzy.pm blib/lib/Bio/Location/Fuzzy.pm
cp Bio/SeqIO.pm blib/lib/Bio/SeqIO.pm
cp Bio/AnalysisI.pm blib/lib/Bio/AnalysisI.pm
cp Bio/LiveSeq/AARange.pm blib/lib/Bio/LiveSeq/AARange.pm
cp Bio/DB/Biblio/biofetch.pm blib/lib/Bio/DB/Biblio/biofetch.pm
cp Bio/Index/Swissprot.pm blib/lib/Bio/Index/Swissprot.pm
cp Bio/Annotation/OntologyTerm.pm blib/lib/Bio/Annotation/OntologyTerm.pm
cp Bio/Map/SimpleMap.pm blib/lib/Bio/Map/SimpleMap.pm
cp Bio/Coordinate/Result/Gap.pm blib/lib/Bio/Coordinate/Result/Gap.pm
cp Bio/Seq/Meta/Array.pm blib/lib/Bio/Seq/Meta/Array.pm
cp Bio/Tools/Run/RemoteBlast.pm blib/lib/Bio/Tools/Run/RemoteBlast.pm
cp Bio/DB/BiblioI.pm blib/lib/Bio/DB/BiblioI.pm
cp Bio/SearchIO/Writer/HSPTableWriter.pm blib/lib/Bio/SearchIO/Writer/HSPTableWriter.pm
cp Bio/MapIO.pm blib/lib/Bio/MapIO.pm
cp Bio/SearchIO/blasttable.pm blib/lib/Bio/SearchIO/blasttable.pm
cp Bio/Graphics/Glyph/segmented_keyglyph.pm blib/lib/Bio/Graphics/Glyph/segmented_keyglyph.pm
cp Bio/SeqFeature/Collection.pm blib/lib/Bio/SeqFeature/Collection.pm
cp Bio/Graphics/Glyph/box.pm blib/lib/Bio/Graphics/Glyph/box.pm
cp Bio/Graphics/Glyph/cds.pm blib/lib/Bio/Graphics/Glyph/cds.pm
cp Bio/Tree/TreeI.pm blib/lib/Bio/Tree/TreeI.pm
cp Bio/Graphics/Glyph/extending_arrow.pm blib/lib/Bio/Graphics/Glyph/extending_arrow.pm
cp Bio/Map/MappableI.pm blib/lib/Bio/Map/MappableI.pm
cp Bio/Seq/BaseSeqProcessor.pm blib/lib/Bio/Seq/BaseSeqProcessor.pm
cp Bio/SeqIO/fastq.pm blib/lib/Bio/SeqIO/fastq.pm
cp Bio/LiveSeq/SeqI.pm blib/lib/Bio/LiveSeq/SeqI.pm
cp Bio/Tools/Analysis/Protein/ELM.pm blib/lib/Bio/Tools/Analysis/Protein/ELM.pm
cp Bio/Seq/TraceI.pm blib/lib/Bio/Seq/TraceI.pm
cp Bio/Phenotype/Phenotype.pm blib/lib/Bio/Phenotype/Phenotype.pm
cp Bio/Seq/PrimaryQual.pm blib/lib/Bio/Seq/PrimaryQual.pm
cp Bio/DB/Failover.pm blib/lib/Bio/DB/Failover.pm
cp Bio/Map/CytoMap.pm blib/lib/Bio/Map/CytoMap.pm
cp Bio/Variation/Allele.pm blib/lib/Bio/Variation/Allele.pm
cp Bio/LiveSeq/IO/Loader.pm blib/lib/Bio/LiveSeq/IO/Loader.pm
cp Bio/Search/Hit/PsiBlastHit.pm blib/lib/Bio/Search/Hit/PsiBlastHit.pm
cp Bio/LiveSeq/Repeat_Unit.pm blib/lib/Bio/LiveSeq/Repeat_Unit.pm
cp Bio/Restriction/Enzyme/MultiCut.pm blib/lib/Bio/Restriction/Enzyme/MultiCut.pm
cp Bio/DB/GFF/Adaptor/memory.pm blib/lib/Bio/DB/GFF/Adaptor/memory.pm
cp Bio/DB/UpdateableSeqI.pm blib/lib/Bio/DB/UpdateableSeqI.pm
cp Bio/Restriction/IO/base.pm blib/lib/Bio/Restriction/IO/base.pm
cp Bio/DB/RefSeq.pm blib/lib/Bio/DB/RefSeq.pm
cp Bio/Tools/RepeatMasker.pm blib/lib/Bio/Tools/RepeatMasker.pm
cp Bio/Coordinate/Result/Match.pm blib/lib/Bio/Coordinate/Result/Match.pm
cp Bio/Search/Result/HMMERResult.pm blib/lib/Bio/Search/Result/HMMERResult.pm
cp Bio/SearchIO/wise.pm blib/lib/Bio/SearchIO/wise.pm
cp Bio/Seq/PrimedSeq.pm blib/lib/Bio/Seq/PrimedSeq.pm
cp Bio/Structure/Chain.pm blib/lib/Bio/Structure/Chain.pm
cp Bio/AlignIO/prodom.pm blib/lib/Bio/AlignIO/prodom.pm
cp Bio/Assembly/ContigAnalysis.pm blib/lib/Bio/Assembly/ContigAnalysis.pm
cp Bio/Coordinate/ExtrapolatingPair.pm blib/lib/Bio/Coordinate/ExtrapolatingPair.pm
cp Bio/SimpleAnalysisI.pm blib/lib/Bio/SimpleAnalysisI.pm
cp Bio/Graphics/Glyph/group.pm blib/lib/Bio/Graphics/Glyph/group.pm
cp Bio/IdCollectionI.pm blib/lib/Bio/IdCollectionI.pm
cp Bio/Tools/Gel.pm blib/lib/Bio/Tools/Gel.pm
cp Bio/Tree/AlleleNode.pm blib/lib/Bio/Tree/AlleleNode.pm
cp Bio/DB/NCBIHelper.pm blib/lib/Bio/DB/NCBIHelper.pm
cp Bio/Biblio/BiblioBase.pm blib/lib/Bio/Biblio/BiblioBase.pm
cp Bio/Biblio/IO.pm blib/lib/Bio/Biblio/IO.pm
cp Bio/DB/GFF/Feature.pm blib/lib/Bio/DB/GFF/Feature.pm
cp Bio/Phenotype/OMIM/MiniMIMentry.pm blib/lib/Bio/Phenotype/OMIM/MiniMIMentry.pm
cp Bio/UpdateableSeqI.pm blib/lib/Bio/UpdateableSeqI.pm
cp Bio/Tools/Phylo/PAML/ModelResult.pm blib/lib/Bio/Tools/Phylo/PAML/ModelResult.pm
cp Bio/Event/EventHandlerI.pm blib/lib/Bio/Event/EventHandlerI.pm
cp Bio/Biblio/Thesis.pm blib/lib/Bio/Biblio/Thesis.pm
cp Bio/Graphics/Glyph/processed_transcript.pm blib/lib/Bio/Graphics/Glyph/processed_transcript.pm
cp Bio/Graphics/ConfiguratorI.pm blib/lib/Bio/Graphics/ConfiguratorI.pm
cp Bio/DB/Fasta.pm blib/lib/Bio/DB/Fasta.pm
cp Bio/Graphics/Glyph/minmax.pm blib/lib/Bio/Graphics/Glyph/minmax.pm
cp Bio/TreeIO/lintree.pm blib/lib/Bio/TreeIO/lintree.pm
cp Bio/Biblio.pm blib/lib/Bio/Biblio.pm
cp Bio/Phenotype/OMIM/OMIMparser.pm blib/lib/Bio/Phenotype/OMIM/OMIMparser.pm
cp Bio/DB/GFF/Adaptor/memory_iterator.pm blib/lib/Bio/DB/GFF/Adaptor/memory_iterator.pm
cp Bio/Restriction/Enzyme.pm blib/lib/Bio/Restriction/Enzyme.pm
cp Bio/SeqIO/game/seqHandler.pm blib/lib/Bio/SeqIO/game/seqHandler.pm
cp Bio/Matrix/PSM/InstanceSite.pm blib/lib/Bio/Matrix/PSM/InstanceSite.pm
cp Bio/Tree/TreeFunctionsI.pm blib/lib/Bio/Tree/TreeFunctionsI.pm
cp Bio/Matrix/MatrixI.pm blib/lib/Bio/Matrix/MatrixI.pm
cp Bio/SeqIO/largefasta.pm blib/lib/Bio/SeqIO/largefasta.pm
cp Bio/AlignIO/emboss.pm blib/lib/Bio/AlignIO/emboss.pm
cp Bio/Annotation/SimpleValue.pm blib/lib/Bio/Annotation/SimpleValue.pm
cp Bio/Align/AlignI.pm blib/lib/Bio/Align/AlignI.pm
cp Bio/Graphics/Glyph/generic.pm blib/lib/Bio/Graphics/Glyph/generic.pm
cp Bio/DB/Query/WebQuery.pm blib/lib/Bio/DB/Query/WebQuery.pm
cp Bio/Ontology/OntologyI.pm blib/lib/Bio/Ontology/OntologyI.pm
cp Bio/SearchIO/hmmer.pm blib/lib/Bio/SearchIO/hmmer.pm
cp Bio/SeqIO/ctf.pm blib/lib/Bio/SeqIO/ctf.pm
cp Bio/LiveSeq/IO/SRS.pm blib/lib/Bio/LiveSeq/IO/SRS.pm
cp Bio/Tools/SeqPattern.pm blib/lib/Bio/Tools/SeqPattern.pm
cp Bio/SearchIO/psl.pm blib/lib/Bio/SearchIO/psl.pm
cp Bio/LiveSeq/DNA.pm blib/lib/Bio/LiveSeq/DNA.pm
cp Bio/Index/AbstractSeq.pm blib/lib/Bio/Index/AbstractSeq.pm
cp Bio/AlignIO.pm blib/lib/Bio/AlignIO.pm
cp Bio/Tree/NodeI.pm blib/lib/Bio/Tree/NodeI.pm
cp Bio/Tools/Prints.pm blib/lib/Bio/Tools/Prints.pm
cp Bio/SeqFeature/Gene/Exon.pm blib/lib/Bio/SeqFeature/Gene/Exon.pm
cp Bio/Matrix/PSM/IO.pm blib/lib/Bio/Matrix/PSM/IO.pm
cp Bio/TreeIO/svggraph.pm blib/lib/Bio/TreeIO/svggraph.pm
cp Bio/Taxonomy/Tree.pm blib/lib/Bio/Taxonomy/Tree.pm
cp Bio/Ontology/RelationshipType.pm blib/lib/Bio/Ontology/RelationshipType.pm
cp Bio/Cluster/UniGene.pm blib/lib/Bio/Cluster/UniGene.pm
cp Bio/CodonUsage/Table.pm blib/lib/Bio/CodonUsage/Table.pm
cp Bio/SeqFeature/Generic.pm blib/lib/Bio/SeqFeature/Generic.pm
cp Bio/PopGen/PopulationI.pm blib/lib/Bio/PopGen/PopulationI.pm
cp Bio/Root/Global.pm blib/lib/Bio/Root/Global.pm
cp Bio/SeqFeature/SimilarityPair.pm blib/lib/Bio/SeqFeature/SimilarityPair.pm
cp Bio/SeqIO/raw.pm blib/lib/Bio/SeqIO/raw.pm
cp Bio/Search/Processor.pm blib/lib/Bio/Search/Processor.pm
cp Bio/Tools/Analysis/Protein/GOR4.pm blib/lib/Bio/Tools/Analysis/Protein/GOR4.pm
cp Bio/Seq.pm blib/lib/Bio/Seq.pm
cp Bio/Biblio/Article.pm blib/lib/Bio/Biblio/Article.pm
cp Bio/Tools/HMMER/Results.pm blib/lib/Bio/Tools/HMMER/Results.pm
cp Bio/Biblio/Organisation.pm blib/lib/Bio/Biblio/Organisation.pm
cp Bio/Search/BlastUtils.pm blib/lib/Bio/Search/BlastUtils.pm
cp Bio/Tree/RandomFactory.pm blib/lib/Bio/Tree/RandomFactory.pm
cp Bio/Structure/IO/pdb.pm blib/lib/Bio/Structure/IO/pdb.pm
cp Bio/Tools/Phylo/PAML/Result.pm blib/lib/Bio/Tools/Phylo/PAML/Result.pm
cp Bio/DescribableI.pm blib/lib/Bio/DescribableI.pm
cp Bio/Structure/StructureI.pm blib/lib/Bio/Structure/StructureI.pm
cp Bio/Search/Result/ResultI.pm blib/lib/Bio/Search/Result/ResultI.pm
cp Bio/Symbol/AlphabetI.pm blib/lib/Bio/Symbol/AlphabetI.pm
cp Bio/Graphics/Glyph/rndrect.pm blib/lib/Bio/Graphics/Glyph/rndrect.pm
cp Bio/RangeI.pm blib/lib/Bio/RangeI.pm
cp Bio/Matrix/PSM/InstanceSiteI.pm blib/lib/Bio/Matrix/PSM/InstanceSiteI.pm
cp Bio/Location/SplitLocationI.pm blib/lib/Bio/Location/SplitLocationI.pm
cp Bio/SeqFeature/Gene/NC_Feature.pm blib/lib/Bio/SeqFeature/Gene/NC_Feature.pm
cp Bio/SeqIO/metafasta.pm blib/lib/Bio/SeqIO/metafasta.pm
cp Bio/OntologyIO.pm blib/lib/Bio/OntologyIO.pm
cp Bio/Ontology/RelationshipI.pm blib/lib/Bio/Ontology/RelationshipI.pm
cp Bio/Graphics/Feature.pm blib/lib/Bio/Graphics/Feature.pm
cp Bio/Search/HSP/PsiBlastHSP.pm blib/lib/Bio/Search/HSP/PsiBlastHSP.pm
cp Bio/Index/GenBank.pm blib/lib/Bio/Index/GenBank.pm
cp Bio/Restriction/IO/itype2.pm blib/lib/Bio/Restriction/IO/itype2.pm
cp Bio/Biblio/MedlineJournalArticle.pm blib/lib/Bio/Biblio/MedlineJournalArticle.pm
cp Bio/CodonUsage/IO.pm blib/lib/Bio/CodonUsage/IO.pm
cp Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm blib/lib/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm
cp Bio/Taxonomy/Node.pm blib/lib/Bio/Taxonomy/Node.pm
cp Bio/Variation/IO/xml.pm blib/lib/Bio/Variation/IO/xml.pm
cp Bio/DB/GFF/Aggregator/alignment.pm blib/lib/Bio/DB/GFF/Aggregator/alignment.pm
cp Bio/Matrix/Generic.pm blib/lib/Bio/Matrix/Generic.pm
cp Bio/FeatureHolderI.pm blib/lib/Bio/FeatureHolderI.pm
cp Bio/Tools/dpAlign.pm blib/lib/Bio/Tools/dpAlign.pm
cp Bio/SeqFeature/Gene/TranscriptI.pm blib/lib/Bio/SeqFeature/Gene/TranscriptI.pm
cp Bio/Restriction/IO.pm blib/lib/Bio/Restriction/IO.pm
cp Bio/Cluster/FamilyI.pm blib/lib/Bio/Cluster/FamilyI.pm
cp Bio/DB/RandomAccessI.pm blib/lib/Bio/DB/RandomAccessI.pm
cp Bio/SeqIO/qual.pm blib/lib/Bio/SeqIO/qual.pm
cp Bio/SeqIO/kegg.pm blib/lib/Bio/SeqIO/kegg.pm
cp Bio/SearchIO/axt.pm blib/lib/Bio/SearchIO/axt.pm
cp Bio/SeqIO/pln.pm blib/lib/Bio/SeqIO/pln.pm
cp Bio/Ontology/TermI.pm blib/lib/Bio/Ontology/TermI.pm
cp Bio/AnalysisResultI.pm blib/lib/Bio/AnalysisResultI.pm
cp Bio/Search/Result/BlastResult.pm blib/lib/Bio/Search/Result/BlastResult.pm
cp Bio/PopGen/Simulation/Coalescent.pm blib/lib/Bio/PopGen/Simulation/Coalescent.pm
cp Bio/Assembly/ScaffoldI.pm blib/lib/Bio/Assembly/ScaffoldI.pm
cp Bio/Annotation/AnnotationFactory.pm blib/lib/Bio/Annotation/AnnotationFactory.pm
cp Bio/SeqIO/locuslink.pm blib/lib/Bio/SeqIO/locuslink.pm
cp Bio/Phenotype/MeSH/Twig.pm blib/lib/Bio/Phenotype/MeSH/Twig.pm
cp Bio/Tools/Sim4/Exon.pm blib/lib/Bio/Tools/Sim4/Exon.pm
cp Bio/Structure/Atom.pm blib/lib/Bio/Structure/Atom.pm
cp Bio/PopGen/Genotype.pm blib/lib/Bio/PopGen/Genotype.pm
cp Bio/Tools/pICalculator.pm blib/lib/Bio/Tools/pICalculator.pm
cp Bio/Graphics/Glyph/ex.pm blib/lib/Bio/Graphics/Glyph/ex.pm
cp Bio/Tools/Phylo/Molphy/Result.pm blib/lib/Bio/Tools/Phylo/Molphy/Result.pm
cp Bio/DB/GFF/Aggregator/match.pm blib/lib/Bio/DB/GFF/Aggregator/match.pm
cp Bio/DB/GFF/Aggregator/ucsc_softberry.pm blib/lib/Bio/DB/GFF/Aggregator/ucsc_softberry.pm
cp Bio/Map/PositionI.pm blib/lib/Bio/Map/PositionI.pm
cp Bio/Biblio/BookArticle.pm blib/lib/Bio/Biblio/BookArticle.pm
cp Bio/Restriction/IO/withrefm.pm blib/lib/Bio/Restriction/IO/withrefm.pm
cp Bio/DB/Flat/BDB/swiss.pm blib/lib/Bio/DB/Flat/BDB/swiss.pm
cp Bio/Tools/SeqStats.pm blib/lib/Bio/Tools/SeqStats.pm
cp Bio/LiveSeq/Transcript.pm blib/lib/Bio/LiveSeq/Transcript.pm
cp Bio/Ontology/OntologyEngineI.pm blib/lib/Bio/Ontology/OntologyEngineI.pm
cp Bio/Search/HSP/FastaHSP.pm blib/lib/Bio/Search/HSP/FastaHSP.pm
cp Bio/Ontology/Term.pm blib/lib/Bio/Ontology/Term.pm
cp Bio/Tools/Primer/Assessor/Base.pm blib/lib/Bio/Tools/Primer/Assessor/Base.pm
cp Bio/Graphics/Util.pm blib/lib/Bio/Graphics/Util.pm
cp Bio/DB/Flat/BDB.pm blib/lib/Bio/DB/Flat/BDB.pm
cp Bio/AlignIO/mase.pm blib/lib/Bio/AlignIO/mase.pm
cp Bio/Graphics/Glyph/diamond.pm blib/lib/Bio/Graphics/Glyph/diamond.pm
cp Bio/SeqFeature/Gene/Transcript.pm blib/lib/Bio/SeqFeature/Gene/Transcript.pm
cp Bio/SeqFeature/Tools/TypeMapper.pm blib/lib/Bio/SeqFeature/Tools/TypeMapper.pm
cp Bio/Graphics/Glyph/ellipse.pm blib/lib/Bio/Graphics/Glyph/ellipse.pm
cp Bio/SeqIO/scf.pm blib/lib/Bio/SeqIO/scf.pm
cp Bio/Taxonomy/FactoryI.pm blib/lib/Bio/Taxonomy/FactoryI.pm
cp Bio/OntologyIO/InterProParser.pm blib/lib/Bio/OntologyIO/InterProParser.pm
cp Bio/Ontology/OntologyStore.pm blib/lib/Bio/Ontology/OntologyStore.pm
cp Bio/MapIO/mapmaker.pm blib/lib/Bio/MapIO/mapmaker.pm
cp Bio/Tools/Analysis/Protein/HNN.pm blib/lib/Bio/Tools/Analysis/Protein/HNN.pm
cp Bio/DB/GFF/Adaptor/dbi/caching_handle.pm blib/lib/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
cp Bio/Location/Atomic.pm blib/lib/Bio/Location/Atomic.pm
cp Bio/Tools/QRNA.pm blib/lib/Bio/Tools/QRNA.pm
cp Bio/PopGen/IO/prettybase.pm blib/lib/Bio/PopGen/IO/prettybase.pm
cp Bio/Ontology/Ontology.pm blib/lib/Bio/Ontology/Ontology.pm
cp Bio/SeqIO/fasta.pm blib/lib/Bio/SeqIO/fasta.pm
cp Bio/Root/Root.pm blib/lib/Bio/Root/Root.pm
cp Bio/Graphics/Glyph/oval.pm blib/lib/Bio/Graphics/Glyph/oval.pm
cp Bio/DB/GFF/Aggregator/ucsc_twinscan.pm blib/lib/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm
cp Bio/Graphics/Glyph/anchored_arrow.pm blib/lib/Bio/Graphics/Glyph/anchored_arrow.pm
cp Bio/SeqFeature/Similarity.pm blib/lib/Bio/SeqFeature/Similarity.pm
cp Bio/Tools/Sigcleave.pm blib/lib/Bio/Tools/Sigcleave.pm
cp Bio/Tools/Alignment/Trim.pm blib/lib/Bio/Tools/Alignment/Trim.pm
cp Bio/Tools/Alignment/Consed.pm blib/lib/Bio/Tools/Alignment/Consed.pm
cp Bio/Restriction/EnzymeI.pm blib/lib/Bio/Restriction/EnzymeI.pm
cp Bio/SearchIO/sim4.pm blib/lib/Bio/SearchIO/sim4.pm
cp Bio/Phenotype/OMIM/OMIMentry.pm blib/lib/Bio/Phenotype/OMIM/OMIMentry.pm
cp Bio/Map/MarkerI.pm blib/lib/Bio/Map/MarkerI.pm
cp Bio/SearchIO/waba.pm blib/lib/Bio/SearchIO/waba.pm
cp Bio/DB/Flat/BDB/genbank.pm blib/lib/Bio/DB/Flat/BDB/genbank.pm
cp Bio/DB/Taxonomy/entrez.pm blib/lib/Bio/DB/Taxonomy/entrez.pm
cp Bio/Tools/ESTScan.pm blib/lib/Bio/Tools/ESTScan.pm
cp Bio/AlignIO/phylip.pm blib/lib/Bio/AlignIO/phylip.pm
cp Bio/Variation/SeqDiff.pm blib/lib/Bio/Variation/SeqDiff.pm
cp Bio/SeqIO/phd.pm blib/lib/Bio/SeqIO/phd.pm
cp Bio/DB/BioFetch.pm blib/lib/Bio/DB/BioFetch.pm
cp Bio/SeqFeature/AnnotationAdaptor.pm blib/lib/Bio/SeqFeature/AnnotationAdaptor.pm
cp Bio/Factory/LocationFactoryI.pm blib/lib/Bio/Factory/LocationFactoryI.pm
cp Bio/DB/MANIFEST blib/lib/Bio/DB/MANIFEST
cp Bio/SeqIO/embl.pm blib/lib/Bio/SeqIO/embl.pm
cp Bio/SeqIO/tigr.pm blib/lib/Bio/SeqIO/tigr.pm
cp Bio/Biblio/IO/medline2ref.pm blib/lib/Bio/Biblio/IO/medline2ref.pm
cp Bio/SeqIO/asciitree.pm blib/lib/Bio/SeqIO/asciitree.pm
cp Bio/Graphics/Glyph/pinsertion.pm blib/lib/Bio/Graphics/Glyph/pinsertion.pm
cp Bio/Tools/AnalysisResult.pm blib/lib/Bio/Tools/AnalysisResult.pm
cp Bio/Graphics/Glyph/toomany.pm blib/lib/Bio/Graphics/Glyph/toomany.pm
cp Bio/Biblio/Journal.pm blib/lib/Bio/Biblio/Journal.pm
cp Bio/DB/GFF/Aggregator/transcript.pm blib/lib/Bio/DB/GFF/Aggregator/transcript.pm
cp Bio/Search/HSP/GenericHSP.pm blib/lib/Bio/Search/HSP/GenericHSP.pm
cp Bio/Factory/DriverFactory.pm blib/lib/Bio/Factory/DriverFactory.pm
cp Bio/Coordinate/Result.pm blib/lib/Bio/Coordinate/Result.pm
cp Bio/Biblio/PubmedJournalArticle.pm blib/lib/Bio/Biblio/PubmedJournalArticle.pm
cp Bio/PopGen/IO.pm blib/lib/Bio/PopGen/IO.pm
cp Bio/SeqAnalysisParserI.pm blib/lib/Bio/SeqAnalysisParserI.pm
cp Bio/Variation/RNAChange.pm blib/lib/Bio/Variation/RNAChange.pm
cp Bio/Factory/ObjectFactoryI.pm blib/lib/Bio/Factory/ObjectFactoryI.pm
cp Bio/AnalysisParserI.pm blib/lib/Bio/AnalysisParserI.pm
cp Bio/SearchIO.pm blib/lib/Bio/SearchIO.pm
cp Bio/Search/Result/WABAResult.pm blib/lib/Bio/Search/Result/WABAResult.pm
cp Bio/Matrix/PSM/IO/transfac.pm blib/lib/Bio/Matrix/PSM/IO/transfac.pm
cp Bio/Matrix/PSM/PsmHeader.pm blib/lib/Bio/Matrix/PSM/PsmHeader.pm
cp Bio/Tools/Analysis/Protein/Sopma.pm blib/lib/Bio/Tools/Analysis/Protein/Sopma.pm
cp Bio/SearchDist.pm blib/lib/Bio/SearchDist.pm
cp Bio/Expression/FeatureGroup/FeatureGroupMas50.pm blib/lib/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm
cp Bio/Tools/ECnumber.pm blib/lib/Bio/Tools/ECnumber.pm
cp Bio/LiveSeq/Range.pm blib/lib/Bio/LiveSeq/Range.pm
cp Bio/Restriction/EnzymeCollection.pm blib/lib/Bio/Restriction/EnzymeCollection.pm
cp Bio/Matrix/IO/phylip.pm blib/lib/Bio/Matrix/IO/phylip.pm
cp Bio/Tools/Pseudowise.pm blib/lib/Bio/Tools/Pseudowise.pm
cp Bio/Tools/Genscan.pm blib/lib/Bio/Tools/Genscan.pm
cp Bio/OntologyIO/soflat.pm blib/lib/Bio/OntologyIO/soflat.pm
cp Bio/Tools/Blast.pm blib/lib/Bio/Tools/Blast.pm
cp Bio/Tools/GFF.pm blib/lib/Bio/Tools/GFF.pm
cp Bio/DB/GFF/Util/Rearrange.pm blib/lib/Bio/DB/GFF/Util/Rearrange.pm
cp Bio/AnnotationCollectionI.pm blib/lib/Bio/AnnotationCollectionI.pm
cp Bio/Das/SegmentI.pm blib/lib/Bio/Das/SegmentI.pm
cp Bio/SeqFeatureI.pm blib/lib/Bio/SeqFeatureI.pm
cp Bio/Das/FeatureTypeI.pm blib/lib/Bio/Das/FeatureTypeI.pm
cp Bio/Graphics/Glyph/graded_segments.pm blib/lib/Bio/Graphics/Glyph/graded_segments.pm
cp bptutorial.pl blib/lib/bptutorial.pl
cp Bio/Graphics/Glyph/dna.pm blib/lib/Bio/Graphics/Glyph/dna.pm
cp Bio/Structure/Model.pm blib/lib/Bio/Structure/Model.pm
cp Bio/Restriction/Analysis.pm blib/lib/Bio/Restriction/Analysis.pm
cp Bio/Seq/SeqFastaSpeedFactory.pm blib/lib/Bio/Seq/SeqFastaSpeedFactory.pm
cp Bio/Tree/Node.pm blib/lib/Bio/Tree/Node.pm
cp Bio/LiveSeq/Repeat_Region.pm blib/lib/Bio/LiveSeq/Repeat_Region.pm
cp Bio/Tools/RandomDistFunctions.pm blib/lib/Bio/Tools/RandomDistFunctions.pm
cp Bio/Annotation/Reference.pm blib/lib/Bio/Annotation/Reference.pm
cp Bio/Coordinate/MapperI.pm blib/lib/Bio/Coordinate/MapperI.pm
cp Bio/Phenotype/MeSH/Term.pm blib/lib/Bio/Phenotype/MeSH/Term.pm
cp Bio/DB/WebDBSeqI.pm blib/lib/Bio/DB/WebDBSeqI.pm
cp Bio/TreeIO/tabtree.pm blib/lib/Bio/TreeIO/tabtree.pm
cp Bio/Tools/Primer3.pm blib/lib/Bio/Tools/Primer3.pm
cp Bio/DB/GFF/Adaptor/dbi/pg.pm blib/lib/Bio/DB/GFF/Adaptor/dbi/pg.pm
cp Bio/Seq/SeqFactory.pm blib/lib/Bio/Seq/SeqFactory.pm
cp Bio/AlignIO/maf.pm blib/lib/Bio/AlignIO/maf.pm
cp Bio/Tools/Seg.pm blib/lib/Bio/Tools/Seg.pm
cp Bio/Graphics/Pictogram.pm blib/lib/Bio/Graphics/Pictogram.pm
cp Bio/Search/Result/ResultFactory.pm blib/lib/Bio/Search/Result/ResultFactory.pm
cp Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm blib/lib/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm
cp Bio/Tools/Phylo/Phylip/ProtDist.pm blib/lib/Bio/Tools/Phylo/Phylip/ProtDist.pm
cp Bio/SeqIO/genbank.pm blib/lib/Bio/SeqIO/genbank.pm
cp Bio/PrimarySeq.pm blib/lib/Bio/PrimarySeq.pm
cp Bio/AlignIO/pfam.pm blib/lib/Bio/AlignIO/pfam.pm
cp Bio/AlignIO/nexus.pm blib/lib/Bio/AlignIO/nexus.pm
cp Bio/DB/GFF/Aggregator/none.pm blib/lib/Bio/DB/GFF/Aggregator/none.pm
cp Bio/DB/GFF/Adaptor/dbi.pm blib/lib/Bio/DB/GFF/Adaptor/dbi.pm
cp Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm blib/lib/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
cp Bio/Tools/Signalp.pm blib/lib/Bio/Tools/Signalp.pm
cp Bio/Location/CoordinatePolicyI.pm blib/lib/Bio/Location/CoordinatePolicyI.pm
cp biodesign.pod blib/lib/biodesign.pod
cp Bio/PopGen/Population.pm blib/lib/Bio/PopGen/Population.pm
cp Bio/SearchIO/Writer/GbrowseGFF.pm blib/lib/Bio/SearchIO/Writer/GbrowseGFF.pm
cp Bio/AlignIO/bl2seq.pm blib/lib/Bio/AlignIO/bl2seq.pm
cp Bio/Root/HTTPget.pm blib/lib/Bio/Root/HTTPget.pm
cp Bio/Ontology/SimpleOntologyEngine.pm blib/lib/Bio/Ontology/SimpleOntologyEngine.pm
cp Bio/Tools/BPbl2seq.pm blib/lib/Bio/Tools/BPbl2seq.pm
cp Bio/Ontology/PathI.pm blib/lib/Bio/Ontology/PathI.pm
cp Bio/Root/Storable.pm blib/lib/Bio/Root/Storable.pm
cp Bio/Variation/IO.pm blib/lib/Bio/Variation/IO.pm
cp Bio/AnnotationI.pm blib/lib/Bio/AnnotationI.pm
cp Bio/Restriction/IO/bairoch.pm blib/lib/Bio/Restriction/IO/bairoch.pm
cp Bio/Tools/WWW.pm blib/lib/Bio/Tools/WWW.pm
cp Bio/Seq/LargePrimarySeq.pm blib/lib/Bio/Seq/LargePrimarySeq.pm
cp Bio/SeqIO/game/gameSubs.pm blib/lib/Bio/SeqIO/game/gameSubs.pm
cp Bio/SearchIO/Writer/BSMLResultWriter.pm blib/lib/Bio/SearchIO/Writer/BSMLResultWriter.pm
cp Bio/Annotation/Collection.pm blib/lib/Bio/Annotation/Collection.pm
cp Bio/Tools/IUPAC.pm blib/lib/Bio/Tools/IUPAC.pm
cp Bio/DB/Taxonomy/flatfile.pm blib/lib/Bio/DB/Taxonomy/flatfile.pm
cp Bio/Graphics/Glyph/triangle.pm blib/lib/Bio/Graphics/Glyph/triangle.pm
cp Bio/Graphics.pm blib/lib/Bio/Graphics.pm
cp Bio/SeqIO/abi.pm blib/lib/Bio/SeqIO/abi.pm
cp Bio/DB/GFF/Aggregator/ucsc_refgene.pm blib/lib/Bio/DB/GFF/Aggregator/ucsc_refgene.pm
cp Bio/AlignIO/msf.pm blib/lib/Bio/AlignIO/msf.pm
cp Bio/LiveSeq/Intron.pm blib/lib/Bio/LiveSeq/Intron.pm
cp Bio/DB/GFF/Aggregator/clone.pm blib/lib/Bio/DB/GFF/Aggregator/clone.pm
cp Bio/Map/Position.pm blib/lib/Bio/Map/Position.pm
cp Bio/PrimarySeqI.pm blib/lib/Bio/PrimarySeqI.pm
cp Bio/Graphics/Glyph/alignment.pm blib/lib/Bio/Graphics/Glyph/alignment.pm
cp Bio/Root/IOManager.pm blib/lib/Bio/Root/IOManager.pm
cp Bio/LiveSeq/Gene.pm blib/lib/Bio/LiveSeq/Gene.pm
cp Bio/Ontology/Relationship.pm blib/lib/Bio/Ontology/Relationship.pm
cp Bio/Search/Hit/HitFactory.pm blib/lib/Bio/Search/Hit/HitFactory.pm
cp Bio/Factory/HitFactoryI.pm blib/lib/Bio/Factory/HitFactoryI.pm
cp Bio/SearchIO/exonerate.pm blib/lib/Bio/SearchIO/exonerate.pm
cp Bio/SimpleAlign.pm blib/lib/Bio/SimpleAlign.pm
cp Bio/Matrix/PSM/SiteMatrix.pm blib/lib/Bio/Matrix/PSM/SiteMatrix.pm
cp Bio/Expression/FeatureSet/FeatureSetMas50.pm blib/lib/Bio/Expression/FeatureSet/FeatureSetMas50.pm
cp Bio/Graphics/RendererI.pm blib/lib/Bio/Graphics/RendererI.pm
cp Bio/Tools/Phylo/PAML.pm blib/lib/Bio/Tools/Phylo/PAML.pm
cp Bio/Tools/Blast/Sbjct.pm blib/lib/Bio/Tools/Blast/Sbjct.pm
cp Bio/Graphics/FeatureFile/Iterator.pm blib/lib/Bio/Graphics/FeatureFile/Iterator.pm
cp Bio/Factory/ApplicationFactoryI.pm blib/lib/Bio/Factory/ApplicationFactoryI.pm
cp Bio/DB/GFF/Typename.pm blib/lib/Bio/DB/GFF/Typename.pm
cp Bio/Search/HSP/HSPFactory.pm blib/lib/Bio/Search/HSP/HSPFactory.pm
cp Bio/DB/GFF/Homol.pm blib/lib/Bio/DB/GFF/Homol.pm
cp Bio/Event/EventGeneratorI.pm blib/lib/Bio/Event/EventGeneratorI.pm
cp Bio/AlignIO/psi.pm blib/lib/Bio/AlignIO/psi.pm
cp Bio/Graphics/Glyph/redgreen_box.pm blib/lib/Bio/Graphics/Glyph/redgreen_box.pm
cp Bio/Tools/BPlite/Sbjct.pm blib/lib/Bio/Tools/BPlite/Sbjct.pm
cp biodatabases.pod blib/lib/biodatabases.pod
cp Bio/Graphics/FeatureFile.pm blib/lib/Bio/Graphics/FeatureFile.pm
cp Bio/Map/Microsatellite.pm blib/lib/Bio/Map/Microsatellite.pm
cp Bio/LiveSeq/Translation.pm blib/lib/Bio/LiveSeq/Translation.pm
cp Bio/Search/Hit/HitI.pm blib/lib/Bio/Search/Hit/HitI.pm
cp Bio/DB/SeqI.pm blib/lib/Bio/DB/SeqI.pm
cp Bio/Search/Iteration/GenericIteration.pm blib/lib/Bio/Search/Iteration/GenericIteration.pm
cp Bio/Index/SwissPfam.pm blib/lib/Bio/Index/SwissPfam.pm
cp Bio/DB/GenBank.pm blib/lib/Bio/DB/GenBank.pm
cp Bio/DB/Flat/BDB/fasta.pm blib/lib/Bio/DB/Flat/BDB/fasta.pm
cp Bio/Seq/SequenceTrace.pm blib/lib/Bio/Seq/SequenceTrace.pm
cp Bio/Tools/BPlite/HSP.pm blib/lib/Bio/Tools/BPlite/HSP.pm
cp Bio/PopGen/IndividualI.pm blib/lib/Bio/PopGen/IndividualI.pm
cp Bio/DB/MeSH.pm blib/lib/Bio/DB/MeSH.pm
cp Bio/DB/GFF/Aggregator/coding.pm blib/lib/Bio/DB/GFF/Aggregator/coding.pm
cp Bio/Index/EMBL.pm blib/lib/Bio/Index/EMBL.pm
cp Bio/SeqFeature/Gene/GeneStructureI.pm blib/lib/Bio/SeqFeature/Gene/GeneStructureI.pm
cp Bio/ClusterIO.pm blib/lib/Bio/ClusterIO.pm
cp Bio/DB/EMBL.pm blib/lib/Bio/DB/EMBL.pm
cp Bio/DB/DBFetch.pm blib/lib/Bio/DB/DBFetch.pm
cp Bio/DB/Taxonomy.pm blib/lib/Bio/DB/Taxonomy.pm
cp Bio/Tools/Blast/README blib/lib/Bio/Tools/Blast/README
cp Bio/Matrix/Scoring.pm blib/lib/Bio/Matrix/Scoring.pm
cp Bio/Map/CytoPosition.pm blib/lib/Bio/Map/CytoPosition.pm
cp Bio/Seq/Meta.pm blib/lib/Bio/Seq/Meta.pm
cp Bio/Tools/SiRNA.pm blib/lib/Bio/Tools/SiRNA.pm
cp Bio/Phenotype/Correlate.pm blib/lib/Bio/Phenotype/Correlate.pm
cp Bio/Graphics/Glyph/Factory.pm blib/lib/Bio/Graphics/Glyph/Factory.pm
cp Bio/SeqFeature/SiRNA/Oligo.pm blib/lib/Bio/SeqFeature/SiRNA/Oligo.pm
cp Bio/Assembly/IO/phrap.pm blib/lib/Bio/Assembly/IO/phrap.pm
cp Bio/Ontology/Path.pm blib/lib/Bio/Ontology/Path.pm
cp Bio/SeqFeature/Tools/Unflattener.pm blib/lib/Bio/SeqFeature/Tools/Unflattener.pm
cp Bio/LiveSeq/Prim_Transcript.pm blib/lib/Bio/LiveSeq/Prim_Transcript.pm
cp Bio/Tools/Promoterwise.pm blib/lib/Bio/Tools/Promoterwise.pm
cp Bio/Tools/Geneid.pm blib/lib/Bio/Tools/Geneid.pm
cp Bio/Root/Version.pm blib/lib/Bio/Root/Version.pm
cp Bio/Tree/NodeNHX.pm blib/lib/Bio/Tree/NodeNHX.pm
cp Bio/AlignIO/clustalw.pm blib/lib/Bio/AlignIO/clustalw.pm
cp Bio/DB/Ace.pm blib/lib/Bio/DB/Ace.pm
cp Bio/DB/GFF/Adaptor/dbi/mysql.pm blib/lib/Bio/DB/GFF/Adaptor/dbi/mysql.pm
cp Bio/Factory/FTLocationFactory.pm blib/lib/Bio/Factory/FTLocationFactory.pm
cp Bio/Align/DNAStatistics.pm blib/lib/Bio/Align/DNAStatistics.pm
cp Bio/Coordinate/Utils.pm blib/lib/Bio/Coordinate/Utils.pm
cp Bio/Root/Vector.pm blib/lib/Bio/Root/Vector.pm
cp Bio/LiveSeq/IO/BioPerl.pm blib/lib/Bio/LiveSeq/IO/BioPerl.pm
cp Bio/Variation/IO/flat.pm blib/lib/Bio/Variation/IO/flat.pm
cp Bio/SeqIO/chadoxml.pm blib/lib/Bio/SeqIO/chadoxml.pm
cp Bio/PopGen/PopStats.pm blib/lib/Bio/PopGen/PopStats.pm
cp Bio/Biblio/Ref.pm blib/lib/Bio/Biblio/Ref.pm
cp Bio/DB/Query/GenBank.pm blib/lib/Bio/DB/Query/GenBank.pm
cp Bio/Search/GenericDatabase.pm blib/lib/Bio/Search/GenericDatabase.pm
cp Bio/Factory/SequenceProcessorI.pm blib/lib/Bio/Factory/SequenceProcessorI.pm
cp Bio/Location/AvWithinCoordPolicy.pm blib/lib/Bio/Location/AvWithinCoordPolicy.pm
cp Bio/Structure/SecStr/DSSP/Res.pm blib/lib/Bio/Structure/SecStr/DSSP/Res.pm
cp Bio/Biblio/TechReport.pm blib/lib/Bio/Biblio/TechReport.pm
cp Bio/Graphics/Glyph/translation.pm blib/lib/Bio/Graphics/Glyph/translation.pm
cp Bio/SeqIO/gcg.pm blib/lib/Bio/SeqIO/gcg.pm
cp Bio/SeqIO/alf.pm blib/lib/Bio/SeqIO/alf.pm
cp Bio/SeqI.pm blib/lib/Bio/SeqI.pm
cp Bio/Location/Simple.pm blib/lib/Bio/Location/Simple.pm
cp Bio/SearchIO/SearchResultEventBuilder.pm blib/lib/Bio/SearchIO/SearchResultEventBuilder.pm
cp Bio/Seq/QualI.pm blib/lib/Bio/Seq/QualI.pm
cp Bio/Map/LinkagePosition.pm blib/lib/Bio/Map/LinkagePosition.pm
cp Bio/Ontology/SimpleGOEngine.pm blib/lib/Bio/Ontology/SimpleGOEngine.pm
cp Bio/Cluster/ClusterFactory.pm blib/lib/Bio/Cluster/ClusterFactory.pm
cp Bio/PopGen/IO/csv.pm blib/lib/Bio/PopGen/IO/csv.pm
cp Bio/SeqFeature/Gene/Poly_A_site.pm blib/lib/Bio/SeqFeature/Gene/Poly_A_site.pm
cp Bio/Matrix/PSM/SiteMatrixI.pm blib/lib/Bio/Matrix/PSM/SiteMatrixI.pm
cp Bio/SeqFeature/Gene/ExonI.pm blib/lib/Bio/SeqFeature/Gene/ExonI.pm
cp Bio/Tools/Hmmpfam.pm blib/lib/Bio/Tools/Hmmpfam.pm
cp Bio/Expression/FeatureGroup.pm blib/lib/Bio/Expression/FeatureGroup.pm
cp Bio/Graphics/Glyph/primers.pm blib/lib/Bio/Graphics/Glyph/primers.pm
cp Bio/DB/GFF/Aggregator/ucsc_genscan.pm blib/lib/Bio/DB/GFF/Aggregator/ucsc_genscan.pm
cp Bio/IdentifiableI.pm blib/lib/Bio/IdentifiableI.pm
cp Bio/Graphics/Glyph/heterogeneous_segments.pm blib/lib/Bio/Graphics/Glyph/heterogeneous_segments.pm
cp Bio/Ontology/InterProTerm.pm blib/lib/Bio/Ontology/InterProTerm.pm
cp Bio/Graphics/Glyph/crossbox.pm blib/lib/Bio/Graphics/Glyph/crossbox.pm
cp Bio/Tools/Blast/HTML.pm blib/lib/Bio/Tools/Blast/HTML.pm
cp Bio/Tools/Grail.pm blib/lib/Bio/Tools/Grail.pm
cp Bio/Coordinate/Chain.pm blib/lib/Bio/Coordinate/Chain.pm
cp Bio/DB/InMemoryCache.pm blib/lib/Bio/DB/InMemoryCache.pm
cp Bio/PopGen/GenotypeI.pm blib/lib/Bio/PopGen/GenotypeI.pm
cp Bio/DB/GFF/Segment.pm blib/lib/Bio/DB/GFF/Segment.pm
cp Bio/Symbol/DNAAlphabet.pm blib/lib/Bio/Symbol/DNAAlphabet.pm
cp Bio/OntologyIO/goflat.pm blib/lib/Bio/OntologyIO/goflat.pm
cp Bio/Tools/Blast/HSP.pm blib/lib/Bio/Tools/Blast/HSP.pm
cp Bio/DB/FileCache.pm blib/lib/Bio/DB/FileCache.pm
cp Bio/DB/GFF/Util/Binning.pm blib/lib/Bio/DB/GFF/Util/Binning.pm
cp Bio/SearchIO/blast.pm blib/lib/Bio/SearchIO/blast.pm
cp Bio/Tools/Primer/AssessorI.pm blib/lib/Bio/Tools/Primer/AssessorI.pm
cp Bio/Species.pm blib/lib/Bio/Species.pm
cp Bio/DB/GFF/Adaptor/biofetch_oracle.pm blib/lib/Bio/DB/GFF/Adaptor/biofetch_oracle.pm
cp Bio/Biblio/Person.pm blib/lib/Bio/Biblio/Person.pm
cp Bio/Map/Marker.pm blib/lib/Bio/Map/Marker.pm
cp Bio/Tools/CodonTable.pm blib/lib/Bio/Tools/CodonTable.pm
cp Bio/Matrix/PSM/PsmHeaderI.pm blib/lib/Bio/Matrix/PSM/PsmHeaderI.pm
cp Bio/SeqIO/bsml.pm blib/lib/Bio/SeqIO/bsml.pm
cp Bio/Tools/AlignFactory.pm blib/lib/Bio/Tools/AlignFactory.pm
cp Bio/DB/QueryI.pm blib/lib/Bio/DB/QueryI.pm
cp Bio/Graphics/Glyph/segments.pm blib/lib/Bio/Graphics/Glyph/segments.pm
cp Bio/Annotation/DBLink.pm blib/lib/Bio/Annotation/DBLink.pm
cp Bio/Seq/SeqWithQuality.pm blib/lib/Bio/Seq/SeqWithQuality.pm
cp Bio/SearchIO/FastHitEventBuilder.pm blib/lib/Bio/SearchIO/FastHitEventBuilder.pm
cp Bio/DB/XEMBL.pm blib/lib/Bio/DB/XEMBL.pm
cp Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm
cp Bio/Search/Hit/BlastHit.pm blib/lib/Bio/Search/Hit/BlastHit.pm
cp Bio/Graphics/Glyph/redgreen_segment.pm blib/lib/Bio/Graphics/Glyph/redgreen_segment.pm
cp Bio/Variation/AAReverseMutate.pm blib/lib/Bio/Variation/AAReverseMutate.pm
cp Bio/Tools/Prediction/Gene.pm blib/lib/Bio/Tools/Prediction/Gene.pm
cp Bio/SeqFeature/Primer.pm blib/lib/Bio/SeqFeature/Primer.pm
cp Bio/Search/SearchUtils.pm blib/lib/Bio/Search/SearchUtils.pm
cp Bio/Biblio/WebResource.pm blib/lib/Bio/Biblio/WebResource.pm
cp Bio/AlignIO/fasta.pm blib/lib/Bio/AlignIO/fasta.pm
cp Bio/Tools/Phylo/Molphy.pm blib/lib/Bio/Tools/Phylo/Molphy.pm
cp Bio/Search/Hit/HMMERHit.pm blib/lib/Bio/Search/Hit/HMMERHit.pm
cp Bio/Tools/Run/StandAloneBlast.pm blib/lib/Bio/Tools/Run/StandAloneBlast.pm
cp Bio/Tools/MZEF.pm blib/lib/Bio/Tools/MZEF.pm
cp Bio/Root/Err.pm blib/lib/Bio/Root/Err.pm
cp Bio/SearchIO/Writer/ResultTableWriter.pm blib/lib/Bio/SearchIO/Writer/ResultTableWriter.pm
cp Bio/Tools/Primer/Feature.pm blib/lib/Bio/Tools/Primer/Feature.pm
cp Bio/Ontology/RelationshipFactory.pm blib/lib/Bio/Ontology/RelationshipFactory.pm
cp Bio/Seq/RichSeqI.pm blib/lib/Bio/Seq/RichSeqI.pm
cp Bio/Tools/Prediction/Exon.pm blib/lib/Bio/Tools/Prediction/Exon.pm
cp Bio/SearchIO/EventHandlerI.pm blib/lib/Bio/SearchIO/EventHandlerI.pm
cp Bio/SearchIO/Writer/HitTableWriter.pm blib/lib/Bio/SearchIO/Writer/HitTableWriter.pm
cp Bio/DB/GFF/Adaptor/biofetch.pm blib/lib/Bio/DB/GFF/Adaptor/biofetch.pm
cp Bio/Tools/Est2Genome.pm blib/lib/Bio/Tools/Est2Genome.pm
cp Bio/Search/HSP/HMMERHSP.pm blib/lib/Bio/Search/HSP/HMMERHSP.pm
cp Bio/Variation/DNAMutation.pm blib/lib/Bio/Variation/DNAMutation.pm
cp Bio/Factory/MapFactoryI.pm blib/lib/Bio/Factory/MapFactoryI.pm
cp Bio/Symbol/README.Symbol blib/lib/Bio/Symbol/README.Symbol
cp Bio/Tree/Tree.pm blib/lib/Bio/Tree/Tree.pm
cp Bio/Tools/EMBOSS/Palindrome.pm blib/lib/Bio/Tools/EMBOSS/Palindrome.pm
cp Bio/Structure/IO.pm blib/lib/Bio/Structure/IO.pm
cp Bio/SeqIO/game/gameWriter.pm blib/lib/Bio/SeqIO/game/gameWriter.pm
cp bioperl.pod blib/lib/bioperl.pod
cp Bio/Variation/SNP.pm blib/lib/Bio/Variation/SNP.pm
cp Bio/Factory/AnalysisI.pm blib/lib/Bio/Factory/AnalysisI.pm
cp Bio/SearchIO/SearchWriterI.pm blib/lib/Bio/SearchIO/SearchWriterI.pm
cp Bio/SeqFeature/Gene/Promoter.pm blib/lib/Bio/SeqFeature/Gene/Promoter.pm
cp Bio/SeqFeature/FeaturePair.pm blib/lib/Bio/SeqFeature/FeaturePair.pm
cp Bio/Graphics/Glyph/transcript2.pm blib/lib/Bio/Graphics/Glyph/transcript2.pm
cp Bio/Location/Split.pm blib/lib/Bio/Location/Split.pm
cp Bio/SeqIO/exp.pm blib/lib/Bio/SeqIO/exp.pm
cp Bio/Graphics/Glyph/transcript.pm blib/lib/Bio/Graphics/Glyph/transcript.pm
cp Bio/Biblio/IO/pubmedxml.pm blib/lib/Bio/Biblio/IO/pubmedxml.pm
cp Bio/Search/Result/GenericResult.pm blib/lib/Bio/Search/Result/GenericResult.pm
cp Bio/Cluster/SequenceFamily.pm blib/lib/Bio/Cluster/SequenceFamily.pm
cp Bio/SeqIO/swiss.pm blib/lib/Bio/SeqIO/swiss.pm
cp Bio/DB/Makefile.PL blib/lib/Bio/DB/Makefile.PL
cp Bio/Tools/Analysis/DNA/ESEfinder.pm blib/lib/Bio/Tools/Analysis/DNA/ESEfinder.pm
cp Bio/ClusterIO/unigene.pm blib/lib/Bio/ClusterIO/unigene.pm
cp Bio/DB/XEMBLService.pm blib/lib/Bio/DB/XEMBLService.pm
cp Bio/Tools/PrositeScan.pm blib/lib/Bio/Tools/PrositeScan.pm
cp Bio/Annotation/StructuredValue.pm blib/lib/Bio/Annotation/StructuredValue.pm
cp Bio/DB/Flat/BinarySearch.pm blib/lib/Bio/DB/Flat/BinarySearch.pm
cp Bio/Tools/FootPrinter.pm blib/lib/Bio/Tools/FootPrinter.pm
cp Bio/SeqIO/FTHelper.pm blib/lib/Bio/SeqIO/FTHelper.pm
cp Bio/Graphics/Glyph/dot.pm blib/lib/Bio/Graphics/Glyph/dot.pm
cp Bio/Tools/Coil.pm blib/lib/Bio/Tools/Coil.pm
cp Bio/Restriction/Enzyme/MultiSite.pm blib/lib/Bio/Restriction/Enzyme/MultiSite.pm
cp Bio/Root/IO.pm blib/lib/Bio/Root/IO.pm
cp Bio/Coordinate/Collection.pm blib/lib/Bio/Coordinate/Collection.pm
cp Bio/Tools/Lucy.pm blib/lib/Bio/Tools/Lucy.pm
cp Bio/Matrix/PSM/IO/mast.pm blib/lib/Bio/Matrix/PSM/IO/mast.pm
cp Bio/Biblio/MedlineBook.pm blib/lib/Bio/Biblio/MedlineBook.pm
cp Bio/Ontology/GOterm.pm blib/lib/Bio/Ontology/GOterm.pm
cp Bio/Symbol/Symbol.pm blib/lib/Bio/Symbol/Symbol.pm
cp Bio/DB/GFF/Featname.pm blib/lib/Bio/DB/GFF/Featname.pm
cp Bio/Graphics/Glyph/xyplot.pm blib/lib/Bio/Graphics/Glyph/xyplot.pm
cp Bio/Symbol/Alphabet.pm blib/lib/Bio/Symbol/Alphabet.pm
cp Bio/LocatableSeq.pm blib/lib/Bio/LocatableSeq.pm
cp Bio/DB/CUTG.pm blib/lib/Bio/DB/CUTG.pm
cp Bio/Matrix/IO/scoring.pm blib/lib/Bio/Matrix/IO/scoring.pm
cp Bio/Factory/ObjectBuilderI.pm blib/lib/Bio/Factory/ObjectBuilderI.pm
cp Bio/DB/Universal.pm blib/lib/Bio/DB/Universal.pm
cp Bio/SeqIO/ztr.pm blib/lib/Bio/SeqIO/ztr.pm
cp Bio/Structure/Entry.pm blib/lib/Bio/Structure/Entry.pm
cp Bio/Tools/OddCodes.pm blib/lib/Bio/Tools/OddCodes.pm
cp Bio/Matrix/PSM/IO/meme.pm blib/lib/Bio/Matrix/PSM/IO/meme.pm
cp Bio/Biblio/JournalArticle.pm blib/lib/Bio/Biblio/JournalArticle.pm
cp Bio/Coordinate/Pair.pm blib/lib/Bio/Coordinate/Pair.pm
cp Bio/DB/GFF/Aggregator/processed_transcript.pm blib/lib/Bio/DB/GFF/Aggregator/processed_transcript.pm
cp Bio/Coordinate/ResultI.pm blib/lib/Bio/Coordinate/ResultI.pm
cp Bio/Tools/Primer/Pair.pm blib/lib/Bio/Tools/Primer/Pair.pm
cp Bio/PopGen/Statistics.pm blib/lib/Bio/PopGen/Statistics.pm
cp Bio/Tools/Analysis/SimpleAnalysisBase.pm blib/lib/Bio/Tools/Analysis/SimpleAnalysisBase.pm
cp Bio/Tools/Analysis/Protein/NetPhos.pm blib/lib/Bio/Tools/Analysis/Protein/NetPhos.pm
cp Bio/Tools/Analysis/Protein/Scansite.pm blib/lib/Bio/Tools/Analysis/Protein/Scansite.pm
cp Bio/Graphics/Glyph/arrow.pm blib/lib/Bio/Graphics/Glyph/arrow.pm
cp Bio/DB/Flat/BDB/swissprot.pm blib/lib/Bio/DB/Flat/BDB/swissprot.pm
cp Bio/Graphics/Panel.pm blib/lib/Bio/Graphics/Panel.pm
cp Bio/ClusterI.pm blib/lib/Bio/ClusterI.pm
cp Bio/Index/Fasta.pm blib/lib/Bio/Index/Fasta.pm
cp Bio/Align/StatisticsI.pm blib/lib/Bio/Align/StatisticsI.pm
cp Bio/SeqFeature/PositionProxy.pm blib/lib/Bio/SeqFeature/PositionProxy.pm
cp Bio/Tools/SeqAnal.pm blib/lib/Bio/Tools/SeqAnal.pm
cp Bio/LiveSeq/IO/README blib/lib/Bio/LiveSeq/IO/README
cp Bio/DB/GFF/Adaptor/ace.pm blib/lib/Bio/DB/GFF/Adaptor/ace.pm
cp Bio/Structure/SecStr/STRIDE/Res.pm blib/lib/Bio/Structure/SecStr/STRIDE/Res.pm
cp Bio/Graphics/Glyph/ruler_arrow.pm blib/lib/Bio/Graphics/Glyph/ruler_arrow.pm
cp Bio/Biblio/MedlineBookArticle.pm blib/lib/Bio/Biblio/MedlineBookArticle.pm
cp Bio/Biblio/Patent.pm blib/lib/Bio/Biblio/Patent.pm
cp Bio/Tools/Genemark.pm blib/lib/Bio/Tools/Genemark.pm
cp Bio/Matrix/IO.pm blib/lib/Bio/Matrix/IO.pm
cp Bio/Seq/RichSeq.pm blib/lib/Bio/Seq/RichSeq.pm
cp Bio/DB/GFF/Aggregator.pm blib/lib/Bio/DB/GFF/Aggregator.pm
cp Bio/DB/GFF.pm blib/lib/Bio/DB/GFF.pm
cp Bio/SeqFeature/SiRNA/Pair.pm blib/lib/Bio/SeqFeature/SiRNA/Pair.pm
cp Bio/Tools/BPpsilite.pm blib/lib/Bio/Tools/BPpsilite.pm
cp Bio/Graphics/Glyph/track.pm blib/lib/Bio/Graphics/Glyph/track.pm
cp Bio/PopGen/Simulation/GeneticDrift.pm blib/lib/Bio/PopGen/Simulation/GeneticDrift.pm
cp Bio/Factory/ResultFactoryI.pm blib/lib/Bio/Factory/ResultFactoryI.pm
cp Bio/SeqFeature/CollectionI.pm blib/lib/Bio/SeqFeature/CollectionI.pm
cp Bio/Biblio/MedlineArticle.pm blib/lib/Bio/Biblio/MedlineArticle.pm
cp Bio/Phenotype/PhenotypeI.pm blib/lib/Bio/Phenotype/PhenotypeI.pm
cp Bio/AlignIO/metafasta.pm blib/lib/Bio/AlignIO/metafasta.pm
cp Bio/Taxonomy/Taxon.pm blib/lib/Bio/Taxonomy/Taxon.pm
cp Bio/Seq/LargeSeq.pm blib/lib/Bio/Seq/LargeSeq.pm
cp Bio/DB/GDB.pm blib/lib/Bio/DB/GDB.pm
cp Bio/Tools/Profile.pm blib/lib/Bio/Tools/Profile.pm
cp Bio/Seq/EncodedSeq.pm blib/lib/Bio/Seq/EncodedSeq.pm
cp Bio/Tools/Analysis/Protein/Domcut.pm blib/lib/Bio/Tools/Analysis/Protein/Domcut.pm
cp Bio/Variation/README blib/lib/Bio/Variation/README
cp bioscripts.pod blib/lib/bioscripts.pod
cp Bio/DB/Registry.pm blib/lib/Bio/DB/Registry.pm
cp Bio/Variation/VariantI.pm blib/lib/Bio/Variation/VariantI.pm
cp Bio/Tools/Glimmer.pm blib/lib/Bio/Tools/Glimmer.pm
cp Bio/Root/Utilities.pm blib/lib/Bio/Root/Utilities.pm
cp Bio/Graphics/Glyph/line.pm blib/lib/Bio/Graphics/Glyph/line.pm
cp Bio/Factory/SequenceFactoryI.pm blib/lib/Bio/Factory/SequenceFactoryI.pm
cp Bio/Search/Hit/GenericHit.pm blib/lib/Bio/Search/Hit/GenericHit.pm
cp Bio/Map/LinkageMap.pm blib/lib/Bio/Map/LinkageMap.pm
cp Bio/Tools/RestrictionEnzyme.pm blib/lib/Bio/Tools/RestrictionEnzyme.pm
cp Bio/OntologyIO/Handlers/InterProHandler.pm blib/lib/Bio/OntologyIO/Handlers/InterProHandler.pm
cp Bio/AlignIO/stockholm.pm blib/lib/Bio/AlignIO/stockholm.pm
cp Bio/PopGen/Individual.pm blib/lib/Bio/PopGen/Individual.pm
cp Bio/DB/GFF/Adaptor/dbi/mysqlace.pm blib/lib/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm
cp Bio/Seq/MetaI.pm blib/lib/Bio/Seq/MetaI.pm
cp Bio/SeqFeature/Computation.pm blib/lib/Bio/SeqFeature/Computation.pm
cp Bio/Graphics/Glyph/splice_site.pm blib/lib/Bio/Graphics/Glyph/splice_site.pm
cp Bio/DasI.pm blib/lib/Bio/DasI.pm
cp Bio/Tools/Analysis/Protein/Mitoprot.pm blib/lib/Bio/Tools/Analysis/Protein/Mitoprot.pm
cp Bio/OntologyIO/simplehierarchy.pm blib/lib/Bio/OntologyIO/simplehierarchy.pm
cp Bio/Assembly/Scaffold.pm blib/lib/Bio/Assembly/Scaffold.pm
cp Bio/Assembly/Contig.pm blib/lib/Bio/Assembly/Contig.pm
cp Bio/SeqUtils.pm blib/lib/Bio/SeqUtils.pm
cp Bio/TreeIO/nhx.pm blib/lib/Bio/TreeIO/nhx.pm
cp Bio/Structure/Residue.pm blib/lib/Bio/Structure/Residue.pm
cp Bio/DB/GFF/Adaptor/dbi/iterator.pm blib/lib/Bio/DB/GFF/Adaptor/dbi/iterator.pm
cp Bio/Tools/Sim4/Results.pm blib/lib/Bio/Tools/Sim4/Results.pm
cp Bio/OntologyIO/Handlers/BaseSAXHandler.pm blib/lib/Bio/OntologyIO/Handlers/BaseSAXHandler.pm
cp Bio/Variation/AAChange.pm blib/lib/Bio/Variation/AAChange.pm
cp Bio/Index/Fastq.pm blib/lib/Bio/Index/Fastq.pm
cp Bio/SearchIO/Writer/TextResultWriter.pm blib/lib/Bio/SearchIO/Writer/TextResultWriter.pm
cp Bio/Range.pm blib/lib/Bio/Range.pm
cp Bio/OntologyIO/dagflat.pm blib/lib/Bio/OntologyIO/dagflat.pm
cp Bio/SeqIO/pir.pm blib/lib/Bio/SeqIO/pir.pm
cp Bio/Factory/SequenceStreamI.pm blib/lib/Bio/Factory/SequenceStreamI.pm
cp Bio/Matrix/PhylipDist.pm blib/lib/Bio/Matrix/PhylipDist.pm
cp Bio/Annotation/Comment.pm blib/lib/Bio/Annotation/Comment.pm
cp Bio/Tools/BPlite.pm blib/lib/Bio/Tools/BPlite.pm
cp Bio/Biblio/PubmedArticle.pm blib/lib/Bio/Biblio/PubmedArticle.pm
cp Bio/Symbol/ProteinAlphabet.pm blib/lib/Bio/Symbol/ProteinAlphabet.pm
cp Bio/Tools/Genewise.pm blib/lib/Bio/Tools/Genewise.pm
cp Bio/Search/HSP/HSPI.pm blib/lib/Bio/Search/HSP/HSPI.pm
cp Bio/Perl.pm blib/lib/Bio/Perl.pm
cp Bio/LiveSeq/Exon.pm blib/lib/Bio/LiveSeq/Exon.pm
cp Bio/SeqIO/game/gameHandler.pm blib/lib/Bio/SeqIO/game/gameHandler.pm
cp Bio/LiveSeq/Chain.pm blib/lib/Bio/LiveSeq/Chain.pm
cp Bio/ClusterIO/dbsnp.pm blib/lib/Bio/ClusterIO/dbsnp.pm
cp Bio/SearchIO/IteratedSearchResultEventBuilder.pm blib/lib/Bio/SearchIO/IteratedSearchResultEventBuilder.pm
cp Bio/Root/Xref.pm blib/lib/Bio/Root/Xref.pm
cp Bio/AlignIO/meme.pm blib/lib/Bio/AlignIO/meme.pm
cp Bio/Tools/Run/WrapperBase.pm blib/lib/Bio/Tools/Run/WrapperBase.pm
cp Bio/Map/MapI.pm blib/lib/Bio/Map/MapI.pm
cp Bio/PopGen/Marker.pm blib/lib/Bio/PopGen/Marker.pm
cp Bio/Location/WidestCoordPolicy.pm blib/lib/Bio/Location/WidestCoordPolicy.pm
cp Bio/Tools/Genomewise.pm blib/lib/Bio/Tools/Genomewise.pm
cp Bio/DB/Flat/BDB/embl.pm blib/lib/Bio/DB/Flat/BDB/embl.pm
cp Bio/Search/HSP/BlastHSP.pm blib/lib/Bio/Search/HSP/BlastHSP.pm
cp Bio/LiveSeq/Mutator.pm blib/lib/Bio/LiveSeq/Mutator.pm
cp Bio/Phenotype/Measure.pm blib/lib/Bio/Phenotype/Measure.pm
cp Bio/DB/GFF/RelSegment.pm blib/lib/Bio/DB/GFF/RelSegment.pm
cp Bio/SeqFeature/Gene/Intron.pm blib/lib/Bio/SeqFeature/Gene/Intron.pm
cp Bio/Tools/Eponine.pm blib/lib/Bio/Tools/Eponine.pm
cp Bio/Map/OrderedPosition.pm blib/lib/Bio/Map/OrderedPosition.pm
cp Bio/Annotation/TypeManager.pm blib/lib/Bio/Annotation/TypeManager.pm
cp Bio/DB/GFF/Aggregator/ucsc_ensgene.pm blib/lib/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm
cp Bio/SeqIO/MultiFile.pm blib/lib/Bio/SeqIO/MultiFile.pm
cp Bio/Tools/Tmhmm.pm blib/lib/Bio/Tools/Tmhmm.pm
cp Bio/Factory/SeqAnalysisParserFactory.pm blib/lib/Bio/Factory/SeqAnalysisParserFactory.pm
cp Bio/Map/CytoMarker.pm blib/lib/Bio/Map/CytoMarker.pm
cp Bio/AlignIO/selex.pm blib/lib/Bio/AlignIO/selex.pm
cp Bio/SeqFeature/Gene/UTR.pm blib/lib/Bio/SeqFeature/Gene/UTR.pm
cp Bio/Seq/SeqBuilder.pm blib/lib/Bio/Seq/SeqBuilder.pm
cp Bio/Biblio/Service.pm blib/lib/Bio/Biblio/Service.pm
cp Bio/Biblio/MedlineJournal.pm blib/lib/Bio/Biblio/MedlineJournal.pm
cp Bio/DB/GenPept.pm blib/lib/Bio/DB/GenPept.pm
cp Bio/Search/DatabaseI.pm blib/lib/Bio/Search/DatabaseI.pm
cp Bio/Index/Blast.pm blib/lib/Bio/Index/Blast.pm
cp Bio/SeqIO/game/featHandler.pm blib/lib/Bio/SeqIO/game/featHandler.pm
cp Bio/Tools/Blat.pm blib/lib/Bio/Tools/Blat.pm
cp Bio/Graphics/Glyph.pm blib/lib/Bio/Graphics/Glyph.pm
cp Bio/Symbol/SymbolI.pm blib/lib/Bio/Symbol/SymbolI.pm
cp Bio/Tools/EPCR.pm blib/lib/Bio/Tools/EPCR.pm
cp Bio/Location/NarrowestCoordPolicy.pm blib/lib/Bio/Location/NarrowestCoordPolicy.pm
cp Bio/Tools/pSW.pm blib/lib/Bio/Tools/pSW.pm
cp Bio/AnnotatableI.pm blib/lib/Bio/AnnotatableI.pm
cp Bio/Biblio/Proceeding.pm blib/lib/Bio/Biblio/Proceeding.pm
cp Bio/TreeIO/newick.pm blib/lib/Bio/TreeIO/newick.pm
cp Bio/Biblio/Book.pm blib/lib/Bio/Biblio/Book.pm
cp Bio/SeqFeature/Gene/GeneStructure.pm blib/lib/Bio/SeqFeature/Gene/GeneStructure.pm
cp Bio/SearchIO/Writer/HTMLResultWriter.pm blib/lib/Bio/SearchIO/Writer/HTMLResultWriter.pm
cp Bio/Tools/BPlite/Iteration.pm blib/lib/Bio/Tools/BPlite/Iteration.pm
cp Bio/Tree/Statistics.pm blib/lib/Bio/Tree/Statistics.pm
cp Bio/Align/PairwiseStatistics.pm blib/lib/Bio/Align/PairwiseStatistics.pm
cp Bio/Assembly/IO.pm blib/lib/Bio/Assembly/IO.pm
cp Bio/Graphics/Glyph/span.pm blib/lib/Bio/Graphics/Glyph/span.pm
cp Bio/Ontology/TermFactory.pm blib/lib/Bio/Ontology/TermFactory.pm
cp Bio/Tools/SeqWords.pm blib/lib/Bio/Tools/SeqWords.pm
cp Bio/DB/GFF/Adaptor/dbi/oracleace.pm blib/lib/Bio/DB/GFF/Adaptor/dbi/oracleace.pm
cp Bio/Expression/FeatureI.pm blib/lib/Bio/Expression/FeatureI.pm
cp Bio/Map/OrderedPositionWithDistance.pm blib/lib/Bio/Map/OrderedPositionWithDistance.pm
cp Bio/Biblio/IO/pubmed2ref.pm blib/lib/Bio/Biblio/IO/pubmed2ref.pm
cp Bio/SeqIO/game.pm blib/lib/Bio/SeqIO/game.pm
cp Bio/Index/Abstract.pm blib/lib/Bio/Index/Abstract.pm
cp Bio/SearchIO/blastxml.pm blib/lib/Bio/SearchIO/blastxml.pm
cp Bio/Search/Iteration/IterationI.pm blib/lib/Bio/Search/Iteration/IterationI.pm
cp Bio/Tools/HMMER/Domain.pm blib/lib/Bio/Tools/HMMER/Domain.pm
cp Bio/DB/GFF/Adaptor/dbi/oracle.pm blib/lib/Bio/DB/GFF/Adaptor/dbi/oracle.pm
cp Bio/Coordinate/GeneMapper.pm blib/lib/Bio/Coordinate/GeneMapper.pm
cp Bio/Biblio/IO/medlinexml.pm blib/lib/Bio/Biblio/IO/medlinexml.pm
cp Bio/Location/FuzzyLocationI.pm blib/lib/Bio/Location/FuzzyLocationI.pm
cp Bio/SeqIO/ace.pm blib/lib/Bio/SeqIO/ace.pm
cp Bio/Search/Hit/Fasta.pm blib/lib/Bio/Search/Hit/Fasta.pm
cp Bio/Root/Exception.pm blib/lib/Bio/Root/Exception.pm
cp Bio/Factory/TreeFactoryI.pm blib/lib/Bio/Factory/TreeFactoryI.pm
cp Bio/Assembly/IO/ace.pm blib/lib/Bio/Assembly/IO/ace.pm
cp Bio/DB/Biblio/soap.pm blib/lib/Bio/DB/Biblio/soap.pm
cp Bio/Root/Object.pm blib/lib/Bio/Root/Object.pm
cp Bio/SeqIO/tab.pm blib/lib/Bio/SeqIO/tab.pm
cp ./scripts_temp/bp_heterogeneity_test.pl blib/script/bp_heterogeneity_test.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_heterogeneity_test.pl
cp ./scripts_temp/bp_biogetseq.pl blib/script/bp_biogetseq.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_biogetseq.pl
cp ./scripts_temp/bp_biblio.pl blib/script/bp_biblio.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_biblio.pl
cp ./scripts_temp/bp_extract_feature_seq.pl blib/script/bp_extract_feature_seq.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_extract_feature_seq.pl
cp ./scripts_temp/bp_process_gadfly.pl blib/script/bp_process_gadfly.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_process_gadfly.pl
cp ./scripts_temp/bp_aacomp.pl blib/script/bp_aacomp.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_aacomp.pl
cp ./scripts_temp/bp_nrdb.pl blib/script/bp_nrdb.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_nrdb.pl
cp ./scripts_temp/bp_mrtrans.pl blib/script/bp_mrtrans.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_mrtrans.pl
cp ./scripts_temp/bp_load_gff.pl blib/script/bp_load_gff.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_load_gff.pl
cp ./scripts_temp/bp_process_sgd.pl blib/script/bp_process_sgd.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_process_sgd.pl
cp ./scripts_temp/bp_gccalc.pl blib/script/bp_gccalc.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_gccalc.pl
cp ./scripts_temp/bp_feature_draw.pl blib/script/bp_feature_draw.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_feature_draw.pl
cp ./scripts_temp/bp_sreformat.pl blib/script/bp_sreformat.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_sreformat.pl
cp ./scripts_temp/bp_oligo_count.pl blib/script/bp_oligo_count.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_oligo_count.pl
cp ./scripts_temp/bp_translate_seq.pl blib/script/bp_translate_seq.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_translate_seq.pl
cp ./scripts_temp/bp_flanks.pl blib/script/bp_flanks.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_flanks.pl
cp ./scripts_temp/bp_index.pl blib/script/bp_index.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_index.pl
cp ./scripts_temp/bp_seq_length.pl blib/script/bp_seq_length.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_seq_length.pl
cp ./scripts_temp/bp_search2alnblocks.pl blib/script/bp_search2alnblocks.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_search2alnblocks.pl
cp ./scripts_temp/bp_search2tribe.pl blib/script/bp_search2tribe.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_search2tribe.pl
cp ./scripts_temp/bp_generate_histogram.pl blib/script/bp_generate_histogram.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_generate_histogram.pl
cp ./scripts_temp/bp_dbsplit.pl blib/script/bp_dbsplit.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_dbsplit.pl
cp ./scripts_temp/bp_composite_LD.pl blib/script/bp_composite_LD.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_composite_LD.pl
cp ./scripts_temp/bp_filter_search.pl blib/script/bp_filter_search.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_filter_search.pl
cp ./scripts_temp/bp_mutate.pl blib/script/bp_mutate.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_mutate.pl
cp ./scripts_temp/bp_bioflat_index.pl blib/script/bp_bioflat_index.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_bioflat_index.pl
cp ./scripts_temp/bp_seqconvert.pl blib/script/bp_seqconvert.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_seqconvert.pl
cp ./scripts_temp/bp_local_taxonomydb_query.pl blib/script/bp_local_taxonomydb_query.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_local_taxonomydb_query.pl
cp ./scripts_temp/bp_process_ncbi_human.pl blib/script/bp_process_ncbi_human.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_process_ncbi_human.pl
cp ./scripts_temp/bp_fetch.pl blib/script/bp_fetch.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_fetch.pl
cp ./scripts_temp/bp_search2gff.pl blib/script/bp_search2gff.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_search2gff.pl
cp ./scripts_temp/bp_process_wormbase.pl blib/script/bp_process_wormbase.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_process_wormbase.pl
cp ./scripts_temp/bp_fast_load_gff.pl blib/script/bp_fast_load_gff.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_fast_load_gff.pl
cp ./scripts_temp/bp_split_seq.pl blib/script/bp_split_seq.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_split_seq.pl
cp ./scripts_temp/bp_bulk_load_gff.pl blib/script/bp_bulk_load_gff.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_bulk_load_gff.pl
cp ./scripts_temp/bp_pg_bulk_load_gff.pl blib/script/bp_pg_bulk_load_gff.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_pg_bulk_load_gff.pl
cp ./scripts_temp/bp_blast2tree.pl blib/script/bp_blast2tree.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_blast2tree.pl
cp ./scripts_temp/bp_chaos_plot.pl blib/script/bp_chaos_plot.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_chaos_plot.pl
cp ./scripts_temp/bp_search2BSML.pl blib/script/bp_search2BSML.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_search2BSML.pl
cp ./scripts_temp/bp_remote_blast.pl blib/script/bp_remote_blast.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_remote_blast.pl
cp ./scripts_temp/bp_frend.pl blib/script/bp_frend.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_frend.pl
cp ./scripts_temp/bp_mask_by_search.pl blib/script/bp_mask_by_search.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_mask_by_search.pl
cp ./scripts_temp/bp_search_overview.pl blib/script/bp_search_overview.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_search_overview.pl
cp ./scripts_temp/bp_genbank2gff.pl blib/script/bp_genbank2gff.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_genbank2gff.pl
cp ./scripts_temp/bp_pairwise_kaks.pl blib/script/bp_pairwise_kaks.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_pairwise_kaks.pl
cp ./scripts_temp/bp_biofetch_genbank_proxy.pl blib/script/bp_biofetch_genbank_proxy.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_biofetch_genbank_proxy.pl
cp ./scripts_temp/bp_taxid4species.pl blib/script/bp_taxid4species.pl
/home/cpan/perl588/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/bp_taxid4species.pl

[ERROR] [Mon Jul 28 10:35:28 2008] MAKE TEST failed:  PERL_DL_NONLAZY=1 /home/cpan/perl588/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/AAChange.....................ok
t/AAReverseMutate..............ok
t/AlignIO......................ok
t/AlignStats...................ok
t/Allele.......................ok
t/Alphabet.....................ok
t/Annotation...................ok
t/AnnotationAdaptor............ok
t/Assembly.....................ok
t/Biblio.......................SOAP::Lite not installed. Skipping some tests.
XML::Parser not installed. Skipping some tests.
ok
t/Biblio_biofetch..............ok
t/BiblioReferences.............ok
t/BioDBGFF.....................ok
t/BioFetch_DB..................Can't locate LWP/UserAgent.pm in @INC (@INC contains: t . ./blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib /home/cpan/perl588/lib/5.8.8/OpenBSD.i386-openbsd-thread-multi-64int /home/cpan/perl588/lib/5.8.8 /home/cpan/perl588/lib/site_perl/5.8.8/OpenBSD.i386-openbsd-thread-multi-64int /home/cpan/perl588/lib/site_perl/5.8.8 /home/cpan/perl588/lib/site_perl) at Bio/DB/WebDBSeqI.pm line 86.
BEGIN failed--compilation aborted at Bio/DB/WebDBSeqI.pm line 86.
Compilation failed in require at Bio/DB/BioFetch.pm line 16.
BEGIN failed--compilation aborted at Bio/DB/BioFetch.pm line 16.
Compilation failed in require at t/BioFetch_DB.t line 51.
 Dubious, test returned 2 (wstat 512, 0x200)
 All 27 subtests passed 
t/BioGraphics..................GD or Text::Shellwords modules are not installed. This means that Bio::Graphics module is unusable. Skipping tests.
ok
t/BlastIndex...................ok
t/BPbl2seq.....................ok
t/BPlite.......................ok
t/BPpsilite....................ok
t/Chain........................ok
t/cigarstring..................ok
t/ClusterIO....................XML::Parser::PerlSAX not loaded. This means ClusterIO::dbsnp test cannot be executed. Skipping
ok
t/Coalescent...................ok
t/CodonTable...................ok
t/consed.......................ok
t/CoordinateGraph..............ok
t/CoordinateMapper.............ok
t/Correlate....................ok
t/CytoMap......................ok
t/DB...........................IO::String or LWP::UserAgent or HTTP::Request not installed. This means the Bio::DB::* modules are not usable. Skipping tests.
ok
t/DBCUTG.......................IO::String or LWP::UserAgent not installed. This means that the module is not usable. Skipping tests at t/DBCUTG.t line 31.
ok
t/DBFasta......................ok
t/DNAMutation..................ok
t/Domcut.......................IO::String or LWP::UserAgent not installed. This means that the module is not usable. Skipping tests at t/Domcut.t line 31.
ok
t/ECnumber.....................ok
t/ELM..........................IO::String or LWP::UserAgent not installed. This means that the module is not usable. Skipping tests at t/ELM.t line 30.
ok
t/EMBL_DB......................Can't locate HTTP/Request/Common.pm in @INC (@INC contains: t /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib /home/cpan/perl588/lib/5.8.8/OpenBSD.i386-openbsd-thread-multi-64int /home/cpan/perl588/lib/5.8.8 /home/cpan/perl588/lib/site_perl/5.8.8/OpenBSD.i386-openbsd-thread-multi-64int /home/cpan/perl588/lib/site_perl/5.8.8 /home/cpan/perl588/lib/site_perl .) at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/DB/DBFetch.pm line 74.
BEGIN failed--compilation aborted at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/DB/DBFetch.pm line 74.
Compilation failed in require at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/DB/EMBL.pm line 103.
BEGIN failed--compilation aborted at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/DB/EMBL.pm line 103.
Compilation failed in require at t/EMBL_DB.t line 46.
 Dubious, test returned 2 (wstat 512, 0x200)
 All 15 subtests passed 
t/EMBOSS_Tools.................ok
t/EncodedSeq...................ok
t/ePCR.........................ok
t/ESEfinder....................IO::String or LWP::UserAgent not installed. This means that the module is not usable. Skipping tests at t/ESEfinder.t line 32.
Can't locate HTTP/Request/Common.pm in @INC (@INC contains: t /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib /home/cpan/perl588/lib/5.8.8/OpenBSD.i386-openbsd-thread-multi-64int /home/cpan/perl588/lib/5.8.8 /home/cpan/perl588/lib/site_perl/5.8.8/OpenBSD.i386-openbsd-thread-multi-64int /home/cpan/perl588/lib/site_perl/5.8.8 /home/cpan/perl588/lib/site_perl .) at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/Tools/Analysis/DNA/ESEfinder.pm line 138.
BEGIN failed--compilation aborted at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/Tools/Analysis/DNA/ESEfinder.pm line 138.
Compilation failed in require at t/ESEfinder.t line 55.
BEGIN failed--compilation aborted at t/ESEfinder.t line 55.
 Dubious, test returned 2 (wstat 512, 0x200)
 All 12 subtests passed 
t/est2genome...................ok
t/Exception....................ok
t/Exonerate....................ok
t/flat.........................ok
t/FootPrinter..................ok
t/game.........................XML::Parser::PerlSAX not loaded. This means game test cannot be executed. Skipping
ok
t/GDB..........................Cannot load LWP::UserAgent or HTML::Parser, skipping tests
ok
t/GeneCoordinateMapper.........
-------------------- WARNING ---------------------
MSG: sorted sublocation array requested but root location doesn't define seq_id (at least one sublocation does!)
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: sorted sublocation array requested but root location doesn't define seq_id (at least one sublocation does!)
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/Coordinate/GeneMapper.pm line 814.
ok
t/Geneid.......................ok
t/Genewise.....................ok
t/Genomewise...................ok
t/Genpred......................ok
t/GFF..........................Filehandle GEN0 opened only for output at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/Root/IO.pm line 440.
Filehandle GEN1 opened only for output at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/Root/IO.pm line 440.
ok
t/GOR4.........................IO::String or LWP::UserAgent not installed. This means that the module is not usable. Skipping tests at t/GOR4.t line 30.
ok
t/GOterm.......................ok
t/GuessSeqFormat...............Bio::SeqIO: game cannot be found
Exception 
------------- EXCEPTION  -------------
MSG: Failed to load module Bio::SeqIO::game. Can't locate XML/Parser/PerlSAX.pm in @INC (@INC contains: t .. /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib /home/cpan/perl588/lib/5.8.8/OpenBSD.i386-openbsd-thread-multi-64int /home/cpan/perl588/lib/5.8.8 /home/cpan/perl588/lib/site_perl/5.8.8/OpenBSD.i386-openbsd-thread-multi-64int /home/cpan/perl588/lib/site_perl/5.8.8 /home/cpan/perl588/lib/site_perl .) at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/SeqIO/game/gameSubs.pm line 70.
BEGIN failed--compilation aborted at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/SeqIO/game/gameSubs.pm line 70.
Compilation failed in require at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/SeqIO/game/gameHandler.pm line 62.
BEGIN failed--compilation aborted at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/SeqIO/game/gameHandler.pm line 62.
Compilation failed in require at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/SeqIO/game.pm line 76.
BEGIN failed--compilation aborted at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/SeqIO/game.pm line 76.
Compilation failed in require at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/Root/Root.pm line 394.

STACK Bio::Root::Root::_load_module /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/Root/Root.pm:396
STACK (eval) /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/SeqIO.pm:549
STACK Bio::SeqIO::_load_format_module /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/SeqIO.pm:548
STACK Bio::SeqIO::new /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/SeqIO.pm:377
STACK (eval) t/GuessSeqFormat.t:61
STACK toplevel t/GuessSeqFormat.t:60

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

For more information about the SeqIO system please see the SeqIO docs.
This includes ways of checking for formats at compile time, not run time
 Failed 1/46 subtests 
t/hmmer........................ok
t/HNN..........................IO::String or LWP::UserAgent not installed. This means that the module is not usable. Skipping tests at t/HNN.t line 30.
ok
t/Index........................ok
t/InstanceSite.................ok
t/InterProParser...............XML::Parser not installed. This means that InterPro Ontology Parsing module is not usable. Skipping tests.
ok
t/IUPAC........................ok
t/largefasta...................ok
t/largepseq....................ok
t/LinkageMap...................ok
t/LiveSeq......................ok
t/LocatableSeq.................ok
t/Location.....................ok
t/LocationFactory..............ok
t/LocusLink....................ok
t/lucy.........................ok
t/Map..........................ok
t/MapIO........................ok
t/Matrix.......................ok
t/Measure......................ok
t/MeSH.........................IO::String or LWP::UserAgent or HTTP::Request not installed. This means the MeSH modules are not usable. Skipping tests.
ok
t/MetaSeq......................ok
t/MicrosatelliteMarker.........ok
t/MiniMIMentry.................ok
t/MitoProt.....................IO::String or LWP::UserAgent not installed. This means that the module is not usable. Skipping tests at t/MitoProt.t line 29.
ok
t/Molphy.......................ok
t/multiple_fasta...............ok
t/Mutation.....................ok
t/Mutator......................ok
t/NetPhos......................IO::String or LWP::UserAgent not installed. This means that the module is not usable. Skipping tests at t/NetPhos.t line 31.
ok
t/Node.........................ok
t/OddCodes.....................ok
t/OMIMentry....................ok
t/OMIMentryAllelicVariant......ok
t/OMIMparser...................ok
t/Ontology.....................
Graph.pm doesn't seem to be installed on this system -- the GO Parser needs it...

ok
t/OntologyEngine...............ok
t/PAML.........................ok
t/Perl.........................ok
t/phd..........................ok
t/Phenotype....................ok
t/PhylipDist...................ok
t/pICalculator.................ok
t/Pictogram....................SVG not installed, skipping tests at t/Pictogram.t line 29.
ok
t/PopGen.......................ok
t/PopGenSims...................ok
t/primaryqual..................ok
t/PrimarySeq...................ok
t/primedseq....................ok
t/Primer.......................ok
t/primer3......................ok
t/Promoterwise.................ok
t/ProtDist.....................ok
t/psm..........................ok
t/QRNA.........................ok
t/qual.........................ok
t/RandDistFunctions............ok
t/RandomTreeFactory............ok
t/Range........................ok
t/RangeI.......................ok
t/RefSeq.......................Can't locate HTTP/Request/Common.pm in @INC (@INC contains: t /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib /home/cpan/perl588/lib/5.8.8/OpenBSD.i386-openbsd-thread-multi-64int /home/cpan/perl588/lib/5.8.8 /home/cpan/perl588/lib/site_perl/5.8.8/OpenBSD.i386-openbsd-thread-multi-64int /home/cpan/perl588/lib/site_perl/5.8.8 /home/cpan/perl588/lib/site_perl .) at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/DB/DBFetch.pm line 74.
BEGIN failed--compilation aborted at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/DB/DBFetch.pm line 74.
Compilation failed in require at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/DB/RefSeq.pm line 108.
BEGIN failed--compilation aborted at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/DB/RefSeq.pm line 108.
Compilation failed in require at t/RefSeq.t line 46.
 Dubious, test returned 2 (wstat 512, 0x200)
 All 13 subtests passed 
t/Registry.....................DB_File and BerkeleyDB not found. Skipping DB_File tests

-------------------- WARNING ---------------------
MSG: Couldn't call new_from_registry on [Bio::DB::BioFetch]
Can't locate object method "new_from_registry" via package "Bio::DB::BioFetch" at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/DB/Registry.pm line 182.

---------------------------------------------------
ok
t/Relationship.................ok
t/RelationshipType.............ok
t/RemoteBlast..................Can't locate LWP.pm in @INC (@INC contains: t /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib/lib /home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib/arch /home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib /home/cpan/perl588/lib/5.8.8/OpenBSD.i386-openbsd-thread-multi-64int /home/cpan/perl588/lib/5.8.8 /home/cpan/perl588/lib/site_perl/5.8.8/OpenBSD.i386-openbsd-thread-multi-64int /home/cpan/perl588/lib/site_perl/5.8.8 /home/cpan/perl588/lib/site_perl .) at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/Tools/Run/RemoteBlast.pm line 144.
BEGIN failed--compilation aborted at /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib/Bio/Tools/Run/RemoteBlast.pm line 144.
Compilation failed in require at t/RemoteBlast.t line 38.
 Dubious, test returned 2 (wstat 512, 0x200)
 All 6 subtests passed 
t/RepeatMasker.................ok
t/RestrictionAnalysis..........ok
t/RestrictionEnzyme............ok
t/RestrictionIO................ok
t/RNAChange....................ok
t/RootI........................ok
t/RootIO.......................ok
t/RootStorable.................ok
t/Scansite.....................IO::String or LWP::UserAgent not installed. This means that the module is not usable. Skipping tests at t/Scansite.t line 29.
ok
t/scf..........................ok
t/SearchDist...................ok
t/SearchIO.....................XML::Parser::PerlSAX or HTML::Entities not loaded. This means SearchIO::blastxml test cannot be executed. Skipping
ok
t/Seq..........................ok
t/SeqAnalysisParser............ok
t/SeqBuilder...................ok
t/SeqDiff......................ok
t/SeqFeatCollection............ok
t/SeqFeature...................skipping DB tests...
Can't locate object method "new" via package "Bio::DB::GenBank" at t/SeqFeature.t line 338, <GEN1> line 125.
 Dubious, test returned 255 (wstat 65280, 0xff00)
 All 74 subtests passed 
t/seqfeaturePrimer.............ok
t/SeqIO........................ok
t/SeqPattern...................ok
t/SeqStats.....................ok
t/SequenceFamily...............ok
t/sequencetrace................ok
t/SeqUtils.....................ok
t/seqwithquality...............ok
t/SeqWords.....................ok
t/Sigcleave....................ok
t/Sim4.........................ok
t/SimilarityPair...............ok
t/SimpleAlign..................ok
t/simpleGOparser...............
Graph.pm doesn't seem to be installed on this system -- the GO Parser needs it...

ok
t/sirna........................ok
t/SiteMatrix...................ok
t/SNP..........................ok
t/Sopma........................IO::String or LWP::UserAgent not installed. This means that the module is not usable. Skipping tests at t/Sopma.t line 30.
ok
t/Species......................ok
t/splicedseq...................Skipping remote location tests
ok
t/StandAloneBlast..............ok
t/StructIO.....................ok
t/Structure....................ok
t/Swiss........................ok
t/Symbol.......................ok
t/Taxonomy.....................ok
t/Tempfile.....................ok
t/Term.........................ok
t/Tools........................ok
t/Tree.........................ok
t/TreeIO.......................ok
t/trim.........................ok
t/tutorial.....................Warning: Couldn't connect to Genbank with Bio::DB::GenBank.pm!
Probably no network access.
Skipping method 'access_remote_db'.
Cannot run demo_xml
	Problem parsing GAME format or missing necessary installed modules XML::Parser XML::Parser::PerlSAX
ok
t/UCSCParsers..................ok
t/Unflattener..................ok
t/Unflattener2.................ok
t/UniGene......................ok
t/Variation_IO.................
The XML-format conversion requires the CPAN modules XML::Twig, XML::Writer, and IO::String to be installed on your system, which they probably aren't. Skipping these tests.
ok
t/WABA.........................ok
t/XEMBL_DB.....................SOAP::Lite and/or XML::DOM not installed. This means that Bio::DB::XEMBL module is not usable. Skipping tests.
ok

Test Summary Report
-------------------
t/BioFetch_DB.t            (Wstat: 512 Tests: 27 Failed: 0)
  Non-zero exit status: 2
t/EMBL_DB.t                (Wstat: 512 Tests: 15 Failed: 0)
  Non-zero exit status: 2
t/ESEfinder.t              (Wstat: 512 Tests: 12 Failed: 0)
  Non-zero exit status: 2
t/GuessSeqFormat.t         (Wstat: 0 Tests: 46 Failed: 1)
  Failed test:  11
t/RefSeq.t                 (Wstat: 512 Tests: 13 Failed: 0)
  Non-zero exit status: 2
t/RemoteBlast.t            (Wstat: 512 Tests: 6 Failed: 0)
  Non-zero exit status: 2
t/SeqFeature.t             (Wstat: 65280 Tests: 74 Failed: 0)
  Non-zero exit status: 255
Files=179, Tests=8122, 829 wallclock secs ( 8.50 usr  9.51 sys + 199.84 cusr 55.56 csys = 273.41 CPU)
Result: FAIL
Failed 7/179 test programs. 1/8122 subtests failed.
*** Error code 255

Stop in /home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4 (line 3974 of Makefile).

[MSG] [Mon Jul 28 10:35:30 2008] DEFAULT 'proceed_on_test_failure' HANDLER RETURNING 'sub return value'


MISSING PREREQUISITES:

It was observed that the test suite seem to fail without these modules:

LWP::UserAgent
HTTP::Request::Common
XML::Parser::PerlSAX
LWP

As such, adding the prerequisite module(s) to 'PREREQ_PM' in your
Makefile.PL should solve this problem.  For example:

WriteMakefile(
    AUTHOR      => 'Ewan Birney (birney@sanger.ac.uk)',
    ... # other information
    PREREQ_PM   => {
	'LWP::UserAgent'	=> '0', # or a minimum working version
	'HTTP::Request::Common'	=> '0', # or a minimum working version
	'XML::Parser::PerlSAX'	=> '0', # or a minimum working version
	'LWP'	=> '0', # or a minimum working version
    }
);

If you are interested in making a more flexible Makefile.PL that can
probe for missing dependencies and install them, ExtUtils::AutoInstall
at <http://search.cpan.org/dist/ExtUtils-AutoInstall/> may be
worth a look.

Thanks! :-)

PREREQUISITES:

Here is a list of prerequisites you specified and versions we 
managed to load:
                                
	  Module Name                        Have     Want
	  DB_File                           1.814        0
	  File::Spec                         3.12        0
	  File::Temp                         0.16        0
	  HTML::Entities                     1.35        0
	  IO::Scalar                        2.110        0
	  IO::String                         1.08        0

******************************** NOTE ********************************
The comments above are created mechanically, possibly without manual
checking by the sender.  As there are many people performing automatic
tests on each upload to CPAN, it is likely that you will receive 
identical messages about the same problem.

If you believe that the message is mistaken, please reply to the first
one with correction and/or additional informations, and do not take
it personally.  We appreciate your patience. :)
**********************************************************************

Additional comments:
 

This report was machine-generated by CPANPLUS::Dist::YACSmoke 0.02.

------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------

Environment variables:

    AUTOMATED_TESTING = 1
    PATH = /home/cpan/bin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/X11R6/bin:/usr/local/bin:/usr/local/sbin:/usr/games:.
    PERL5LIB = :/home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib/lib:/home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib/arch:/home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib:/home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib/lib:/home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib/arch:/home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Tagset-3.20/blib:/home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib/lib:/home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib/arch:/home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib:/home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib/lib:/home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib/arch:/home/cpan/perl588/.cpanplus/5.8.8/build/HTML-Parser-3.56/blib:/home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib/lib:/home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib/arch:/home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib:/home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib/lib:/home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib/arch:/home/cpan/perl588/.cpanplus/5.8.8/build/IO-stringy-2.110/blib:/home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib/lib:/home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib/arch:/home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib:/home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib/lib:/home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib/arch:/home/cpan/perl588/.cpanplus/5.8.8/build/IO-String-1.08/blib:/home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/lib:/home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib/arch:/home/cpan/perl588/.cpanplus/5.8.8/build/bioperl-1.4/blib
    PERL5_CPANPLUS_IS_RUNNING = 11729
    PERL5_CPANPLUS_IS_VERSION = 0.84
    PERL5_CPANPLUS_VERBOSE = 1
    PERL_MM_USE_DEFAULT = 1
    SHELL = /bin/ksh
    TERM = screen

Perl special variables (and OS-specific diagnostics, for MSWin32):

    Perl: $^X = /home/cpan/perl588/bin/perl
    UID:  $<  = 1000
    EUID: $>  = 1000
    GID:  $(  = 1000 0 1000
    EGID: $)  = 1000 0 1000


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


--

Summary of my perl5 (revision 5 version 8 subversion 8) configuration:
  Platform:
    osname=openbsd, osvers=4.2, archname=OpenBSD.i386-openbsd-thread-multi-64int
    uname='openbsd wynionyn.bingosnet.co.uk 4.2 generic#375 i386 '
    config_args='-Dprefix=/home/cpan/perl588 -Dusethreads -Duse64bitint -Uusemymalloc'
    hint=recommended, useposix=true, d_sigaction=define
    usethreads=define use5005threads=undef useithreads=define usemultiplicity=define
    useperlio=define d_sfio=undef uselargefiles=define usesocks=undef
    use64bitint=define use64bitall=undef uselongdouble=undef
    usemymalloc=n, bincompat5005=undef
  Compiler:
    cc='cc', ccflags ='-pthread -fno-strict-aliasing -fno-delete-null-pointer-checks -pipe -I/usr/local/include',
    optimize='-O2',
    cppflags='-pthread -fno-strict-aliasing -fno-delete-null-pointer-checks -pipe -I/usr/local/include'
    ccversion='', gccversion='3.3.5 (propolice)', gccosandvers='openbsd4.2'
    intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=12345678
    d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12
    ivtype='long long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
    alignbytes=4, prototype=define
  Linker and Libraries:
    ld='cc', ldflags ='-pthread -Wl,-E  -L/usr/local/lib'
    libpth=/usr/local/lib /usr/lib
    libs=-lm -lutil -lc
    perllibs=-lm -lutil -lc
    libc=/usr/lib/libc.so.41.0, so=so, useshrplib=false, libperl=libperl.a
    gnulibc_version=''
  Dynamic Linking:
    dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags=' '
Thread Next
FAIL bioperl-1.4 OpenBSD.i386-openbsd-thread-multi-64int 4.2 by chris
FAIL bioperl-1.4 OpenBSD.i386-openbsd-thread-multi-64int 4.2 by chris
Comments to Ask Bjørn Hansen at ask@perl.org | Group listing | About