FAIL bioperl-1.4 darwin-thread-multi-64int-2level 8.10.0

Front page | perl.cpan.testers | Postings from April 2008
FAIL bioperl-1.4 darwin-thread-multi-64int-2level 8.10.0

From:
chris
Date:
April 20, 2008 05:40
Subject:
FAIL bioperl-1.4 darwin-thread-multi-64int-2level 8.10.0
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/

Please cc any replies to cpan-testers@perl.org to keep other
test volunteers informed and to prevent any duplicate effort.

--

Dear 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] [Sun Apr 20 13:16:34 2008] Trying to get 'http://www.cpan.org/authors/id/B/BI/BIRNEY/bioperl-1.4.tar.gz'
[MSG] [Sun Apr 20 13:17:16 2008] Trying to get 'http://www.cpan.org/authors/id/B/BI/BIRNEY/CHECKSUMS'
[MSG] [Sun Apr 20 13:17:17 2008] Checksum matches for 'bioperl-1.4.tar.gz'
[MSG] [Sun Apr 20 13:17:45 2008] Extracted 'bioperl-1.4/'
[MSG] [Sun Apr 20 13:17:45 2008] Extracted 'bioperl-1.4/DEPRECATED'
[MSG] [Sun Apr 20 13:17:45 2008] Extracted 'bioperl-1.4/AUTHORS'
[MSG] [Sun Apr 20 13:17:45 2008] Extracted 'bioperl-1.4/BUGS'
[MSG] [Sun Apr 20 13:17:45 2008] Extracted 'bioperl-1.4/Changes'
[MSG] [Sun Apr 20 13:17:45 2008] Extracted 'bioperl-1.4/INSTALL'
[MSG] [Sun Apr 20 13:17:45 2008] Extracted 'bioperl-1.4/FAQ'
[MSG] [Sun Apr 20 13:17:45 2008] Extracted 'bioperl-1.4/Bio/'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/Align/'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/Align/AlignI.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/Align/DNAStatistics.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/Align/PairwiseStatistics.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/Align/StatisticsI.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/Align/Utilities.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/AlignIO.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/AnalysisI.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/AnalysisParserI.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/AnalysisResultI.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/AnnotatableI.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/AnnotationCollectionI.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/AnnotationI.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/Biblio.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/ClusterI.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/ClusterIO.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/DBLinkContainerI.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/DasI.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/DescribableI.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/FeatureHolderI.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/Graphics.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/IdCollectionI.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/IdentifiableI.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/LocatableSeq.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/LocationI.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/MapIO.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/OntologyIO.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/Perl.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/PrimarySeq.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/PrimarySeqI.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/Range.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/RangeI.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/SearchDist.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/SearchIO.pm'
[MSG] [Sun Apr 20 13:17:46 2008] Extracted 'bioperl-1.4/Bio/Seq.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/SeqAnalysisParserI.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/SeqFeatureI.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/SeqI.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/SeqIO.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/SeqUtils.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/SimpleAlign.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/SimpleAnalysisI.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/Species.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/Taxonomy.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/TreeIO.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/UpdateableSeqI.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/WebAgent.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/AlignIO/'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/AlignIO/bl2seq.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/AlignIO/clustalw.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/AlignIO/emboss.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/AlignIO/fasta.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/AlignIO/maf.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/AlignIO/mase.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/AlignIO/mega.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/AlignIO/meme.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/AlignIO/metafasta.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/AlignIO/msf.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/AlignIO/nexus.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/AlignIO/pfam.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/AlignIO/phylip.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/AlignIO/prodom.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/AlignIO/psi.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/AlignIO/selex.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/AlignIO/stockholm.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/Annotation/'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/Annotation/AnnotationFactory.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/Annotation/Collection.pm'
[MSG] [Sun Apr 20 13:17:47 2008] Extracted 'bioperl-1.4/Bio/Annotation/Comment.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Annotation/DBLink.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Annotation/OntologyTerm.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Annotation/Reference.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Annotation/SimpleValue.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Annotation/StructuredValue.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Annotation/TypeManager.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Assembly/'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Assembly/IO/'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Assembly/IO/phrap.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Assembly/IO/ace.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Assembly/Contig.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Assembly/ContigAnalysis.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Assembly/IO.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Assembly/Scaffold.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Assembly/ScaffoldI.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Biblio/'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Biblio/IO/'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Biblio/IO/medline2ref.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Biblio/IO/medlinexml.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Biblio/IO/pubmed2ref.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Biblio/IO/pubmedxml.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Biblio/Article.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Biblio/BiblioBase.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Biblio/Book.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Biblio/BookArticle.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Biblio/IO.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Biblio/Journal.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Biblio/JournalArticle.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Biblio/MedlineArticle.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Biblio/MedlineBook.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Biblio/MedlineBookArticle.pm'
[MSG] [Sun Apr 20 13:17:48 2008] Extracted 'bioperl-1.4/Bio/Biblio/MedlineJournal.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Biblio/MedlineJournalArticle.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Biblio/Organisation.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Biblio/Patent.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Biblio/Person.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Biblio/Proceeding.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Biblio/Provider.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Biblio/PubmedArticle.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Biblio/PubmedBookArticle.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Biblio/PubmedJournalArticle.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Biblio/Ref.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Biblio/Service.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Biblio/TechReport.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Biblio/Thesis.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Biblio/WebResource.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Cluster/'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Cluster/ClusterFactory.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Cluster/FamilyI.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Cluster/SequenceFamily.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Cluster/UniGene.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Cluster/UniGeneI.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/ClusterIO/'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/ClusterIO/dbsnp.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/ClusterIO/unigene.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/CodonUsage/'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/CodonUsage/Table.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/CodonUsage/IO.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Coordinate/'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Coordinate/Result/'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Coordinate/Result/Match.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Coordinate/Result/Gap.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Coordinate/Chain.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Coordinate/Collection.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Coordinate/ExtrapolatingPair.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Coordinate/GeneMapper.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Coordinate/Graph.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Coordinate/MapperI.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Coordinate/Pair.pm'
[MSG] [Sun Apr 20 13:17:49 2008] Extracted 'bioperl-1.4/Bio/Coordinate/Result.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/Coordinate/ResultI.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/Coordinate/Utils.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/BiblioI.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/Ace.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/Biblio/'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/Biblio/biofetch.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/Biblio/soap.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/BioFetch.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/CUTG.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/DBFetch.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/EMBL.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/Failover.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/Fasta.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/FileCache.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/Flat.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/GDB.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/GFF.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/GenBank.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/GenPept.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/InMemoryCache.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/MANIFEST'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/Makefile.PL'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/MeSH.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/NCBIHelper.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/QueryI.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/RandomAccessI.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/RefSeq.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/Registry.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/SeqI.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/SwissProt.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/Taxonomy.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/Universal.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/UpdateableSeqI.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/WebDBSeqI.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/XEMBL.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/XEMBLService.pm'
[MSG] [Sun Apr 20 13:17:50 2008] Extracted 'bioperl-1.4/Bio/DB/Flat/'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/fasta.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/embl.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/genbank.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/swiss.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/swissprot.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/Flat/BinarySearch.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/biofetch.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/ace.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/iterator.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/mysql.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/oracle.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/oracleace.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/pg.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/biofetch_oracle.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/memory.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/memory_iterator.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Featname.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Feature.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Homol.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/RelSegment.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Segment.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Typename.pm'
[MSG] [Sun Apr 20 13:17:51 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/alignment.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/clone.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/coding.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/match.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/none.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/processed_transcript.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/transcript.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_acembly.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_genscan.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_refgene.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_softberry.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_unigene.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Util/'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Util/Binning.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Util/Rearrange.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/Query/'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/Query/GenBank.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/Query/WebQuery.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/Taxonomy/'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/Taxonomy/entrez.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/DB/Taxonomy/flatfile.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/Das/'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/Das/FeatureTypeI.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/Das/SegmentI.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/Event/'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/Event/EventGeneratorI.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/Event/EventHandlerI.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/Expression/'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/Expression/FeatureGroup/'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/Expression/FeatureGroup.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/Expression/FeatureI.pm'
[MSG] [Sun Apr 20 13:17:52 2008] Extracted 'bioperl-1.4/Bio/Expression/FeatureSet/'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Expression/FeatureSet/FeatureSetMas50.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Factory/'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Factory/AnalysisI.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Factory/ApplicationFactoryI.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Factory/DriverFactory.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Factory/FTLocationFactory.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Factory/HitFactoryI.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Factory/LocationFactoryI.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Factory/MapFactoryI.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Factory/ObjectBuilderI.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Factory/ObjectFactory.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Factory/ObjectFactoryI.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Factory/ResultFactoryI.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Factory/SeqAnalysisParserFactory.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Factory/SeqAnalysisParserFactoryI.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Factory/SequenceFactoryI.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Factory/SequenceProcessorI.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Factory/SequenceStreamI.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Factory/TreeFactoryI.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Graphics/'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Graphics/FeatureFile/'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Graphics/FeatureFile/Iterator.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Graphics/ConfiguratorI.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Graphics/Feature.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Graphics/FeatureFile.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Graphics/Panel.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Graphics/Pictogram.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Graphics/RendererI.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Graphics/Util.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/Factory.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/alignment.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/anchored_arrow.pm'
[MSG] [Sun Apr 20 13:17:53 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/arrow.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/box.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/cds.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/crossbox.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/diamond.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/dna.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/dot.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/ellipse.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/ex.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/extending_arrow.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/generic.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/graded_segments.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/group.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/heterogeneous_segments.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/line.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/minmax.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/oval.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/pinsertion.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/primers.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/processed_transcript.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/redgreen_box.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/redgreen_segment.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/rndrect.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/ruler_arrow.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/segmented_keyglyph.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/segments.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/span.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/splice_site.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/toomany.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/track.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/transcript.pm'
[MSG] [Sun Apr 20 13:17:54 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/transcript2.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/translation.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/triangle.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/xyplot.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/Index/'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/Index/Abstract.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/Index/AbstractSeq.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/Index/Blast.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/Index/EMBL.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/Index/Fasta.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/Index/Fastq.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/Index/GenBank.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/Index/SwissPfam.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/Index/Swissprot.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/BioPerl.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/Loader.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/README'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/SRS.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/AARange.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Chain.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/ChainI.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/DNA.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Exon.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Gene.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Intron.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Mutation.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Mutator.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Prim_Transcript.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Range.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Repeat_Region.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Repeat_Unit.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/SeqI.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Transcript.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Translation.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/Location/'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/Location/Atomic.pm'
[MSG] [Sun Apr 20 13:17:55 2008] Extracted 'bioperl-1.4/Bio/Location/AvWithinCoordPolicy.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Location/CoordinatePolicyI.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Location/Fuzzy.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Location/FuzzyLocationI.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Location/NarrowestCoordPolicy.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Location/Simple.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Location/Split.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Location/SplitLocationI.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Location/WidestCoordPolicy.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Map/'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Map/CytoMap.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Map/CytoMarker.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Map/CytoPosition.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Map/LinkageMap.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Map/LinkagePosition.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Map/MapI.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Map/MappableI.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Map/Marker.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Map/MarkerI.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Map/Microsatellite.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Map/OrderedPosition.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Map/OrderedPositionWithDistance.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Map/Position.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Map/PositionI.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Map/SimpleMap.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/MapIO/'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/MapIO/mapmaker.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Matrix/'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Matrix/IO/'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Matrix/IO/phylip.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Matrix/IO/scoring.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/PsmHeader.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/Psm.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/InstanceSite.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/InstanceSiteI.pm'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/'
[MSG] [Sun Apr 20 13:17:56 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/transfac.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/mast.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/meme.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/PsmHeaderI.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/PsmI.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/SiteMatrix.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/SiteMatrixI.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Matrix/Generic.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Matrix/IO.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Matrix/MatrixI.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Matrix/PhylipDist.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Matrix/Scoring.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Ontology/'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Ontology/GOterm.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Ontology/InterProTerm.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Ontology/Ontology.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Ontology/OntologyEngineI.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Ontology/OntologyI.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Ontology/OntologyStore.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Ontology/Path.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Ontology/PathI.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Ontology/Relationship.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Ontology/RelationshipFactory.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Ontology/RelationshipI.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Ontology/RelationshipType.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Ontology/SimpleGOEngine.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Ontology/SimpleOntologyEngine.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Ontology/Term.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Ontology/TermFactory.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/Ontology/TermI.pm'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/'
[MSG] [Sun Apr 20 13:17:57 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/BaseSAXHandler.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/InterProHandler.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/InterProParser.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/dagflat.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/goflat.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/simplehierarchy.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/soflat.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/Phenotype/'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/Phenotype/MeSH/'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/Phenotype/MeSH/Term.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/Phenotype/MeSH/Twig.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/MiniMIMentry.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/OMIMentry.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/OMIMparser.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/Phenotype/Correlate.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/Phenotype/Measure.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/Phenotype/Phenotype.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/Phenotype/PhenotypeI.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/PopGen/'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/PopGen/IO/'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/PopGen/IO/csv.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/PopGen/IO/prettybase.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/PopGen/Genotype.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/PopGen/GenotypeI.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/PopGen/IO.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/PopGen/Individual.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/PopGen/IndividualI.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/PopGen/Marker.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/PopGen/MarkerI.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/PopGen/PopStats.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/PopGen/Population.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/PopGen/PopulationI.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/PopGen/Statistics.pm'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/PopGen/Simulation/'
[MSG] [Sun Apr 20 13:17:58 2008] Extracted 'bioperl-1.4/Bio/PopGen/Simulation/Coalescent.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/PopGen/Simulation/GeneticDrift.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Restriction/'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme/'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme/MultiCut.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme/MultiSite.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Restriction/Analysis.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Restriction/EnzymeCollection.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Restriction/EnzymeI.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Restriction/IO.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Restriction/IO/'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Restriction/IO/bairoch.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Restriction/IO/base.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Restriction/IO/itype2.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Restriction/IO/withrefm.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Root/'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Root/Exception.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Root/Err.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Root/Global.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Root/HTTPget.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Root/IO.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Root/IOManager.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Root/Object.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Root/Root.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Root/RootI.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Root/Storable.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Root/Utilities.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Root/Vector.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Root/Version.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Root/Xref.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Search/'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/BlastHSP.pm'
[MSG] [Sun Apr 20 13:17:59 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/FastaHSP.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/GenericHSP.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/HMMERHSP.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/HSPFactory.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/HSPI.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/PSLHSP.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/PsiBlastHSP.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/WABAHSP.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/Hit/'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/Hit/BlastHit.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/Hit/Fasta.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/Hit/GenericHit.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/Hit/HMMERHit.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/Hit/HitFactory.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/Hit/HitI.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/Hit/PsiBlastHit.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/BlastUtils.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/DatabaseI.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/GenericDatabase.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/Processor.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/SearchUtils.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/Iteration/'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/Iteration/GenericIteration.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/Iteration/IterationI.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/Result/'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/Result/BlastResult.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/Result/GenericResult.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/Result/HMMERResult.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/Result/ResultFactory.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/Result/ResultI.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/Search/Result/WABAResult.pm'
[MSG] [Sun Apr 20 13:18:00 2008] Extracted 'bioperl-1.4/Bio/SearchIO/'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/BSMLResultWriter.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/GbrowseGFF.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/HSPTableWriter.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/HTMLResultWriter.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/HitTableWriter.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/ResultTableWriter.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/TextResultWriter.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/EventHandlerI.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/FastHitEventBuilder.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/IteratedSearchResultEventBuilder.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/SearchResultEventBuilder.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/SearchWriterI.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/axt.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/blast.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/blasttable.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/blastxml.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/exonerate.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/fasta.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/hmmer.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/megablast.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/psl.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/sim4.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/waba.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/SearchIO/wise.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/Seq/'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/Seq/Meta/'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/Seq/Meta/Array.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/Seq/BaseSeqProcessor.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/Seq/EncodedSeq.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/Seq/LargePrimarySeq.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/Seq/LargeSeq.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/Seq/Meta.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/Seq/MetaI.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/Seq/PrimaryQual.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/Seq/PrimedSeq.pm'
[MSG] [Sun Apr 20 13:18:01 2008] Extracted 'bioperl-1.4/Bio/Seq/QualI.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/Seq/RichSeq.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/Seq/RichSeqI.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/Seq/SeqBuilder.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/Seq/SeqFactory.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/Seq/SeqFastaSpeedFactory.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/Seq/SeqWithQuality.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/Seq/SequenceTrace.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/Seq/TraceI.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/ExonI.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Exon.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/GeneStructure.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/GeneStructureI.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Intron.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/NC_Feature.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Poly_A_site.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Promoter.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Transcript.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/TranscriptI.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/UTR.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/AnnotationAdaptor.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Collection.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/CollectionI.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Computation.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/FeaturePair.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Generic.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/PositionProxy.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Primer.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Similarity.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/SimilarityPair.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/SiRNA/'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/SiRNA/Oligo.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/SiRNA/Pair.pm'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Tools/'
[MSG] [Sun Apr 20 13:18:02 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Tools/TypeMapper.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Tools/Unflattener.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/game/'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/game/featHandler.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/game/gameHandler.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/game/gameSubs.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/game/gameWriter.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/game/seqHandler.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/FTHelper.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/MultiFile.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/abi.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/ace.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/alf.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/asciitree.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/bsml.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/chadoxml.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/ctf.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/embl.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/exp.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/fasta.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/fastq.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/game.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/gcg.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/genbank.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/kegg.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/largefasta.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/locuslink.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/metafasta.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/phd.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/pir.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/pln.pm'
[MSG] [Sun Apr 20 13:18:03 2008] Extracted 'bioperl-1.4/Bio/SeqIO/qual.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/SeqIO/raw.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/SeqIO/scf.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/SeqIO/swiss.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/SeqIO/tab.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/SeqIO/tigr.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/SeqIO/ztr.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Structure/'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Structure/Chain.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Structure/Atom.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Structure/IO/'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Structure/IO/pdb.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Structure/Entry.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Structure/IO.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Structure/Model.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Structure/Residue.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Structure/StructureI.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Structure/SecStr/'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Structure/SecStr/DSSP/'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Structure/SecStr/DSSP/Res.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Structure/SecStr/STRIDE/'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Structure/SecStr/STRIDE/Res.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Symbol/'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Symbol/Alphabet.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Symbol/AlphabetI.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Symbol/DNAAlphabet.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Symbol/ProteinAlphabet.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Symbol/README.Symbol'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Symbol/Symbol.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Symbol/SymbolI.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Taxonomy/'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Taxonomy/FactoryI.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Taxonomy/Node.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Taxonomy/Taxon.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Taxonomy/Tree.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Tools/'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Tools/Alignment/'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Tools/Alignment/Consed.pm'
[MSG] [Sun Apr 20 13:18:04 2008] Extracted 'bioperl-1.4/Bio/Tools/Alignment/Trim.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/AlignFactory.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/AnalysisResult.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/BPbl2seq.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/BPlite.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/BPpsilite.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/Blast.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/Blat.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/CodonTable.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/Coil.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/ECnumber.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/EPCR.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/ESTScan.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/Eponine.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/Est2Genome.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/FootPrinter.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/GFF.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/Gel.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/Geneid.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/Genemark.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/Genewise.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/Genomewise.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/Genscan.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/Glimmer.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/Grail.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/GuessSeqFormat.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/Hmmpfam.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/IUPAC.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/Lucy.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/MZEF.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/OddCodes.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/Primer3.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/Prints.pm'
[MSG] [Sun Apr 20 13:18:05 2008] Extracted 'bioperl-1.4/Bio/Tools/Profile.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Promoterwise.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/PrositeScan.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Pseudowise.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/QRNA.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/RandomDistFunctions.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/RepeatMasker.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/RestrictionEnzyme.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Seg.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/SeqAnal.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/SeqPattern.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/SeqStats.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/SeqWords.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/SiRNA.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Sigcleave.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Signalp.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Tmhmm.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/WWW.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/dpAlign.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/pICalculator.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/pSW.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/DNA/'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/DNA/ESEfinder.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/SimpleAnalysisBase.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Domcut.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/ELM.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/GOR4.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/HNN.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Mitoprot.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/NetPhos.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Scansite.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Sopma.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/BPlite/'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/BPlite/Iteration.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/BPlite/HSP.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/BPlite/Sbjct.pm'
[MSG] [Sun Apr 20 13:18:06 2008] Extracted 'bioperl-1.4/Bio/Tools/Blast/'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Blast/Sbjct.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Blast/CHANGES'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Blast/HSP.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Blast/HTML.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Blast/README'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/EMBOSS/'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/EMBOSS/Palindrome.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/HMMER/'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/HMMER/Domain.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/HMMER/Results.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/HMMER/Set.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Molphy/'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Molphy/Result.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Molphy.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML/'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML/ModelResult.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML/Result.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Phylip/'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Phylip/ProtDist.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Prediction/'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Prediction/Exon.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Prediction/Gene.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Primer/'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Primer/Assessor/'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Primer/Assessor/Base.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Primer/AssessorI.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Primer/Feature.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Primer/Pair.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Run/'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Run/README'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Run/RemoteBlast.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Run/StandAloneBlast.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Run/WrapperBase.pm'
[MSG] [Sun Apr 20 13:18:07 2008] Extracted 'bioperl-1.4/Bio/Tools/Sim4/'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Tools/Sim4/Results.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Tools/Sim4/Exon.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Tree/'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Tree/AlleleNode.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Tree/Node.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Tree/NodeI.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Tree/NodeNHX.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Tree/RandomFactory.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Tree/Statistics.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Tree/Tree.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Tree/TreeFunctionsI.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Tree/TreeI.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/TreeIO/'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/TreeIO/TreeEventBuilder.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/TreeIO/lintree.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/TreeIO/newick.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/TreeIO/nexus.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/TreeIO/nhx.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/TreeIO/svggraph.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/TreeIO/tabtree.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Variation/'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Variation/IO/'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Variation/IO/flat.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Variation/IO/xml.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Variation/AAChange.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Variation/AAReverseMutate.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Variation/Allele.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Variation/DNAMutation.pm'
[MSG] [Sun Apr 20 13:18:08 2008] Extracted 'bioperl-1.4/Bio/Variation/IO.pm'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/Bio/Variation/README'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/Bio/Variation/RNAChange.pm'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/Bio/Variation/SNP.pm'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/Bio/Variation/SeqDiff.pm'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/Bio/Variation/VariantI.pm'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/faq/'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/faq/faq.html'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/faq/faq.dtd'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/faq/faq.pl'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/faq/faq.xml'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/makedoc.PL'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/howto/'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/howto/examples/'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/blastn.out'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/data1.txt'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/embl2picture.pl'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/factor7.embl'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast1.pl'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast2.pl'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast3.pl'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast4.pl'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_features.pl'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/howto/examples/README'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/howto/figs/'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/howto/figs/graphics/'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig1.png'
[MSG] [Sun Apr 20 13:18:09 2008] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig2.png'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig3.png'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig4.png'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig5.png'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig6.png'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/figs/README'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/html/'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/html/images/'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/html/images/tip.png'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/html/Flat_Databases.html'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/html/Graphics-HOWTO.html'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/html/OBDA_Access.html'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/html/PAML.html'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/html/README'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/html/SearchIO.html'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/html/SeqIO.html'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/html/SimpleWebAnalysis.html'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/html/e-novative.css'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/pdf/'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/pdf/Flat_Databases.pdf'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/pdf/Graphics-HOWTO.pdf'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/pdf/OBDA_Access.pdf'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/pdf/PAML.pdf'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/pdf/SearchIO.pdf'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/pdf/SeqIO.pdf'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/pdf/SimpleWebAnalysis.pdf'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/pdf/Trees.pdf'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/sgml/'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/sgml/Feature-Annotation.sgml'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/sgml/Flat_Databases.sgml'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/sgml/Graphics-HOWTO.sgml'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/sgml/OBDA_Access.sgml'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/sgml/PAML.sgml'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/sgml/README'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/sgml/SearchIO.sgml'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/sgml/SeqIO.sgml'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/sgml/SimpleWebAnalysis.sgml'
[MSG] [Sun Apr 20 13:18:10 2008] Extracted 'bioperl-1.4/doc/howto/sgml/Trees.sgml'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/doc/howto/txt/'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/doc/howto/txt/Flat_Databases.txt'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/doc/howto/txt/SimpleWebAnalysis.txt'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/INSTALL.WIN'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/LICENSE'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/MANIFEST.SKIP'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/Makefile.PL'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/PLATFORMS'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/README'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/biodatabases.pod'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/biodesign.pod'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/bioperl.lisp'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/bioperl.pod'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/bioscripts.pod'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/bptutorial.pl'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/Bio-DB-GFF/'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/Bio-DB-GFF/load_ucsc.pl'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/bioperl.pl'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/generate_random_seq.pl'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/longorf.pl'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/make_mrna_protein.pl'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/make_primers.pl'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/rev_and_trans.pl'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/revcom_dir.pl'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/subsequence.cgi'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/align/'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/align/align_on_codons.pl'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/align/aligntutorial.pl'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/align/clustalw.pl'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/align/simplealign.pl'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/biblio/'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/biblio/biblio_examples.pl'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/biblio/biblio_soap.pl'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/biographics/'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/biographics/all_glyphs.pl'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/biographics/dynamic_glyphs.pl'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/biographics/feature_data.gff'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/biographics/feature_data.txt'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/biographics/lots_of_glyphs.pl'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/biographics/render_sequence.pl'
[MSG] [Sun Apr 20 13:18:11 2008] Extracted 'bioperl-1.4/examples/cluster/'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/cluster/dbsnp.pl'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/contributed/'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/contributed/nmrpdb_parse.pl'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/contributed/prosite2perl.pl'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/contributed/rebase2list.pl'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/db/'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/db/get_seqs.pl'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/db/dbfetch'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/db/est_tissue_query.pl'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/db/gb2features.pl'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/db/getGenBank.pl'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/db/rfetch.pl'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/db/use_registry.pl'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/liveseq/'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/liveseq/change_gene.pl'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/popgen/'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/popgen/parse_calc_stats.pl'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/root/'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/root/lib/'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/root/lib/Bio/'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/root/lib/Bio/PrimarySeq.pm'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/root/lib/Bio/PrimarySeqI.pm'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/root/lib/Bio/Seq.pm'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/root/lib/Bio/SeqI.pm'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/root/lib/Error.pm'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/root/lib/TestInterface.pm'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/root/lib/TestObject.pm'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/root/README'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/root/exceptions1.pl'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/root/exceptions2.pl'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/root/exceptions3.pl'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/root/exceptions4.pl'
[MSG] [Sun Apr 20 13:18:12 2008] Extracted 'bioperl-1.4/examples/searchio/'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/searchio/blast_example.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/searchio/custom_writer.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/searchio/hitwriter.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/searchio/hspwriter.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/searchio/htmlwriter.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/searchio/psiblast_features.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/searchio/psiblast_iterations.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/searchio/rawwriter.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/searchio/resultwriter.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/searchio/waba2gff.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/sirna/'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/sirna/TAG'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/sirna/rnai_finder.cgi'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/tk/'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/tk/gsequence.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/tk/hitdisplay.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/tools/'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/tools/gb_to_gff.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/tools/gff2ps.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/tools/parse_codeml.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/tools/psw.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/tools/restriction.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/tools/run_genscan.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/tools/seq_pattern.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/tools/standaloneblast.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/tree/'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/examples/tree/paup2phylip.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/maintenance/'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/maintenance/authors.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/maintenance/README'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/maintenance/modules.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/maintenance/pod.pl'
[MSG] [Sun Apr 20 13:18:13 2008] Extracted 'bioperl-1.4/models/'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/models/biblio.dia'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/models/README'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/models/bio_liveseq_variation.dia'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/models/bio_map.dia'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/models/bio_restriction.dia'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/models/bioperl.dia'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/models/coordinatemapper.dia'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/models/map_proposal.txt'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/models/maps_and_markers.dia'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/models/popgen.dia'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/models/population_proposal.txt'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/load_gff.PLS'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/README'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/TAG'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/bp_genbank2gff.PLS'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/bulk_load_gff.PLS'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/fast_load_gff.PLS'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/generate_histogram.PLS'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/load_ucsc.pl'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/pg_bulk_load_gff.PLS'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_gadfly.PLS'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_ncbi_human.PLS'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_sgd.PLS'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_wormbase.PLS'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/install_bioperl_scripts.pl'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/DB/'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/DB/TAG'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/DB/biofetch_genbank_proxy.PLS'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/DB/bioflat_index.PLS'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/DB/biogetseq.PLS'
[MSG] [Sun Apr 20 13:18:14 2008] Extracted 'bioperl-1.4/scripts/DB/flanks.PLS'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/biblio/'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/biblio/TAG'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/biblio/biblio.PLS'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/das/'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/das/README'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/das/TAG'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/graphics/'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/graphics/frend.PLS'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/graphics/README'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/graphics/TAG'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/graphics/feature_draw.PLS'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/graphics/search_overview.PLS'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/index/'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/index/TAG'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/index/bp_fetch.PLS'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/index/bp_index.PLS'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/popgen/'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/popgen/composite_LD.PLS'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/popgen/heterogeneity_test.PLS'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/searchio/'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/searchio/filter_search.PLS'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/seq/'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/seq/TAG'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/seq/extract_feature_seq.PLS'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/seq/seqconvert.PLS'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/seq/split_seq.PLS'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/seq/translate_seq.PLS'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/seqstats/'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/seqstats/TAG'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/seqstats/aacomp.PLS'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/seqstats/chaos_plot.PLS'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/seqstats/gccalc.PLS'
[MSG] [Sun Apr 20 13:18:15 2008] Extracted 'bioperl-1.4/scripts/seqstats/oligo_count.PLS'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/taxa/'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/taxa/TAG'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/taxa/local_taxonomydb_query.PLS'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/taxa/taxid4species.PLS'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/tree/'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/tree/TAG'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/tree/blast2tree.PLS'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/utilities/'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/utilities/bp_nrdb.PLS'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/utilities/README'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/utilities/TAG'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/utilities/bp_mrtrans.PLS'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/utilities/bp_sreformat.PLS'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/utilities/dbsplit.PLS'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/utilities/mask_by_search.PLS'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/utilities/mutate.PLS'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/utilities/pairwise_kaks.PLS'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/utilities/remote_blast.PLS'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/utilities/search2BSML.PLS'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/utilities/search2alnblocks.PLS'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/utilities/search2gff.PLS'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/utilities/search2tribe.PLS'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/scripts/utilities/seq_length.PLS'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/t/'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/t/data/'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/t/data/biodbgff/'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/t/data/biodbgff/test.gff'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/t/data/503384.MEGABLAST.0'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/t/data/503384.MEGABLAST.2'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/t/data/5X_1895.FASTXY'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/t/data/AAC12660.fa'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/t/data/AB077698.gb'
[MSG] [Sun Apr 20 13:18:16 2008] Extracted 'bioperl-1.4/t/data/AE003528_ecoli.bls'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/AE003644_Adh-genomic.gb'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/AF032047.gbk'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/AF165282.gb'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/AHCYL1.kegg'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/ATF14F8.gbk'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/AY095303S1.gbk'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/AnnIX-v003.gbk'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/BK000016-tpa.gbk'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/BLOSUM50'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/BN000066-tpa.embl'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/D10483.gbk'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/D12555.gbk'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/ECAPAH02.embl'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/GO.defs.test'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/GO.defs.test2'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/Genscan.FastA'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.FASTA'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.fa'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.gff'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.grail'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.grailexp'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.mzef'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.tblastx'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/L77119.hmmer'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/LL-sample.seq'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/LOAD_Ccd1.dnd'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/LittleChrY.dbsnp.xml'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/MmCT'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/NM_002254.gb'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/NT_021877.gbk'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/PAM250'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/SwissProt.dat'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/U58726.gb'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/X98338_Adh-mRNA.gb'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/a_thaliana.blastn'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/aaml.mlc'
[MSG] [Sun Apr 20 13:18:17 2008] Extracted 'bioperl-1.4/t/data/aaml_pairwise.mlc'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/acefile.ace.1'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/acefile.singlets'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/alnfile.fasta'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/amino.fa'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/ar.embl'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/bl2seq.blastn'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/bl2seq.blastn.rev'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/bl2seq.blastx.out'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/bl2seq.bug940.out'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/bl2seq.out'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/bl2seq.tblastx.out'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/blast.report'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/blat.psLayout3'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/c200-vs-yeast.BLASTN'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/c200-vs-yeast.BLASTN.m8'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/chad100.scf'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/codeml.mlc'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/codeml_nssites.mlc'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/compLD_missingtest.prettybase'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/compLD_test.prettybase'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/component.ontology.test'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/component.ontology.test2'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/crab.dat.cn'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/crab.nj'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/crab.njb'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/crypto.sim4-0'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/crypto.sim4-3'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/crypto.sim4-4'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/cys1_dicdi.water'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/cysprot.fa'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/cysprot.msf'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/cysprot.needle'
[MSG] [Sun Apr 20 13:18:18 2008] Extracted 'bioperl-1.4/t/data/cysprot.tblastn'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/cysprot.water'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/cysprot1.FASTA'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/cysprot1.fa'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/cysprot1a.fa'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/cysprot1a.msf'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/cysprot1b.fa'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/cysprot1b.hmmsearch'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/cysprot1b.msf'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/cysprot1b.newick'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/cysprot_vs_gadfly.FASTA'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/dmel_2Lchunk.gb'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/dna1.fa'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/dna2.fa'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/dnaE-bsub-prot.fa'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/dnaE-bsub.fa'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/dnaEbsub_ecoli.wublastx'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/dnaEbsub_ecoli.wutblastn'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/dnaEbsub_ecoli.wutblastx'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/ecoli-trna-qrna.out'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/ecoli_domains.rps.xml'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/ecoli_domains.rpsblast'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/ecolitst.bls'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/ecolitst.fa'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/ecolitst.wublastp'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/empty.bl2seq'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/expected.blast.out'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/factor7.embl'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/footprinter.out'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/geneid_1.0.out'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/genemark.out'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/genewise.out'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/genewise_output.paracel_btk'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/genomewise.out'
[MSG] [Sun Apr 20 13:18:19 2008] Extracted 'bioperl-1.4/t/data/genomic-seq.epcr'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/genomic-seq.fasta'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/genomic-seq.genscan'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/genomic-seq.mzef'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/gf-s71.needle'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/glimmer.out'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/hemoglobinA.meg'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/hg16_chroms.gff'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/hmmpfam.out'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/hmmsearch.out'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/hs_est.est2genome'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/hs_fugu.newick'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/hs_owlmonkey.fas'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/hs_owlmonkey.fasta'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/hsinsulin.blastcl3.blastn'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/humor.maf'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/humts1.pal'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/insulin.water'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/interpro_short.xml'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/lucy.info'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/lucy.qual'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/lucy.seq'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/lucy.stderr'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/lysozyme6.protml'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/lysozyme6.simple.protml'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/mapmaker.out'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/mast.dat'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/megablast_output.paracel_btk'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/meme.dat'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/mpath.ontology.test'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/multi_1.fa'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/multi_2.fa'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/multi_blast.bls'
[MSG] [Sun Apr 20 13:18:20 2008] Extracted 'bioperl-1.4/t/data/multifa.seq'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/multiseq.bls'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/mus.bls.xml'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/mutations.dat'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/mutations.xml'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/myco_sites.gff'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/nei_gojobori_test.aln'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/neighbor.dist'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/no-genes.genscan'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/no_hsps.blastp'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/noninterleaved.phy'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/omim_genemap_test'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/omim_text_test'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/pdb1bpt.ent'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/phi.out'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/phipsi.out'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/phredfile.phd'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/phylipdist-36.out'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/phylipdist.out'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/pictogram.fa'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/plague_yeast.bls.xml'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/polymorphism.dat'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/polymorphism.xml'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/popgen_saureus.dat'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/popgen_saureus.multidat'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/popstats.prettybase'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/roa1.dat'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/primedseq.fa'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/primer3_infile.txt'
[MSG] [Sun Apr 20 13:18:21 2008] Extracted 'bioperl-1.4/t/data/primer3_outfile.txt'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/primer3_output.txt'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/promoterwise.out'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/protpars.phy'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/psiblastreport.out'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/qrna-relloc.out'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/qualfile.qual'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/rebase.itype2'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/rebase.withrefm'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/repeatmasker.fa.out'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/revcomp_mrna.gb'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/roa1.genbank'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/roa1.swiss'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/sbay_c545-yeast.BLASTZ.PSL'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/seqdatabase.ini'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/seqfile.pir'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/seqs.fas'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/sequencefamily.dat'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/short.blx'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/sim4.for.for'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/sim4.for.rev'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/sim4.rev'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/sofa.ontology'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/sparsealn.needle'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/stress_test_medline.xml'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/stress_test_pubmed.xml'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/swiss.dat'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/swisspfam.data'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/test.ace'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/test.embl'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/test.fasta'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/test.game'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/test.gcg'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/test.gcgblast'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/test.gcgfasta'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/test.genbank'
[MSG] [Sun Apr 20 13:18:22 2008] Extracted 'bioperl-1.4/t/data/test.genbank.noseq'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/test.mase'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/test.metafasta'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/test.nh'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/test.nhx'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/test.pfam'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/test.pir'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/test.raw'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/test.swiss'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/test.tab'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/test.txt'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/test.waba'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/test_badlf.gcg'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/testaln.aln'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/testaln.fasta'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/testaln.mase'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/testaln.metafasta'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/testaln.msf'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/testaln.nexus'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/testaln.pfam'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/testaln.phylip'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/testaln.prodom'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/testaln.selex'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/testaln.stockholm'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/testdat.exonerate'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/testdbaccnums.out'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/testfuzzy.genbank'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/transfac.dat'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/unigene.data'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/version2.scf'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/version3.scf'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/worm_fam_2785.cdna'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/yn00.mlc'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/biographics/'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version1.gif'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version1.png'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version2.gif'
[MSG] [Sun Apr 20 13:18:23 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version2.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version3.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version4.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version5.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version6.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version7.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version8.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version1.gif'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version1.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version10.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version11.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version12.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version13.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version14.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version2.gif'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version2.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version3.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version4.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version5.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version6.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version7.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version8.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version9.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/feature_data.txt'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/version1.gif'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/version1.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/version2.gif'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/version2.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/version3.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/version4.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/version5.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/version6.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/version7.png'
[MSG] [Sun Apr 20 13:18:24 2008] Extracted 'bioperl-1.4/t/data/consed_project/'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.contigs'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.log'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.ace.1'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs.qual'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.log'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.problems'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.problems.qual'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.qual'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.singlets'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.view'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.newtags'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.phrap.out'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.screen.out'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_projectNewChromats.fof'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project_to_alu.cross'
[MSG] [Sun Apr 20 13:18:25 2008] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4922R.phd.1'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4924F.phd.1'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4924R.phd.1'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4947F.phd.1'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/data/dbfa/'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/data/dbfa/1.fa'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/data/dbfa/2.fa'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/data/dbfa/3.fa'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/data/dbfa/4.fa'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/data/dbfa/5.fa'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/data/dbfa/6.fa'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/data/dbfa/7.fa'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/data/registry/'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/data/registry/bdb/'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/data/registry/bdb/seqdatabase.ini'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/data/registry/flat/'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/data/registry/flat/seqdatabase.ini'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/AAChange.t'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/AAReverseMutate.t'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/AlignIO.t'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/AlignStats.t'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/Allele.t'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/Alphabet.t'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/Annotation.t'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/AnnotationAdaptor.t'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/Assembly.t'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/BPbl2seq.t'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/BPlite.t'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/BPpsilite.t'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/Biblio.t'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/BiblioReferences.t'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/Biblio_biofetch.t'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/BioDBGFF.t'
[MSG] [Sun Apr 20 13:18:26 2008] Extracted 'bioperl-1.4/t/BioFetch_DB.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/BioGraphics.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/BlastIndex.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/Chain.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/ClusterIO.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/Coalescent.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/CodonTable.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/CoordinateGraph.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/CoordinateMapper.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/Correlate.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/CytoMap.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/DB.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/DBCUTG.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/DBFasta.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/DNAMutation.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/Domcut.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/ECnumber.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/ELM.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/EMBL_DB.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/EMBOSS_Tools.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/ESEfinder.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/EncodedSeq.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/Exception.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/Exonerate.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/FootPrinter.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/GDB.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/GFF.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/GOR4.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/GOterm.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/GeneCoordinateMapper.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/Geneid.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/Genewise.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/Genomewise.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/Genpred.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/GuessSeqFormat.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/HNN.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/IUPAC.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/Index.t'
[MSG] [Sun Apr 20 13:18:27 2008] Extracted 'bioperl-1.4/t/InstanceSite.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/InterProParser.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/LinkageMap.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/LiveSeq.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/LocatableSeq.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/Location.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/LocationFactory.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/LocusLink.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/Map.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/MapIO.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/Matrix.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/MeSH.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/Measure.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/MetaSeq.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/MicrosatelliteMarker.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/MiniMIMentry.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/MitoProt.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/Molphy.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/Mutation.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/Mutator.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/NetPhos.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/Node.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/OMIMentry.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/OMIMentryAllelicVariant.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/OMIMparser.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/OddCodes.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/Ontology.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/OntologyEngine.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/PAML.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/Perl.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/Phenotype.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/PhylipDist.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/Pictogram.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/PopGen.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/PopGenSims.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/PrimarySeq.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/Primer.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/Promoterwise.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/ProtDist.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/QRNA.t'
[MSG] [Sun Apr 20 13:18:28 2008] Extracted 'bioperl-1.4/t/RNAChange.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/RandDistFunctions.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/RandomTreeFactory.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/Range.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/RangeI.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/RefSeq.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/Registry.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/Relationship.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/RelationshipType.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/RemoteBlast.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/RepeatMasker.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/RestrictionAnalysis.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/RestrictionEnzyme.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/RestrictionIO.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/RootI.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/RootIO.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/RootStorable.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/SNP.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/Scansite.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/SearchDist.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/SearchIO.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/Seq.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/SeqAnalysisParser.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/SeqBuilder.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/SeqDiff.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/SeqFeatCollection.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/SeqFeature.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/SeqIO.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/SeqPattern.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/SeqStats.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/SeqUtils.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/SeqWords.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/SequenceFamily.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/Sigcleave.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/Sim4.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/SimilarityPair.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/SimpleAlign.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/SiteMatrix.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/Sopma.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/Species.t'
[MSG] [Sun Apr 20 13:18:29 2008] Extracted 'bioperl-1.4/t/StandAloneBlast.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/StructIO.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/Structure.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/Swiss.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/Symbol.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/Taxonomy.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/Tempfile.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/Term.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/Test.pm'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/Tools.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/Tree.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/TreeIO.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/UCSCParsers.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/Unflattener.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/Unflattener2.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/UniGene.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/Variation_IO.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/WABA.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/XEMBL_DB.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/cigarstring.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/consed.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/ePCR.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/est2genome.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/flat.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/game.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/hmmer.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/largefasta.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/largepseq.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/lucy.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/multiple_fasta.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/pICalculator.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/phd.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/primaryqual.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/primedseq.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/primer3.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/psm.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/qual.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/scf.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/seqfeaturePrimer.t'
[MSG] [Sun Apr 20 13:18:30 2008] Extracted 'bioperl-1.4/t/sequencetrace.t'
[MSG] [Sun Apr 20 13:18:31 2008] Extracted 'bioperl-1.4/t/seqwithquality.t'
[MSG] [Sun Apr 20 13:18:31 2008] Extracted 'bioperl-1.4/t/simpleGOparser.t'
[MSG] [Sun Apr 20 13:18:31 2008] Extracted 'bioperl-1.4/t/sirna.t'
[MSG] [Sun Apr 20 13:18:31 2008] Extracted 'bioperl-1.4/t/splicedseq.t'
[MSG] [Sun Apr 20 13:18:31 2008] Extracted 'bioperl-1.4/t/testformats.pl'
[MSG] [Sun Apr 20 13:18:31 2008] Extracted 'bioperl-1.4/t/trim.t'
[MSG] [Sun Apr 20 13:18:31 2008] Extracted 'bioperl-1.4/t/tutorial.t'
[MSG] [Sun Apr 20 13:18:31 2008] Extracted 'bioperl-1.4/MANIFEST'
[MSG] [Sun Apr 20 13:18:31 2008] Extracted 'bioperl-1.4/Makefile.old'
[MSG] [Sun Apr 20 13:18:35 2008] Extracted 'bioperl' to '/Volumes/Media/smoke/blead/.cpanplus/5.11.0/build/bioperl-1.4'
[MSG] [Sun Apr 20 13:18:43 2008] Generated sub tests. go make show_tests to see available subtests

*** Script Install Section ****

Bioperl comes with a number of useful scripts which you may wish to install.
Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively? [a] a

* Script Directory biblio *
These are scripts to manipulate bibliographic repositories using the
Bio::Biblio modules.
	Activating bp_biblio.pl....

* Script Directory Bio-DB-GFF *
These are scripts that go with the Bio::DB::GFF module, a basic
seqfeature database.  Install these scripts if you wish to use the
LDAS distributed annotation server or the Generic Genome Browser.

	Activating bp_genbank2gff.pl....
	Activating bp_bulk_load_gff.pl....
	Activating bp_fast_load_gff.pl....
	Activating bp_generate_histogram.pl....
	Activating bp_load_gff.pl....
	Activating bp_pg_bulk_load_gff.pl....
	Activating bp_process_gadfly.pl....
	Activating bp_process_ncbi_human.pl....
	Activating bp_process_sgd.pl....
	Activating bp_process_wormbase.pl....

* Script Directory das *
This directory is currently empty.  For the Lightweight Distributed
Annotation System (LDAS) server, see http://www.biodas.org/servers/

* Script Directory DB *
These are scripts to fetch sequence data from local and remote
sequence repositories using the Open Bio Database Access registry
protocol (http://obda.open-bio.org).
	Activating bp_biofe