FAIL bioperl-1.4 i386-netbsd-thread-multi-64int 3.1

Front page | perl.cpan.testers | Postings from August 2007
FAIL bioperl-1.4 i386-netbsd-thread-multi-64int 3.1

Thread Previous | Thread Next
From:
chris
Date:
August 21, 2007 16:04
Subject:
FAIL bioperl-1.4 i386-netbsd-thread-multi-64int 3.1
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 Ewan Birney,
    
This is a computer-generated error report created automatically by
CPANPLUS, version 0.80. 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] [Tue Aug 21 23:56:41 2007] Trying to get 'http://www.cpan.org/authors/id/L/LI/LIMAONE/CHECKSUMS'
[MSG] [Tue Aug 21 23:56:42 2007] Checksum matches for 'Bio-Grep-v0.10.0.tar.gz'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/README'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/TODO'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/lib/'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Backend/'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Backend/Vmatch.pm'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Backend/RE.pm'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Backend/GUUGle.pm'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Backend/Agrep.pm'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Backend/BackendI.pm'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Benchmarks.pod'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Cookbook.pod'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Root.pm'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Filter/'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Filter/FilterI.pm'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/Filter/FilterRemoveDuplicates.pm'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/SearchSettings.pm'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep/SearchResult.pm'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/lib/Bio/Grep.pm'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/META.yml'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/Makefile.PL'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/script/'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/script/bgrep'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/script/benchmark.pl'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/Build.PL'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/pod-coverage.t'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/Test.fasta'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/Test_pep.fasta'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/pod.t'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/TestFilter.pm'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/00.checkprereq.t'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/00.load.t'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/50.synopsis.t'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/perlcritic.t'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/Test2.fasta'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/11.backends.guugle.t'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/40.utils.t'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/Test_query_revcom.fasta'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/11.backends.re.t'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/BioGrepTest.pm'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/10.backends.all.t'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/30.features.alignments.t'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/TestGUUGleExtend.fasta'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/20.filter.t'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/BioGrepSkip.pm'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/TestRevCom.fasta'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/t/Test_query.fasta'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/Changes'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio-Grep-v0.10.0/MANIFEST'
[MSG] [Tue Aug 21 23:56:43 2007] Extracted 'Bio::Grep' to '/home/cpan/perl581/.cpanplus/5.8.1/build/Bio-Grep-v0.10.0'
[MSG] [Tue Aug 21 23:56:44 2007] Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Root::Version 0 not found.
Warning: prerequisite Carp::Assert 0 not found.
Warning: prerequisite Class::MethodMaker 2.02 not found.
Warning: prerequisite IO::String 1 not found.
Warning: prerequisite ToolSet 0.13 not found.
Warning: prerequisite UNIVERSAL::require 0.11 not found.
Writing Makefile for Bio::Grep

[MSG] [Tue Aug 21 23:56:44 2007] DEFAULT 'filter_prereqs' HANDLER RETURNING 'sub return value'
[MSG] [Tue Aug 21 23:56:44 2007] Module 'Bio::Grep' requires 'Bio::Root::Version' version '0' to be installed 
[MSG] [Tue Aug 21 23:56:44 2007] Module 'Bio::Grep' requires 'Carp::Assert' version '0' to be installed 
[MSG] [Tue Aug 21 23:56:44 2007] Module 'Bio::Grep' requires 'Class::MethodMaker' version '2.02' to be installed 
[MSG] [Tue Aug 21 23:56:44 2007] Module 'Bio::Grep' requires 'IO::String' version '1' to be installed 
[MSG] [Tue Aug 21 23:56:44 2007] Module 'Bio::Grep' requires 'ToolSet' version '0.13' to be installed 
[MSG] [Tue Aug 21 23:56:44 2007] Module 'Bio::Grep' requires 'UNIVERSAL::require' version '0.11' to be installed 
[MSG] [Tue Aug 21 23:56:44 2007] Trying to get 'http://www.cpan.org/authors/id/B/BI/BIRNEY/CHECKSUMS'
[MSG] [Tue Aug 21 23:56:45 2007] Checksum matches for 'bioperl-1.4.tar.gz'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/DEPRECATED'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/AUTHORS'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/BUGS'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Changes'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/INSTALL'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/FAQ'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/Align/'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/Align/AlignI.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/Align/DNAStatistics.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/Align/PairwiseStatistics.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/Align/StatisticsI.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/Align/Utilities.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/AlignIO.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/AnalysisI.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/AnalysisParserI.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/AnalysisResultI.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/AnnotatableI.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/AnnotationCollectionI.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/AnnotationI.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/Biblio.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/ClusterI.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/ClusterIO.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/DBLinkContainerI.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/DasI.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/DescribableI.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/FeatureHolderI.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/Graphics.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/IdCollectionI.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/IdentifiableI.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/LocatableSeq.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/LocationI.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/MapIO.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/OntologyIO.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/Perl.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/PrimarySeq.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/PrimarySeqI.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/Range.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/RangeI.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/SearchDist.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/SearchIO.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/Seq.pm'
[MSG] [Tue Aug 21 23:56:55 2007] Extracted 'bioperl-1.4/Bio/SeqAnalysisParserI.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/SeqFeatureI.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/SeqI.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/SeqIO.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/SeqUtils.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/SimpleAlign.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/SimpleAnalysisI.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Species.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Taxonomy.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/TreeIO.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/UpdateableSeqI.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/WebAgent.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/AlignIO/'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/AlignIO/bl2seq.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/AlignIO/clustalw.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/AlignIO/emboss.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/AlignIO/fasta.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/AlignIO/maf.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/AlignIO/mase.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/AlignIO/mega.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/AlignIO/meme.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/AlignIO/metafasta.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/AlignIO/msf.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/AlignIO/nexus.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/AlignIO/pfam.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/AlignIO/phylip.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/AlignIO/prodom.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/AlignIO/psi.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/AlignIO/selex.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/AlignIO/stockholm.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Annotation/'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Annotation/AnnotationFactory.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Annotation/Collection.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Annotation/Comment.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Annotation/DBLink.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Annotation/OntologyTerm.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Annotation/Reference.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Annotation/SimpleValue.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Annotation/StructuredValue.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Annotation/TypeManager.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Assembly/'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Assembly/IO/'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Assembly/IO/phrap.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Assembly/IO/ace.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Assembly/Contig.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Assembly/ContigAnalysis.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Assembly/IO.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Assembly/Scaffold.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Assembly/ScaffoldI.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/IO/'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/IO/medline2ref.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/IO/medlinexml.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/IO/pubmed2ref.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/IO/pubmedxml.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/Article.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/BiblioBase.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/Book.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/BookArticle.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/IO.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/Journal.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/JournalArticle.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/MedlineArticle.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/MedlineBook.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/MedlineBookArticle.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/MedlineJournal.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/MedlineJournalArticle.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/Organisation.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/Patent.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/Person.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/Proceeding.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/Provider.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/PubmedArticle.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/PubmedBookArticle.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/PubmedJournalArticle.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/Ref.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/Service.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/TechReport.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/Thesis.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Biblio/WebResource.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Cluster/'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Cluster/ClusterFactory.pm'
[MSG] [Tue Aug 21 23:56:56 2007] Extracted 'bioperl-1.4/Bio/Cluster/FamilyI.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/Cluster/SequenceFamily.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/Cluster/UniGene.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/Cluster/UniGeneI.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/ClusterIO/'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/ClusterIO/dbsnp.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/ClusterIO/unigene.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/CodonUsage/'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/CodonUsage/Table.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/CodonUsage/IO.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/Coordinate/'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Result/'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Result/Match.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Result/Gap.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Chain.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Collection.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/Coordinate/ExtrapolatingPair.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/Coordinate/GeneMapper.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Graph.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/Coordinate/MapperI.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Pair.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Result.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/Coordinate/ResultI.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Utils.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/BiblioI.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Ace.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Biblio/'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Biblio/biofetch.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Biblio/soap.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/BioFetch.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/CUTG.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/DBFetch.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/EMBL.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Failover.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Fasta.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/FileCache.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Flat.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/GDB.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/GFF.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/GenBank.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/GenPept.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/InMemoryCache.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/MANIFEST'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Makefile.PL'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/MeSH.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/NCBIHelper.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/QueryI.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/RandomAccessI.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/RefSeq.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Registry.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/SeqI.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/SwissProt.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Taxonomy.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Universal.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/UpdateableSeqI.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/WebDBSeqI.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/XEMBL.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/XEMBLService.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/fasta.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/embl.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/genbank.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/swiss.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/swissprot.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BinarySearch.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/biofetch.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/ace.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/iterator.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/mysql.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm'
[MSG] [Tue Aug 21 23:56:57 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/oracle.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/oracleace.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/pg.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/biofetch_oracle.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/memory.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/memory_iterator.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Featname.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Feature.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Homol.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/RelSegment.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Segment.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Typename.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/alignment.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/clone.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/coding.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/match.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/none.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/processed_transcript.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/transcript.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_acembly.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_genscan.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_refgene.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_softberry.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_unigene.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Util/'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Util/Binning.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Util/Rearrange.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/Query/'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/Query/GenBank.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/Query/WebQuery.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/Taxonomy/'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/Taxonomy/entrez.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/DB/Taxonomy/flatfile.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Das/'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Das/FeatureTypeI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Das/SegmentI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Event/'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Event/EventGeneratorI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Event/EventHandlerI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Expression/'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Expression/FeatureGroup/'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Expression/FeatureGroup.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Expression/FeatureI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Expression/FeatureSet/'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Expression/FeatureSet/FeatureSetMas50.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Factory/'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Factory/AnalysisI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Factory/ApplicationFactoryI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Factory/DriverFactory.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Factory/FTLocationFactory.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Factory/HitFactoryI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Factory/LocationFactoryI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Factory/MapFactoryI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Factory/ObjectBuilderI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Factory/ObjectFactory.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Factory/ObjectFactoryI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Factory/ResultFactoryI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Factory/SeqAnalysisParserFactory.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Factory/SeqAnalysisParserFactoryI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Factory/SequenceFactoryI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Factory/SequenceProcessorI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Factory/SequenceStreamI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Factory/TreeFactoryI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Graphics/'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Graphics/FeatureFile/'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Graphics/FeatureFile/Iterator.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Graphics/ConfiguratorI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Graphics/Feature.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Graphics/FeatureFile.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Graphics/Panel.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Graphics/Pictogram.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Graphics/RendererI.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Graphics/Util.pm'
[MSG] [Tue Aug 21 23:56:58 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/Factory.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/alignment.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/anchored_arrow.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/arrow.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/box.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/cds.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/crossbox.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/diamond.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/dna.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/dot.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/ellipse.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/ex.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/extending_arrow.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/generic.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/graded_segments.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/group.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/heterogeneous_segments.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/line.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/minmax.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/oval.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/pinsertion.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/primers.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/processed_transcript.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/redgreen_box.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/redgreen_segment.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/rndrect.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/ruler_arrow.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/segmented_keyglyph.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/segments.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/span.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/splice_site.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/toomany.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/track.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/transcript.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/transcript2.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/translation.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/triangle.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/xyplot.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Index/'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Index/Abstract.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Index/AbstractSeq.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Index/Blast.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Index/EMBL.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Index/Fasta.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Index/Fastq.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Index/GenBank.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Index/SwissPfam.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Index/Swissprot.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/BioPerl.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/Loader.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/README'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/SRS.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/AARange.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Chain.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/ChainI.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/DNA.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Exon.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Gene.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Intron.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Mutation.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Mutator.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Prim_Transcript.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Range.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Repeat_Region.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Repeat_Unit.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/SeqI.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Transcript.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Translation.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Location/'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Location/Atomic.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Location/AvWithinCoordPolicy.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Location/CoordinatePolicyI.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Location/Fuzzy.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Location/FuzzyLocationI.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Location/NarrowestCoordPolicy.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Location/Simple.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Location/Split.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Location/SplitLocationI.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Location/WidestCoordPolicy.pm'
[MSG] [Tue Aug 21 23:56:59 2007] Extracted 'bioperl-1.4/Bio/Map/'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Map/CytoMap.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Map/CytoMarker.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Map/CytoPosition.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Map/LinkageMap.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Map/LinkagePosition.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Map/MapI.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Map/MappableI.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Map/Marker.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Map/MarkerI.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Map/Microsatellite.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Map/OrderedPosition.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Map/OrderedPositionWithDistance.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Map/Position.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Map/PositionI.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Map/SimpleMap.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/MapIO/'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/MapIO/mapmaker.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/IO/'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/IO/phylip.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/IO/scoring.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/PsmHeader.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/Psm.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/InstanceSite.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/InstanceSiteI.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/transfac.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/mast.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/meme.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/PsmHeaderI.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/PsmI.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/SiteMatrix.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/SiteMatrixI.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/Generic.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/IO.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/MatrixI.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/PhylipDist.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Matrix/Scoring.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Ontology/'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Ontology/GOterm.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Ontology/InterProTerm.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Ontology/Ontology.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Ontology/OntologyEngineI.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Ontology/OntologyI.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Ontology/OntologyStore.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Ontology/Path.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Ontology/PathI.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Ontology/Relationship.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Ontology/RelationshipFactory.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Ontology/RelationshipI.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Ontology/RelationshipType.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Ontology/SimpleGOEngine.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Ontology/SimpleOntologyEngine.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Ontology/Term.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Ontology/TermFactory.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Ontology/TermI.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/BaseSAXHandler.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/InterProHandler.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/InterProParser.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/dagflat.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/goflat.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/simplehierarchy.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/soflat.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Phenotype/'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Phenotype/MeSH/'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Phenotype/MeSH/Term.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Phenotype/MeSH/Twig.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/MiniMIMentry.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/OMIMentry.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/OMIMparser.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Phenotype/Correlate.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Phenotype/Measure.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Phenotype/Phenotype.pm'
[MSG] [Tue Aug 21 23:57:00 2007] Extracted 'bioperl-1.4/Bio/Phenotype/PhenotypeI.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/PopGen/'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/PopGen/IO/'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/PopGen/IO/csv.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/PopGen/IO/prettybase.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/PopGen/Genotype.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/PopGen/GenotypeI.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/PopGen/IO.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/PopGen/Individual.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/PopGen/IndividualI.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/PopGen/Marker.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/PopGen/MarkerI.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/PopGen/PopStats.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/PopGen/Population.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/PopGen/PopulationI.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/PopGen/Statistics.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/PopGen/Simulation/'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/PopGen/Simulation/Coalescent.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/PopGen/Simulation/GeneticDrift.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Restriction/'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme/'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme/MultiCut.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme/MultiSite.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Restriction/Analysis.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Restriction/EnzymeCollection.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Restriction/EnzymeI.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Restriction/IO.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Restriction/IO/'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Restriction/IO/bairoch.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Restriction/IO/base.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Restriction/IO/itype2.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Restriction/IO/withrefm.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Root/'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Root/Exception.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Root/Err.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Root/Global.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Root/HTTPget.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Root/IO.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Root/IOManager.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Root/Object.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Root/Root.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Root/RootI.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Root/Storable.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Root/Utilities.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Root/Vector.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Root/Version.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Root/Xref.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/BlastHSP.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/FastaHSP.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/GenericHSP.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/HMMERHSP.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/HSPFactory.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/HSPI.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/PSLHSP.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/PsiBlastHSP.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/WABAHSP.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/BlastHit.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/Fasta.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/GenericHit.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/HMMERHit.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/HitFactory.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/HitI.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/PsiBlastHit.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/BlastUtils.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/DatabaseI.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/GenericDatabase.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/Processor.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/SearchUtils.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/Iteration/'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/Iteration/GenericIteration.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/Iteration/IterationI.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/Result/'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/Result/BlastResult.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/Result/GenericResult.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/Result/HMMERResult.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/Result/ResultFactory.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/Result/ResultI.pm'
[MSG] [Tue Aug 21 23:57:01 2007] Extracted 'bioperl-1.4/Bio/Search/Result/WABAResult.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/BSMLResultWriter.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/GbrowseGFF.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/HSPTableWriter.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/HTMLResultWriter.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/HitTableWriter.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/ResultTableWriter.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/TextResultWriter.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/EventHandlerI.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/FastHitEventBuilder.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/IteratedSearchResultEventBuilder.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/SearchResultEventBuilder.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/SearchWriterI.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/axt.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/blast.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/blasttable.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/blastxml.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/exonerate.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/fasta.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/hmmer.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/megablast.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/psl.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/sim4.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/waba.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SearchIO/wise.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/Meta/'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/Meta/Array.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/BaseSeqProcessor.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/EncodedSeq.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/LargePrimarySeq.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/LargeSeq.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/Meta.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/MetaI.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/PrimaryQual.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/PrimedSeq.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/QualI.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/RichSeq.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/RichSeqI.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/SeqBuilder.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/SeqFactory.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/SeqFastaSpeedFactory.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/SeqWithQuality.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/SequenceTrace.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/Seq/TraceI.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/ExonI.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Exon.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/GeneStructure.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/GeneStructureI.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Intron.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/NC_Feature.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Poly_A_site.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Promoter.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Transcript.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/TranscriptI.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/UTR.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/AnnotationAdaptor.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Collection.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/CollectionI.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Computation.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/FeaturePair.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Generic.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/PositionProxy.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Primer.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Similarity.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/SimilarityPair.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/SiRNA/'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/SiRNA/Oligo.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/SiRNA/Pair.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Tools/'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Tools/TypeMapper.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Tools/Unflattener.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqIO/'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game/'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game/featHandler.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game/gameHandler.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game/gameSubs.pm'
[MSG] [Tue Aug 21 23:57:02 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game/gameWriter.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game/seqHandler.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/FTHelper.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/MultiFile.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/abi.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/ace.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/alf.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/asciitree.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/bsml.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/chadoxml.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/ctf.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/embl.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/exp.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/fasta.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/fastq.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/gcg.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/genbank.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/kegg.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/largefasta.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/locuslink.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/metafasta.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/phd.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/pir.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/pln.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/qual.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/raw.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/scf.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/swiss.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/tab.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/tigr.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/SeqIO/ztr.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Structure/'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Structure/Chain.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Structure/Atom.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Structure/IO/'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Structure/IO/pdb.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Structure/Entry.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Structure/IO.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Structure/Model.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Structure/Residue.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Structure/StructureI.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Structure/SecStr/'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Structure/SecStr/DSSP/'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Structure/SecStr/DSSP/Res.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Structure/SecStr/STRIDE/'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Structure/SecStr/STRIDE/Res.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Symbol/'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Symbol/Alphabet.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Symbol/AlphabetI.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Symbol/DNAAlphabet.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Symbol/ProteinAlphabet.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Symbol/README.Symbol'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Symbol/Symbol.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Symbol/SymbolI.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Taxonomy/'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Taxonomy/FactoryI.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Taxonomy/Node.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Taxonomy/Taxon.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Taxonomy/Tree.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/Alignment/'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/Alignment/Consed.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/Alignment/Trim.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/AlignFactory.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/AnalysisResult.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/BPbl2seq.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/BPlite.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/BPpsilite.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/Blat.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/CodonTable.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/Coil.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/ECnumber.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/EPCR.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/ESTScan.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/Eponine.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/Est2Genome.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/FootPrinter.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/GFF.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/Gel.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/Geneid.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/Genemark.pm'
[MSG] [Tue Aug 21 23:57:03 2007] Extracted 'bioperl-1.4/Bio/Tools/Genewise.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Genomewise.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Genscan.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Glimmer.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Grail.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/GuessSeqFormat.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Hmmpfam.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/IUPAC.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Lucy.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/MZEF.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/OddCodes.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer3.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Prints.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Profile.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Promoterwise.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/PrositeScan.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Pseudowise.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/QRNA.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/RandomDistFunctions.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/RepeatMasker.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/RestrictionEnzyme.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Seg.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/SeqAnal.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/SeqPattern.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/SeqStats.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/SeqWords.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/SiRNA.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Sigcleave.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Signalp.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Tmhmm.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/WWW.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/dpAlign.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/pICalculator.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/pSW.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/DNA/'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/DNA/ESEfinder.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/SimpleAnalysisBase.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Domcut.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/ELM.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/GOR4.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/HNN.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Mitoprot.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/NetPhos.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Scansite.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Sopma.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/BPlite/'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/BPlite/Iteration.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/BPlite/HSP.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/BPlite/Sbjct.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast/'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast/Sbjct.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast/CHANGES'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast/HSP.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast/HTML.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast/README'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/EMBOSS/'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/EMBOSS/Palindrome.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/HMMER/'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/HMMER/Domain.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/HMMER/Results.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/HMMER/Set.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Molphy/'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Molphy/Result.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Molphy.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML/'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML/ModelResult.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML/Result.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Phylip/'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Phylip/ProtDist.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Prediction/'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Prediction/Exon.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Prediction/Gene.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer/'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer/Assessor/'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer/Assessor/Base.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer/AssessorI.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer/Feature.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer/Pair.pm'
[MSG] [Tue Aug 21 23:57:04 2007] Extracted 'bioperl-1.4/Bio/Tools/Run/'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Tools/Run/README'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Tools/Run/RemoteBlast.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Tools/Run/StandAloneBlast.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Tools/Run/WrapperBase.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Tools/Sim4/'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Tools/Sim4/Results.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Tools/Sim4/Exon.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Tree/'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Tree/AlleleNode.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Tree/Node.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Tree/NodeI.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Tree/NodeNHX.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Tree/RandomFactory.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Tree/Statistics.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Tree/Tree.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Tree/TreeFunctionsI.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Tree/TreeI.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/TreeIO/'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/TreeIO/TreeEventBuilder.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/TreeIO/lintree.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/TreeIO/newick.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/TreeIO/nexus.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/TreeIO/nhx.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/TreeIO/svggraph.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/TreeIO/tabtree.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Variation/'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Variation/IO/'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Variation/IO/flat.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Variation/IO/xml.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Variation/AAChange.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Variation/AAReverseMutate.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Variation/Allele.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Variation/DNAMutation.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Variation/IO.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Variation/README'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Variation/RNAChange.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Variation/SNP.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Variation/SeqDiff.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/Bio/Variation/VariantI.pm'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/faq/'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/faq/faq.html'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/faq/faq.dtd'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/faq/faq.pl'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/faq/faq.xml'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/makedoc.PL'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/examples/'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/blastn.out'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/data1.txt'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/embl2picture.pl'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/factor7.embl'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast1.pl'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast2.pl'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast3.pl'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast4.pl'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_features.pl'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/examples/README'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/figs/'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig1.png'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig2.png'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig3.png'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig4.png'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig5.png'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig6.png'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/figs/README'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/html/'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/html/images/'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/html/images/tip.png'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/html/Flat_Databases.html'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/html/Graphics-HOWTO.html'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/html/OBDA_Access.html'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/html/PAML.html'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/html/README'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/html/SearchIO.html'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/html/SeqIO.html'
[MSG] [Tue Aug 21 23:57:05 2007] Extracted 'bioperl-1.4/doc/howto/html/SimpleWebAnalysis.html'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/html/e-novative.css'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/pdf/'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/pdf/Flat_Databases.pdf'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/pdf/Graphics-HOWTO.pdf'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/pdf/OBDA_Access.pdf'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/pdf/PAML.pdf'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/pdf/SearchIO.pdf'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/pdf/SeqIO.pdf'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/pdf/SimpleWebAnalysis.pdf'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/pdf/Trees.pdf'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/sgml/'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/sgml/Feature-Annotation.sgml'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/sgml/Flat_Databases.sgml'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/sgml/Graphics-HOWTO.sgml'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/sgml/OBDA_Access.sgml'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/sgml/PAML.sgml'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/sgml/README'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/sgml/SearchIO.sgml'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/sgml/SeqIO.sgml'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/sgml/SimpleWebAnalysis.sgml'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/sgml/Trees.sgml'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/txt/'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/txt/Flat_Databases.txt'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/doc/howto/txt/SimpleWebAnalysis.txt'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/INSTALL.WIN'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/LICENSE'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/MANIFEST.SKIP'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/Makefile.PL'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/PLATFORMS'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/README'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/biodatabases.pod'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/biodesign.pod'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/bioperl.lisp'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/bioperl.pod'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/bioscripts.pod'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/bptutorial.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/Bio-DB-GFF/'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/Bio-DB-GFF/load_ucsc.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/bioperl.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/generate_random_seq.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/longorf.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/make_mrna_protein.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/make_primers.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/rev_and_trans.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/revcom_dir.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/subsequence.cgi'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/align/'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/align/align_on_codons.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/align/aligntutorial.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/align/clustalw.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/align/simplealign.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/biblio/'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/biblio/biblio_examples.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/biblio/biblio_soap.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/biographics/'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/biographics/all_glyphs.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/biographics/dynamic_glyphs.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/biographics/feature_data.gff'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/biographics/feature_data.txt'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/biographics/lots_of_glyphs.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/biographics/render_sequence.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/cluster/'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/cluster/dbsnp.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/contributed/'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/contributed/nmrpdb_parse.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/contributed/prosite2perl.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/contributed/rebase2list.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/db/'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/db/get_seqs.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/db/dbfetch'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/db/est_tissue_query.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/db/gb2features.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/db/getGenBank.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/db/rfetch.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/db/use_registry.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/liveseq/'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/liveseq/change_gene.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/popgen/'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/popgen/parse_calc_stats.pl'
[MSG] [Tue Aug 21 23:57:06 2007] Extracted 'bioperl-1.4/examples/root/'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/root/lib/'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/root/lib/Bio/'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/root/lib/Bio/PrimarySeq.pm'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/root/lib/Bio/PrimarySeqI.pm'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/root/lib/Bio/Seq.pm'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/root/lib/Bio/SeqI.pm'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/root/lib/Error.pm'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/root/lib/TestInterface.pm'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/root/lib/TestObject.pm'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/root/README'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/root/exceptions1.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/root/exceptions2.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/root/exceptions3.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/root/exceptions4.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/searchio/'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/searchio/blast_example.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/searchio/custom_writer.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/searchio/hitwriter.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/searchio/hspwriter.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/searchio/htmlwriter.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/searchio/psiblast_features.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/searchio/psiblast_iterations.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/searchio/rawwriter.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/searchio/resultwriter.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/searchio/waba2gff.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/sirna/'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/sirna/TAG'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/sirna/rnai_finder.cgi'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/tk/'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/tk/gsequence.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/tk/hitdisplay.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/tools/'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/tools/gb_to_gff.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/tools/gff2ps.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/tools/parse_codeml.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/tools/psw.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/tools/restriction.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/tools/run_genscan.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/tools/seq_pattern.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/tools/standaloneblast.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/tree/'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/examples/tree/paup2phylip.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/maintenance/'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/maintenance/authors.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/maintenance/README'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/maintenance/modules.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/maintenance/pod.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/models/'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/models/biblio.dia'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/models/README'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/models/bio_liveseq_variation.dia'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/models/bio_map.dia'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/models/bio_restriction.dia'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/models/bioperl.dia'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/models/coordinatemapper.dia'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/models/map_proposal.txt'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/models/maps_and_markers.dia'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/models/popgen.dia'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/models/population_proposal.txt'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/load_gff.PLS'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/README'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/TAG'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/bp_genbank2gff.PLS'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/bulk_load_gff.PLS'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/fast_load_gff.PLS'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/generate_histogram.PLS'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/load_ucsc.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/pg_bulk_load_gff.PLS'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_gadfly.PLS'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_ncbi_human.PLS'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_sgd.PLS'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_wormbase.PLS'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/install_bioperl_scripts.pl'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/DB/'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/DB/TAG'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/DB/biofetch_genbank_proxy.PLS'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/DB/bioflat_index.PLS'
[MSG] [Tue Aug 21 23:57:07 2007] Extracted 'bioperl-1.4/scripts/DB/biogetseq.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/DB/flanks.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/biblio/'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/biblio/TAG'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/biblio/biblio.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/das/'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/das/README'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/das/TAG'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/graphics/'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/graphics/frend.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/graphics/README'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/graphics/TAG'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/graphics/feature_draw.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/graphics/search_overview.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/index/'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/index/TAG'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/index/bp_fetch.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/index/bp_index.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/popgen/'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/popgen/composite_LD.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/popgen/heterogeneity_test.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/searchio/'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/searchio/filter_search.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/seq/'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/seq/TAG'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/seq/extract_feature_seq.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/seq/seqconvert.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/seq/split_seq.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/seq/translate_seq.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/seqstats/'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/seqstats/TAG'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/seqstats/aacomp.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/seqstats/chaos_plot.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/seqstats/gccalc.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/seqstats/oligo_count.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/taxa/'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/taxa/TAG'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/taxa/local_taxonomydb_query.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/taxa/taxid4species.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/tree/'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/tree/TAG'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/tree/blast2tree.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/utilities/'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/utilities/bp_nrdb.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/utilities/README'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/utilities/TAG'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/utilities/bp_mrtrans.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/utilities/bp_sreformat.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/utilities/dbsplit.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/utilities/mask_by_search.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/utilities/mutate.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/utilities/pairwise_kaks.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/utilities/remote_blast.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/utilities/search2BSML.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/utilities/search2alnblocks.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/utilities/search2gff.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/utilities/search2tribe.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/scripts/utilities/seq_length.PLS'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/biodbgff/'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/biodbgff/test.gff'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/503384.MEGABLAST.0'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/503384.MEGABLAST.2'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/5X_1895.FASTXY'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/AAC12660.fa'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/AB077698.gb'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/AE003528_ecoli.bls'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/AE003644_Adh-genomic.gb'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/AF032047.gbk'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/AF165282.gb'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/AHCYL1.kegg'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/ATF14F8.gbk'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/AY095303S1.gbk'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/AnnIX-v003.gbk'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/BK000016-tpa.gbk'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/BLOSUM50'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/BN000066-tpa.embl'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/D10483.gbk'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/D12555.gbk'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/ECAPAH02.embl'
[MSG] [Tue Aug 21 23:57:08 2007] Extracted 'bioperl-1.4/t/data/GO.defs.test'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/GO.defs.test2'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/Genscan.FastA'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.FASTA'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.fa'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.gff'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.grail'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.grailexp'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.mzef'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.tblastx'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/L77119.hmmer'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/LL-sample.seq'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/LOAD_Ccd1.dnd'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/LittleChrY.dbsnp.xml'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/MmCT'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/NM_002254.gb'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/NT_021877.gbk'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/PAM250'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/SwissProt.dat'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/U58726.gb'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/X98338_Adh-mRNA.gb'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/a_thaliana.blastn'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/aaml.mlc'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/aaml_pairwise.mlc'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/acefile.ace.1'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/acefile.singlets'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/alnfile.fasta'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/amino.fa'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/ar.embl'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/bl2seq.blastn'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/bl2seq.blastn.rev'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/bl2seq.blastx.out'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/bl2seq.bug940.out'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/bl2seq.out'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/bl2seq.tblastx.out'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/blast.report'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/blat.psLayout3'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/c200-vs-yeast.BLASTN'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/c200-vs-yeast.BLASTN.m8'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/chad100.scf'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/codeml.mlc'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/codeml_nssites.mlc'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/compLD_missingtest.prettybase'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/compLD_test.prettybase'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/component.ontology.test'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/component.ontology.test2'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/crab.dat.cn'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/crab.nj'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/crab.njb'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/crypto.sim4-0'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/crypto.sim4-3'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/crypto.sim4-4'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/cys1_dicdi.water'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/cysprot.fa'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/cysprot.msf'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/cysprot.needle'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/cysprot.tblastn'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/cysprot.water'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/cysprot1.FASTA'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/cysprot1.fa'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/cysprot1a.fa'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/cysprot1a.msf'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/cysprot1b.fa'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/cysprot1b.hmmsearch'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/cysprot1b.msf'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/cysprot1b.newick'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/cysprot_vs_gadfly.FASTA'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/dmel_2Lchunk.gb'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/dna1.fa'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/dna2.fa'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/dnaE-bsub-prot.fa'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/dnaE-bsub.fa'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/dnaEbsub_ecoli.wublastx'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/dnaEbsub_ecoli.wutblastn'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/dnaEbsub_ecoli.wutblastx'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/ecoli-trna-qrna.out'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/ecoli_domains.rps.xml'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/ecoli_domains.rpsblast'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/ecolitst.bls'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/ecolitst.fa'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/ecolitst.wublastp'
[MSG] [Tue Aug 21 23:57:09 2007] Extracted 'bioperl-1.4/t/data/empty.bl2seq'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/expected.blast.out'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/factor7.embl'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/footprinter.out'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/geneid_1.0.out'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/genemark.out'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/genewise.out'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/genewise_output.paracel_btk'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/genomewise.out'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/genomic-seq.epcr'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/genomic-seq.fasta'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/genomic-seq.genscan'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/genomic-seq.mzef'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/gf-s71.needle'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/glimmer.out'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/hemoglobinA.meg'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/hg16_chroms.gff'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/hmmpfam.out'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/hmmsearch.out'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/hs_est.est2genome'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/hs_fugu.newick'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/hs_owlmonkey.fas'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/hs_owlmonkey.fasta'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/hsinsulin.blastcl3.blastn'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/humor.maf'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/humts1.pal'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/insulin.water'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/interpro_short.xml'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/lucy.info'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/lucy.qual'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/lucy.seq'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/lucy.stderr'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/lysozyme6.protml'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/lysozyme6.simple.protml'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/mapmaker.out'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/mast.dat'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/megablast_output.paracel_btk'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/meme.dat'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/mpath.ontology.test'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/multi_1.fa'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/multi_2.fa'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/multi_blast.bls'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/multifa.seq'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/multiseq.bls'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/mus.bls.xml'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/mutations.dat'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/mutations.xml'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/myco_sites.gff'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/nei_gojobori_test.aln'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/neighbor.dist'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/no-genes.genscan'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/no_hsps.blastp'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/noninterleaved.phy'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/omim_genemap_test'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/omim_text_test'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/pdb1bpt.ent'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/phi.out'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/phipsi.out'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/phredfile.phd'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/phylipdist-36.out'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/phylipdist.out'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/pictogram.fa'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/plague_yeast.bls.xml'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/polymorphism.dat'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/polymorphism.xml'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/popgen_saureus.dat'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/popgen_saureus.multidat'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/popstats.prettybase'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/roa1.dat'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/primedseq.fa'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/primer3_infile.txt'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/primer3_outfile.txt'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/primer3_output.txt'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/promoterwise.out'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/protpars.phy'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/psiblastreport.out'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/qrna-relloc.out'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/qualfile.qual'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/rebase.itype2'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/rebase.withrefm'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/repeatmasker.fa.out'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/revcomp_mrna.gb'
[MSG] [Tue Aug 21 23:57:10 2007] Extracted 'bioperl-1.4/t/data/roa1.genbank'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/roa1.swiss'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/sbay_c545-yeast.BLASTZ.PSL'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/seqdatabase.ini'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/seqfile.pir'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/seqs.fas'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/sequencefamily.dat'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/short.blx'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/sim4.for.for'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/sim4.for.rev'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/sim4.rev'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/sofa.ontology'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/sparsealn.needle'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/stress_test_medline.xml'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/stress_test_pubmed.xml'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/swiss.dat'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/swisspfam.data'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.ace'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.embl'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.fasta'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.game'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.gcg'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.gcgblast'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.gcgfasta'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.genbank'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.genbank.noseq'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.mase'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.metafasta'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.nh'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.nhx'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.pfam'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.pir'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.raw'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.swiss'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.tab'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.txt'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test.waba'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/test_badlf.gcg'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/testaln.aln'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/testaln.fasta'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/testaln.mase'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/testaln.metafasta'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/testaln.msf'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/testaln.nexus'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/testaln.pfam'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/testaln.phylip'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/testaln.prodom'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/testaln.selex'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/testaln.stockholm'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/testdat.exonerate'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/testdbaccnums.out'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/testfuzzy.genbank'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/transfac.dat'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/unigene.data'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/version2.scf'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/version3.scf'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/worm_fam_2785.cdna'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/yn00.mlc'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version1.gif'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version1.png'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version2.gif'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version2.png'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version3.png'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version4.png'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version5.png'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version6.png'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version7.png'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version8.png'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version1.gif'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version1.png'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version10.png'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version11.png'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version12.png'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version13.png'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version14.png'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version2.gif'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version2.png'
[MSG] [Tue Aug 21 23:57:11 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version3.png'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version4.png'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version5.png'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version6.png'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version7.png'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version8.png'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version9.png'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/biographics/feature_data.txt'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version1.gif'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version1.png'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version2.gif'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version2.png'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version3.png'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version4.png'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version5.png'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version6.png'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version7.png'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.contigs'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.log'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.ace.1'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs.qual'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.log'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.problems'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.problems.qual'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.qual'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.singlets'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.view'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.newtags'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.phrap.out'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.screen.out'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_projectNewChromats.fof'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project_to_alu.cross'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4922R.phd.1'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4924F.phd.1'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4924R.phd.1'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4947F.phd.1'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/dbfa/'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/dbfa/1.fa'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/dbfa/2.fa'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/dbfa/3.fa'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/dbfa/4.fa'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/dbfa/5.fa'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/dbfa/6.fa'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/dbfa/7.fa'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/registry/'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/registry/bdb/'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/registry/bdb/seqdatabase.ini'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/registry/flat/'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/data/registry/flat/seqdatabase.ini'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/AAChange.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/AAReverseMutate.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/AlignIO.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/AlignStats.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/Allele.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/Alphabet.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/Annotation.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/AnnotationAdaptor.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/Assembly.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/BPbl2seq.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/BPlite.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/BPpsilite.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/Biblio.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/BiblioReferences.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/Biblio_biofetch.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/BioDBGFF.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/BioFetch_DB.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/BioGraphics.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/BlastIndex.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/Chain.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/ClusterIO.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/Coalescent.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/CodonTable.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/CoordinateGraph.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/CoordinateMapper.t'
[MSG] [Tue Aug 21 23:57:12 2007] Extracted 'bioperl-1.4/t/Correlate.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/CytoMap.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/DB.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/DBCUTG.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/DBFasta.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/DNAMutation.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Domcut.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/ECnumber.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/ELM.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/EMBL_DB.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/EMBOSS_Tools.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/ESEfinder.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/EncodedSeq.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Exception.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Exonerate.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/FootPrinter.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/GDB.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/GFF.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/GOR4.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/GOterm.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/GeneCoordinateMapper.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Geneid.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Genewise.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Genomewise.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Genpred.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/GuessSeqFormat.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/HNN.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/IUPAC.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Index.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/InstanceSite.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/InterProParser.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/LinkageMap.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/LiveSeq.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/LocatableSeq.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Location.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/LocationFactory.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/LocusLink.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Map.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/MapIO.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Matrix.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/MeSH.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Measure.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/MetaSeq.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/MicrosatelliteMarker.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/MiniMIMentry.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/MitoProt.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Molphy.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Mutation.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Mutator.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/NetPhos.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Node.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/OMIMentry.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/OMIMentryAllelicVariant.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/OMIMparser.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/OddCodes.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Ontology.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/OntologyEngine.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/PAML.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Perl.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Phenotype.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/PhylipDist.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Pictogram.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/PopGen.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/PopGenSims.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/PrimarySeq.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Primer.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Promoterwise.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/ProtDist.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/QRNA.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/RNAChange.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/RandDistFunctions.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/RandomTreeFactory.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Range.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/RangeI.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/RefSeq.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Registry.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/Relationship.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/RelationshipType.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/RemoteBlast.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/RepeatMasker.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/RestrictionAnalysis.t'
[MSG] [Tue Aug 21 23:57:13 2007] Extracted 'bioperl-1.4/t/RestrictionEnzyme.t'
[MSG] [Tue Aug 21 23:57:14 2007] Extracted 'bioperl-1.4/t/RestrictionIO.t'
[MSG] [Tue Aug 21 23:57:14 2007] Extracted 'bioperl-1.4/t/RootI.t'
[MSG] [Tue Aug 21 23:57:14 2007] Extracted 'bioperl-1.4/t/RootIO.t'
[MSG] [Tue Aug 21 23:57:14 2007] Extracted 'bioperl-1.4/t/RootStorable.t'
[MSG] [Tue Aug 21 23:57:14 2007] Extracted 'bioperl-1.4/t/SNP.t'
[MSG] [Tue Aug 21 23:57:14 2007] Extracted 'bioperl-1.4/t/Scansite.t'
[MSG] [Tue Aug 21 23:57:14 2007] Extracted 'bioperl-1.4/t/SearchDist.t'
[MSG] [Tue Aug 21 23:57:14 2007] Extracted 'bioperl-1.4/t/SearchIO.t'
[MSG] [Tue Aug 21 23:57:14 2007] Extracted 'bioperl-1.4/t/Seq.t'
[MSG] [Tue Aug 21 23:57:14 2007] Extracted 'bioperl-1.4/t/SeqAnalysisParser.t'
[MSG] [Tue Aug 21 23:57:14 2007] Extracted 'bioperl-1.4/t/SeqBuilder.t'
[MSG] [Tue Aug 21 23:57:14 2007] Extracted 'bioperl-1.4/t/SeqDiff.t'
[MSG] [Tue Aug 21 23:57:14 2007] Extracted 'bioperl-1.4/t/SeqFeatCollection.t'
[MSG] [Tue Aug 21 23:57:14 2007] Extracted 'bioperl-1.4/t/SeqFeature.t'
[MSG] [Tue Aug 21 23:57:14 2007] Extracted 'bioperl-1.4/t/SeqIO.t'
[MSG] [Tue Aug 21 23:57:14 2007] Extracted 'bioperl-1.4/t/SeqPattern.t'
[MSG] [Tue Aug 21 23:57:14 2007] Extracted 'bioperl-1.4/t/SeqStats.