FAIL bioperl-1.4 i686-linux-thread-multi-64int 2.6.21.5-smp

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 0.81_01. Testers personal comments may appear 
at the end of this report.


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

TEST RESULTS:

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

[MSG] [Mon Sep 17 08:27:32 2007] Trying to get 'http://www.cpan.org/authors/id/L/LI/LIMAONE/Bio-Grep-v0.10.1.tar.gz'
[MSG] [Mon Sep 17 08:27:34 2007] Trying to get 'http://www.cpan.org/authors/id/L/LI/LIMAONE/CHECKSUMS'
[MSG] [Mon Sep 17 08:27:35 2007] Checksum matches for 'Bio-Grep-v0.10.1.tar.gz'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/README'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/TODO'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/examples/'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/examples/bgrep'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/examples/Benchmarks.tt'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/examples/benchmark.pl'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/lib/'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/lib/Bio/'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/lib/Bio/Grep/'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/lib/Bio/Grep/Backend/'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/lib/Bio/Grep/Backend/Vmatch.pm'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/lib/Bio/Grep/Backend/RE.pm'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/lib/Bio/Grep/Backend/GUUGle.pm'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/lib/Bio/Grep/Backend/Agrep.pm'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/lib/Bio/Grep/Backend/BackendI.pm'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/lib/Bio/Grep/Benchmarks.pod'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/lib/Bio/Grep/Cookbook.pod'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/lib/Bio/Grep/Root.pm'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/lib/Bio/Grep/Filter/'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/lib/Bio/Grep/Filter/FilterI.pm'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/lib/Bio/Grep/Filter/FilterRemoveDuplicates.pm'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/lib/Bio/Grep/SearchSettings.pm'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/lib/Bio/Grep/SearchResult.pm'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/lib/Bio/Grep.pm'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/META.yml'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/Makefile.PL'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/Build.PL'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/pod-coverage.t'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/Test.fasta'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/Test_pep.fasta'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/pod.t'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/TestFilter.pm'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/00.checkprereq.t'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/00.load.t'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/50.synopsis.t'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/perlcritic.t'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/Test2.fasta'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/11.backends.guugle.t'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/40.utils.t'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/Test_query_revcom.fasta'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/11.backends.re.t'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/BioGrepTest.pm'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/10.backends.all.t'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/30.features.alignments.t'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/TestGUUGleExtend.fasta'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/20.filter.t'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/BioGrepSkip.pm'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/TestRevCom.fasta'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/t/Test_query.fasta'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/Changes'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio-Grep-v0.10.1/MANIFEST'
[MSG] [Mon Sep 17 08:27:35 2007] Extracted 'Bio::Grep' to '/home/cpan/perl595/.cpanplus/5.9.5/build/Bio-Grep-v0.10.1'
[MSG] [Mon Sep 17 08:27:36 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] [Mon Sep 17 08:27:36 2007] DEFAULT 'filter_prereqs' HANDLER RETURNING 'sub return value'
[MSG] [Mon Sep 17 08:27:36 2007] Module 'Bio::Grep' requires 'Bio::Root::Version' version '0' to be installed 
[MSG] [Mon Sep 17 08:27:36 2007] Module 'Bio::Grep' requires 'Carp::Assert' version '0' to be installed 
[MSG] [Mon Sep 17 08:27:36 2007] Module 'Bio::Grep' requires 'Class::MethodMaker' version '2.02' to be installed 
[MSG] [Mon Sep 17 08:27:36 2007] Module 'Bio::Grep' requires 'IO::String' version '1' to be installed 
[MSG] [Mon Sep 17 08:27:36 2007] Module 'Bio::Grep' requires 'ToolSet' version '0.13' to be installed 
[MSG] [Mon Sep 17 08:27:36 2007] Module 'Bio::Grep' requires 'UNIVERSAL::require' version '0.11' to be installed 
[MSG] [Mon Sep 17 08:27:36 2007] Trying to get 'http://www.cpan.org/authors/id/B/BI/BIRNEY/bioperl-1.4.tar.gz'
[MSG] [Mon Sep 17 08:28:01 2007] Trying to get 'http://www.cpan.org/authors/id/B/BI/BIRNEY/CHECKSUMS'
[MSG] [Mon Sep 17 08:28:02 2007] Checksum matches for 'bioperl-1.4.tar.gz'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/DEPRECATED'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/AUTHORS'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/BUGS'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Changes'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/INSTALL'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/FAQ'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/Align/'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/Align/AlignI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/Align/DNAStatistics.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/Align/PairwiseStatistics.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/Align/StatisticsI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/Align/Utilities.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/AlignIO.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/AnalysisI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/AnalysisParserI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/AnalysisResultI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/AnnotatableI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/AnnotationCollectionI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/AnnotationI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/Biblio.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/ClusterI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/ClusterIO.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/DBLinkContainerI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/DasI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/DescribableI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/FeatureHolderI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/Graphics.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/IdCollectionI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/IdentifiableI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/LocatableSeq.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/LocationI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/MapIO.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/OntologyIO.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/Perl.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/PrimarySeq.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/PrimarySeqI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/Range.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/RangeI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/SearchDist.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/SearchIO.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/Seq.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/SeqAnalysisParserI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/SeqFeatureI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/SeqI.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/SeqIO.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/SeqUtils.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/SimpleAlign.pm'
[MSG] [Mon Sep 17 08:28:06 2007] Extracted 'bioperl-1.4/Bio/SimpleAnalysisI.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Species.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Taxonomy.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/TreeIO.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/UpdateableSeqI.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/WebAgent.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/AlignIO/'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/AlignIO/bl2seq.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/AlignIO/clustalw.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/AlignIO/emboss.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/AlignIO/fasta.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/AlignIO/maf.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/AlignIO/mase.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/AlignIO/mega.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/AlignIO/meme.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/AlignIO/metafasta.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/AlignIO/msf.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/AlignIO/nexus.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/AlignIO/pfam.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/AlignIO/phylip.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/AlignIO/prodom.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/AlignIO/psi.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/AlignIO/selex.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/AlignIO/stockholm.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Annotation/'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Annotation/AnnotationFactory.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Annotation/Collection.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Annotation/Comment.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Annotation/DBLink.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Annotation/OntologyTerm.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Annotation/Reference.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Annotation/SimpleValue.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Annotation/StructuredValue.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Annotation/TypeManager.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Assembly/'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Assembly/IO/'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Assembly/IO/phrap.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Assembly/IO/ace.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Assembly/Contig.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Assembly/ContigAnalysis.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Assembly/IO.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Assembly/Scaffold.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Assembly/ScaffoldI.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Biblio/'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Biblio/IO/'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Biblio/IO/medline2ref.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Biblio/IO/medlinexml.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Biblio/IO/pubmed2ref.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Biblio/IO/pubmedxml.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Biblio/Article.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Biblio/BiblioBase.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Biblio/Book.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Biblio/BookArticle.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Biblio/IO.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Biblio/Journal.pm'
[MSG] [Mon Sep 17 08:28:07 2007] Extracted 'bioperl-1.4/Bio/Biblio/JournalArticle.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Biblio/MedlineArticle.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Biblio/MedlineBook.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Biblio/MedlineBookArticle.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Biblio/MedlineJournal.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Biblio/MedlineJournalArticle.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Biblio/Organisation.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Biblio/Patent.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Biblio/Person.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Biblio/Proceeding.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Biblio/Provider.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Biblio/PubmedArticle.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Biblio/PubmedBookArticle.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Biblio/PubmedJournalArticle.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Biblio/Ref.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Biblio/Service.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Biblio/TechReport.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Biblio/Thesis.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Biblio/WebResource.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Cluster/'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Cluster/ClusterFactory.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Cluster/FamilyI.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Cluster/SequenceFamily.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Cluster/UniGene.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Cluster/UniGeneI.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/ClusterIO/'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/ClusterIO/dbsnp.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/ClusterIO/unigene.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/CodonUsage/'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/CodonUsage/Table.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/CodonUsage/IO.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Coordinate/'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Result/'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Result/Match.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Result/Gap.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Chain.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Collection.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Coordinate/ExtrapolatingPair.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Coordinate/GeneMapper.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Graph.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Coordinate/MapperI.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Pair.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Result.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Coordinate/ResultI.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/Coordinate/Utils.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/DB/'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/DB/BiblioI.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/DB/Ace.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/DB/Biblio/'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/DB/Biblio/biofetch.pm'
[MSG] [Mon Sep 17 08:28:08 2007] Extracted 'bioperl-1.4/Bio/DB/Biblio/soap.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/BioFetch.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/CUTG.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/DBFetch.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/EMBL.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/Failover.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/Fasta.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/FileCache.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/Flat.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/GDB.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/GFF.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/GenBank.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/GenPept.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/InMemoryCache.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/MANIFEST'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/Makefile.PL'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/MeSH.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/NCBIHelper.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/QueryI.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/RandomAccessI.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/RefSeq.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/Registry.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/SeqI.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/SwissProt.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/Taxonomy.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/Universal.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/UpdateableSeqI.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/WebDBSeqI.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/XEMBL.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/XEMBLService.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/fasta.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/embl.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/genbank.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/swiss.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/swissprot.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/Flat/BinarySearch.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/biofetch.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/ace.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/iterator.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/mysql.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/oracle.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/oracleace.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/pg.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/biofetch_oracle.pm'
[MSG] [Mon Sep 17 08:28:09 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/memory.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/memory_iterator.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Featname.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Feature.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Homol.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/RelSegment.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Segment.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Typename.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/alignment.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/clone.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/coding.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/match.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/none.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/processed_transcript.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/transcript.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_acembly.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_genscan.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_refgene.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_softberry.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_unigene.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Util/'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Util/Binning.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/GFF/Util/Rearrange.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/Query/'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/Query/GenBank.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/Query/WebQuery.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/Taxonomy/'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/Taxonomy/entrez.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/DB/Taxonomy/flatfile.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/Das/'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/Das/FeatureTypeI.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/Das/SegmentI.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/Event/'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/Event/EventGeneratorI.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/Event/EventHandlerI.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/Expression/'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/Expression/FeatureGroup/'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/Expression/FeatureGroup.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/Expression/FeatureI.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/Expression/FeatureSet/'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/Expression/FeatureSet/FeatureSetMas50.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/Factory/'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/Factory/AnalysisI.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/Factory/ApplicationFactoryI.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/Factory/DriverFactory.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/Factory/FTLocationFactory.pm'
[MSG] [Mon Sep 17 08:28:10 2007] Extracted 'bioperl-1.4/Bio/Factory/HitFactoryI.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Factory/LocationFactoryI.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Factory/MapFactoryI.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Factory/ObjectBuilderI.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Factory/ObjectFactory.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Factory/ObjectFactoryI.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Factory/ResultFactoryI.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Factory/SeqAnalysisParserFactory.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Factory/SeqAnalysisParserFactoryI.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Factory/SequenceFactoryI.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Factory/SequenceProcessorI.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Factory/SequenceStreamI.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Factory/TreeFactoryI.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/FeatureFile/'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/FeatureFile/Iterator.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/ConfiguratorI.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Feature.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/FeatureFile.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Panel.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Pictogram.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/RendererI.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Util.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/Factory.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/alignment.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/anchored_arrow.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/arrow.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/box.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/cds.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/crossbox.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/diamond.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/dna.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/dot.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/ellipse.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/ex.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/extending_arrow.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/generic.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/graded_segments.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/group.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/heterogeneous_segments.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/line.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/minmax.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/oval.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/pinsertion.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/primers.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/processed_transcript.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/redgreen_box.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/redgreen_segment.pm'
[MSG] [Mon Sep 17 08:28:11 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/rndrect.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/ruler_arrow.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/segmented_keyglyph.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/segments.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/span.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/splice_site.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/toomany.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/track.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/transcript.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/transcript2.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/translation.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/triangle.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/xyplot.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Index/'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Index/Abstract.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Index/AbstractSeq.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Index/Blast.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Index/EMBL.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Index/Fasta.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Index/Fastq.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Index/GenBank.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Index/SwissPfam.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Index/Swissprot.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/BioPerl.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/Loader.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/README'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/SRS.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/AARange.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Chain.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/ChainI.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/DNA.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Exon.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Gene.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Intron.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Mutation.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Mutator.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Prim_Transcript.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Range.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Repeat_Region.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Repeat_Unit.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/SeqI.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Transcript.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/LiveSeq/Translation.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Location/'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Location/Atomic.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Location/AvWithinCoordPolicy.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Location/CoordinatePolicyI.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Location/Fuzzy.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Location/FuzzyLocationI.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Location/NarrowestCoordPolicy.pm'
[MSG] [Mon Sep 17 08:28:12 2007] Extracted 'bioperl-1.4/Bio/Location/Simple.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Location/Split.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Location/SplitLocationI.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Location/WidestCoordPolicy.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Map/'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Map/CytoMap.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Map/CytoMarker.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Map/CytoPosition.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Map/LinkageMap.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Map/LinkagePosition.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Map/MapI.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Map/MappableI.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Map/Marker.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Map/MarkerI.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Map/Microsatellite.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Map/OrderedPosition.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Map/OrderedPositionWithDistance.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Map/Position.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Map/PositionI.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Map/SimpleMap.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/MapIO/'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/MapIO/mapmaker.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/IO/'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/IO/phylip.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/IO/scoring.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/PsmHeader.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/Psm.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/InstanceSite.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/InstanceSiteI.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/transfac.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/mast.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/meme.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/PsmHeaderI.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/PsmI.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/SiteMatrix.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/PSM/SiteMatrixI.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/Generic.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/IO.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/MatrixI.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/PhylipDist.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Matrix/Scoring.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Ontology/'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Ontology/GOterm.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Ontology/InterProTerm.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Ontology/Ontology.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Ontology/OntologyEngineI.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Ontology/OntologyI.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Ontology/OntologyStore.pm'
[MSG] [Mon Sep 17 08:28:13 2007] Extracted 'bioperl-1.4/Bio/Ontology/Path.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/PathI.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/Relationship.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/RelationshipFactory.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/RelationshipI.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/RelationshipType.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/SimpleGOEngine.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/SimpleOntologyEngine.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/Term.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/TermFactory.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Ontology/TermI.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/BaseSAXHandler.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/InterProHandler.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/InterProParser.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/dagflat.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/goflat.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/simplehierarchy.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/OntologyIO/soflat.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/MeSH/'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/MeSH/Term.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/MeSH/Twig.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/MiniMIMentry.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/OMIMentry.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/OMIMparser.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/Correlate.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/Measure.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/Phenotype.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Phenotype/PhenotypeI.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/IO/'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/IO/csv.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/IO/prettybase.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/Genotype.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/GenotypeI.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/IO.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/Individual.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/IndividualI.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/Marker.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/MarkerI.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/PopStats.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/Population.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/PopulationI.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/Statistics.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/Simulation/'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/Simulation/Coalescent.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/PopGen/Simulation/GeneticDrift.pm'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Restriction/'
[MSG] [Mon Sep 17 08:28:14 2007] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme/'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme/MultiCut.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme/MultiSite.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Restriction/Analysis.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Restriction/EnzymeCollection.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Restriction/EnzymeI.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Restriction/IO.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Restriction/IO/'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Restriction/IO/bairoch.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Restriction/IO/base.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Restriction/IO/itype2.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Restriction/IO/withrefm.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Root/'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Root/Exception.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Root/Err.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Root/Global.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Root/HTTPget.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Root/IO.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Root/IOManager.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Root/Object.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Root/Root.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Root/RootI.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Root/Storable.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Root/Utilities.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Root/Vector.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Root/Version.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Root/Xref.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/BlastHSP.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/FastaHSP.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/GenericHSP.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/HMMERHSP.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/HSPFactory.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/HSPI.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/PSLHSP.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/PsiBlastHSP.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/HSP/WABAHSP.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/BlastHit.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/Fasta.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/GenericHit.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/HMMERHit.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/HitFactory.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/HitI.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/Hit/PsiBlastHit.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/BlastUtils.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/DatabaseI.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/GenericDatabase.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/Processor.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/SearchUtils.pm'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/Iteration/'
[MSG] [Mon Sep 17 08:28:15 2007] Extracted 'bioperl-1.4/Bio/Search/Iteration/GenericIteration.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Search/Iteration/IterationI.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Search/Result/'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Search/Result/BlastResult.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Search/Result/GenericResult.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Search/Result/HMMERResult.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Search/Result/ResultFactory.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Search/Result/ResultI.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Search/Result/WABAResult.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/BSMLResultWriter.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/GbrowseGFF.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/HSPTableWriter.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/HTMLResultWriter.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/HitTableWriter.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/ResultTableWriter.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/TextResultWriter.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/EventHandlerI.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/FastHitEventBuilder.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/IteratedSearchResultEventBuilder.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/SearchResultEventBuilder.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/SearchWriterI.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/axt.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/blast.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/blasttable.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/blastxml.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/exonerate.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/fasta.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/hmmer.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/megablast.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/psl.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/sim4.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/waba.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/SearchIO/wise.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Seq/'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Seq/Meta/'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Seq/Meta/Array.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Seq/BaseSeqProcessor.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Seq/EncodedSeq.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Seq/LargePrimarySeq.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Seq/LargeSeq.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Seq/Meta.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Seq/MetaI.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Seq/PrimaryQual.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Seq/PrimedSeq.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Seq/QualI.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Seq/RichSeq.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Seq/RichSeqI.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Seq/SeqBuilder.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Seq/SeqFactory.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Seq/SeqFastaSpeedFactory.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Seq/SeqWithQuality.pm'
[MSG] [Mon Sep 17 08:28:16 2007] Extracted 'bioperl-1.4/Bio/Seq/SequenceTrace.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/Seq/TraceI.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/ExonI.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Exon.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/GeneStructure.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/GeneStructureI.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Intron.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/NC_Feature.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Poly_A_site.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Promoter.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Transcript.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/TranscriptI.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/UTR.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/AnnotationAdaptor.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Collection.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/CollectionI.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Computation.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/FeaturePair.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Generic.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/PositionProxy.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Primer.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Similarity.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/SimilarityPair.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/SiRNA/'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/SiRNA/Oligo.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/SiRNA/Pair.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Tools/'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Tools/TypeMapper.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqFeature/Tools/Unflattener.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game/'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game/featHandler.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game/gameHandler.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game/gameSubs.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game/gameWriter.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game/seqHandler.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/FTHelper.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/MultiFile.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/abi.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/ace.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/alf.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/asciitree.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/bsml.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/chadoxml.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/ctf.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/embl.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/exp.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/fasta.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/fastq.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/game.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/gcg.pm'
[MSG] [Mon Sep 17 08:28:17 2007] Extracted 'bioperl-1.4/Bio/SeqIO/genbank.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/SeqIO/kegg.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/SeqIO/largefasta.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/SeqIO/locuslink.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/SeqIO/metafasta.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/SeqIO/phd.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/SeqIO/pir.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/SeqIO/pln.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/SeqIO/qual.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/SeqIO/raw.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/SeqIO/scf.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/SeqIO/swiss.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/SeqIO/tab.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/SeqIO/tigr.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/SeqIO/ztr.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Structure/'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Structure/Chain.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Structure/Atom.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Structure/IO/'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Structure/IO/pdb.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Structure/Entry.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Structure/IO.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Structure/Model.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Structure/Residue.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Structure/StructureI.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Structure/SecStr/'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Structure/SecStr/DSSP/'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Structure/SecStr/DSSP/Res.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Structure/SecStr/STRIDE/'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Structure/SecStr/STRIDE/Res.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Symbol/'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Symbol/Alphabet.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Symbol/AlphabetI.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Symbol/DNAAlphabet.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Symbol/ProteinAlphabet.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Symbol/README.Symbol'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Symbol/Symbol.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Symbol/SymbolI.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Taxonomy/'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Taxonomy/FactoryI.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Taxonomy/Node.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Taxonomy/Taxon.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Taxonomy/Tree.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Tools/'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Tools/Alignment/'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Tools/Alignment/Consed.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Tools/Alignment/Trim.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Tools/AlignFactory.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Tools/AnalysisResult.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Tools/BPbl2seq.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Tools/BPlite.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Tools/BPpsilite.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Tools/Blat.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Tools/CodonTable.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Tools/Coil.pm'
[MSG] [Mon Sep 17 08:28:18 2007] Extracted 'bioperl-1.4/Bio/Tools/ECnumber.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/EPCR.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/ESTScan.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Eponine.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Est2Genome.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/FootPrinter.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/GFF.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Gel.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Geneid.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Genemark.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Genewise.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Genomewise.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Genscan.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Glimmer.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Grail.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/GuessSeqFormat.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Hmmpfam.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/IUPAC.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Lucy.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/MZEF.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/OddCodes.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer3.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Prints.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Profile.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Promoterwise.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/PrositeScan.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Pseudowise.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/QRNA.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/RandomDistFunctions.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/RepeatMasker.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/RestrictionEnzyme.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Seg.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/SeqAnal.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/SeqPattern.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/SeqStats.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/SeqWords.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/SiRNA.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Sigcleave.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Signalp.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Tmhmm.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/WWW.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/dpAlign.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/pICalculator.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/pSW.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/DNA/'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/DNA/ESEfinder.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/SimpleAnalysisBase.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Domcut.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/ELM.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/GOR4.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/HNN.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Mitoprot.pm'
[MSG] [Mon Sep 17 08:28:19 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/NetPhos.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Scansite.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Sopma.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/BPlite/'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/BPlite/Iteration.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/BPlite/HSP.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/BPlite/Sbjct.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast/'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast/Sbjct.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast/CHANGES'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast/HSP.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast/HTML.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Blast/README'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/EMBOSS/'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/EMBOSS/Palindrome.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/HMMER/'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/HMMER/Domain.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/HMMER/Results.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/HMMER/Set.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Molphy/'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Molphy/Result.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Molphy.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML/'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML/ModelResult.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML/Result.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Phylip/'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Phylip/ProtDist.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Prediction/'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Prediction/Exon.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Prediction/Gene.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer/'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer/Assessor/'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer/Assessor/Base.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer/AssessorI.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer/Feature.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Primer/Pair.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Run/'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Run/README'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Run/RemoteBlast.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Run/StandAloneBlast.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Run/WrapperBase.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Sim4/'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Sim4/Results.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tools/Sim4/Exon.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tree/'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tree/AlleleNode.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tree/Node.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tree/NodeI.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tree/NodeNHX.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tree/RandomFactory.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tree/Statistics.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tree/Tree.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tree/TreeFunctionsI.pm'
[MSG] [Mon Sep 17 08:28:20 2007] Extracted 'bioperl-1.4/Bio/Tree/TreeI.pm'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/TreeIO/'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/TreeIO/TreeEventBuilder.pm'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/TreeIO/lintree.pm'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/TreeIO/newick.pm'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/TreeIO/nexus.pm'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/TreeIO/nhx.pm'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/TreeIO/svggraph.pm'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/TreeIO/tabtree.pm'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/Variation/'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/Variation/IO/'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/Variation/IO/flat.pm'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/Variation/IO/xml.pm'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/Variation/AAChange.pm'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/Variation/AAReverseMutate.pm'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/Variation/Allele.pm'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/Variation/DNAMutation.pm'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/Variation/IO.pm'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/Variation/README'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/Variation/RNAChange.pm'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/Variation/SNP.pm'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/Variation/SeqDiff.pm'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/Bio/Variation/VariantI.pm'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/faq/'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/faq/faq.html'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/faq/faq.dtd'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/faq/faq.pl'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/faq/faq.xml'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/makedoc.PL'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/examples/'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/blastn.out'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/data1.txt'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/embl2picture.pl'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/factor7.embl'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast1.pl'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast2.pl'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast3.pl'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast4.pl'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_features.pl'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/examples/README'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/figs/'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig1.png'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig2.png'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig3.png'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig4.png'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig5.png'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig6.png'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/figs/README'
[MSG] [Mon Sep 17 08:28:21 2007] Extracted 'bioperl-1.4/doc/howto/html/'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/html/images/'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/html/images/tip.png'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/html/Flat_Databases.html'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/html/Graphics-HOWTO.html'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/html/OBDA_Access.html'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/html/PAML.html'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/html/README'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/html/SearchIO.html'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/html/SeqIO.html'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/html/SimpleWebAnalysis.html'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/html/e-novative.css'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/pdf/'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/pdf/Flat_Databases.pdf'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/pdf/Graphics-HOWTO.pdf'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/pdf/OBDA_Access.pdf'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/pdf/PAML.pdf'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/pdf/SearchIO.pdf'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/pdf/SeqIO.pdf'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/pdf/SimpleWebAnalysis.pdf'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/pdf/Trees.pdf'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/sgml/'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/sgml/Feature-Annotation.sgml'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/sgml/Flat_Databases.sgml'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/sgml/Graphics-HOWTO.sgml'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/sgml/OBDA_Access.sgml'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/sgml/PAML.sgml'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/sgml/README'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/sgml/SearchIO.sgml'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/sgml/SeqIO.sgml'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/sgml/SimpleWebAnalysis.sgml'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/sgml/Trees.sgml'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/txt/'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/txt/Flat_Databases.txt'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/doc/howto/txt/SimpleWebAnalysis.txt'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/INSTALL.WIN'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/LICENSE'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/MANIFEST.SKIP'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/Makefile.PL'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/PLATFORMS'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/README'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/biodatabases.pod'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/biodesign.pod'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/bioperl.lisp'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/bioperl.pod'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/bioscripts.pod'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/bptutorial.pl'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/examples/'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/examples/Bio-DB-GFF/'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/examples/Bio-DB-GFF/load_ucsc.pl'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/examples/bioperl.pl'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/examples/generate_random_seq.pl'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/examples/longorf.pl'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/examples/make_mrna_protein.pl'
[MSG] [Mon Sep 17 08:28:22 2007] Extracted 'bioperl-1.4/examples/make_primers.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/rev_and_trans.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/revcom_dir.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/subsequence.cgi'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/align/'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/align/align_on_codons.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/align/aligntutorial.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/align/clustalw.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/align/simplealign.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/biblio/'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/biblio/biblio_examples.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/biblio/biblio_soap.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/biographics/'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/biographics/all_glyphs.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/biographics/dynamic_glyphs.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/biographics/feature_data.gff'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/biographics/feature_data.txt'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/biographics/lots_of_glyphs.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/biographics/render_sequence.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/cluster/'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/cluster/dbsnp.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/contributed/'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/contributed/nmrpdb_parse.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/contributed/prosite2perl.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/contributed/rebase2list.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/db/'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/db/get_seqs.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/db/dbfetch'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/db/est_tissue_query.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/db/gb2features.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/db/getGenBank.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/db/rfetch.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/db/use_registry.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/liveseq/'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/liveseq/change_gene.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/popgen/'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/popgen/parse_calc_stats.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/root/'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/root/lib/'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/root/lib/Bio/'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/root/lib/Bio/PrimarySeq.pm'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/root/lib/Bio/PrimarySeqI.pm'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/root/lib/Bio/Seq.pm'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/root/lib/Bio/SeqI.pm'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/root/lib/Error.pm'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/root/lib/TestInterface.pm'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/root/lib/TestObject.pm'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/root/README'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/root/exceptions1.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/root/exceptions2.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/root/exceptions3.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/root/exceptions4.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/searchio/'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/searchio/blast_example.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/searchio/custom_writer.pl'
[MSG] [Mon Sep 17 08:28:23 2007] Extracted 'bioperl-1.4/examples/searchio/hitwriter.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/searchio/hspwriter.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/searchio/htmlwriter.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/searchio/psiblast_features.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/searchio/psiblast_iterations.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/searchio/rawwriter.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/searchio/resultwriter.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/searchio/waba2gff.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/sirna/'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/sirna/TAG'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/sirna/rnai_finder.cgi'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/tk/'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/tk/gsequence.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/tk/hitdisplay.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/tools/'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/tools/gb_to_gff.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/tools/gff2ps.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/tools/parse_codeml.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/tools/psw.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/tools/restriction.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/tools/run_genscan.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/tools/seq_pattern.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/tools/standaloneblast.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/tree/'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/examples/tree/paup2phylip.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/maintenance/'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/maintenance/authors.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/maintenance/README'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/maintenance/modules.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/maintenance/pod.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/models/'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/models/biblio.dia'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/models/README'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/models/bio_liveseq_variation.dia'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/models/bio_map.dia'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/models/bio_restriction.dia'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/models/bioperl.dia'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/models/coordinatemapper.dia'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/models/map_proposal.txt'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/models/maps_and_markers.dia'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/models/popgen.dia'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/models/population_proposal.txt'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/scripts/'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/load_gff.PLS'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/README'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/TAG'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/bp_genbank2gff.PLS'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/bulk_load_gff.PLS'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/fast_load_gff.PLS'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/generate_histogram.PLS'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/load_ucsc.pl'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/pg_bulk_load_gff.PLS'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_gadfly.PLS'
[MSG] [Mon Sep 17 08:28:24 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_ncbi_human.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_sgd.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_wormbase.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/install_bioperl_scripts.pl'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/DB/'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/DB/TAG'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/DB/biofetch_genbank_proxy.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/DB/bioflat_index.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/DB/biogetseq.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/DB/flanks.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/biblio/'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/biblio/TAG'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/biblio/biblio.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/das/'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/das/README'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/das/TAG'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/graphics/'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/graphics/frend.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/graphics/README'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/graphics/TAG'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/graphics/feature_draw.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/graphics/search_overview.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/index/'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/index/TAG'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/index/bp_fetch.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/index/bp_index.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/popgen/'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/popgen/composite_LD.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/popgen/heterogeneity_test.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/searchio/'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/searchio/filter_search.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/seq/'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/seq/TAG'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/seq/extract_feature_seq.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/seq/seqconvert.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/seq/split_seq.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/seq/translate_seq.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/seqstats/'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/seqstats/TAG'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/seqstats/aacomp.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/seqstats/chaos_plot.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/seqstats/gccalc.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/seqstats/oligo_count.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/taxa/'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/taxa/TAG'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/taxa/local_taxonomydb_query.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/taxa/taxid4species.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/tree/'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/tree/TAG'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/tree/blast2tree.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/utilities/'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/utilities/bp_nrdb.PLS'
[MSG] [Mon Sep 17 08:28:25 2007] Extracted 'bioperl-1.4/scripts/utilities/README'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/scripts/utilities/TAG'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/scripts/utilities/bp_mrtrans.PLS'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/scripts/utilities/bp_sreformat.PLS'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/scripts/utilities/dbsplit.PLS'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/scripts/utilities/mask_by_search.PLS'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/scripts/utilities/mutate.PLS'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/scripts/utilities/pairwise_kaks.PLS'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/scripts/utilities/remote_blast.PLS'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/scripts/utilities/search2BSML.PLS'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/scripts/utilities/search2alnblocks.PLS'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/scripts/utilities/search2gff.PLS'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/scripts/utilities/search2tribe.PLS'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/scripts/utilities/seq_length.PLS'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/biodbgff/'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/biodbgff/test.gff'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/503384.MEGABLAST.0'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/503384.MEGABLAST.2'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/5X_1895.FASTXY'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/AAC12660.fa'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/AB077698.gb'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/AE003528_ecoli.bls'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/AE003644_Adh-genomic.gb'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/AF032047.gbk'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/AF165282.gb'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/AHCYL1.kegg'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/ATF14F8.gbk'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/AY095303S1.gbk'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/AnnIX-v003.gbk'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/BK000016-tpa.gbk'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/BLOSUM50'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/BN000066-tpa.embl'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/D10483.gbk'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/D12555.gbk'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/ECAPAH02.embl'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/GO.defs.test'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/GO.defs.test2'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/Genscan.FastA'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.FASTA'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.fa'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.gff'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.grail'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.grailexp'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.mzef'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.tblastx'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/L77119.hmmer'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/LL-sample.seq'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/LOAD_Ccd1.dnd'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/LittleChrY.dbsnp.xml'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/MmCT'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/NM_002254.gb'
[MSG] [Mon Sep 17 08:28:26 2007] Extracted 'bioperl-1.4/t/data/NT_021877.gbk'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/PAM250'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/SwissProt.dat'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/U58726.gb'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/X98338_Adh-mRNA.gb'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/a_thaliana.blastn'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/aaml.mlc'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/aaml_pairwise.mlc'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/acefile.ace.1'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/acefile.singlets'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/alnfile.fasta'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/amino.fa'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/ar.embl'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/bl2seq.blastn'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/bl2seq.blastn.rev'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/bl2seq.blastx.out'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/bl2seq.bug940.out'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/bl2seq.out'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/bl2seq.tblastx.out'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/blast.report'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/blat.psLayout3'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/c200-vs-yeast.BLASTN'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/c200-vs-yeast.BLASTN.m8'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/chad100.scf'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/codeml.mlc'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/codeml_nssites.mlc'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/compLD_missingtest.prettybase'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/compLD_test.prettybase'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/component.ontology.test'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/component.ontology.test2'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/crab.dat.cn'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/crab.nj'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/crab.njb'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/crypto.sim4-0'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/crypto.sim4-3'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/crypto.sim4-4'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/cys1_dicdi.water'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/cysprot.fa'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/cysprot.msf'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/cysprot.needle'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/cysprot.tblastn'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/cysprot.water'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/cysprot1.FASTA'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/cysprot1.fa'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/cysprot1a.fa'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/cysprot1a.msf'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/cysprot1b.fa'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/cysprot1b.hmmsearch'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/cysprot1b.msf'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/cysprot1b.newick'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/cysprot_vs_gadfly.FASTA'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/dmel_2Lchunk.gb'
[MSG] [Mon Sep 17 08:28:27 2007] Extracted 'bioperl-1.4/t/data/dna1.fa'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/dna2.fa'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/dnaE-bsub-prot.fa'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/dnaE-bsub.fa'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/dnaEbsub_ecoli.wublastx'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/dnaEbsub_ecoli.wutblastn'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/dnaEbsub_ecoli.wutblastx'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/ecoli-trna-qrna.out'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/ecoli_domains.rps.xml'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/ecoli_domains.rpsblast'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/ecolitst.bls'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/ecolitst.fa'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/ecolitst.wublastp'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/empty.bl2seq'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/expected.blast.out'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/factor7.embl'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/footprinter.out'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/geneid_1.0.out'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/genemark.out'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/genewise.out'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/genewise_output.paracel_btk'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/genomewise.out'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/genomic-seq.epcr'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/genomic-seq.fasta'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/genomic-seq.genscan'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/genomic-seq.mzef'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/gf-s71.needle'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/glimmer.out'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/hemoglobinA.meg'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/hg16_chroms.gff'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/hmmpfam.out'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/hmmsearch.out'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/hs_est.est2genome'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/hs_fugu.newick'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/hs_owlmonkey.fas'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/hs_owlmonkey.fasta'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/hsinsulin.blastcl3.blastn'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/humor.maf'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/humts1.pal'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/insulin.water'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/interpro_short.xml'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/lucy.info'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/lucy.qual'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/lucy.seq'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/lucy.stderr'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/lysozyme6.protml'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/lysozyme6.simple.protml'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/mapmaker.out'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/mast.dat'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/megablast_output.paracel_btk'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/meme.dat'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/mpath.ontology.test'
[MSG] [Mon Sep 17 08:28:28 2007] Extracted 'bioperl-1.4/t/data/multi_1.fa'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/multi_2.fa'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/multi_blast.bls'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/multifa.seq'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/multiseq.bls'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/mus.bls.xml'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/mutations.dat'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/mutations.xml'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/myco_sites.gff'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/nei_gojobori_test.aln'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/neighbor.dist'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/no-genes.genscan'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/no_hsps.blastp'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/noninterleaved.phy'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/omim_genemap_test'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/omim_text_test'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/pdb1bpt.ent'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/phi.out'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/phipsi.out'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/phredfile.phd'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/phylipdist-36.out'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/phylipdist.out'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/pictogram.fa'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/plague_yeast.bls.xml'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/polymorphism.dat'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/polymorphism.xml'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/popgen_saureus.dat'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/popgen_saureus.multidat'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/popstats.prettybase'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/roa1.dat'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/primedseq.fa'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/primer3_infile.txt'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/primer3_outfile.txt'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/primer3_output.txt'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/promoterwise.out'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/protpars.phy'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/psiblastreport.out'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/qrna-relloc.out'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/qualfile.qual'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/rebase.itype2'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/rebase.withrefm'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/repeatmasker.fa.out'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/revcomp_mrna.gb'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/roa1.genbank'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/roa1.swiss'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/sbay_c545-yeast.BLASTZ.PSL'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/seqdatabase.ini'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/seqfile.pir'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/seqs.fas'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/sequencefamily.dat'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/short.blx'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/sim4.for.for'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/sim4.for.rev'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/sim4.rev'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/sofa.ontology'
[MSG] [Mon Sep 17 08:28:29 2007] Extracted 'bioperl-1.4/t/data/sparsealn.needle'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/stress_test_medline.xml'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/stress_test_pubmed.xml'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/swiss.dat'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/swisspfam.data'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.ace'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.embl'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.fasta'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.game'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.gcg'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.gcgblast'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.gcgfasta'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.genbank'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.genbank.noseq'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.mase'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.metafasta'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.nh'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.nhx'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.pfam'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.pir'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.raw'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.swiss'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.tab'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.txt'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test.waba'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/test_badlf.gcg'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/testaln.aln'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/testaln.fasta'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/testaln.mase'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/testaln.metafasta'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/testaln.msf'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/testaln.nexus'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/testaln.pfam'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/testaln.phylip'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/testaln.prodom'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/testaln.selex'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/testaln.stockholm'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/testdat.exonerate'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/testdbaccnums.out'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/testfuzzy.genbank'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/transfac.dat'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/unigene.data'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/version2.scf'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/version3.scf'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/worm_fam_2785.cdna'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/yn00.mlc'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/biographics/'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version1.gif'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version1.png'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version2.gif'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version2.png'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version3.png'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version4.png'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version5.png'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version6.png'
[MSG] [Mon Sep 17 08:28:30 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version7.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t1/version8.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version1.gif'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version1.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version10.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version11.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version12.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version13.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version14.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version2.gif'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version2.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version3.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version4.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version5.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version6.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version7.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version8.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t2/version9.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/feature_data.txt'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version1.gif'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version1.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version2.gif'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version2.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version3.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version4.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version5.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version6.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/biographics/t3/version7.png'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.contigs'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.log'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.ace.1'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs.qual'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.log'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.problems'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.problems.qual'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.qual'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.singlets'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.view'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.newtags'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.phrap.out'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.screen.out'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_projectNewChromats.fof'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project_to_alu.cross'
[MSG] [Mon Sep 17 08:28:31 2007] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4922R.phd.1'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4924F.phd.1'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4924R.phd.1'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4947F.phd.1'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/data/dbfa/'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/data/dbfa/1.fa'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/data/dbfa/2.fa'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/data/dbfa/3.fa'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/data/dbfa/4.fa'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/data/dbfa/5.fa'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/data/dbfa/6.fa'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/data/dbfa/7.fa'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/data/registry/'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/data/registry/bdb/'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/data/registry/bdb/seqdatabase.ini'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/data/registry/flat/'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/data/registry/flat/seqdatabase.ini'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/AAChange.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/AAReverseMutate.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/AlignIO.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/AlignStats.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/Allele.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/Alphabet.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/Annotation.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/AnnotationAdaptor.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/Assembly.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/BPbl2seq.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/BPlite.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/BPpsilite.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/Biblio.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/BiblioReferences.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/Biblio_biofetch.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/BioDBGFF.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/BioFetch_DB.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/BioGraphics.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/BlastIndex.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/Chain.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/ClusterIO.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/Coalescent.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/CodonTable.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/CoordinateGraph.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/CoordinateMapper.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/Correlate.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/CytoMap.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/DB.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/DBCUTG.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/DBFasta.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/DNAMutation.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/Domcut.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/ECnumber.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/ELM.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/EMBL_DB.t'
[MSG] [Mon Sep 17 08:28:32 2007] Extracted 'bioperl-1.4/t/EMBOSS_Tools.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/ESEfinder.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/EncodedSeq.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/Exception.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/Exonerate.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/FootPrinter.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/GDB.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/GFF.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/GOR4.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/GOterm.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/GeneCoordinateMapper.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/Geneid.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/Genewise.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/Genomewise.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/Genpred.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/GuessSeqFormat.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/HNN.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/IUPAC.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/Index.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/InstanceSite.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/InterProParser.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/LinkageMap.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/LiveSeq.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/LocatableSeq.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/Location.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/LocationFactory.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/LocusLink.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/Map.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/MapIO.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/Matrix.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/MeSH.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/Measure.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/MetaSeq.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/MicrosatelliteMarker.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/MiniMIMentry.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/MitoProt.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/Molphy.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/Mutation.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/Mutator.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/NetPhos.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/Node.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/OMIMentry.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/OMIMentryAllelicVariant.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/OMIMparser.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/OddCodes.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/Ontology.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/OntologyEngine.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/PAML.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/Perl.t'
[MSG] [Mon Sep 17 08:28:33 2007] Extracted 'bioperl-1.4/t/Phenotype.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/PhylipDist.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/Pictogram.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/PopGen.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/PopGenSims.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/PrimarySeq.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/Primer.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/Promoterwise.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/ProtDist.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/QRNA.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/RNAChange.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/RandDistFunctions.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/RandomTreeFactory.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/Range.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/RangeI.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/RefSeq.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/Registry.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/Relationship.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/RelationshipType.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/RemoteBlast.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/RepeatMasker.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/RestrictionAnalysis.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/RestrictionEnzyme.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/RestrictionIO.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/RootI.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/RootIO.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/RootStorable.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/SNP.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/Scansite.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/SearchDist.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/SearchIO.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/Seq.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/SeqAnalysisParser.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/SeqBuilder.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/SeqDiff.t'
[MSG] [Mon Sep 17 08:28:34 2007] Extracted 'bioperl-1.4/t/SeqFeatCollection.t'
[MSG