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

This distribution has been tested as part of the cpan-testers
effort to test as many new uploads to CPAN as possible.  See
http://testers.cpan.org/

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

--

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


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

TEST RESULTS:

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

[MSG] [Fri Apr 25 16:44:46 2008] Trying to get 'http://www.cpan.org/authors/id/L/LI/LIMAONE/CHECKSUMS'
[MSG] [Fri Apr 25 16:44:46 2008] Checksum matches for 'Bio-Grep-0.10.3.tar.gz'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/README'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/TODO'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/examples/'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/examples/bgrep'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/examples/Benchmarks.tt'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/examples/benchmark.pl'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/lib/'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Backend/'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Backend/Vmatch.pm'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Backend/RE.pm'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Backend/GUUGle.pm'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Backend/Agrep.pm'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Backend/BackendI.pm'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Benchmarks.pod'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Cookbook.pod'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Root.pm'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Filter/'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Filter/FilterI.pm'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Filter/FilterRemoveDuplicates.pm'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/SearchSettings.pm'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/SearchResult.pm'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep.pm'
[MSG] [Fri Apr 25 16:44:48 2008] Extracted 'Bio-Grep-0.10.3/META.yml'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/Makefile.PL'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/Build.PL'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/Test_DB_Extend.fasta'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/pod-coverage.t'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/perlcriticrc'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/pod.t'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/TestFilter.pm'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/00.checkprereq.t'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/Test_DB_RevCom.fasta'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/Test_DB_Big.fasta'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/00.load.t'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/50.synopsis.t'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/perlcritic.t'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/Test_DB_Small.fasta'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/Test_DB_Protein.fasta'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/11.backends.guugle.t'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/40.utils.t'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/Test_query_revcom.fasta'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/11.backends.re.t'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/BioGrepTest.pm'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/10.backends.all.t'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/30.features.alignments.t'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/20.filter.t'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/BioGrepSkip.pm'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/Test_query.fasta'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/t/30.features.updownstream.t'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/Changes'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/MANIFEST'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio-Grep-0.10.3/LICENSE'
[MSG] [Fri Apr 25 16:44:49 2008] Extracted 'Bio::Grep' to '/Volumes/Media/smoke/perl588/.cpanplus/5.8.8/build/Bio-Grep-0.10.3'
[MSG] [Fri Apr 25 16:44:52 2008] Warning: prerequisite Bio::AlignIO 0 not found.
Warning: prerequisite Bio::Factory::EMBOSS 0 not found.
Warning: prerequisite Bio::Index::Fasta 0 not found.
Warning: prerequisite Bio::Root::Root 0 not found.
Warning: prerequisite Bio::Root::Version 0 not found.
Warning: prerequisite Bio::Seq 0 not found.
Warning: prerequisite Bio::SeqIO 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] [Fri Apr 25 16:44:52 2008] DEFAULT 'filter_prereqs' HANDLER RETURNING 'sub return value'
[ERROR] [Fri Apr 25 16:44:52 2008] No such module 'Bio::AlignIO' found on CPAN
[MSG] [Fri Apr 25 16:44:52 2008] Module 'Bio::Grep' requires 'Bio::Factory::EMBOSS' version '0' to be installed 
[ERROR] [Fri Apr 25 16:44:52 2008] No such module 'Bio::Index::Fasta' found on CPAN
[ERROR] [Fri Apr 25 16:44:53 2008] No such module 'Bio::Root::Root' found on CPAN
[MSG] [Fri Apr 25 16:44:53 2008] Module 'Bio::Grep' requires 'Bio::Root::Version' version '0' to be installed 
[MSG] [Fri Apr 25 16:44:53 2008] Module 'Bio::Grep' requires 'Bio::Seq' version '0' to be installed 
[ERROR] [Fri Apr 25 16:44:53 2008] No such module 'Bio::SeqIO' found on CPAN
[MSG] [Fri Apr 25 16:44:53 2008] Module 'Bio::Grep' requires 'Carp::Assert' version '0' to be installed 
[MSG] [Fri Apr 25 16:44:53 2008] Module 'Bio::Grep' requires 'Class::MethodMaker' version '2.02' to be installed 
[MSG] [Fri Apr 25 16:44:53 2008] Module 'Bio::Grep' requires 'IO::String' version '1' to be installed 
[MSG] [Fri Apr 25 16:44:53 2008] Module 'Bio::Grep' requires 'ToolSet' version '0.13' to be installed 
[MSG] [Fri Apr 25 16:44:53 2008] Module 'Bio::Grep' requires 'UNIVERSAL::require' version '0.11' to be installed 
[MSG] [Fri Apr 25 16:44:53 2008] Known uninstallable prereqs bioperl-run-1.4 - aborting install

[MSG] [Fri Apr 25 16:44:53 2008] Will not install prerequisite 'Bio::Factory::EMBOSS' -- Note that the overall install may fail due to this
[MSG] [Fri Apr 25 16:44:59 2008] Trying to get 'http://www.cpan.org/authors/id/B/BI/BIRNEY/CHECKSUMS'
[MSG] [Fri Apr 25 16:44:59 2008] Checksum matches for 'bioperl-1.4.tar.gz'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/DEPRECATED'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/AUTHORS'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/BUGS'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/Changes'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/INSTALL'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/FAQ'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/Bio/'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/Bio/Align/'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/Bio/Align/AlignI.pm'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/Bio/Align/DNAStatistics.pm'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/Bio/Align/PairwiseStatistics.pm'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/Bio/Align/StatisticsI.pm'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/Bio/Align/Utilities.pm'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/Bio/AlignIO.pm'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/Bio/AnalysisI.pm'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/Bio/AnalysisParserI.pm'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/Bio/AnalysisResultI.pm'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/Bio/AnnotatableI.pm'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/Bio/AnnotationCollectionI.pm'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/Bio/AnnotationI.pm'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/Bio/Biblio.pm'
[MSG] [Fri Apr 25 16:45:24 2008] Extracted 'bioperl-1.4/Bio/ClusterI.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/ClusterIO.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/DBLinkContainerI.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/DasI.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/DescribableI.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/FeatureHolderI.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/Graphics.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/IdCollectionI.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/IdentifiableI.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/LocatableSeq.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/LocationI.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/MapIO.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/OntologyIO.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/Perl.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/PrimarySeq.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/PrimarySeqI.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/Range.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/RangeI.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/SearchDist.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/SearchIO.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/Seq.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/SeqAnalysisParserI.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/SeqFeatureI.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/SeqI.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/SeqIO.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/SeqUtils.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/SimpleAlign.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/SimpleAnalysisI.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/Species.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/Taxonomy.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/TreeIO.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/UpdateableSeqI.pm'
[MSG] [Fri Apr 25 16:45:25 2008] Extracted 'bioperl-1.4/Bio/WebAgent.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/AlignIO/'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/AlignIO/bl2seq.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/AlignIO/clustalw.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/AlignIO/emboss.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/AlignIO/fasta.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/AlignIO/maf.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/AlignIO/mase.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/AlignIO/mega.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/AlignIO/meme.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/AlignIO/metafasta.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/AlignIO/msf.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/AlignIO/nexus.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/AlignIO/pfam.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/AlignIO/phylip.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/AlignIO/prodom.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/AlignIO/psi.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/AlignIO/selex.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/AlignIO/stockholm.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/Annotation/'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/Annotation/AnnotationFactory.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/Annotation/Collection.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/Annotation/Comment.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/Annotation/DBLink.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/Annotation/OntologyTerm.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/Annotation/Reference.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/Annotation/SimpleValue.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/Annotation/StructuredValue.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/Annotation/TypeManager.pm'
[MSG] [Fri Apr 25 16:45:26 2008] Extracted 'bioperl-1.4/Bio/Assembly/'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Assembly/IO/'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Assembly/IO/phrap.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Assembly/IO/ace.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Assembly/Contig.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Assembly/ContigAnalysis.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Assembly/IO.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Assembly/Scaffold.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Assembly/ScaffoldI.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/IO/'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/IO/medline2ref.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/IO/medlinexml.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/IO/pubmed2ref.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/IO/pubmedxml.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/Article.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/BiblioBase.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/Book.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/BookArticle.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/IO.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/Journal.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/JournalArticle.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/MedlineArticle.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/MedlineBook.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/MedlineBookArticle.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/MedlineJournal.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/MedlineJournalArticle.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/Organisation.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/Patent.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/Person.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/Proceeding.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/Provider.pm'
[MSG] [Fri Apr 25 16:45:27 2008] Extracted 'bioperl-1.4/Bio/Biblio/PubmedArticle.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Biblio/PubmedBookArticle.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Biblio/PubmedJournalArticle.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Biblio/Ref.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Biblio/Service.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Biblio/TechReport.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Biblio/Thesis.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Biblio/WebResource.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Cluster/'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Cluster/ClusterFactory.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Cluster/FamilyI.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Cluster/SequenceFamily.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Cluster/UniGene.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Cluster/UniGeneI.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/ClusterIO/'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/ClusterIO/dbsnp.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/ClusterIO/unigene.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/CodonUsage/'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/CodonUsage/Table.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/CodonUsage/IO.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Coordinate/'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Coordinate/Result/'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Coordinate/Result/Match.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Coordinate/Result/Gap.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Coordinate/Chain.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Coordinate/Collection.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Coordinate/ExtrapolatingPair.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Coordinate/GeneMapper.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Coordinate/Graph.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Coordinate/MapperI.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Coordinate/Pair.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Coordinate/Result.pm'
[MSG] [Fri Apr 25 16:45:28 2008] Extracted 'bioperl-1.4/Bio/Coordinate/ResultI.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/Coordinate/Utils.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/BiblioI.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/Ace.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/Biblio/'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/Biblio/biofetch.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/Biblio/soap.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/BioFetch.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/CUTG.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/DBFetch.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/EMBL.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/Failover.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/Fasta.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/FileCache.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/Flat.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/GDB.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/GFF.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/GenBank.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/GenPept.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/InMemoryCache.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/MANIFEST'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/Makefile.PL'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/MeSH.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/NCBIHelper.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/QueryI.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/RandomAccessI.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/RefSeq.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/Registry.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/SeqI.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/SwissProt.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/Taxonomy.pm'
[MSG] [Fri Apr 25 16:45:29 2008] Extracted 'bioperl-1.4/Bio/DB/Universal.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/UpdateableSeqI.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/WebDBSeqI.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/XEMBL.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/XEMBLService.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/Flat/'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/fasta.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/embl.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/genbank.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/swiss.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/swissprot.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/Flat/BinarySearch.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/biofetch.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/ace.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/iterator.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/mysql.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/oracle.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/oracleace.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/pg.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/biofetch_oracle.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/memory.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/memory_iterator.pm'
[MSG] [Fri Apr 25 16:45:30 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Featname.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Feature.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Homol.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/RelSegment.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Segment.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Typename.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/alignment.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/clone.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/coding.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/match.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/none.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/processed_transcript.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/transcript.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_acembly.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_genscan.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_refgene.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_softberry.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_unigene.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Util/'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Util/Binning.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/GFF/Util/Rearrange.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/Query/'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/Query/GenBank.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/Query/WebQuery.pm'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/Taxonomy/'
[MSG] [Fri Apr 25 16:45:31 2008] Extracted 'bioperl-1.4/Bio/DB/Taxonomy/entrez.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/DB/Taxonomy/flatfile.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Das/'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Das/FeatureTypeI.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Das/SegmentI.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Event/'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Event/EventGeneratorI.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Event/EventHandlerI.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Expression/'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Expression/FeatureGroup/'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Expression/FeatureGroup.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Expression/FeatureI.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Expression/FeatureSet/'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Expression/FeatureSet/FeatureSetMas50.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Factory/'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Factory/AnalysisI.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Factory/ApplicationFactoryI.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Factory/DriverFactory.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Factory/FTLocationFactory.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Factory/HitFactoryI.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Factory/LocationFactoryI.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Factory/MapFactoryI.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Factory/ObjectBuilderI.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Factory/ObjectFactory.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Factory/ObjectFactoryI.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Factory/ResultFactoryI.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Factory/SeqAnalysisParserFactory.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Factory/SeqAnalysisParserFactoryI.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Factory/SequenceFactoryI.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Factory/SequenceProcessorI.pm'
[MSG] [Fri Apr 25 16:45:32 2008] Extracted 'bioperl-1.4/Bio/Factory/SequenceStreamI.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Factory/TreeFactoryI.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/FeatureFile/'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/FeatureFile/Iterator.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/ConfiguratorI.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Feature.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/FeatureFile.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Panel.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Pictogram.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/RendererI.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Util.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/Factory.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/alignment.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/anchored_arrow.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/arrow.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/box.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/cds.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/crossbox.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/diamond.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/dna.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/dot.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/ellipse.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/ex.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/extending_arrow.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/generic.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/graded_segments.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/group.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/heterogeneous_segments.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/line.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/minmax.pm'
[MSG] [Fri Apr 25 16:45:33 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/oval.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/pinsertion.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/primers.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/processed_transcript.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/redgreen_box.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/redgreen_segment.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/rndrect.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/ruler_arrow.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/segmented_keyglyph.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/segments.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/span.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/splice_site.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/toomany.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/track.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/transcript.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/transcript2.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/translation.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/triangle.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/xyplot.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Index/'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Index/Abstract.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Index/AbstractSeq.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Index/Blast.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Index/EMBL.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Index/Fasta.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Index/Fastq.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Index/GenBank.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Index/SwissPfam.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/Index/Swissprot.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/BioPerl.pm'
[MSG] [Fri Apr 25 16:45:34 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/Loader.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/README'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/SRS.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/AARange.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Chain.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/ChainI.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/DNA.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Exon.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Gene.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Intron.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Mutation.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Mutator.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Prim_Transcript.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Range.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Repeat_Region.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Repeat_Unit.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/SeqI.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Transcript.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/LiveSeq/Translation.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/Location/'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/Location/Atomic.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/Location/AvWithinCoordPolicy.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/Location/CoordinatePolicyI.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/Location/Fuzzy.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/Location/FuzzyLocationI.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/Location/NarrowestCoordPolicy.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/Location/Simple.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/Location/Split.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/Location/SplitLocationI.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/Location/WidestCoordPolicy.pm'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/Map/'
[MSG] [Fri Apr 25 16:45:35 2008] Extracted 'bioperl-1.4/Bio/Map/CytoMap.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Map/CytoMarker.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Map/CytoPosition.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Map/LinkageMap.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Map/LinkagePosition.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Map/MapI.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Map/MappableI.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Map/Marker.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Map/MarkerI.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Map/Microsatellite.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Map/OrderedPosition.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Map/OrderedPositionWithDistance.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Map/Position.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Map/PositionI.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Map/SimpleMap.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/MapIO/'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/MapIO/mapmaker.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Matrix/'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Matrix/IO/'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Matrix/IO/phylip.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Matrix/IO/scoring.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/PsmHeader.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/Psm.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/InstanceSite.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/InstanceSiteI.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/transfac.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/mast.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/meme.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/PsmHeaderI.pm'
[MSG] [Fri Apr 25 16:45:36 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/PsmI.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/SiteMatrix.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Matrix/PSM/SiteMatrixI.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Matrix/Generic.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Matrix/IO.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Matrix/MatrixI.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Matrix/PhylipDist.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Matrix/Scoring.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Ontology/'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Ontology/GOterm.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Ontology/InterProTerm.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Ontology/Ontology.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Ontology/OntologyEngineI.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Ontology/OntologyI.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Ontology/OntologyStore.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Ontology/Path.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Ontology/PathI.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Ontology/Relationship.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Ontology/RelationshipFactory.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Ontology/RelationshipI.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Ontology/RelationshipType.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Ontology/SimpleGOEngine.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Ontology/SimpleOntologyEngine.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Ontology/Term.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Ontology/TermFactory.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/Ontology/TermI.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/BaseSAXHandler.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/InterProHandler.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm'
[MSG] [Fri Apr 25 16:45:37 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/InterProParser.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/dagflat.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/goflat.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/simplehierarchy.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/OntologyIO/soflat.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/Phenotype/'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/Phenotype/MeSH/'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/Phenotype/MeSH/Term.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/Phenotype/MeSH/Twig.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/MiniMIMentry.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/OMIMentry.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/OMIMparser.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/Phenotype/Correlate.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/Phenotype/Measure.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/Phenotype/Phenotype.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/Phenotype/PhenotypeI.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/PopGen/'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/PopGen/IO/'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/PopGen/IO/csv.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/PopGen/IO/prettybase.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/PopGen/Genotype.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/PopGen/GenotypeI.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/PopGen/IO.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/PopGen/Individual.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/PopGen/IndividualI.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/PopGen/Marker.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/PopGen/MarkerI.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/PopGen/PopStats.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/PopGen/Population.pm'
[MSG] [Fri Apr 25 16:45:38 2008] Extracted 'bioperl-1.4/Bio/PopGen/PopulationI.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/PopGen/Statistics.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/PopGen/Simulation/'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/PopGen/Simulation/Coalescent.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/PopGen/Simulation/GeneticDrift.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Restriction/'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme/'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme/MultiCut.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme/MultiSite.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Restriction/Analysis.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Restriction/EnzymeCollection.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Restriction/EnzymeI.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Restriction/IO.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Restriction/IO/'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Restriction/IO/bairoch.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Restriction/IO/base.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Restriction/IO/itype2.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Restriction/IO/withrefm.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Root/'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Root/Exception.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Root/Err.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Root/Global.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Root/HTTPget.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Root/IO.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Root/IOManager.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Root/Object.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Root/Root.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Root/RootI.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Root/Storable.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Root/Utilities.pm'
[MSG] [Fri Apr 25 16:45:39 2008] Extracted 'bioperl-1.4/Bio/Root/Vector.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Root/Version.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Root/Xref.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/BlastHSP.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/FastaHSP.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/GenericHSP.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/HMMERHSP.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/HSPFactory.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/HSPI.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/PSLHSP.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/PsiBlastHSP.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/HSP/WABAHSP.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/Hit/'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/Hit/BlastHit.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/Hit/Fasta.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/Hit/GenericHit.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/Hit/HMMERHit.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/Hit/HitFactory.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/Hit/HitI.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/Hit/PsiBlastHit.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/BlastUtils.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/DatabaseI.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/GenericDatabase.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/Processor.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/SearchUtils.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/Iteration/'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/Iteration/GenericIteration.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/Iteration/IterationI.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/Result/'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/Result/BlastResult.pm'
[MSG] [Fri Apr 25 16:45:40 2008] Extracted 'bioperl-1.4/Bio/Search/Result/GenericResult.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/Search/Result/HMMERResult.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/Search/Result/ResultFactory.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/Search/Result/ResultI.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/Search/Result/WABAResult.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/BSMLResultWriter.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/GbrowseGFF.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/HSPTableWriter.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/HTMLResultWriter.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/HitTableWriter.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/ResultTableWriter.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/TextResultWriter.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/EventHandlerI.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/FastHitEventBuilder.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/IteratedSearchResultEventBuilder.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/SearchResultEventBuilder.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/SearchWriterI.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/axt.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/blast.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/blasttable.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/blastxml.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/exonerate.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/fasta.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/hmmer.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/megablast.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/psl.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/sim4.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/waba.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/SearchIO/wise.pm'
[MSG] [Fri Apr 25 16:45:41 2008] Extracted 'bioperl-1.4/Bio/Seq/'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/Seq/Meta/'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/Seq/Meta/Array.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/Seq/BaseSeqProcessor.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/Seq/EncodedSeq.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/Seq/LargePrimarySeq.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/Seq/LargeSeq.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/Seq/Meta.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/Seq/MetaI.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/Seq/PrimaryQual.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/Seq/PrimedSeq.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/Seq/QualI.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/Seq/RichSeq.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/Seq/RichSeqI.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/Seq/SeqBuilder.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/Seq/SeqFactory.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/Seq/SeqFastaSpeedFactory.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/Seq/SeqWithQuality.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/Seq/SequenceTrace.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/Seq/TraceI.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/ExonI.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Exon.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/GeneStructure.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/GeneStructureI.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Intron.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/NC_Feature.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Poly_A_site.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Promoter.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Transcript.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/TranscriptI.pm'
[MSG] [Fri Apr 25 16:45:42 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/UTR.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/AnnotationAdaptor.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Collection.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/CollectionI.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Computation.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/FeaturePair.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Generic.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/PositionProxy.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Primer.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Similarity.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/SimilarityPair.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/SiRNA/'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/SiRNA/Oligo.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/SiRNA/Pair.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Tools/'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Tools/TypeMapper.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqFeature/Tools/Unflattener.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqIO/'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqIO/game/'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqIO/game/featHandler.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqIO/game/gameHandler.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqIO/game/gameSubs.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqIO/game/gameWriter.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqIO/game/seqHandler.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqIO/FTHelper.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqIO/MultiFile.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqIO/abi.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqIO/ace.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqIO/alf.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqIO/asciitree.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqIO/bsml.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqIO/chadoxml.pm'
[MSG] [Fri Apr 25 16:45:43 2008] Extracted 'bioperl-1.4/Bio/SeqIO/ctf.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/embl.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/exp.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/fasta.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/fastq.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/game.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/gcg.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/genbank.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/kegg.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/largefasta.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/locuslink.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/metafasta.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/phd.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/pir.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/pln.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/qual.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/raw.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/scf.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/swiss.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/tab.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/tigr.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/SeqIO/ztr.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/Structure/'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/Structure/Chain.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/Structure/Atom.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/Structure/IO/'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/Structure/IO/pdb.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/Structure/Entry.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/Structure/IO.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/Structure/Model.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/Structure/Residue.pm'
[MSG] [Fri Apr 25 16:45:44 2008] Extracted 'bioperl-1.4/Bio/Structure/StructureI.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Structure/SecStr/'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Structure/SecStr/DSSP/'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Structure/SecStr/DSSP/Res.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Structure/SecStr/STRIDE/'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Structure/SecStr/STRIDE/Res.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Symbol/'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Symbol/Alphabet.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Symbol/AlphabetI.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Symbol/DNAAlphabet.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Symbol/ProteinAlphabet.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Symbol/README.Symbol'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Symbol/Symbol.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Symbol/SymbolI.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Taxonomy/'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Taxonomy/FactoryI.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Taxonomy/Node.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Taxonomy/Taxon.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Taxonomy/Tree.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Tools/'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Tools/Alignment/'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Tools/Alignment/Consed.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Tools/Alignment/Trim.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Tools/AlignFactory.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Tools/AnalysisResult.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Tools/BPbl2seq.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Tools/BPlite.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Tools/BPpsilite.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Tools/Blast.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Tools/Blat.pm'
[MSG] [Fri Apr 25 16:45:45 2008] Extracted 'bioperl-1.4/Bio/Tools/CodonTable.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/Coil.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/ECnumber.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/EPCR.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/ESTScan.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/Eponine.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/Est2Genome.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/FootPrinter.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/GFF.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/Gel.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/Geneid.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/Genemark.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/Genewise.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/Genomewise.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/Genscan.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/Glimmer.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/Grail.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/GuessSeqFormat.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/Hmmpfam.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/IUPAC.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/Lucy.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/MZEF.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/OddCodes.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/Primer3.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/Prints.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/Profile.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/Promoterwise.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/PrositeScan.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/Pseudowise.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/QRNA.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/RandomDistFunctions.pm'
[MSG] [Fri Apr 25 16:45:46 2008] Extracted 'bioperl-1.4/Bio/Tools/RepeatMasker.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/RestrictionEnzyme.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/Seg.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/SeqAnal.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/SeqPattern.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/SeqStats.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/SeqWords.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/SiRNA.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/Sigcleave.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/Signalp.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/Tmhmm.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/WWW.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/dpAlign.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/pICalculator.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/pSW.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/DNA/'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/DNA/ESEfinder.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/SimpleAnalysisBase.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Domcut.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/ELM.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/GOR4.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/HNN.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Mitoprot.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/NetPhos.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Scansite.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Sopma.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/BPlite/'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/BPlite/Iteration.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/BPlite/HSP.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/BPlite/Sbjct.pm'
[MSG] [Fri Apr 25 16:45:47 2008] Extracted 'bioperl-1.4/Bio/Tools/Blast/'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Blast/Sbjct.pm'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Blast/CHANGES'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Blast/HSP.pm'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Blast/HTML.pm'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Blast/README'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/EMBOSS/'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/EMBOSS/Palindrome.pm'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/HMMER/'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/HMMER/Domain.pm'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/HMMER/Results.pm'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/HMMER/Set.pm'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Molphy/'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Molphy/Result.pm'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Molphy.pm'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML.pm'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML/'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML/ModelResult.pm'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML/Result.pm'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Phylip/'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Phylip/ProtDist.pm'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Prediction/'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Prediction/Exon.pm'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Prediction/Gene.pm'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Primer/'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Primer/Assessor/'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Primer/Assessor/Base.pm'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Primer/AssessorI.pm'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Primer/Feature.pm'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Primer/Pair.pm'
[MSG] [Fri Apr 25 16:45:48 2008] Extracted 'bioperl-1.4/Bio/Tools/Run/'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Tools/Run/README'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Tools/Run/RemoteBlast.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Tools/Run/StandAloneBlast.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Tools/Run/WrapperBase.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Tools/Sim4/'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Tools/Sim4/Results.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Tools/Sim4/Exon.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Tree/'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Tree/AlleleNode.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Tree/Node.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Tree/NodeI.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Tree/NodeNHX.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Tree/RandomFactory.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Tree/Statistics.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Tree/Tree.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Tree/TreeFunctionsI.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Tree/TreeI.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/TreeIO/'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/TreeIO/TreeEventBuilder.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/TreeIO/lintree.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/TreeIO/newick.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/TreeIO/nexus.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/TreeIO/nhx.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/TreeIO/svggraph.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/TreeIO/tabtree.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Variation/'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Variation/IO/'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Variation/IO/flat.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Variation/IO/xml.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Variation/AAChange.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Variation/AAReverseMutate.pm'
[MSG] [Fri Apr 25 16:45:49 2008] Extracted 'bioperl-1.4/Bio/Variation/Allele.pm'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/Bio/Variation/DNAMutation.pm'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/Bio/Variation/IO.pm'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/Bio/Variation/README'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/Bio/Variation/RNAChange.pm'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/Bio/Variation/SNP.pm'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/Bio/Variation/SeqDiff.pm'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/Bio/Variation/VariantI.pm'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/faq/'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/faq/faq.html'
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[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/faq/faq.pl'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/faq/faq.xml'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/makedoc.PL'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/howto/'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/howto/examples/'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/blastn.out'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/data1.txt'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/embl2picture.pl'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/factor7.embl'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast1.pl'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast2.pl'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast3.pl'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast4.pl'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_features.pl'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/howto/examples/README'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/howto/figs/'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/howto/figs/graphics/'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig1.png'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig2.png'
[MSG] [Fri Apr 25 16:45:50 2008] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig3.png'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig4.png'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig5.png'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig6.png'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/figs/README'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/html/'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/html/images/'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/html/images/tip.png'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/html/Flat_Databases.html'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/html/Graphics-HOWTO.html'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/html/OBDA_Access.html'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/html/PAML.html'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/html/README'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/html/SearchIO.html'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/html/SeqIO.html'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/html/SimpleWebAnalysis.html'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/html/e-novative.css'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/pdf/'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/pdf/Flat_Databases.pdf'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/pdf/Graphics-HOWTO.pdf'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/pdf/OBDA_Access.pdf'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/pdf/PAML.pdf'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/pdf/SearchIO.pdf'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/pdf/SeqIO.pdf'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/pdf/SimpleWebAnalysis.pdf'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/pdf/Trees.pdf'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/sgml/'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/sgml/Feature-Annotation.sgml'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/sgml/Flat_Databases.sgml'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/sgml/Graphics-HOWTO.sgml'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/sgml/OBDA_Access.sgml'
[MSG] [Fri Apr 25 16:45:51 2008] Extracted 'bioperl-1.4/doc/howto/sgml/PAML.sgml'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/doc/howto/sgml/README'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/doc/howto/sgml/SearchIO.sgml'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/doc/howto/sgml/SeqIO.sgml'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/doc/howto/sgml/SimpleWebAnalysis.sgml'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/doc/howto/sgml/Trees.sgml'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/doc/howto/txt/'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/doc/howto/txt/Flat_Databases.txt'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/doc/howto/txt/SimpleWebAnalysis.txt'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/INSTALL.WIN'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/LICENSE'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/MANIFEST.SKIP'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/Makefile.PL'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/PLATFORMS'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/README'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/biodatabases.pod'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/biodesign.pod'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/bioperl.lisp'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/bioperl.pod'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/bioscripts.pod'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/bptutorial.pl'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/examples/'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/examples/Bio-DB-GFF/'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/examples/Bio-DB-GFF/load_ucsc.pl'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/examples/bioperl.pl'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/examples/generate_random_seq.pl'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/examples/longorf.pl'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/examples/make_mrna_protein.pl'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/examples/make_primers.pl'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/examples/rev_and_trans.pl'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/examples/revcom_dir.pl'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/examples/subsequence.cgi'
[MSG] [Fri Apr 25 16:45:52 2008] Extracted 'bioperl-1.4/examples/align/'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/align/align_on_codons.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/align/aligntutorial.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/align/clustalw.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/align/simplealign.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/biblio/'
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[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/biblio/biblio_soap.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/biographics/'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/biographics/all_glyphs.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/biographics/dynamic_glyphs.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/biographics/feature_data.gff'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/biographics/feature_data.txt'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/biographics/lots_of_glyphs.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/biographics/render_sequence.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/cluster/'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/cluster/dbsnp.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/contributed/'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/contributed/nmrpdb_parse.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/contributed/prosite2perl.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/contributed/rebase2list.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/db/'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/db/get_seqs.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/db/dbfetch'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/db/est_tissue_query.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/db/gb2features.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/db/getGenBank.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/db/rfetch.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/db/use_registry.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/liveseq/'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/liveseq/change_gene.pl'
[MSG] [Fri Apr 25 16:45:53 2008] Extracted 'bioperl-1.4/examples/popgen/'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/popgen/parse_calc_stats.pl'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/root/'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/root/lib/'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/root/lib/Bio/'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/root/lib/Bio/PrimarySeq.pm'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/root/lib/Bio/PrimarySeqI.pm'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/root/lib/Bio/Seq.pm'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/root/lib/Bio/SeqI.pm'
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[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/root/lib/TestInterface.pm'
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[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/root/README'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/root/exceptions1.pl'
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[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/searchio/'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/searchio/blast_example.pl'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/searchio/custom_writer.pl'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/searchio/hitwriter.pl'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/searchio/hspwriter.pl'
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[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/searchio/psiblast_features.pl'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/searchio/psiblast_iterations.pl'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/searchio/rawwriter.pl'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/searchio/resultwriter.pl'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/searchio/waba2gff.pl'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/sirna/'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/sirna/TAG'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/sirna/rnai_finder.cgi'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/tk/'
[MSG] [Fri Apr 25 16:45:54 2008] Extracted 'bioperl-1.4/examples/tk/gsequence.pl'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/examples/tk/hitdisplay.pl'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/examples/tools/'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/examples/tools/gb_to_gff.pl'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/examples/tools/gff2ps.pl'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/examples/tools/parse_codeml.pl'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/examples/tools/psw.pl'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/examples/tools/restriction.pl'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/examples/tools/run_genscan.pl'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/examples/tools/seq_pattern.pl'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/examples/tools/standaloneblast.pl'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/examples/tree/'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/examples/tree/paup2phylip.pl'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/maintenance/'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/maintenance/authors.pl'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/maintenance/README'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/maintenance/modules.pl'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/maintenance/pod.pl'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/models/'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/models/biblio.dia'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/models/README'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/models/bio_liveseq_variation.dia'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/models/bio_map.dia'
[MSG] [Fri Apr 25 16:45:55 2008] Extracted 'bioperl-1.4/models/bio_restriction.dia'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/models/bioperl.dia'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/models/coordinatemapper.dia'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/models/map_proposal.txt'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/models/maps_and_markers.dia'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/models/popgen.dia'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/models/population_proposal.txt'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/load_gff.PLS'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/README'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/TAG'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/bp_genbank2gff.PLS'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/bulk_load_gff.PLS'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/fast_load_gff.PLS'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/generate_histogram.PLS'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/load_ucsc.pl'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/pg_bulk_load_gff.PLS'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_gadfly.PLS'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_ncbi_human.PLS'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_sgd.PLS'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_wormbase.PLS'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/install_bioperl_scripts.pl'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/DB/'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/DB/TAG'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/DB/biofetch_genbank_proxy.PLS'
[MSG] [Fri Apr 25 16:45:56 2008] Extracted 'bioperl-1.4/scripts/DB/bioflat_index.PLS'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/DB/biogetseq.PLS'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/DB/flanks.PLS'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/biblio/'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/biblio/TAG'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/biblio/biblio.PLS'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/das/'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/das/README'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/das/TAG'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/graphics/'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/graphics/frend.PLS'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/graphics/README'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/graphics/TAG'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/graphics/feature_draw.PLS'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/graphics/search_overview.PLS'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/index/'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/index/TAG'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/index/bp_fetch.PLS'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/index/bp_index.PLS'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/popgen/'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/popgen/composite_LD.PLS'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/popgen/heterogeneity_test.PLS'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/searchio/'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/searchio/filter_search.PLS'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/seq/'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/seq/TAG'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/seq/extract_feature_seq.PLS'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/seq/seqconvert.PLS'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/seq/split_seq.PLS'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/seq/translate_seq.PLS'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/seqstats/'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/seqstats/TAG'
[MSG] [Fri Apr 25 16:45:57 2008] Extracted 'bioperl-1.4/scripts/seqstats/aacomp.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/seqstats/chaos_plot.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/seqstats/gccalc.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/seqstats/oligo_count.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/taxa/'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/taxa/TAG'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/taxa/local_taxonomydb_query.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/taxa/taxid4species.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/tree/'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/tree/TAG'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/tree/blast2tree.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/utilities/'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/utilities/bp_nrdb.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/utilities/README'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/utilities/TAG'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/utilities/bp_mrtrans.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/utilities/bp_sreformat.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/utilities/dbsplit.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/utilities/mask_by_search.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/utilities/mutate.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/utilities/pairwise_kaks.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/utilities/remote_blast.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/utilities/search2BSML.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/utilities/search2alnblocks.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/utilities/search2gff.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/utilities/search2tribe.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/scripts/utilities/seq_length.PLS'
[MSG] [Fri Apr 25 16:45:58 2008] Extracted 'bioperl-1.4/t/'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/biodbgff/'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/biodbgff/test.gff'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/503384.MEGABLAST.0'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/503384.MEGABLAST.2'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/5X_1895.FASTXY'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/AAC12660.fa'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/AB077698.gb'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/AE003528_ecoli.bls'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/AE003644_Adh-genomic.gb'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/AF032047.gbk'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/AF165282.gb'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/AHCYL1.kegg'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/ATF14F8.gbk'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/AY095303S1.gbk'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/AnnIX-v003.gbk'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/BK000016-tpa.gbk'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/BLOSUM50'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/BN000066-tpa.embl'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/D10483.gbk'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/D12555.gbk'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/ECAPAH02.embl'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/GO.defs.test'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/GO.defs.test2'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/Genscan.FastA'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.FASTA'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.fa'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.gff'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.grail'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.grailexp'
[MSG] [Fri Apr 25 16:45:59 2008] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.mzef'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.tblastx'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/L77119.hmmer'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/LL-sample.seq'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/LOAD_Ccd1.dnd'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/LittleChrY.dbsnp.xml'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/MmCT'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/NM_002254.gb'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/NT_021877.gbk'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/PAM250'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/SwissProt.dat'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/U58726.gb'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/X98338_Adh-mRNA.gb'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/a_thaliana.blastn'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/aaml.mlc'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/aaml_pairwise.mlc'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/acefile.ace.1'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/acefile.singlets'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/alnfile.fasta'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/amino.fa'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/ar.embl'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/bl2seq.blastn'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/bl2seq.blastn.rev'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/bl2seq.blastx.out'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/bl2seq.bug940.out'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/bl2seq.out'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/bl2seq.tblastx.out'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/blast.report'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/blat.psLayout3'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/c200-vs-yeast.BLASTN'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/c200-vs-yeast.BLASTN.m8'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/chad100.scf'
[MSG] [Fri Apr 25 16:46:00 2008] Extracted 'bioperl-1.4/t/data/codeml.mlc'
[MSG] [Fri Apr 25 16:46:01 2008] Extracted 'bioperl-1.4/t/data/codeml_nssites.mlc'
[MSG] [Fri Apr 25 16:46:01 2008] Extracted 'bioperl-1.4/t/data/compLD_missingtest.prettybase'
[MSG] [Fri Apr 25 16:46:01 2008] Extracted 'bioperl-1.4/t/data/compLD_test.prettybase'
[MSG] [Fri Apr 25 16:46:01 2008] Extracted 'bioperl-1.4/t/data/component.ontology.test'
[MSG] [Fri Apr 25 16:46:01 2008] Extracted 'bioperl-1.4/t/data/component.ontology.test2'
[MSG] [Fri Apr 25 16:46:01 2008] Extracted 'bioperl-1.4/t/data/crab.dat.cn'
[MSG] [Fri Apr 25 16:46:01 2008] Extracted 'bioperl-1.4/t/data/crab.nj'
[MSG] [Fri Apr 25 16:46:01 2008] Extracted 'bioperl-1.4/t/data/crab.njb'
[MSG] [Fri Apr 25 16:46:01 2008] Extracted 'bioperl-1.4/t/data/crypto.sim4-0'
[MSG] [Fri Apr 25 16:46:01 2008] Extracted 'bioperl-1.4/t/data/crypto.sim4-3'
[MSG] [Fri Apr 25 16:46:01 2008] Extracted 'bioperl-1.4/t/data/crypto.sim4-4'
[MSG] [Fri Apr 25 16:46:01 2008] Extracted 'bioperl-1.4/t/data/cys1_dicdi.water'
[MSG] [Fri Apr 25 16:46:01 2008] Extracted 'bioperl-1.4/t/data/cysprot.fa'
[MSG] [Fri Apr 25 16:46:01 2008] Extracted 'bioperl-1.4/t/data/cysprot.msf'
[MSG] [Fri Apr 25 16:46:01 2008] Extracted 'bioperl-1.4/t/data/cysprot.needle'
[MSG] [Fri Apr 25 16:46:01 2008] Extracted 'bioperl-1.4/t/data/cysprot.tblastn'
[MSG] [Fri Apr 25 16:46:01 2008] Extracted 'bioperl-1.4/t/data/cysprot.water'
[MSG] [Fri Apr 25 16:46:01 2008] Extracted 'bioperl-1.4/t/data/cysprot1.FASTA'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/cysprot1.fa'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/cysprot1a.fa'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/cysprot1a.msf'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/cysprot1b.fa'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/cysprot1b.hmmsearch'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/cysprot1b.msf'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/cysprot1b.newick'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/cysprot_vs_gadfly.FASTA'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/dmel_2Lchunk.gb'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/dna1.fa'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/dna2.fa'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/dnaE-bsub-prot.fa'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/dnaE-bsub.fa'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/dnaEbsub_ecoli.wublastx'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/dnaEbsub_ecoli.wutblastn'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/dnaEbsub_ecoli.wutblastx'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/ecoli-trna-qrna.out'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/ecoli_domains.rps.xml'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/ecoli_domains.rpsblast'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/ecolitst.bls'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/ecolitst.fa'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/ecolitst.wublastp'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/empty.bl2seq'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/expected.blast.out'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/factor7.embl'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/footprinter.out'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/geneid_1.0.out'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/genemark.out'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/genewise.out'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/genewise_output.paracel_btk'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/genomewise.out'
[MSG] [Fri Apr 25 16:46:02 2008] Extracted 'bioperl-1.4/t/data/genomic-seq.epcr'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/genomic-seq.fasta'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/genomic-seq.genscan'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/genomic-seq.mzef'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/gf-s71.needle'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/glimmer.out'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/hemoglobinA.meg'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/hg16_chroms.gff'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/hmmpfam.out'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/hmmsearch.out'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/hs_est.est2genome'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/hs_fugu.newick'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/hs_owlmonkey.fas'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/hs_owlmonkey.fasta'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/hsinsulin.blastcl3.blastn'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/humor.maf'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/humts1.pal'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/insulin.water'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/interpro_short.xml'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/lucy.info'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/lucy.qual'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/lucy.seq'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/lucy.stderr'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/lysozyme6.protml'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/lysozyme6.simple.protml'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/mapmaker.out'
[MSG] [Fri Apr 25 16:46:03 2008] Extracted 'bioperl-1.4/t/data/mast.dat'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/megablast_output.paracel_btk'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/meme.dat'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/mpath.ontology.test'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/multi_1.fa'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/multi_2.fa'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/multi_blast.bls'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/multifa.seq'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/multiseq.bls'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/mus.bls.xml'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/mutations.dat'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/mutations.xml'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/myco_sites.gff'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/nei_gojobori_test.aln'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/neighbor.dist'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/no-genes.genscan'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/no_hsps.blastp'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/noninterleaved.phy'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/omim_genemap_test'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/omim_text_test'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/pdb1bpt.ent'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/phi.out'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/phipsi.out'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/phredfile.phd'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/phylipdist-36.out'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/phylipdist.out'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/pictogram.fa'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/plague_yeast.bls.xml'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/polymorphism.dat'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/polymorphism.xml'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/popgen_saureus.dat'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/popgen_saureus.multidat'
[MSG] [Fri Apr 25 16:46:04 2008] Extracted 'bioperl-1.4/t/data/popstats.prettybase'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/roa1.dat'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/primedseq.fa'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/primer3_infile.txt'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/primer3_outfile.txt'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/primer3_output.txt'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/promoterwise.out'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/protpars.phy'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/psiblastreport.out'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/qrna-relloc.out'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/qualfile.qual'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/rebase.itype2'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/rebase.withrefm'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/repeatmasker.fa.out'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/revcomp_mrna.gb'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/roa1.genbank'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/roa1.swiss'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/sbay_c545-yeast.BLASTZ.PSL'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/seqdatabase.ini'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/seqfile.pir'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/seqs.fas'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/sequencefamily.dat'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/short.blx'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/sim4.for.for'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/sim4.for.rev'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/sim4.rev'
[MSG] [Fri Apr 25 16:46:05 2008] Extracted 'bioperl-1.4/t/data/sofa.ontology'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/sparsealn.needle'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/stress_test_medline.xml'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/stress_test_pubmed.xml'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/swiss.dat'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/swisspfam.data'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/test.ace'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/test.embl'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/test.fasta'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/test.game'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/test.gcg'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/test.gcgblast'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/test.gcgfasta'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/test.genbank'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/test.genbank.noseq'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/test.mase'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/test.metafasta'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/test.nh'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/test.nhx'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/test.pfam'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/test.pir'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/test.raw'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/test.swiss'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/test.tab'
[MSG] [Fri Apr 25 16:46:06 2008] Extracted 'bioperl-1.4/t/data/test.txt'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/test.waba'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/test_badlf.gcg'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/testaln.aln'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/testaln.fasta'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/testaln.mase'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/testaln.metafasta'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/testaln.msf'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/testaln.nexus'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/testaln.pfam'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/testaln.phylip'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/testaln.prodom'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/testaln.selex'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/testaln.stockholm'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/testdat.exonerate'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/testdbaccnums.out'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/testfuzzy.genbank'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/transfac.dat'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/unigene.data'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/version2.scf'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/version3.scf'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/worm_fam_2785.cdna'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/yn00.mlc'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/biographics/'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version1.gif'
[MSG] [Fri Apr 25 16:46:07 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version1.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version2.gif'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version2.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version3.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version4.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version5.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version6.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version7.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t1/version8.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version1.gif'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version1.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version10.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version11.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version12.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version13.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version14.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version2.gif'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version2.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version3.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version4.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version5.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version6.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version7.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version8.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t2/version9.png'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/feature_data.txt'
[MSG] [Fri Apr 25 16:46:08 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/version1.gif'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/version1.png'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/version2.gif'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/version2.png'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/version3.png'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/version4.png'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/version5.png'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/version6.png'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/biographics/t3/version7.png'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/consed_project/'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.contigs'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.log'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.ace.1'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.contigs.qual'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.log'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.problems'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.problems.qual'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.qual'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.singlets'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta.screen.view'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.newtags'
[MSG] [Fri Apr 25 16:46:09 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.phrap.out'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.screen.out'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_projectNewChromats.fof'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project_to_alu.cross'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4922R.phd.1'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4924F.phd.1'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4924R.phd.1'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/consed_project/phd_dir/ML4947F.phd.1'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/dbfa/'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/dbfa/1.fa'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/dbfa/2.fa'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/dbfa/3.fa'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/dbfa/4.fa'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/dbfa/5.fa'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/dbfa/6.fa'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/dbfa/7.fa'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/registry/'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/registry/bdb/'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/registry/bdb/seqdatabase.ini'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/registry/flat/'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/data/registry/flat/seqdatabase.ini'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/AAChange.t'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/AAReverseMutate.t'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/AlignIO.t'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/AlignStats.t'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/Allele.t'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/Alphabet.t'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/Annotation.t'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/AnnotationAdaptor.t'
[MSG] [Fri Apr 25 16:46:10 2008] Extracted 'bioperl-1.4/t/Assembly.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/BPbl2seq.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/BPlite.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/BPpsilite.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/Biblio.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/BiblioReferences.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/Biblio_biofetch.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/BioDBGFF.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/BioFetch_DB.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/BioGraphics.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/BlastIndex.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/Chain.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/ClusterIO.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/Coalescent.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/CodonTable.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/CoordinateGraph.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/CoordinateMapper.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/Correlate.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/CytoMap.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/DB.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/DBCUTG.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/DBFasta.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/DNAMutation.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/Domcut.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/ECnumber.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/ELM.t'
[MSG] [Fri Apr 25 16:46:11 2008] Extracted 'bioperl-1.4/t/EMBL_DB.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/EMBOSS_Tools.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/ESEfinder.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/EncodedSeq.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/Exception.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/Exonerate.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/FootPrinter.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/GDB.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/GFF.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/GOR4.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/GOterm.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/GeneCoordinateMapper.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/Geneid.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/Genewise.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/Genomewise.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/Genpred.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/GuessSeqFormat.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/HNN.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/IUPAC.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/Index.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/InstanceSite.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/InterProParser.t'
[MSG] [Fri Apr 25 16:46:12 2008] Extracted 'bioperl-1.4/t/LinkageMap.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/LiveSeq.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/LocatableSeq.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/Location.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/LocationFactory.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/LocusLink.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/Map.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/MapIO.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/Matrix.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/MeSH.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/Measure.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/MetaSeq.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/MicrosatelliteMarker.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/MiniMIMentry.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/MitoProt.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/Molphy.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/Mutation.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/Mutator.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/NetPhos.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/Node.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/OMIMentry.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/OMIMentryAllelicVariant.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/OMIMparser.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/OddCodes.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/Ontology.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/OntologyEngine.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/PAML.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/Perl.t'
[MSG] [Fri Apr 25 16:46:13 2008] Extracted 'bioperl-1.4/t/Phenotype.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/PhylipDist.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/Pictogram.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/PopGen.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/PopGenSims.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/PrimarySeq.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/Primer.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/Promoterwise.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/ProtDist.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/QRNA.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/RNAChange.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/RandDistFunctions.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/RandomTreeFactory.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/Range.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/RangeI.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/RefSeq.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/Registry.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/Relationship.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/RelationshipType.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/RemoteBlast.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/RepeatMasker.t'
[MSG] [Fri Apr 25 16:46:14 2008] Extracted 'bioperl-1.4/t/RestrictionAnalysis.t'
[MSG] [Fri Apr 25