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Postings from December 2006
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 0.076. 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] [Thu Dec 7 06:30:41 2006] Trying to get 'http://www.cpan.org/authors/id/S/SE/SENDU/bioperl-db-1.5.2_100.tar.gz'
[MSG] [Thu Dec 7 06:30:43 2006] Trying to get 'http://www.cpan.org/authors/id/S/SE/SENDU/CHECKSUMS'
[MSG] [Thu Dec 7 06:30:43 2006] Checksum matches for 'bioperl-db-1.5.2_100.tar.gz'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/BioEntry.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioDB.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/BaseDriver.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/BasePersistenceAdaptor.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/BioNamespaceAdaptor.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/BiosequenceAdaptor.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/ClusterAdaptor.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/CommentAdaptor.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/DBAdaptor.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/DBLinkAdaptor.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/LocationAdaptor.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/MultiDB.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/mysql/'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/mysql/AnnotationCollectionAdaptorDriver.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/mysql/BasePersistenceAdaptorDriver.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/mysql/BiosequenceAdaptorDriver.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/mysql/PathAdaptorDriver.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/mysql/SpeciesAdaptorDriver.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/mysql/TermAdaptorDriver.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/OBDA.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/OntologyAdaptor.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/Oracle/'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/Oracle/AnnotationCollectionAdaptorDriver.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/Oracle/BasePersistenceAdaptorDriver.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/Oracle/BiosequenceAdaptorDriver.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/Oracle/PathAdaptorDriver.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/Oracle/SpeciesAdaptorDriver.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/Oracle/TermAdaptorDriver.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/PathAdaptor.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/Pg/'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/Pg/AnnotationCollectionAdaptorDriver.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/Pg/BasePersistenceAdaptorDriver.pm'
[MSG] [Thu Dec 7 06:30:45 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/Pg/BiosequenceAdaptorDriver.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/Pg/PathAdaptorDriver.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/Pg/SpeciesAdaptorDriver.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/Pg/TermAdaptorDriver.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/PrimarySeqAdaptor.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/ReferenceAdaptor.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/RelationshipAdaptor.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/SeqAdaptor.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/SeqFeatureAdaptor.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/SimpleValueAdaptor.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/SpeciesAdaptor.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/BioSQL/TermAdaptor.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/CacheServer/'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/CacheServer/SeqDB.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/DBAdaptorI.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/DBContextI.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/DBD.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/DBI/'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/DBI/base.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/DBI/mysql.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/DBI/Oracle.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/DBI/Pg.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/DBI/Transaction.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/DBI/TransactionListener.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/DBI.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/EasyArgv.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/PersistenceAdaptorI.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/Persistent/'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/Persistent/BioNamespace.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/Persistent/ObjectRelMapperI.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/Persistent/PersistentObject.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/Persistent/PersistentObjectFactory.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/Persistent/PrimarySeq.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/Persistent/Seq.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/Persistent/SeqFeature.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/PersistentObjectI.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/Query/'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/Query/AbstractQuery.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/Query/BioQuery.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/Query/DBQueryResult.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/Query/PrebuiltResult.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/Query/QueryConstraint.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/Query/QueryResultI.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/Query/SqlGenerator.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/Query/SqlQuery.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Bio/DB/SimpleDBContext.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/BUGS'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Build.PL'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Changes'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/docs/'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/docs/HOWTO-MySQL.html'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/INSTALL'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/LICENSE'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/Makefile.PL'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/MANIFEST'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/META.yml'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/model/'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/model/bioperl-maps.dia'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/ModuleBuildBioperl.pm'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/onto-term.patch'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/README'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/biosql/'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/biosql/bioentry2flat.pl'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/biosql/cgi-bin/'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/biosql/cgi-bin/getentry.pl'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/biosql/clean_ontology.pl'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/biosql/del-assocs-sql.pl'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/biosql/drop_mysql_biosql_test_dbs'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/biosql/freshen-annot.pl'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/biosql/load_interpro.pl'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/biosql/load_ontology.pl'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/biosql/load_seqdatabase.pl'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/biosql/merge-unique-ann.pl'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/biosql/terms/'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/biosql/terms/add-term-annot.pl'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/biosql/terms/conf.xml'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/biosql/terms/importrelation.pl'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/biosql/terms/interpro2go.pl'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/biosql/update-on-new-date.pl'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/biosql/update-on-new-version.pl'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/corba/'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/corba/bioenv_server.pl'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/corba/caching_corba_server.pl'
[MSG] [Thu Dec 7 06:30:46 2006] Extracted 'bioperl-db-1.5.2_100/scripts/corba/test_bioenv.pl'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/sql/'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/sql/bibliography-mysql.sql'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/sql/markerdb-mysql.sql'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/sql/rawdata-mysql.sql'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/01dbadaptor.t'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/02species.t'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/03simpleseq.t'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/04swiss.t'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/05seqfeature.t'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/06comment.t'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/07dblink.t'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/08genbank.t'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/09fuzzy2.t'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/10ensembl.t'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/11locuslink.t'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/12ontology.t'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/13remove.t'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/14query.t'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/15cluster.t'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/16obda.t'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/BioSQLBase.pm'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/data/'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/data/AB030700.embl'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/data/AP000868.gb'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/data/LL-sample.seq'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/data/parkin.fasta'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/data/parkin.gb'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/data/sofa.ontology'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/data/swiss.dat'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/data/test.genbank'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/data/Titin.fasta'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/data/unigene.data'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/DBHarness.conf.example'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/DBTestHarness.pm'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl-db-1.5.2_100/t/Test.pm'
[MSG] [Thu Dec 7 06:30:47 2006] Extracted 'bioperl::db' to '/home/hybrid/perl588/.cpanplus/5.8.8/build/bioperl-db-1.5.2_100'
[MSG] [Thu Dec 7 06:30:55 2006] !--
Bioperl is transitioning from Makefile.PL-based installations to Build.PL
This Makefile.PL should still work fine, but please try Build.PL instead,
especially if you run into any non-test-related problems:
perl Build.PL
./Build test
./Build install
If you're seeing this message whilst installing with CPAN, consider
stopping this installation and changing your CPAN configuration before
trying to install again:
cpan>install CPAN
cpan>reload CPAN
cpan>install Module::Build
cpan>o conf prefer_installer MB
cpan>o conf commit
cpan>q
Otherwise, if you would like to install the optional dependencies,
install Bundle::BioPerl v2.1.8 or greater
--!
. . . . .
Generated sub tests. go make show_tests to see available subtests
*** Optional dependencies section ***
External Module 'Bio::Root::Version' >= 1.005002 (Bioperl) is not installed on this computer.
The following Bioperl-run modules need it for basic functionality:
* Everything
Additionally, it is absolutely required and therefore most if not all tests will fail!
External Module 'DBI' >= 0.0 (Database Access) is not installed on this computer.
The following Bioperl-run modules need it for basic functionality:
* Everything
Additionally, it is absolutely required and therefore most if not all tests will fail!
Information:
Some perl modules are missing, listed above and below. The only
functionality that will be affected is described above;
the rest of bioperl will work fine without them.
The installation of these external packages is very simple. You
can read more about bioperl external dependencies in the INSTALL
file or at:
http://bioperl.org/wiki/Installing_BioPerl
Enjoy the rest of bioperl, which you can use after going 'make install'
NB: BioSQL also needs to be installed for this package to work; see the INSTALL file
Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::Root::Version 1.005002 not found.
Warning: prerequisite DBI 0.0 not found.
Writing Makefile for Bio
[MSG] [Thu Dec 7 06:30:55 2006] DEFAULT 'filter_prereqs' HANDLER RETURNING 'sub return value'
[ERROR] [Thu Dec 7 06:30:55 2006] This distribution depends on Bio::Root::Version, but the latest version of Bio::Root::Version on CPAN (0.0) doesn't satisfy the specific version dependency (1.005002). You may have to resolve this dependency manually.
[MSG] [Thu Dec 7 06:30:55 2006] Module 'bioperl::db' requires 'Bio::Root::Version' version '1.005002' to be installed
[MSG] [Thu Dec 7 06:30:55 2006] Module 'bioperl::db' requires 'DBI' version '0.0' to be installed
[ERROR] [Thu Dec 7 06:30:55 2006] This distribution depends on Bio::Root::Version, but the latest version of Bio::Root::Version on CPAN (0.0) doesn't satisfy the specific version dependency (1.005002). You may have to resolve this dependency manually.
[MSG] [Thu Dec 7 06:30:55 2006] Trying to get 'http://www.cpan.org/authors/id/B/BI/BIRNEY/bioperl-1.4.tar.gz'
[MSG] [Thu Dec 7 06:31:03 2006] Trying to get 'http://www.cpan.org/authors/id/B/BI/BIRNEY/CHECKSUMS'
[MSG] [Thu Dec 7 06:31:04 2006] Checksum matches for 'bioperl-1.4.tar.gz'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/DEPRECATED'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/AUTHORS'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/BUGS'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Changes'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/INSTALL'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/FAQ'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/Align/'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/Align/AlignI.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/Align/DNAStatistics.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/Align/PairwiseStatistics.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/Align/StatisticsI.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/Align/Utilities.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/AlignIO.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/AnalysisI.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/AnalysisParserI.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/AnalysisResultI.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/AnnotatableI.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/AnnotationCollectionI.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/AnnotationI.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/Biblio.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/ClusterI.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/ClusterIO.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/DBLinkContainerI.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/DasI.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/DescribableI.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/FeatureHolderI.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/Graphics.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/IdCollectionI.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/IdentifiableI.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/LocatableSeq.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/LocationI.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/MapIO.pm'
[MSG] [Thu Dec 7 06:31:14 2006] Extracted 'bioperl-1.4/Bio/OntologyIO.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Perl.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/PrimarySeq.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/PrimarySeqI.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Range.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/RangeI.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/SearchDist.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/SearchIO.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Seq.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/SeqAnalysisParserI.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/SeqFeatureI.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/SeqI.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/SeqIO.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/SeqUtils.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/SimpleAlign.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/SimpleAnalysisI.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Species.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Taxonomy.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/TreeIO.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/UpdateableSeqI.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/WebAgent.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/AlignIO/'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/AlignIO/bl2seq.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/AlignIO/clustalw.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/AlignIO/emboss.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/AlignIO/fasta.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/AlignIO/maf.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/AlignIO/mase.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/AlignIO/mega.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/AlignIO/meme.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/AlignIO/metafasta.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/AlignIO/msf.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/AlignIO/nexus.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/AlignIO/pfam.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/AlignIO/phylip.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/AlignIO/prodom.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/AlignIO/psi.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/AlignIO/selex.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/AlignIO/stockholm.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Annotation/'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Annotation/AnnotationFactory.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Annotation/Collection.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Annotation/Comment.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Annotation/DBLink.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Annotation/OntologyTerm.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Annotation/Reference.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Annotation/SimpleValue.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Annotation/StructuredValue.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Annotation/TypeManager.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Assembly/'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Assembly/IO/'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Assembly/IO/phrap.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Assembly/IO/ace.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Assembly/Contig.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Assembly/ContigAnalysis.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Assembly/IO.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Assembly/Scaffold.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Assembly/ScaffoldI.pm'
[MSG] [Thu Dec 7 06:31:15 2006] Extracted 'bioperl-1.4/Bio/Biblio/'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/IO/'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/IO/medline2ref.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/IO/medlinexml.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/IO/pubmed2ref.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/IO/pubmedxml.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/Article.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/BiblioBase.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/Book.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/BookArticle.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/IO.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/Journal.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/JournalArticle.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/MedlineArticle.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/MedlineBook.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/MedlineBookArticle.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/MedlineJournal.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/MedlineJournalArticle.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/Organisation.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/Patent.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/Person.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/Proceeding.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/Provider.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/PubmedArticle.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/PubmedBookArticle.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/PubmedJournalArticle.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/Ref.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/Service.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/TechReport.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/Thesis.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Biblio/WebResource.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Cluster/'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Cluster/ClusterFactory.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Cluster/FamilyI.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Cluster/SequenceFamily.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Cluster/UniGene.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Cluster/UniGeneI.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/ClusterIO/'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/ClusterIO/dbsnp.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/ClusterIO/unigene.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/CodonUsage/'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/CodonUsage/Table.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/CodonUsage/IO.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Coordinate/'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Coordinate/Result/'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Coordinate/Result/Match.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Coordinate/Result/Gap.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Coordinate/Chain.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Coordinate/Collection.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Coordinate/ExtrapolatingPair.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Coordinate/GeneMapper.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Coordinate/Graph.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Coordinate/MapperI.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Coordinate/Pair.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Coordinate/Result.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Coordinate/ResultI.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/Coordinate/Utils.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/DB/'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/DB/BiblioI.pm'
[MSG] [Thu Dec 7 06:31:16 2006] Extracted 'bioperl-1.4/Bio/DB/Ace.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/Biblio/'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/Biblio/biofetch.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/Biblio/soap.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/BioFetch.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/CUTG.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/DBFetch.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/EMBL.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/Failover.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/Fasta.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/FileCache.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/Flat.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GDB.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GFF.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GenBank.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GenPept.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/InMemoryCache.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/MANIFEST'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/Makefile.PL'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/MeSH.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/NCBIHelper.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/QueryI.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/RandomAccessI.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/RefSeq.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/Registry.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/SeqI.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/SwissProt.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/Taxonomy.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/Universal.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/UpdateableSeqI.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/WebDBSeqI.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/XEMBL.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/XEMBLService.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/Flat/'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/fasta.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/embl.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/genbank.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/swiss.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB/swissprot.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/Flat/BDB.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/Flat/BinarySearch.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/biofetch.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/ace.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/iterator.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/mysql.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/mysqlace.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/oracle.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/oracleace.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi/pg.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/biofetch_oracle.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/dbi.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/memory.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Adaptor/memory_iterator.pm'
[MSG] [Thu Dec 7 06:31:17 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Featname.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Feature.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Homol.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/RelSegment.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Segment.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Typename.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/alignment.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/clone.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/coding.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/match.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/none.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/processed_transcript.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/transcript.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_acembly.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_ensgene.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_genscan.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_refgene.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_sanger22.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_softberry.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_twinscan.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Aggregator/ucsc_unigene.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Util/'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Util/Binning.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/GFF/Util/Rearrange.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/Query/'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/Query/GenBank.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/Query/WebQuery.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/Taxonomy/'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/Taxonomy/entrez.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/DB/Taxonomy/flatfile.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Das/'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Das/FeatureTypeI.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Das/SegmentI.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Event/'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Event/EventGeneratorI.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Event/EventHandlerI.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Expression/'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Expression/FeatureGroup/'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Expression/FeatureGroup.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Expression/FeatureI.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Expression/FeatureSet/'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Expression/FeatureSet/FeatureSetMas50.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Factory/'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Factory/AnalysisI.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Factory/ApplicationFactoryI.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Factory/DriverFactory.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Factory/FTLocationFactory.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Factory/HitFactoryI.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Factory/LocationFactoryI.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Factory/MapFactoryI.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Factory/ObjectBuilderI.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Factory/ObjectFactory.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Factory/ObjectFactoryI.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Factory/ResultFactoryI.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Factory/SeqAnalysisParserFactory.pm'
[MSG] [Thu Dec 7 06:31:18 2006] Extracted 'bioperl-1.4/Bio/Factory/SeqAnalysisParserFactoryI.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Factory/SequenceFactoryI.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Factory/SequenceProcessorI.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Factory/SequenceStreamI.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Factory/TreeFactoryI.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/FeatureFile/'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/FeatureFile/Iterator.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/ConfiguratorI.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Feature.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/FeatureFile.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Panel.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Pictogram.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/RendererI.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Util.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/Factory.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/alignment.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/anchored_arrow.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/arrow.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/box.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/cds.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/crossbox.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/diamond.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/dna.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/dot.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/ellipse.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/ex.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/extending_arrow.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/generic.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/graded_segments.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/group.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/heterogeneous_segments.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/line.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/minmax.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/oval.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/pinsertion.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/primers.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/processed_transcript.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/redgreen_box.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/redgreen_segment.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/rndrect.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/ruler_arrow.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/segmented_keyglyph.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/segments.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/span.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/splice_site.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/toomany.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/track.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/transcript.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/transcript2.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/translation.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/triangle.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Graphics/Glyph/xyplot.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Index/'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Index/Abstract.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Index/AbstractSeq.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Index/Blast.pm'
[MSG] [Thu Dec 7 06:31:19 2006] Extracted 'bioperl-1.4/Bio/Index/EMBL.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Index/Fasta.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Index/Fastq.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Index/GenBank.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Index/SwissPfam.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Index/Swissprot.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/BioPerl.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/Loader.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/README'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/IO/SRS.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/AARange.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/Chain.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/ChainI.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/DNA.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/Exon.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/Gene.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/Intron.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/Mutation.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/Mutator.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/Prim_Transcript.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/Range.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/Repeat_Region.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/Repeat_Unit.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/SeqI.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/Transcript.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/LiveSeq/Translation.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Location/'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Location/Atomic.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Location/AvWithinCoordPolicy.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Location/CoordinatePolicyI.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Location/Fuzzy.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Location/FuzzyLocationI.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Location/NarrowestCoordPolicy.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Location/Simple.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Location/Split.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Location/SplitLocationI.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Location/WidestCoordPolicy.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Map/'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Map/CytoMap.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Map/CytoMarker.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Map/CytoPosition.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Map/LinkageMap.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Map/LinkagePosition.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Map/MapI.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Map/MappableI.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Map/Marker.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Map/MarkerI.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Map/Microsatellite.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Map/OrderedPosition.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Map/OrderedPositionWithDistance.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Map/Position.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Map/PositionI.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Map/SimpleMap.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/MapIO/'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/MapIO/mapmaker.pm'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Matrix/'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Matrix/IO/'
[MSG] [Thu Dec 7 06:31:20 2006] Extracted 'bioperl-1.4/Bio/Matrix/IO/phylip.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/IO/scoring.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/PSM/'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/PSM/PsmHeader.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/PSM/Psm.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/PSM/InstanceSite.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/PSM/InstanceSiteI.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/transfac.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/mast.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/PSM/IO/meme.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/PSM/PsmHeaderI.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/PSM/PsmI.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/PSM/SiteMatrix.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/PSM/SiteMatrixI.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/Generic.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/IO.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/MatrixI.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/PhylipDist.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Matrix/Scoring.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Ontology/'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Ontology/GOterm.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Ontology/InterProTerm.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Ontology/Ontology.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Ontology/OntologyEngineI.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Ontology/OntologyI.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Ontology/OntologyStore.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Ontology/Path.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Ontology/PathI.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Ontology/Relationship.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Ontology/RelationshipFactory.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Ontology/RelationshipI.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Ontology/RelationshipType.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Ontology/SimpleGOEngine.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Ontology/SimpleOntologyEngine.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Ontology/Term.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Ontology/TermFactory.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Ontology/TermI.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/OntologyIO/'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/BaseSAXHandler.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/InterProHandler.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/OntologyIO/InterProParser.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/OntologyIO/dagflat.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/OntologyIO/goflat.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/OntologyIO/simplehierarchy.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/OntologyIO/soflat.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Phenotype/'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Phenotype/MeSH/'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Phenotype/MeSH/Term.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Phenotype/MeSH/Twig.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/MiniMIMentry.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/OMIMentry.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/OMIMentryAllelicVariant.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Phenotype/OMIM/OMIMparser.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Phenotype/Correlate.pm'
[MSG] [Thu Dec 7 06:31:21 2006] Extracted 'bioperl-1.4/Bio/Phenotype/Measure.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Phenotype/Phenotype.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Phenotype/PhenotypeI.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/PopGen/'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/PopGen/IO/'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/PopGen/IO/csv.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/PopGen/IO/prettybase.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/PopGen/Genotype.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/PopGen/GenotypeI.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/PopGen/IO.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/PopGen/Individual.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/PopGen/IndividualI.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/PopGen/Marker.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/PopGen/MarkerI.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/PopGen/PopStats.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/PopGen/Population.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/PopGen/PopulationI.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/PopGen/Statistics.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/PopGen/Simulation/'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/PopGen/Simulation/Coalescent.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/PopGen/Simulation/GeneticDrift.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Restriction/'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme/'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme/MultiCut.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme/MultiSite.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Restriction/Analysis.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Restriction/Enzyme.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Restriction/EnzymeCollection.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Restriction/EnzymeI.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Restriction/IO.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Restriction/IO/'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Restriction/IO/bairoch.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Restriction/IO/base.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Restriction/IO/itype2.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Restriction/IO/withrefm.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Root/'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Root/Exception.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Root/Err.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Root/Global.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Root/HTTPget.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Root/IO.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Root/IOManager.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Root/Object.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Root/Root.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Root/RootI.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Root/Storable.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Root/Utilities.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Root/Vector.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Root/Version.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Root/Xref.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Search/'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Search/HSP/'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Search/HSP/BlastHSP.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Search/HSP/FastaHSP.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Search/HSP/GenericHSP.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Search/HSP/HMMERHSP.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Search/HSP/HSPFactory.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Search/HSP/HSPI.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Search/HSP/PSLHSP.pm'
[MSG] [Thu Dec 7 06:31:22 2006] Extracted 'bioperl-1.4/Bio/Search/HSP/PsiBlastHSP.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/HSP/WABAHSP.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/Hit/'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/Hit/BlastHit.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/Hit/Fasta.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/Hit/GenericHit.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/Hit/HMMERHit.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/Hit/HitFactory.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/Hit/HitI.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/Hit/PsiBlastHit.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/BlastUtils.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/DatabaseI.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/GenericDatabase.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/Processor.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/SearchUtils.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/Iteration/'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/Iteration/GenericIteration.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/Iteration/IterationI.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/Result/'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/Result/BlastResult.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/Result/GenericResult.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/Result/HMMERResult.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/Result/ResultFactory.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/Result/ResultI.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Search/Result/WABAResult.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/BSMLResultWriter.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/GbrowseGFF.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/HSPTableWriter.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/HTMLResultWriter.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/HitTableWriter.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/ResultTableWriter.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/Writer/TextResultWriter.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/EventHandlerI.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/FastHitEventBuilder.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/IteratedSearchResultEventBuilder.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/SearchResultEventBuilder.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/SearchWriterI.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/axt.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/blast.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/blasttable.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/blastxml.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/exonerate.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/fasta.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/hmmer.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/megablast.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/psl.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/sim4.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/waba.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/SearchIO/wise.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Seq/'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Seq/Meta/'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Seq/Meta/Array.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Seq/BaseSeqProcessor.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Seq/EncodedSeq.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Seq/LargePrimarySeq.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Seq/LargeSeq.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Seq/Meta.pm'
[MSG] [Thu Dec 7 06:31:23 2006] Extracted 'bioperl-1.4/Bio/Seq/MetaI.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/Seq/PrimaryQual.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/Seq/PrimedSeq.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/Seq/QualI.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/Seq/RichSeq.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/Seq/RichSeqI.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/Seq/SeqBuilder.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/Seq/SeqFactory.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/Seq/SeqFastaSpeedFactory.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/Seq/SeqWithQuality.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/Seq/SequenceTrace.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/Seq/TraceI.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/ExonI.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Exon.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/GeneStructure.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/GeneStructureI.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Intron.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/NC_Feature.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Poly_A_site.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Promoter.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/Transcript.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/TranscriptI.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Gene/UTR.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/AnnotationAdaptor.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Collection.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/CollectionI.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Computation.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/FeaturePair.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Generic.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/PositionProxy.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Primer.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Similarity.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/SimilarityPair.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/SiRNA/'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/SiRNA/Oligo.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/SiRNA/Pair.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Tools/'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Tools/TypeMapper.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqFeature/Tools/Unflattener.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqIO/'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqIO/game/'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqIO/game/featHandler.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqIO/game/gameHandler.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqIO/game/gameSubs.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqIO/game/gameWriter.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqIO/game/seqHandler.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqIO/FTHelper.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqIO/MultiFile.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqIO/abi.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqIO/ace.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqIO/alf.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqIO/asciitree.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqIO/bsml.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqIO/chadoxml.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqIO/ctf.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqIO/embl.pm'
[MSG] [Thu Dec 7 06:31:24 2006] Extracted 'bioperl-1.4/Bio/SeqIO/exp.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/SeqIO/fasta.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/SeqIO/fastq.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/SeqIO/game.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/SeqIO/gcg.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/SeqIO/genbank.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/SeqIO/kegg.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/SeqIO/largefasta.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/SeqIO/locuslink.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/SeqIO/metafasta.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/SeqIO/phd.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/SeqIO/pir.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/SeqIO/pln.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/SeqIO/qual.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/SeqIO/raw.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/SeqIO/scf.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/SeqIO/swiss.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/SeqIO/tab.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/SeqIO/tigr.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/SeqIO/ztr.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Structure/'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Structure/Chain.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Structure/Atom.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Structure/IO/'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Structure/IO/pdb.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Structure/Entry.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Structure/IO.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Structure/Model.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Structure/Residue.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Structure/StructureI.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Structure/SecStr/'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Structure/SecStr/DSSP/'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Structure/SecStr/DSSP/Res.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Structure/SecStr/STRIDE/'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Structure/SecStr/STRIDE/Res.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Symbol/'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Symbol/Alphabet.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Symbol/AlphabetI.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Symbol/DNAAlphabet.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Symbol/ProteinAlphabet.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Symbol/README.Symbol'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Symbol/Symbol.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Symbol/SymbolI.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Taxonomy/'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Taxonomy/FactoryI.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Taxonomy/Node.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Taxonomy/Taxon.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Taxonomy/Tree.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Tools/'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Tools/Alignment/'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Tools/Alignment/Consed.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Tools/Alignment/Trim.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Tools/AlignFactory.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Tools/AnalysisResult.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Tools/BPbl2seq.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Tools/BPlite.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Tools/BPpsilite.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Tools/Blast.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Tools/Blat.pm'
[MSG] [Thu Dec 7 06:31:25 2006] Extracted 'bioperl-1.4/Bio/Tools/CodonTable.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Coil.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/ECnumber.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/EPCR.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/ESTScan.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Eponine.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Est2Genome.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/FootPrinter.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/GFF.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Gel.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Geneid.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Genemark.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Genewise.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Genomewise.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Genscan.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Glimmer.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Grail.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/GuessSeqFormat.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Hmmpfam.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/IUPAC.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Lucy.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/MZEF.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/OddCodes.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Primer3.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Prints.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Profile.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Promoterwise.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/PrositeScan.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Pseudowise.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/QRNA.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/RandomDistFunctions.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/RepeatMasker.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/RestrictionEnzyme.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Seg.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/SeqAnal.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/SeqPattern.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/SeqStats.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/SeqWords.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/SiRNA.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Sigcleave.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Signalp.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Tmhmm.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/WWW.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/dpAlign.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/pICalculator.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/pSW.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Analysis/'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Analysis/DNA/'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Analysis/DNA/ESEfinder.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Analysis/SimpleAnalysisBase.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Domcut.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/ELM.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/GOR4.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/HNN.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Mitoprot.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/NetPhos.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Scansite.pm'
[MSG] [Thu Dec 7 06:31:26 2006] Extracted 'bioperl-1.4/Bio/Tools/Analysis/Protein/Sopma.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/BPlite/'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/BPlite/Iteration.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/BPlite/HSP.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/BPlite/Sbjct.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Blast/'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Blast/Sbjct.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Blast/CHANGES'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Blast/HSP.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Blast/HTML.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Blast/README'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/EMBOSS/'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/EMBOSS/Palindrome.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/HMMER/'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/HMMER/Domain.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/HMMER/Results.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/HMMER/Set.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Phylo/'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Molphy/'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Molphy/Result.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Molphy.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML/'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML/ModelResult.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Phylo/PAML/Result.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Phylip/'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Phylo/Phylip/ProtDist.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Prediction/'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Prediction/Exon.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Prediction/Gene.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Primer/'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Primer/Assessor/'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Primer/Assessor/Base.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Primer/AssessorI.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Primer/Feature.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Primer/Pair.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Run/'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Run/README'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Run/RemoteBlast.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Run/StandAloneBlast.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Run/WrapperBase.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Sim4/'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Sim4/Results.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tools/Sim4/Exon.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tree/'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tree/AlleleNode.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tree/Node.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tree/NodeI.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tree/NodeNHX.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tree/RandomFactory.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tree/Statistics.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tree/Tree.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tree/TreeFunctionsI.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/Tree/TreeI.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/TreeIO/'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/TreeIO/TreeEventBuilder.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/TreeIO/lintree.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/TreeIO/newick.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/TreeIO/nexus.pm'
[MSG] [Thu Dec 7 06:31:27 2006] Extracted 'bioperl-1.4/Bio/TreeIO/nhx.pm'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/Bio/TreeIO/svggraph.pm'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/Bio/TreeIO/tabtree.pm'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/Bio/Variation/'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/Bio/Variation/IO/'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/Bio/Variation/IO/flat.pm'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/Bio/Variation/IO/xml.pm'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/Bio/Variation/AAChange.pm'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/Bio/Variation/AAReverseMutate.pm'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/Bio/Variation/Allele.pm'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/Bio/Variation/DNAMutation.pm'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/Bio/Variation/IO.pm'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/Bio/Variation/README'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/Bio/Variation/RNAChange.pm'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/Bio/Variation/SNP.pm'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/Bio/Variation/SeqDiff.pm'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/Bio/Variation/VariantI.pm'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/faq/'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/faq/faq.html'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/faq/faq.dtd'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/faq/faq.pl'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/faq/faq.xml'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/makedoc.PL'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/examples/'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/examples/graphics/'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/examples/graphics/blastn.out'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/examples/graphics/data1.txt'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/examples/graphics/embl2picture.pl'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/examples/graphics/factor7.embl'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast1.pl'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast2.pl'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast3.pl'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_blast4.pl'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/examples/graphics/render_features.pl'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/examples/README'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/figs/'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/figs/graphics/'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig1.png'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig2.png'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig3.png'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig4.png'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig5.png'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/figs/graphics/fig6.png'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/figs/README'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/html/'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/html/images/'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/html/images/tip.png'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/html/Flat_Databases.html'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/html/Graphics-HOWTO.html'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/html/OBDA_Access.html'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/html/PAML.html'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/html/README'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/html/SearchIO.html'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/html/SeqIO.html'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/html/SimpleWebAnalysis.html'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/html/e-novative.css'
[MSG] [Thu Dec 7 06:31:28 2006] Extracted 'bioperl-1.4/doc/howto/pdf/'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/pdf/Flat_Databases.pdf'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/pdf/Graphics-HOWTO.pdf'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/pdf/OBDA_Access.pdf'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/pdf/PAML.pdf'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/pdf/SearchIO.pdf'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/pdf/SeqIO.pdf'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/pdf/SimpleWebAnalysis.pdf'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/pdf/Trees.pdf'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/sgml/'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/sgml/Feature-Annotation.sgml'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/sgml/Flat_Databases.sgml'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/sgml/Graphics-HOWTO.sgml'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/sgml/OBDA_Access.sgml'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/sgml/PAML.sgml'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/sgml/README'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/sgml/SearchIO.sgml'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/sgml/SeqIO.sgml'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/sgml/SimpleWebAnalysis.sgml'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/sgml/Trees.sgml'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/txt/'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/txt/Flat_Databases.txt'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/doc/howto/txt/SimpleWebAnalysis.txt'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/INSTALL.WIN'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/LICENSE'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/MANIFEST.SKIP'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/Makefile.PL'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/PLATFORMS'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/README'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/biodatabases.pod'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/biodesign.pod'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/bioperl.lisp'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/bioperl.pod'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/bioscripts.pod'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/bptutorial.pl'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/Bio-DB-GFF/'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/Bio-DB-GFF/load_ucsc.pl'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/bioperl.pl'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/generate_random_seq.pl'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/longorf.pl'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/make_mrna_protein.pl'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/make_primers.pl'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/rev_and_trans.pl'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/revcom_dir.pl'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/subsequence.cgi'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/align/'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/align/align_on_codons.pl'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/align/aligntutorial.pl'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/align/clustalw.pl'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/align/simplealign.pl'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/biblio/'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/biblio/biblio_examples.pl'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/biblio/biblio_soap.pl'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/biographics/'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/biographics/all_glyphs.pl'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/biographics/dynamic_glyphs.pl'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/biographics/feature_data.gff'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/biographics/feature_data.txt'
[MSG] [Thu Dec 7 06:31:29 2006] Extracted 'bioperl-1.4/examples/biographics/lots_of_glyphs.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/biographics/render_sequence.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/cluster/'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/cluster/dbsnp.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/contributed/'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/contributed/nmrpdb_parse.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/contributed/prosite2perl.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/contributed/rebase2list.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/db/'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/db/get_seqs.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/db/dbfetch'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/db/est_tissue_query.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/db/gb2features.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/db/getGenBank.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/db/rfetch.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/db/use_registry.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/liveseq/'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/liveseq/change_gene.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/popgen/'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/popgen/parse_calc_stats.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/root/'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/root/lib/'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/root/lib/Bio/'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/root/lib/Bio/PrimarySeq.pm'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/root/lib/Bio/PrimarySeqI.pm'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/root/lib/Bio/Seq.pm'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/root/lib/Bio/SeqI.pm'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/root/lib/Error.pm'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/root/lib/TestInterface.pm'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/root/lib/TestObject.pm'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/root/README'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/root/exceptions1.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/root/exceptions2.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/root/exceptions3.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/root/exceptions4.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/searchio/'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/searchio/blast_example.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/searchio/custom_writer.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/searchio/hitwriter.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/searchio/hspwriter.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/searchio/htmlwriter.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/searchio/psiblast_features.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/searchio/psiblast_iterations.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/searchio/rawwriter.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/searchio/resultwriter.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/searchio/waba2gff.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/sirna/'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/sirna/TAG'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/sirna/rnai_finder.cgi'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/tk/'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/tk/gsequence.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/tk/hitdisplay.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/tools/'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/tools/gb_to_gff.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/tools/gff2ps.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/tools/parse_codeml.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/tools/psw.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/tools/restriction.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/tools/run_genscan.pl'
[MSG] [Thu Dec 7 06:31:30 2006] Extracted 'bioperl-1.4/examples/tools/seq_pattern.pl'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/examples/tools/standaloneblast.pl'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/examples/tree/'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/examples/tree/paup2phylip.pl'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/maintenance/'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/maintenance/authors.pl'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/maintenance/README'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/maintenance/modules.pl'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/maintenance/pod.pl'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/models/'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/models/biblio.dia'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/models/README'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/models/bio_liveseq_variation.dia'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/models/bio_map.dia'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/models/bio_restriction.dia'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/models/bioperl.dia'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/models/coordinatemapper.dia'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/models/map_proposal.txt'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/models/maps_and_markers.dia'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/models/popgen.dia'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/models/population_proposal.txt'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/load_gff.PLS'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/README'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/TAG'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/bp_genbank2gff.PLS'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/bulk_load_gff.PLS'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/fast_load_gff.PLS'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/generate_histogram.PLS'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/load_ucsc.pl'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/pg_bulk_load_gff.PLS'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_gadfly.PLS'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_ncbi_human.PLS'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_sgd.PLS'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/Bio-DB-GFF/process_wormbase.PLS'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/install_bioperl_scripts.pl'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/DB/'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/DB/TAG'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/DB/biofetch_genbank_proxy.PLS'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/DB/bioflat_index.PLS'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/DB/biogetseq.PLS'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/DB/flanks.PLS'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/biblio/'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/biblio/TAG'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/biblio/biblio.PLS'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/das/'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/das/README'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/das/TAG'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/graphics/'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/graphics/frend.PLS'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/graphics/README'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/graphics/TAG'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/graphics/feature_draw.PLS'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/graphics/search_overview.PLS'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/index/'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/index/TAG'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/index/bp_fetch.PLS'
[MSG] [Thu Dec 7 06:31:31 2006] Extracted 'bioperl-1.4/scripts/index/bp_index.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/popgen/'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/popgen/composite_LD.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/popgen/heterogeneity_test.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/searchio/'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/searchio/filter_search.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/seq/'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/seq/TAG'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/seq/extract_feature_seq.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/seq/seqconvert.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/seq/split_seq.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/seq/translate_seq.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/seqstats/'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/seqstats/TAG'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/seqstats/aacomp.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/seqstats/chaos_plot.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/seqstats/gccalc.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/seqstats/oligo_count.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/taxa/'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/taxa/TAG'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/taxa/local_taxonomydb_query.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/taxa/taxid4species.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/tree/'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/tree/TAG'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/tree/blast2tree.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/utilities/'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/utilities/bp_nrdb.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/utilities/README'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/utilities/TAG'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/utilities/bp_mrtrans.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/utilities/bp_sreformat.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/utilities/dbsplit.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/utilities/mask_by_search.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/utilities/mutate.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/utilities/pairwise_kaks.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/utilities/remote_blast.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/utilities/search2BSML.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/utilities/search2alnblocks.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/utilities/search2gff.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/utilities/search2tribe.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/scripts/utilities/seq_length.PLS'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/t/'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/t/data/'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/t/data/biodbgff/'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/t/data/biodbgff/test.gff'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/t/data/503384.MEGABLAST.0'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/t/data/503384.MEGABLAST.2'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/t/data/5X_1895.FASTXY'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/t/data/AAC12660.fa'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/t/data/AB077698.gb'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/t/data/AE003528_ecoli.bls'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/t/data/AE003644_Adh-genomic.gb'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/t/data/AF032047.gbk'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/t/data/AF165282.gb'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/t/data/AHCYL1.kegg'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/t/data/ATF14F8.gbk'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/t/data/AY095303S1.gbk'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/t/data/AnnIX-v003.gbk'
[MSG] [Thu Dec 7 06:31:32 2006] Extracted 'bioperl-1.4/t/data/BK000016-tpa.gbk'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/BLOSUM50'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/BN000066-tpa.embl'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/D10483.gbk'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/D12555.gbk'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/ECAPAH02.embl'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/GO.defs.test'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/GO.defs.test2'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/Genscan.FastA'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.FASTA'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.fa'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.gff'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.grail'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.grailexp'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.mzef'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/HUMBETGLOA.tblastx'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/L77119.hmmer'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/LL-sample.seq'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/LOAD_Ccd1.dnd'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/LittleChrY.dbsnp.xml'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/MmCT'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/NM_002254.gb'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/NT_021877.gbk'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/PAM250'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/SwissProt.dat'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/U58726.gb'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/X98338_Adh-mRNA.gb'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/a_thaliana.blastn'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/aaml.mlc'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/aaml_pairwise.mlc'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/acefile.ace.1'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/acefile.singlets'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/alnfile.fasta'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/amino.fa'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/ar.embl'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/bl2seq.blastn'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/bl2seq.blastn.rev'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/bl2seq.blastx.out'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/bl2seq.bug940.out'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/bl2seq.out'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/bl2seq.tblastx.out'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/blast.report'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/blat.psLayout3'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/c200-vs-yeast.BLASTN'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/c200-vs-yeast.BLASTN.m8'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/chad100.scf'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/codeml.mlc'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/codeml_nssites.mlc'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/compLD_missingtest.prettybase'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/compLD_test.prettybase'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/component.ontology.test'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/component.ontology.test2'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/crab.dat.cn'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/crab.nj'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/crab.njb'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/crypto.sim4-0'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/crypto.sim4-3'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/crypto.sim4-4'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/cys1_dicdi.water'
[MSG] [Thu Dec 7 06:31:33 2006] Extracted 'bioperl-1.4/t/data/cysprot.fa'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/cysprot.msf'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/cysprot.needle'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/cysprot.tblastn'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/cysprot.water'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/cysprot1.FASTA'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/cysprot1.fa'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/cysprot1a.fa'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/cysprot1a.msf'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/cysprot1b.fa'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/cysprot1b.hmmsearch'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/cysprot1b.msf'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/cysprot1b.newick'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/cysprot_vs_gadfly.FASTA'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/dmel_2Lchunk.gb'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/dna1.fa'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/dna2.fa'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/dnaE-bsub-prot.fa'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/dnaE-bsub.fa'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/dnaEbsub_ecoli.wublastx'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/dnaEbsub_ecoli.wutblastn'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/dnaEbsub_ecoli.wutblastx'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/ecoli-trna-qrna.out'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/ecoli_domains.rps.xml'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/ecoli_domains.rpsblast'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/ecolitst.bls'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/ecolitst.fa'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/ecolitst.wublastp'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/empty.bl2seq'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/expected.blast.out'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/factor7.embl'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/footprinter.out'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/geneid_1.0.out'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/genemark.out'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/genewise.out'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/genewise_output.paracel_btk'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/genomewise.out'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/genomic-seq.epcr'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/genomic-seq.fasta'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/genomic-seq.genscan'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/genomic-seq.mzef'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/gf-s71.needle'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/glimmer.out'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/hemoglobinA.meg'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/hg16_chroms.gff'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/hmmpfam.out'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/hmmsearch.out'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/hs_est.est2genome'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/hs_fugu.newick'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/hs_owlmonkey.fas'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/hs_owlmonkey.fasta'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/hsinsulin.blastcl3.blastn'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/humor.maf'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/humts1.pal'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/insulin.water'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/interpro_short.xml'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/lucy.info'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/lucy.qual'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/lucy.seq'
[MSG] [Thu Dec 7 06:31:34 2006] Extracted 'bioperl-1.4/t/data/lucy.stderr'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/lysozyme6.protml'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/lysozyme6.simple.protml'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/mapmaker.out'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/mast.dat'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/megablast_output.paracel_btk'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/meme.dat'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/mpath.ontology.test'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/multi_1.fa'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/multi_2.fa'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/multi_blast.bls'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/multifa.seq'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/multiseq.bls'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/mus.bls.xml'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/mutations.dat'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/mutations.xml'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/myco_sites.gff'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/nei_gojobori_test.aln'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/neighbor.dist'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/no-genes.genscan'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/no_hsps.blastp'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/noninterleaved.phy'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/omim_genemap_test'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/omim_text_test'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/pdb1bpt.ent'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/phi.out'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/phipsi.out'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/phredfile.phd'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/phylipdist-36.out'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/phylipdist.out'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/pictogram.fa'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/plague_yeast.bls.xml'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/polymorphism.dat'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/polymorphism.xml'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/popgen_saureus.dat'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/popgen_saureus.multidat'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/popstats.prettybase'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/roa1.dat'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/primedseq.fa'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/primer3_infile.txt'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/primer3_outfile.txt'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/primer3_output.txt'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/promoterwise.out'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/protpars.phy'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/psiblastreport.out'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/qrna-relloc.out'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/qualfile.qual'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/rebase.itype2'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/rebase.withrefm'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/repeatmasker.fa.out'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/revcomp_mrna.gb'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/roa1.genbank'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/roa1.swiss'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/sbay_c545-yeast.BLASTZ.PSL'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/seqdatabase.ini'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/seqfile.pir'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/seqs.fas'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/sequencefamily.dat'
[MSG] [Thu Dec 7 06:31:35 2006] Extracted 'bioperl-1.4/t/data/short.blx'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/sim4.for.for'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/sim4.for.rev'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/sim4.rev'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/sofa.ontology'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/sparsealn.needle'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/stress_test_medline.xml'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/stress_test_pubmed.xml'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/swiss.dat'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/swisspfam.data'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.ace'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.embl'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.fasta'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.game'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.gcg'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.gcgblast'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.gcgfasta'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.genbank'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.genbank.noseq'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.mase'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.metafasta'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.nh'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.nhx'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.pfam'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.pir'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.raw'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.swiss'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.tab'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.txt'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test.waba'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/test_badlf.gcg'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/testaln.aln'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/testaln.fasta'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/testaln.mase'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/testaln.metafasta'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/testaln.msf'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/testaln.nexus'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/testaln.pfam'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/testaln.phylip'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/testaln.prodom'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/testaln.selex'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/testaln.stockholm'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/testdat.exonerate'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/testdbaccnums.out'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/testfuzzy.genbank'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/transfac.dat'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/unigene.data'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/version2.scf'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/version3.scf'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/worm_fam_2785.cdna'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/yn00.mlc'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/biographics/'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/biographics/t1/'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/biographics/t1/version1.gif'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/biographics/t1/version1.png'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/biographics/t1/version2.gif'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/biographics/t1/version2.png'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/biographics/t1/version3.png'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/biographics/t1/version4.png'
[MSG] [Thu Dec 7 06:31:36 2006] Extracted 'bioperl-1.4/t/data/biographics/t1/version5.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t1/version6.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t1/version7.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t1/version8.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t2/'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t2/version1.gif'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t2/version1.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t2/version10.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t2/version11.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t2/version12.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t2/version13.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t2/version14.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t2/version2.gif'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t2/version2.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t2/version3.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t2/version4.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t2/version5.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t2/version6.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t2/version7.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t2/version8.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t2/version9.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/feature_data.txt'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t3/'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t3/version1.gif'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t3/version1.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t3/version2.gif'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t3/version2.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t3/version3.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t3/version4.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t3/version5.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t3/version6.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/biographics/t3/version7.png'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/consed_project/'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.contigs'
[MSG] [Thu Dec 7 06:31:37 2006] Extracted 'bioperl-1.4/t/data/consed_project/edit_dir/test_project.fasta'
[MSG] [Thu Dec 7 06:31:37 20