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

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

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

--

Dear Ewan Birney,
    
This is a computer-generated error report created automatically by
CPANPLUS, version 0.80. Testers personal comments may appear 
at the end of this report.


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

TEST RESULTS:

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

[MSG] [Fri Apr 18 12:08:39 2008] Trying to get 'http://www.cpan.org/authors/id/L/LI/LIMAONE/CHECKSUMS'
[MSG] [Fri Apr 18 12:08:40 2008] Checksum matches for 'Bio-Grep-0.10.3.tar.gz'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/README'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/TODO'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/examples/'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/examples/bgrep'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/examples/Benchmarks.tt'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/examples/benchmark.pl'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/lib/'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Backend/'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Backend/Vmatch.pm'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Backend/RE.pm'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Backend/GUUGle.pm'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Backend/Agrep.pm'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Backend/BackendI.pm'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Benchmarks.pod'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Cookbook.pod'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Root.pm'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Filter/'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Filter/FilterI.pm'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Filter/FilterRemoveDuplicates.pm'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/SearchSettings.pm'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/SearchResult.pm'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep.pm'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/META.yml'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/Makefile.PL'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/Build.PL'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/Test_DB_Extend.fasta'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/pod-coverage.t'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/perlcriticrc'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/pod.t'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/TestFilter.pm'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/00.checkprereq.t'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/Test_DB_RevCom.fasta'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/Test_DB_Big.fasta'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/00.load.t'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/50.synopsis.t'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/perlcritic.t'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/Test_DB_Small.fasta'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/Test_DB_Protein.fasta'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/11.backends.guugle.t'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/40.utils.t'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/Test_query_revcom.fasta'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/11.backends.re.t'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/BioGrepTest.pm'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/10.backends.all.t'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/30.features.alignments.t'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/20.filter.t'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/BioGrepSkip.pm'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/Test_query.fasta'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/t/30.features.updownstream.t'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/Changes'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/MANIFEST'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio-Grep-0.10.3/LICENSE'
[MSG] [Fri Apr 18 12:08:41 2008] Extracted 'Bio::Grep' to '/home/cpan/perl586/.cpanplus/5.8.6/build/Bio-Grep-0.10.3'
[MSG] [Fri Apr 18 12:08:43 2008] Checking if your kit is complete...
Looks good
Warning: prerequisite Bio::AlignIO 0 not found.
Warning: prerequisite Bio::Factory::EMBOSS 0 not found.
Warning: prerequisite Bio::Index::Fasta 0 not found.
Warning: prerequisite Bio::Root::Root 0 not found.
Warning: prerequisite Bio::Root::Version 0 not found.
Warning: prerequisite Bio::Seq 0 not found.
Warning: prerequisite Bio::SeqIO 0 not found.
Warning: prerequisite Carp::Assert 0 not found.
Warning: prerequisite Class::MethodMaker 2.02 not found.
Warning: prerequisite IO::String 1 not found.
Warning: prerequisite ToolSet 0.13 not found.
Writing Makefile for Bio::Grep

[MSG] [Fri Apr 18 12:08:43 2008] DEFAULT 'filter_prereqs' HANDLER RETURNING 'sub return value'
[ERROR] [Fri Apr 18 12:08:43 2008] No such module 'Bio::AlignIO' found on CPAN
[MSG] [Fri Apr 18 12:08:43 2008] Module 'Bio::Grep' requires 'Bio::Factory::EMBOSS' version '0' to be installed 
[ERROR] [Fri Apr 18 12:08:43 2008] No such module 'Bio::Index::Fasta' found on CPAN
[ERROR] [Fri Apr 18 12:08:43 2008] No such module 'Bio::Root::Root' found on CPAN
[MSG] [Fri Apr 18 12:08:43 2008] Module 'Bio::Grep' requires 'Bio::Root::Version' version '0' to be installed 
[MSG] [Fri Apr 18 12:08:43 2008] Module 'Bio::Grep' requires 'Bio::Seq' version '0' to be installed 
[ERROR] [Fri Apr 18 12:08:43 2008] No such module 'Bio::SeqIO' found on CPAN
[MSG] [Fri Apr 18 12:08:43 2008] Module 'Bio::Grep' requires 'Carp::Assert' version '0' to be installed 
[MSG] [Fri Apr 18 12:08:43 2008] Module 'Bio::Grep' requires 'Class::MethodMaker' version '2.02' to be installed 
[MSG] [Fri Apr 18 12:08:43 2008] Module 'Bio::Grep' requires 'IO::String' version '1' to be installed 
[MSG] [Fri Apr 18 12:08:43 2008] Module 'Bio::Grep' requires 'ToolSet' version '0.13' to be installed 
[MSG] [Fri Apr 18 12:08:43 2008] Trying to get 'http://www.cpan.org/authors/id/B/BI/BIRNEY/CHECKSUMS'
[MSG] [Fri Apr 18 12:08:43 2008] Checksum matches for 'bioperl-run-1.4.tar.gz'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Makefile.PL'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/AUTHORS'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Changes'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Factory/'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Factory/EMBOSS.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Alignment/'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Alignment/Clustalw.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Alignment/Blat.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Alignment/Lagan.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Alignment/DBA.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Alignment/TCoffee.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Alignment/Sim4.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Alignment/StandAloneFasta.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Analysis.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/AnalysisFactory.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Coil.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/EMBOSSApplication.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/EMBOSSacd.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Eponine.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/FootPrinter.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Genewise.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Genscan.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Hmmer.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Hmmpfam.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Mdust.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseJob.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseJobParser.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseWorkflow.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Primate.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Primer3.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Prints.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Profile.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Promoterwise.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Pseudowise.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/RepeatMasker.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Seg.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Signalp.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Tmhmm.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/TribeMCL.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Vista.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Analysis/'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Analysis/soap.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/AnalysisFactory/'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/AnalysisFactory/Pise.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/AnalysisFactory/soap.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Molphy/'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Molphy/ProtML.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/PAML/'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/PAML/Codeml.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/PAML/Yn00.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/Consense.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/Base.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/Puzzle.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/CSR.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/abiview.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/addquart.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/align2model.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/alistat.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/antigenic.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/assp.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/backtranseq.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/bambe.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/banana.pm'
[MSG] [Fri Apr 18 12:08:47 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/bionj.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/biosed.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/bl2seq.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/blast2.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/blimps.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/blimps_block.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/blimps_matrix.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/boxshade.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/btwisted.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/cai.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/cap.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/cds.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/chaos.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/charge.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/checktrans.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/chips.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/cirdna.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/clique.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/clustalw.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/clustalw_convert.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/codcmp.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/coderet.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/codnocod.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/codontree.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/codonw.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/comalign.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/combat.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/compseq.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/con_filter.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/confmat.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/cons.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/consense.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/consensus.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/cpgplot.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/cpgreport.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/cusp.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/cutseq.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dan.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dca.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/decorate.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/degapseq.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/descseq.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dialign2.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/diffseq.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/digest.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/distmat.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/distquart.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dnadist.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dnapars.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dollop.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/domainer.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dotmatcher.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dotpath.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dottup.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/drawgram.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/drawpyr.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/drawtree.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dreg.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/druid.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dsc.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dssp.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/einverted.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/emma.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/emowse.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/environ.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/eprimer3.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/equicktandem.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/est2genome.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/etandem.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/extractfeat.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/extractseq.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/fasta.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/fastdnaml.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/fastrna.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/filtersites.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/findkm.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/fitch.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/fmtseq.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/freak.pm'
[MSG] [Fri Apr 18 12:08:48 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/fuzznuc.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/fuzzpro.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/fuzztran.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/gb2xml.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/geecee.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/genscan.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/getblock.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/getorf.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/gff2ps.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/gibbs.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/gibbs_scan.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/golden.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/grailclnt.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/gruppi.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/helixturnhelix.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmalign.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmbuild.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmcalibrate.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmconvert.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmemit.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmer2sam.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmfetch.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmpfam.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmscore.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmsearch.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmoment.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/homology.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/html4blast.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/iep.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/infoalign.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/infoseq.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/interface.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/isochore.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/kitsch.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/lassap.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/lgicsearch.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/lindna.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/listor.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/loadseq.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/lvb.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/makehist.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/map.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/marscan.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/maskfeat.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/maskseq.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/matcher.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/megamerger.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/melting.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/merger.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/mfold.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/mix.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/modelfromalign.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/most.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/mreps.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/msa.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/msbar.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/mspcrunch.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/mview_alig.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/mview_blast.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/mwfilter.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/needle.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/neighbor.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/newcpgreport.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/newcpgseek.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/newseq.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/njdist.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/nnssp.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/notseq.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/nrscope.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/nthseq.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/octanol.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/oddcomp.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/palindrome.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pam.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/parciquart.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pars.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pasteseq.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/patmatdb.pm'
[MSG] [Fri Apr 18 12:08:49 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/patmatmotifs.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/patser.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pdbsearch.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pepcoil.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pepinfo.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pepnet.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pepstats.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pepwheel.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pepwindow.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pepwindowall.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pestfind.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pftools.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/phiblast.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pima.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/plotcon.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/plotorf.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/plsearch.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/polydot.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pratt.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/predator.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/preg.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/prettyalign.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/prettyplot.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/prettyseq.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/primersearch.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/primo.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/prodom.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/profit.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/prophecy.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/prophet.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/prose.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/prot_nucml.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/protal2dna.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/protdist.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pscan.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/protpars.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/psiblast.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/psort2.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pyramids.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pyreval.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/qstar.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/quicktree.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/readnexus.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/readseq.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/recoder.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/redata.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/remap.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/repeats.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/restover.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/restrict.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/revseq.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/rnadistance.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/rnaeval.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/rnafold.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/rnaga.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/rnaheat.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/rnainverse.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/rnapdist.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/rnasubopt.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/sam2hmmer.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/sampleseqs.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/saps.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/satellites.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/scan_for_matches.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/scope.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/scopparse.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/seqboot.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/seqgen.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/seqmatchall.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/seqsblast.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/seqstat.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/showalign.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/showfeat.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/showorf.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/showseq.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/shuffleseq.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/sigcleave.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/siggen.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/sigscan.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/silent.pm'
[MSG] [Fri Apr 18 12:08:50 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/sirna.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/splitter.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/sreformat.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/stretcher.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/stride.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/stssearch.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/supermatcher.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/syco.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/tacg.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/tfscan.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/tipdate.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/tmap.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/toppred.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/tranalign.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/transeq.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/treealign.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/trimest.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/trimseq.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/trnascan.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/twofeat.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/unroot.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/vectorstrip.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/water.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/weighbor.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/whichdb.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/wise2.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/wobble.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/wordcount.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/wordmatch.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/wublast2.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/xblast.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/xpound.pm'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/FootPrinter.seq.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/Genscan.FastA'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/NM_002254.gb'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/Primer3.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/Prints_prot.FastA'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/TribeMCL.bls'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/TribeMCL.desc'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/amino.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/blat_dna.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/cel-cbr-fam.aln'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/codeml.mlc'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/coil_protein_input'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/consense.treefile'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/cysprot.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/cysprot.msf'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/cysprot1a.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/cysprot1a.msf'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/cysprot1b.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/cysprot1b.msf'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/dba1a.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/dba1b.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/dba2.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/dna1.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/dna2.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/ecolitst.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/eponine.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/fasta.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/fastalib.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/fastaprot.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/fontfile'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/gf-s85.phylip'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/hmmpfam_protein_input'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/lagan_dna.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/neighbor.dist'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/new_dna.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/new_pep.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/pfam_sample_R11'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/primate_query.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/primate_target.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/prints.dat'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/profile_prot.FastA'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/prosite.dat'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/protpars.phy'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/ps1.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/repeatmasker.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/repeatmasker.fa.out'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/signalp_input_protein'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/sim4_cdna.fa'
[MSG] [Fri Apr 18 12:08:51 2008] Extracted 'bioperl-run-1.4/t/data/sim4_database.fa'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/data/sim4_genomic.fa'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/data/test.txt'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/data/test_prot.FastA'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/data/tree_of_life'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/data/treefile.example'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/data/vista.cls'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/data/vista.gff'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/AnalysisFactory_soap.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Analysis_soap.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Blat.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Clustalw.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Coil.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Consense.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/DBA.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/DrawGram.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/DrawTree.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/EMBOSS.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Eponine.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/FootPrinter.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Genewise.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Genscan.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Hmmer.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Hmmpfam.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Lagan.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Mdust.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Molphy.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Neighbor.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/PAML.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Pise.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Primate.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Primer3.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Prints.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Profile.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Promoterwise.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/ProtDist.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/ProtPars.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Pseudowise.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/RepeatMasker.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Seg.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/SeqBoot.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Signalp.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Sim4.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/StandAloneFasta.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/TCoffee.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Tmhmm.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/TribeMCL.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/t/Vista.t'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/INSTALL.PROGRAMS'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/MANIFEST.SKIP'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/README'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/examples/'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/examples/pise/'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/examples/pise/blast-kun.pl'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/examples/pise/blast2.pl'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/examples/pise/clustalw.pl'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/examples/pise/dnadist.data'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/examples/pise/dnadist.pl'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/examples/pise/genscan.pl'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/examples/pise/needle.pl'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/examples/pise/phylo-kun.pl'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/examples/pise/toppred.pl'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/scripts/'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/scripts/panalysis.PLS'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/scripts/papplmaker.PLS'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/scripts/run_neighbor.PLS'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/scripts/run_protdist.PLS'
[MSG] [Fri Apr 18 12:08:52 2008] Extracted 'bioperl-run-1.4/MANIFEST'
[MSG] [Fri Apr 18 12:08:53 2008] Extracted 'Bio::Factory::EMBOSS' to '/home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4'
[MSG] [Fri Apr 18 12:08:55 2008] Generated sub tests. go make show_tests to see available subtests

External Module XML::Parser::PerlSAX, XML SAX parser,
 is not installed on this computer.
  The Pise::Job module in bioperl-run  needs it for Pise Applications

External Module IO::String, IO handle to read or write to a string,
 is not installed on this computer.
  The Bio::DB::*,Bio::Variation::*,Bio::Tools::Blast::Run::Webblast, Bio::Index::Blast module in bioperl-run  needs it for GenBank+GenPept sequence retrieval, Variation code

External Module Algorithm::Diff, Compute intelligent differences between two files,
 is not installed on this computer.
  The TribeMCL module in bioperl-run  needs it for generating consensus protein family descriptions


Warning:

   There are some external packages and perl modules, listed above, which 
   bioperl-run uses. This only effects the functionality which is listed above:
the rest of bioperl-run will work fine.

   Enjoy the rest of bioperl-run, which you can use after going 'make install'

Checking if your kit is complete...
Looks good
Writing Makefile for Bio

[MSG] [Fri Apr 18 12:08:55 2008] DEFAULT 'filter_prereqs' HANDLER RETURNING 'sub return value'
[MSG] [Fri Apr 18 12:09:17 2008] cp Bio/Tools/Run/PiseApplication/stssearch.pm blib/lib/Bio/Tools/Run/PiseApplication/stssearch.pm
cp Bio/Tools/Run/PiseApplication/filtersites.pm blib/lib/Bio/Tools/Run/PiseApplication/filtersites.pm
cp Bio/Tools/Run/EMBOSSacd.pm blib/lib/Bio/Tools/Run/EMBOSSacd.pm
cp Bio/Tools/Run/PiseApplication/protal2dna.pm blib/lib/Bio/Tools/Run/PiseApplication/protal2dna.pm
cp Bio/Tools/Run/PiseApplication/confmat.pm blib/lib/Bio/Tools/Run/PiseApplication/confmat.pm
cp Bio/Tools/Run/PiseApplication/sam2hmmer.pm blib/lib/Bio/Tools/Run/PiseApplication/sam2hmmer.pm
cp Bio/Tools/Run/PiseApplication/domainer.pm blib/lib/Bio/Tools/Run/PiseApplication/domainer.pm
cp Bio/Tools/Run/PiseApplication/rnainverse.pm blib/lib/Bio/Tools/Run/PiseApplication/rnainverse.pm
cp Bio/Tools/Run/PiseApplication/primo.pm blib/lib/Bio/Tools/Run/PiseApplication/primo.pm
cp Bio/Tools/Run/Alignment/StandAloneFasta.pm blib/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
cp Bio/Tools/Run/PiseApplication/wordmatch.pm blib/lib/Bio/Tools/Run/PiseApplication/wordmatch.pm
cp Bio/Tools/Run/PiseApplication/fuzzpro.pm blib/lib/Bio/Tools/Run/PiseApplication/fuzzpro.pm
cp Bio/Tools/Run/PiseApplication/distquart.pm blib/lib/Bio/Tools/Run/PiseApplication/distquart.pm
cp Bio/Tools/Run/PiseApplication/whichdb.pm blib/lib/Bio/Tools/Run/PiseApplication/whichdb.pm
cp Bio/Tools/Run/PiseApplication/fmtseq.pm blib/lib/Bio/Tools/Run/PiseApplication/fmtseq.pm
cp Bio/Tools/Run/PiseApplication/newcpgreport.pm blib/lib/Bio/Tools/Run/PiseApplication/newcpgreport.pm
cp Bio/Tools/Run/AnalysisFactory.pm blib/lib/Bio/Tools/Run/AnalysisFactory.pm
cp Bio/Tools/Run/PiseApplication/blimps_matrix.pm blib/lib/Bio/Tools/Run/PiseApplication/blimps_matrix.pm
cp Bio/Tools/Run/PiseApplication/redata.pm blib/lib/Bio/Tools/Run/PiseApplication/redata.pm
cp Bio/Tools/Run/AnalysisFactory/Pise.pm blib/lib/Bio/Tools/Run/AnalysisFactory/Pise.pm
cp Bio/Tools/Run/PiseApplication/pscan.pm blib/lib/Bio/Tools/Run/PiseApplication/pscan.pm
cp Bio/Tools/Run/PiseApplication/predator.pm blib/lib/Bio/Tools/Run/PiseApplication/predator.pm
cp Bio/Tools/Run/PiseApplication/tipdate.pm blib/lib/Bio/Tools/Run/PiseApplication/tipdate.pm
cp Bio/Tools/Run/PiseApplication/extractfeat.pm blib/lib/Bio/Tools/Run/PiseApplication/extractfeat.pm
cp Bio/Tools/Run/PiseApplication/most.pm blib/lib/Bio/Tools/Run/PiseApplication/most.pm
cp Bio/Tools/Run/PiseApplication/pepinfo.pm blib/lib/Bio/Tools/Run/PiseApplication/pepinfo.pm
cp Bio/Tools/Run/PiseApplication/golden.pm blib/lib/Bio/Tools/Run/PiseApplication/golden.pm
cp Bio/Tools/Run/PiseApplication/dotmatcher.pm blib/lib/Bio/Tools/Run/PiseApplication/dotmatcher.pm
cp Bio/Tools/Run/Phylo/Phylip/Neighbor.pm blib/lib/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
cp Bio/Tools/Run/AnalysisFactory/soap.pm blib/lib/Bio/Tools/Run/AnalysisFactory/soap.pm
cp Bio/Tools/Run/PiseApplication/wobble.pm blib/lib/Bio/Tools/Run/PiseApplication/wobble.pm
cp Bio/Tools/Run/PiseApplication/silent.pm blib/lib/Bio/Tools/Run/PiseApplication/silent.pm
cp Bio/Tools/Run/PiseApplication/abiview.pm blib/lib/Bio/Tools/Run/PiseApplication/abiview.pm
cp Bio/Tools/Run/Hmmer.pm blib/lib/Bio/Tools/Run/Hmmer.pm
cp Bio/Tools/Run/PiseApplication/maskseq.pm blib/lib/Bio/Tools/Run/PiseApplication/maskseq.pm
cp Bio/Tools/Run/PiseApplication/btwisted.pm blib/lib/Bio/Tools/Run/PiseApplication/btwisted.pm
cp Bio/Tools/Run/PiseApplication/assp.pm blib/lib/Bio/Tools/Run/PiseApplication/assp.pm
cp Bio/Tools/Run/PiseApplication/restover.pm blib/lib/Bio/Tools/Run/PiseApplication/restover.pm
cp Bio/Tools/Run/PiseApplication/supermatcher.pm blib/lib/Bio/Tools/Run/PiseApplication/supermatcher.pm
cp Bio/Tools/Run/PiseApplication/iep.pm blib/lib/Bio/Tools/Run/PiseApplication/iep.pm
cp Bio/Tools/Run/PiseApplication/repeats.pm blib/lib/Bio/Tools/Run/PiseApplication/repeats.pm
cp Bio/Tools/Run/PiseApplication/showalign.pm blib/lib/Bio/Tools/Run/PiseApplication/showalign.pm
cp Bio/Tools/Run/PiseApplication/xblast.pm blib/lib/Bio/Tools/Run/PiseApplication/xblast.pm
cp Bio/Tools/Run/PiseApplication/lassap.pm blib/lib/Bio/Tools/Run/PiseApplication/lassap.pm
cp Bio/Tools/Run/PiseApplication/interface.pm blib/lib/Bio/Tools/Run/PiseApplication/interface.pm
cp Bio/Tools/Run/PiseApplication/emowse.pm blib/lib/Bio/Tools/Run/PiseApplication/emowse.pm
cp Bio/Tools/Run/PiseApplication/con_filter.pm blib/lib/Bio/Tools/Run/PiseApplication/con_filter.pm
cp Bio/Tools/Run/PiseApplication/grailclnt.pm blib/lib/Bio/Tools/Run/PiseApplication/grailclnt.pm
cp Bio/Tools/Run/PiseApplication/fitch.pm blib/lib/Bio/Tools/Run/PiseApplication/fitch.pm
cp Bio/Tools/Run/PiseApplication/emma.pm blib/lib/Bio/Tools/Run/PiseApplication/emma.pm
cp Bio/Tools/Run/PiseApplication/unroot.pm blib/lib/Bio/Tools/Run/PiseApplication/unroot.pm
cp Bio/Tools/Run/PiseApplication/splitter.pm blib/lib/Bio/Tools/Run/PiseApplication/splitter.pm
cp Bio/Tools/Run/PiseApplication/sigcleave.pm blib/lib/Bio/Tools/Run/PiseApplication/sigcleave.pm
cp Bio/Tools/Run/PiseApplication/environ.pm blib/lib/Bio/Tools/Run/PiseApplication/environ.pm
cp Bio/Tools/Run/PiseApplication/newseq.pm blib/lib/Bio/Tools/Run/PiseApplication/newseq.pm
cp Bio/Tools/Run/PiseApplication/xpound.pm blib/lib/Bio/Tools/Run/PiseApplication/xpound.pm
cp Bio/Tools/Run/PiseApplication/prophecy.pm blib/lib/Bio/Tools/Run/PiseApplication/prophecy.pm
cp Bio/Tools/Run/PiseApplication/dotpath.pm blib/lib/Bio/Tools/Run/PiseApplication/dotpath.pm
cp Bio/Tools/Run/PiseApplication/chips.pm blib/lib/Bio/Tools/Run/PiseApplication/chips.pm
cp Bio/Tools/Run/PiseApplication/map.pm blib/lib/Bio/Tools/Run/PiseApplication/map.pm
cp Bio/Tools/Run/PiseApplication/maskfeat.pm blib/lib/Bio/Tools/Run/PiseApplication/maskfeat.pm
cp Bio/Tools/Run/PiseApplication/weighbor.pm blib/lib/Bio/Tools/Run/PiseApplication/weighbor.pm
cp Bio/Tools/Run/PiseApplication/showfeat.pm blib/lib/Bio/Tools/Run/PiseApplication/showfeat.pm
cp Bio/Tools/Run/PiseApplication/lvb.pm blib/lib/Bio/Tools/Run/PiseApplication/lvb.pm
cp Bio/Tools/Run/PiseApplication/kitsch.pm blib/lib/Bio/Tools/Run/PiseApplication/kitsch.pm
cp Bio/Tools/Run/Alignment/Lagan.pm blib/lib/Bio/Tools/Run/Alignment/Lagan.pm
cp Bio/Tools/Run/Phylo/Phylip/DrawGram.pm blib/lib/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
cp Bio/Tools/Run/PiseApplication/msbar.pm blib/lib/Bio/Tools/Run/PiseApplication/msbar.pm
cp Bio/Tools/Run/PiseApplication/bl2seq.pm blib/lib/Bio/Tools/Run/PiseApplication/bl2seq.pm
cp Bio/Tools/Run/PiseApplication/seqgen.pm blib/lib/Bio/Tools/Run/PiseApplication/seqgen.pm
cp Bio/Tools/Run/PiseApplication/dan.pm blib/lib/Bio/Tools/Run/PiseApplication/dan.pm
cp Bio/Tools/Run/PiseApplication/pasteseq.pm blib/lib/Bio/Tools/Run/PiseApplication/pasteseq.pm
cp Bio/Tools/Run/Seg.pm blib/lib/Bio/Tools/Run/Seg.pm
cp Bio/Tools/Run/RepeatMasker.pm blib/lib/Bio/Tools/Run/RepeatMasker.pm
cp Bio/Tools/Run/PiseApplication/listor.pm blib/lib/Bio/Tools/Run/PiseApplication/listor.pm
cp Bio/Tools/Run/Genewise.pm blib/lib/Bio/Tools/Run/Genewise.pm
cp Bio/Tools/Run/PiseApplication/polydot.pm blib/lib/Bio/Tools/Run/PiseApplication/polydot.pm
cp Bio/Tools/Run/PiseApplication/tacg.pm blib/lib/Bio/Tools/Run/PiseApplication/tacg.pm
cp Bio/Tools/Run/PiseApplication/hmmalign.pm blib/lib/Bio/Tools/Run/PiseApplication/hmmalign.pm
cp Bio/Tools/Run/PiseApplication/sreformat.pm blib/lib/Bio/Tools/Run/PiseApplication/sreformat.pm
cp Bio/Tools/Run/PiseApplication/wordcount.pm blib/lib/Bio/Tools/Run/PiseApplication/wordcount.pm
cp Bio/Tools/Run/PiseApplication/prettyplot.pm blib/lib/Bio/Tools/Run/PiseApplication/prettyplot.pm
cp Bio/Tools/Run/Primer3.pm blib/lib/Bio/Tools/Run/Primer3.pm
cp Bio/Tools/Run/PiseApplication/siggen.pm blib/lib/Bio/Tools/Run/PiseApplication/siggen.pm
cp Bio/Tools/Run/PiseApplication/needle.pm blib/lib/Bio/Tools/Run/PiseApplication/needle.pm
cp Bio/Tools/Run/PiseApplication/cutseq.pm blib/lib/Bio/Tools/Run/PiseApplication/cutseq.pm
cp Bio/Tools/Run/PiseApplication/findkm.pm blib/lib/Bio/Tools/Run/PiseApplication/findkm.pm
cp Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm blib/lib/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
cp Bio/Tools/Run/PiseApplication/pam.pm blib/lib/Bio/Tools/Run/PiseApplication/pam.pm
cp Bio/Tools/Run/PiseApplication/prettyseq.pm blib/lib/Bio/Tools/Run/PiseApplication/prettyseq.pm
cp Bio/Tools/Run/PiseApplication/transeq.pm blib/lib/Bio/Tools/Run/PiseApplication/transeq.pm
cp Bio/Tools/Run/PiseApplication/combat.pm blib/lib/Bio/Tools/Run/PiseApplication/combat.pm
cp Bio/Tools/Run/PiseJobParser.pm blib/lib/Bio/Tools/Run/PiseJobParser.pm
cp Bio/Tools/Run/PiseWorkflow.pm blib/lib/Bio/Tools/Run/PiseWorkflow.pm
cp Bio/Tools/Run/Alignment/DBA.pm blib/lib/Bio/Tools/Run/Alignment/DBA.pm
cp Bio/Tools/Run/PiseApplication/restrict.pm blib/lib/Bio/Tools/Run/PiseApplication/restrict.pm
cp Bio/Tools/Run/PiseApplication/patser.pm blib/lib/Bio/Tools/Run/PiseApplication/patser.pm
cp Bio/Tools/Run/Primate.pm blib/lib/Bio/Tools/Run/Primate.pm
cp Bio/Tools/Run/Alignment/Blat.pm blib/lib/Bio/Tools/Run/Alignment/Blat.pm
cp Bio/Tools/Run/PiseApplication/hmmsearch.pm blib/lib/Bio/Tools/Run/PiseApplication/hmmsearch.pm
cp Bio/Tools/Run/PiseApplication/mreps.pm blib/lib/Bio/Tools/Run/PiseApplication/mreps.pm
cp Bio/Tools/Run/PiseApplication/hmmpfam.pm blib/lib/Bio/Tools/Run/PiseApplication/hmmpfam.pm
cp Bio/Tools/Run/PiseApplication/revseq.pm blib/lib/Bio/Tools/Run/PiseApplication/revseq.pm
cp Bio/Tools/Run/PiseApplication/rnaga.pm blib/lib/Bio/Tools/Run/PiseApplication/rnaga.pm
cp Bio/Tools/Run/PiseApplication/blimps.pm blib/lib/Bio/Tools/Run/PiseApplication/blimps.pm
cp Bio/Tools/Run/PiseApplication/gruppi.pm blib/lib/Bio/Tools/Run/PiseApplication/gruppi.pm
cp Bio/Tools/Run/Analysis.pm blib/lib/Bio/Tools/Run/Analysis.pm
cp Bio/Tools/Run/PiseApplication/lindna.pm blib/lib/Bio/Tools/Run/PiseApplication/lindna.pm
cp Bio/Tools/Run/PiseApplication/rnaeval.pm blib/lib/Bio/Tools/Run/PiseApplication/rnaeval.pm
cp Bio/Tools/Run/PiseApplication/palindrome.pm blib/lib/Bio/Tools/Run/PiseApplication/palindrome.pm
cp Bio/Tools/Run/PiseApplication/dnadist.pm blib/lib/Bio/Tools/Run/PiseApplication/dnadist.pm
cp Bio/Tools/Run/PiseApplication/stride.pm blib/lib/Bio/Tools/Run/PiseApplication/stride.pm
cp Bio/Tools/Run/Hmmpfam.pm blib/lib/Bio/Tools/Run/Hmmpfam.pm
cp Bio/Tools/Run/PiseApplication/pepcoil.pm blib/lib/Bio/Tools/Run/PiseApplication/pepcoil.pm
cp Bio/Tools/Run/Alignment/Clustalw.pm blib/lib/Bio/Tools/Run/Alignment/Clustalw.pm
cp Bio/Tools/Run/PiseApplication/clustalw.pm blib/lib/Bio/Tools/Run/PiseApplication/clustalw.pm
cp Bio/Tools/Run/PiseApplication/gibbs_scan.pm blib/lib/Bio/Tools/Run/PiseApplication/gibbs_scan.pm
cp Bio/Tools/Run/PiseApplication/sigscan.pm blib/lib/Bio/Tools/Run/PiseApplication/sigscan.pm
cp Bio/Tools/Run/PiseApplication/modelfromalign.pm blib/lib/Bio/Tools/Run/PiseApplication/modelfromalign.pm
cp Bio/Tools/Run/PiseApplication/hmmemit.pm blib/lib/Bio/Tools/Run/PiseApplication/hmmemit.pm
cp Bio/Tools/Run/PiseApplication/treealign.pm blib/lib/Bio/Tools/Run/PiseApplication/treealign.pm
cp Bio/Tools/Run/PiseApplication/toppred.pm blib/lib/Bio/Tools/Run/PiseApplication/toppred.pm
cp Bio/Tools/Run/PiseApplication/wise2.pm blib/lib/Bio/Tools/Run/PiseApplication/wise2.pm
cp Bio/Tools/Run/PiseApplication/fastdnaml.pm blib/lib/Bio/Tools/Run/PiseApplication/fastdnaml.pm
cp Bio/Tools/Run/TribeMCL.pm blib/lib/Bio/Tools/Run/TribeMCL.pm
cp Bio/Tools/Run/PiseApplication/dca.pm blib/lib/Bio/Tools/Run/PiseApplication/dca.pm
cp Bio/Tools/Run/PiseApplication/vectorstrip.pm blib/lib/Bio/Tools/Run/PiseApplication/vectorstrip.pm
cp Bio/Tools/Run/PiseApplication/prodom.pm blib/lib/Bio/Tools/Run/PiseApplication/prodom.pm
cp Bio/Tools/Run/PiseApplication/tranalign.pm blib/lib/Bio/Tools/Run/PiseApplication/tranalign.pm
cp Bio/Tools/Run/PiseApplication/charge.pm blib/lib/Bio/Tools/Run/PiseApplication/charge.pm
cp Bio/Tools/Run/PiseApplication/njdist.pm blib/lib/Bio/Tools/Run/PiseApplication/njdist.pm
cp Bio/Tools/Run/PiseApplication/hmmfetch.pm blib/lib/Bio/Tools/Run/PiseApplication/hmmfetch.pm
cp Bio/Tools/Run/PiseApplication/hmmscore.pm blib/lib/Bio/Tools/Run/PiseApplication/hmmscore.pm
cp Bio/Tools/Run/PiseApplication/backtranseq.pm blib/lib/Bio/Tools/Run/PiseApplication/backtranseq.pm
cp Bio/Tools/Run/PiseApplication/etandem.pm blib/lib/Bio/Tools/Run/PiseApplication/etandem.pm
cp Bio/Tools/Run/PiseApplication/est2genome.pm blib/lib/Bio/Tools/Run/PiseApplication/est2genome.pm
cp Bio/Tools/Run/PiseApplication/hmmconvert.pm blib/lib/Bio/Tools/Run/PiseApplication/hmmconvert.pm
cp Bio/Tools/Run/PiseApplication/prot_nucml.pm blib/lib/Bio/Tools/Run/PiseApplication/prot_nucml.pm
cp Bio/Tools/Run/PiseApplication/gibbs.pm blib/lib/Bio/Tools/Run/PiseApplication/gibbs.pm
cp Bio/Tools/Run/PiseApplication/rnaheat.pm blib/lib/Bio/Tools/Run/PiseApplication/rnaheat.pm
cp Bio/Tools/Run/PiseApplication/codcmp.pm blib/lib/Bio/Tools/Run/PiseApplication/codcmp.pm
cp Bio/Tools/Run/PiseApplication/comalign.pm blib/lib/Bio/Tools/Run/PiseApplication/comalign.pm
cp Bio/Tools/Run/PiseApplication/bionj.pm blib/lib/Bio/Tools/Run/PiseApplication/bionj.pm
cp Bio/Tools/Run/PiseApplication/rnasubopt.pm blib/lib/Bio/Tools/Run/PiseApplication/rnasubopt.pm
cp Bio/Tools/Run/PiseApplication/preg.pm blib/lib/Bio/Tools/Run/PiseApplication/preg.pm
cp Bio/Tools/Run/PiseApplication/qstar.pm blib/lib/Bio/Tools/Run/PiseApplication/qstar.pm
cp Bio/Tools/Run/Phylo/Phylip/Base.pm blib/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm
cp Bio/Tools/Run/PiseApplication/mview_blast.pm blib/lib/Bio/Tools/Run/PiseApplication/mview_blast.pm
cp Bio/Tools/Run/Phylo/PAML/Yn00.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm
cp Bio/Tools/Run/PiseApplication/hmoment.pm blib/lib/Bio/Tools/Run/PiseApplication/hmoment.pm
cp Bio/Tools/Run/PiseApplication/nnssp.pm blib/lib/Bio/Tools/Run/PiseApplication/nnssp.pm
cp Bio/Tools/Run/PiseApplication/trimseq.pm blib/lib/Bio/Tools/Run/PiseApplication/trimseq.pm
cp Bio/Tools/Run/PiseApplication/matcher.pm blib/lib/Bio/Tools/Run/PiseApplication/matcher.pm
cp Bio/Tools/Run/PiseApplication.pm blib/lib/Bio/Tools/Run/PiseApplication.pm
cp Bio/Tools/Run/PiseApplication/CSR.pm blib/lib/Bio/Tools/Run/PiseApplication/CSR.pm
cp Bio/Tools/Run/PiseApplication/boxshade.pm blib/lib/Bio/Tools/Run/PiseApplication/boxshade.pm
cp Bio/Tools/Run/PiseApplication/consense.pm blib/lib/Bio/Tools/Run/PiseApplication/consense.pm
cp Bio/Tools/Run/PiseJob.pm blib/lib/Bio/Tools/Run/PiseJob.pm
cp Bio/Tools/Run/Phylo/Molphy/ProtML.pm blib/lib/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
cp Bio/Tools/Run/PiseApplication/dsc.pm blib/lib/Bio/Tools/Run/PiseApplication/dsc.pm
cp Bio/Tools/Run/PiseApplication/einverted.pm blib/lib/Bio/Tools/Run/PiseApplication/einverted.pm
cp Bio/Tools/Run/PiseApplication/newcpgseek.pm blib/lib/Bio/Tools/Run/PiseApplication/newcpgseek.pm
cp Bio/Tools/Run/PiseApplication/clustalw_convert.pm blib/lib/Bio/Tools/Run/PiseApplication/clustalw_convert.pm
cp Bio/Tools/Run/PiseApplication/drawtree.pm blib/lib/Bio/Tools/Run/PiseApplication/drawtree.pm
cp Bio/Tools/Run/PiseApplication/nrscope.pm blib/lib/Bio/Tools/Run/PiseApplication/nrscope.pm
cp Bio/Tools/Run/PiseApplication/octanol.pm blib/lib/Bio/Tools/Run/PiseApplication/octanol.pm
cp Bio/Tools/Run/Alignment/Sim4.pm blib/lib/Bio/Tools/Run/Alignment/Sim4.pm
cp Bio/Tools/Run/PiseApplication/bambe.pm blib/lib/Bio/Tools/Run/PiseApplication/bambe.pm
cp Bio/Tools/Run/FootPrinter.pm blib/lib/Bio/Tools/Run/FootPrinter.pm
cp Bio/Tools/Run/PiseApplication/syco.pm blib/lib/Bio/Tools/Run/PiseApplication/syco.pm
cp Bio/Tools/Run/PiseApplication/pratt.pm blib/lib/Bio/Tools/Run/PiseApplication/pratt.pm
cp Bio/Tools/Run/PiseApplication/gff2ps.pm blib/lib/Bio/Tools/Run/PiseApplication/gff2ps.pm
cp Bio/Tools/Run/Phylo/PAML/Codeml.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm
cp Bio/Tools/Run/PiseApplication/tmap.pm blib/lib/Bio/Tools/Run/PiseApplication/tmap.pm
cp Bio/Tools/Run/PiseApplication/pepwindow.pm blib/lib/Bio/Tools/Run/PiseApplication/pepwindow.pm
cp Bio/Tools/Run/PiseApplication/checktrans.pm blib/lib/Bio/Tools/Run/PiseApplication/checktrans.pm
cp Bio/Tools/Run/Genscan.pm blib/lib/Bio/Tools/Run/Genscan.pm
cp Bio/Tools/Run/PiseApplication/protpars.pm blib/lib/Bio/Tools/Run/PiseApplication/protpars.pm
cp Bio/Tools/Run/Analysis/soap.pm blib/lib/Bio/Tools/Run/Analysis/soap.pm
cp Bio/Tools/Run/PiseApplication/notseq.pm blib/lib/Bio/Tools/Run/PiseApplication/notseq.pm
cp Bio/Tools/Run/PiseApplication/blimps_block.pm blib/lib/Bio/Tools/Run/PiseApplication/blimps_block.pm
cp Bio/Tools/Run/PiseApplication/protdist.pm blib/lib/Bio/Tools/Run/PiseApplication/protdist.pm
cp Bio/Tools/Run/PiseApplication/seqstat.pm blib/lib/Bio/Tools/Run/PiseApplication/seqstat.pm
cp Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm blib/lib/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
cp Bio/Tools/Run/PiseApplication/equicktandem.pm blib/lib/Bio/Tools/Run/PiseApplication/equicktandem.pm
cp Bio/Tools/Run/PiseApplication/infoalign.pm blib/lib/Bio/Tools/Run/PiseApplication/infoalign.pm
cp Bio/Tools/Run/PiseApplication/trimest.pm blib/lib/Bio/Tools/Run/PiseApplication/trimest.pm
cp Bio/Tools/Run/PiseApplication/pyreval.pm blib/lib/Bio/Tools/Run/PiseApplication/pyreval.pm
cp Bio/Tools/Run/PiseApplication/trnascan.pm blib/lib/Bio/Tools/Run/PiseApplication/trnascan.pm
cp Bio/Tools/Run/PiseApplication/recoder.pm blib/lib/Bio/Tools/Run/PiseApplication/recoder.pm
cp Bio/Tools/Run/Coil.pm blib/lib/Bio/Tools/Run/Coil.pm
cp Bio/Tools/Run/PiseApplication/seqsblast.pm blib/lib/Bio/Tools/Run/PiseApplication/seqsblast.pm
cp Bio/Tools/Run/Phylo/Phylip/ProtPars.pm blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
cp Bio/Tools/Run/PiseApplication/patmatmotifs.pm blib/lib/Bio/Tools/Run/PiseApplication/patmatmotifs.pm
cp Bio/Tools/Run/PiseApplication/geecee.pm blib/lib/Bio/Tools/Run/PiseApplication/geecee.pm
cp Bio/Tools/Run/PiseApplication/druid.pm blib/lib/Bio/Tools/Run/PiseApplication/druid.pm
cp Bio/Tools/Run/PiseApplication/patmatdb.pm blib/lib/Bio/Tools/Run/PiseApplication/patmatdb.pm
cp Bio/Tools/Run/PiseApplication/seqboot.pm blib/lib/Bio/Tools/Run/PiseApplication/seqboot.pm
cp Bio/Tools/Run/PiseApplication/dnapars.pm blib/lib/Bio/Tools/Run/PiseApplication/dnapars.pm
cp Bio/Tools/Run/PiseApplication/cpgreport.pm blib/lib/Bio/Tools/Run/PiseApplication/cpgreport.pm
cp Bio/Tools/Run/PiseApplication/plsearch.pm blib/lib/Bio/Tools/Run/PiseApplication/plsearch.pm
cp Bio/Tools/Run/PiseApplication/biosed.pm blib/lib/Bio/Tools/Run/PiseApplication/biosed.pm
cp Bio/Tools/Run/PiseApplication/hmmcalibrate.pm blib/lib/Bio/Tools/Run/PiseApplication/hmmcalibrate.pm
cp Bio/Tools/Run/PiseApplication/neighbor.pm blib/lib/Bio/Tools/Run/PiseApplication/neighbor.pm
cp Bio/Tools/Run/PiseApplication/wublast2.pm blib/lib/Bio/Tools/Run/PiseApplication/wublast2.pm
cp Bio/Tools/Run/PiseApplication/dollop.pm blib/lib/Bio/Tools/Run/PiseApplication/dollop.pm
cp Bio/Tools/Run/PiseApplication/gb2xml.pm blib/lib/Bio/Tools/Run/PiseApplication/gb2xml.pm
cp Bio/Tools/Run/PiseApplication/pdbsearch.pm blib/lib/Bio/Tools/Run/PiseApplication/pdbsearch.pm
cp Bio/Tools/Run/PiseApplication/pepstats.pm blib/lib/Bio/Tools/Run/PiseApplication/pepstats.pm
cp Bio/Tools/Run/PiseApplication/loadseq.pm blib/lib/Bio/Tools/Run/PiseApplication/loadseq.pm
cp Bio/Tools/Run/PiseApplication/prettyalign.pm blib/lib/Bio/Tools/Run/PiseApplication/prettyalign.pm
cp Bio/Tools/Run/PiseApplication/cusp.pm blib/lib/Bio/Tools/Run/PiseApplication/cusp.pm
cp Bio/Tools/Run/PiseApplication/mix.pm blib/lib/Bio/Tools/Run/PiseApplication/mix.pm
cp Bio/Tools/Run/PiseApplication/banana.pm blib/lib/Bio/Tools/Run/PiseApplication/banana.pm
cp Bio/Tools/Run/PiseApplication/dottup.pm blib/lib/Bio/Tools/Run/PiseApplication/dottup.pm
cp Bio/Tools/Run/PiseApplication/scopparse.pm blib/lib/Bio/Tools/Run/PiseApplication/scopparse.pm
cp Bio/Tools/Run/PiseApplication/alistat.pm blib/lib/Bio/Tools/Run/PiseApplication/alistat.pm
cp Bio/Tools/Run/PiseApplication/msa.pm blib/lib/Bio/Tools/Run/PiseApplication/msa.pm
cp Bio/Tools/Run/PiseApplication/drawgram.pm blib/lib/Bio/Tools/Run/PiseApplication/drawgram.pm
cp Bio/Tools/Run/Alignment/TCoffee.pm blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm
cp Bio/Tools/Run/PiseApplication/coderet.pm blib/lib/Bio/Tools/Run/PiseApplication/coderet.pm
cp Bio/Tools/Run/Phylo/Phylip/ProtDist.pm blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
cp Bio/Tools/Run/PiseApplication/codnocod.pm blib/lib/Bio/Tools/Run/PiseApplication/codnocod.pm
cp Bio/Tools/Run/PiseApplication/oddcomp.pm blib/lib/Bio/Tools/Run/PiseApplication/oddcomp.pm
cp Bio/Tools/Run/EMBOSSApplication.pm blib/lib/Bio/Tools/Run/EMBOSSApplication.pm
cp Bio/Tools/Run/Signalp.pm blib/lib/Bio/Tools/Run/Signalp.pm
cp Bio/Tools/Run/PiseApplication/cirdna.pm blib/lib/Bio/Tools/Run/PiseApplication/cirdna.pm
cp Bio/Tools/Run/PiseApplication/lgicsearch.pm blib/lib/Bio/Tools/Run/PiseApplication/lgicsearch.pm
cp Bio/Tools/Run/PiseApplication/consensus.pm blib/lib/Bio/Tools/Run/PiseApplication/consensus.pm
cp Bio/Tools/Run/PiseApplication/helixturnhelix.pm blib/lib/Bio/Tools/Run/PiseApplication/helixturnhelix.pm
cp Bio/Tools/Run/PiseApplication/getblock.pm blib/lib/Bio/Tools/Run/PiseApplication/getblock.pm
cp Bio/Tools/Run/PiseApplication/diffseq.pm blib/lib/Bio/Tools/Run/PiseApplication/diffseq.pm
cp Bio/Tools/Run/PiseApplication/sampleseqs.pm blib/lib/Bio/Tools/Run/PiseApplication/sampleseqs.pm
cp Bio/Tools/Run/PiseApplication/codontree.pm blib/lib/Bio/Tools/Run/PiseApplication/codontree.pm
cp Bio/Tools/Run/PiseApplication/pepnet.pm blib/lib/Bio/Tools/Run/PiseApplication/pepnet.pm
cp Bio/Tools/Run/PiseApplication/scope.pm blib/lib/Bio/Tools/Run/PiseApplication/scope.pm
cp Bio/Tools/Run/PiseApplication/rnapdist.pm blib/lib/Bio/Tools/Run/PiseApplication/rnapdist.pm
cp Bio/Tools/Run/PiseApplication/water.pm blib/lib/Bio/Tools/Run/PiseApplication/water.pm
cp Bio/Tools/Run/PiseApplication/parciquart.pm blib/lib/Bio/Tools/Run/PiseApplication/parciquart.pm
cp Bio/Tools/Run/Mdust.pm blib/lib/Bio/Tools/Run/Mdust.pm
cp Bio/Factory/EMBOSS.pm blib/lib/Bio/Factory/EMBOSS.pm
cp Bio/Tools/Run/PiseApplication/hmmbuild.pm blib/lib/Bio/Tools/Run/PiseApplication/hmmbuild.pm
cp Bio/Tools/Run/PiseApplication/align2model.pm blib/lib/Bio/Tools/Run/PiseApplication/align2model.pm
cp Bio/Tools/Run/PiseApplication/cons.pm blib/lib/Bio/Tools/Run/PiseApplication/cons.pm
cp Bio/Tools/Run/PiseApplication/rnadistance.pm blib/lib/Bio/Tools/Run/PiseApplication/rnadistance.pm
cp Bio/Tools/Run/PiseApplication/marscan.pm blib/lib/Bio/Tools/Run/PiseApplication/marscan.pm
cp Bio/Tools/Run/PiseApplication/pars.pm blib/lib/Bio/Tools/Run/PiseApplication/pars.pm
cp Bio/Tools/Run/PiseApplication/homology.pm blib/lib/Bio/Tools/Run/PiseApplication/homology.pm
cp Bio/Tools/Run/PiseApplication/pima.pm blib/lib/Bio/Tools/Run/PiseApplication/pima.pm
cp Bio/Tools/Run/Profile.pm blib/lib/Bio/Tools/Run/Profile.pm
cp Bio/Tools/Run/PiseApplication/tfscan.pm blib/lib/Bio/Tools/Run/PiseApplication/tfscan.pm
cp Bio/Tools/Run/PiseApplication/mfold.pm blib/lib/Bio/Tools/Run/PiseApplication/mfold.pm
cp Bio/Tools/Run/PiseApplication/antigenic.pm blib/lib/Bio/Tools/Run/PiseApplication/antigenic.pm
cp Bio/Tools/Run/PiseApplication/sirna.pm blib/lib/Bio/Tools/Run/PiseApplication/sirna.pm
cp Bio/Tools/Run/PiseApplication/hmmer2sam.pm blib/lib/Bio/Tools/Run/PiseApplication/hmmer2sam.pm
cp Bio/Tools/Run/PiseApplication/plotorf.pm blib/lib/Bio/Tools/Run/PiseApplication/plotorf.pm
cp Bio/Tools/Run/PiseApplication/codonw.pm blib/lib/Bio/Tools/Run/PiseApplication/codonw.pm
cp Bio/Tools/Run/PiseApplication/descseq.pm blib/lib/Bio/Tools/Run/PiseApplication/descseq.pm
cp Bio/Tools/Run/PiseApplication/html4blast.pm blib/lib/Bio/Tools/Run/PiseApplication/html4blast.pm
cp Bio/Tools/Run/PiseApplication/phiblast.pm blib/lib/Bio/Tools/Run/PiseApplication/phiblast.pm
cp Bio/Tools/Run/PiseApplication/megamerger.pm blib/lib/Bio/Tools/Run/PiseApplication/megamerger.pm
cp Bio/Tools/Run/PiseApplication/nthseq.pm blib/lib/Bio/Tools/Run/PiseApplication/nthseq.pm
cp Bio/Tools/Run/PiseApplication/fuzznuc.pm blib/lib/Bio/Tools/Run/PiseApplication/fuzznuc.pm
cp Bio/Tools/Run/PiseApplication/dreg.pm blib/lib/Bio/Tools/Run/PiseApplication/dreg.pm
cp Bio/Tools/Run/PiseApplication/fasta.pm blib/lib/Bio/Tools/Run/PiseApplication/fasta.pm
cp Bio/Tools/Run/PiseApplication/melting.pm blib/lib/Bio/Tools/Run/PiseApplication/melting.pm
cp Bio/Tools/Run/PiseApplication/distmat.pm blib/lib/Bio/Tools/Run/PiseApplication/distmat.pm
cp Bio/Tools/Run/PiseApplication/drawpyr.pm blib/lib/Bio/Tools/Run/PiseApplication/drawpyr.pm
cp Bio/Tools/Run/PiseApplication/fuzztran.pm blib/lib/Bio/Tools/Run/PiseApplication/fuzztran.pm
cp Bio/Tools/Run/Pseudowise.pm blib/lib/Bio/Tools/Run/Pseudowise.pm
cp Bio/Tools/Run/PiseApplication/cai.pm blib/lib/Bio/Tools/Run/PiseApplication/cai.pm
cp Bio/Tools/Run/PiseApplication/showorf.pm blib/lib/Bio/Tools/Run/PiseApplication/showorf.pm
cp Bio/Tools/Run/PiseApplication/pepwindowall.pm blib/lib/Bio/Tools/Run/PiseApplication/pepwindowall.pm
cp Bio/Tools/Run/PiseApplication/degapseq.pm blib/lib/Bio/Tools/Run/PiseApplication/degapseq.pm
cp Bio/Tools/Run/PiseApplication/freak.pm blib/lib/Bio/Tools/Run/PiseApplication/freak.pm
cp Bio/Tools/Run/PiseApplication/readseq.pm blib/lib/Bio/Tools/Run/PiseApplication/readseq.pm
cp Bio/Tools/Run/PiseApplication/primersearch.pm blib/lib/Bio/Tools/Run/PiseApplication/primersearch.pm
cp Bio/Tools/Run/PiseApplication/pftools.pm blib/lib/Bio/Tools/Run/PiseApplication/pftools.pm
cp Bio/Tools/Run/PiseApplication/scan_for_matches.pm blib/lib/Bio/Tools/Run/PiseApplication/scan_for_matches.pm
cp Bio/Tools/Run/PiseApplication/dialign2.pm blib/lib/Bio/Tools/Run/PiseApplication/dialign2.pm
cp Bio/Tools/Run/PiseApplication/seqmatchall.pm blib/lib/Bio/Tools/Run/PiseApplication/seqmatchall.pm
cp Bio/Tools/Run/Phylo/Phylip/DrawTree.pm blib/lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm
cp Bio/Tools/Run/PiseApplication/quicktree.pm blib/lib/Bio/Tools/Run/PiseApplication/quicktree.pm
cp Bio/Tools/Run/PiseApplication/pestfind.pm blib/lib/Bio/Tools/Run/PiseApplication/pestfind.pm
cp Bio/Tools/Run/Prints.pm blib/lib/Bio/Tools/Run/Prints.pm
cp Bio/Tools/Run/PiseApplication/cds.pm blib/lib/Bio/Tools/Run/PiseApplication/cds.pm
cp Bio/Tools/Run/PiseApplication/fastrna.pm blib/lib/Bio/Tools/Run/PiseApplication/fastrna.pm
cp Bio/Tools/Run/PiseApplication/extractseq.pm blib/lib/Bio/Tools/Run/PiseApplication/extractseq.pm
cp Bio/Tools/Run/PiseApplication/genscan.pm blib/lib/Bio/Tools/Run/PiseApplication/genscan.pm
cp Bio/Tools/Run/PiseApplication/getorf.pm blib/lib/Bio/Tools/Run/PiseApplication/getorf.pm
cp Bio/Tools/Run/PiseApplication/dssp.pm blib/lib/Bio/Tools/Run/PiseApplication/dssp.pm
cp Bio/Tools/Run/Vista.pm blib/lib/Bio/Tools/Run/Vista.pm
cp Bio/Tools/Run/PiseApplication/mwfilter.pm blib/lib/Bio/Tools/Run/PiseApplication/mwfilter.pm
cp Bio/Tools/Run/PiseApplication/psiblast.pm blib/lib/Bio/Tools/Run/PiseApplication/psiblast.pm
cp Bio/Tools/Run/PiseApplication/eprimer3.pm blib/lib/Bio/Tools/Run/PiseApplication/eprimer3.pm
cp Bio/Tools/Run/PiseApplication/showseq.pm blib/lib/Bio/Tools/Run/PiseApplication/showseq.pm
cp Bio/Tools/Run/PiseApplication/infoseq.pm blib/lib/Bio/Tools/Run/PiseApplication/infoseq.pm
cp Bio/Tools/Run/PiseApplication/prose.pm blib/lib/Bio/Tools/Run/PiseApplication/prose.pm
cp Bio/Tools/Run/Eponine.pm blib/lib/Bio/Tools/Run/Eponine.pm
cp Bio/Tools/Run/PiseApplication/pyramids.pm blib/lib/Bio/Tools/Run/PiseApplication/pyramids.pm
cp Bio/Tools/Run/PiseApplication/twofeat.pm blib/lib/Bio/Tools/Run/PiseApplication/twofeat.pm
cp Bio/Tools/Run/PiseApplication/clique.pm blib/lib/Bio/Tools/Run/PiseApplication/clique.pm
cp Bio/Tools/Run/PiseApplication/rnafold.pm blib/lib/Bio/Tools/Run/PiseApplication/rnafold.pm
cp Bio/Tools/Run/PiseApplication/addquart.pm blib/lib/Bio/Tools/Run/PiseApplication/addquart.pm
cp Bio/Tools/Run/Promoterwise.pm blib/lib/Bio/Tools/Run/Promoterwise.pm
cp Bio/Tools/Run/PiseApplication/blast2.pm blib/lib/Bio/Tools/Run/PiseApplication/blast2.pm
cp Bio/Tools/Run/PiseApplication/satellites.pm blib/lib/Bio/Tools/Run/PiseApplication/satellites.pm
cp Bio/Tools/Run/Phylo/Phylip/Consense.pm blib/lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm
cp Bio/Tools/Run/PiseApplication/profit.pm blib/lib/Bio/Tools/Run/PiseApplication/profit.pm
cp Bio/Tools/Run/PiseApplication/plotcon.pm blib/lib/Bio/Tools/Run/PiseApplication/plotcon.pm
cp Bio/Tools/Run/PiseApplication/stretcher.pm blib/lib/Bio/Tools/Run/PiseApplication/stretcher.pm
cp Bio/Tools/Run/PiseApplication/makehist.pm blib/lib/Bio/Tools/Run/PiseApplication/makehist.pm
cp Bio/Tools/Run/PiseApplication/digest.pm blib/lib/Bio/Tools/Run/PiseApplication/digest.pm
cp Bio/Tools/Run/PiseApplication/decorate.pm blib/lib/Bio/Tools/Run/PiseApplication/decorate.pm
cp Bio/Tools/Run/PiseApplication/merger.pm blib/lib/Bio/Tools/Run/PiseApplication/merger.pm
cp Bio/Tools/Run/PiseApplication/psort2.pm blib/lib/Bio/Tools/Run/PiseApplication/psort2.pm
cp Bio/Tools/Run/PiseApplication/saps.pm blib/lib/Bio/Tools/Run/PiseApplication/saps.pm
cp Bio/Tools/Run/PiseApplication/prophet.pm blib/lib/Bio/Tools/Run/PiseApplication/prophet.pm
cp Bio/Tools/Run/PiseApplication/mview_alig.pm blib/lib/Bio/Tools/Run/PiseApplication/mview_alig.pm
cp Bio/Tools/Run/PiseApplication/cap.pm blib/lib/Bio/Tools/Run/PiseApplication/cap.pm
cp Bio/Tools/Run/PiseApplication/readnexus.pm blib/lib/Bio/Tools/Run/PiseApplication/readnexus.pm
cp Bio/Tools/Run/PiseApplication/cpgplot.pm blib/lib/Bio/Tools/Run/PiseApplication/cpgplot.pm
cp Bio/Tools/Run/PiseApplication/chaos.pm blib/lib/Bio/Tools/Run/PiseApplication/chaos.pm
cp Bio/Tools/Run/PiseApplication/mspcrunch.pm blib/lib/Bio/Tools/Run/PiseApplication/mspcrunch.pm
cp Bio/Tools/Run/PiseApplication/remap.pm blib/lib/Bio/Tools/Run/PiseApplication/remap.pm
cp Bio/Tools/Run/Tmhmm.pm blib/lib/Bio/Tools/Run/Tmhmm.pm
cp Bio/Tools/Run/PiseApplication/pepwheel.pm blib/lib/Bio/Tools/Run/PiseApplication/pepwheel.pm
cp Bio/Tools/Run/PiseApplication/compseq.pm blib/lib/Bio/Tools/Run/PiseApplication/compseq.pm
cp Bio/Tools/Run/PiseApplication/shuffleseq.pm blib/lib/Bio/Tools/Run/PiseApplication/shuffleseq.pm
cp Bio/Tools/Run/PiseApplication/isochore.pm blib/lib/Bio/Tools/Run/PiseApplication/isochore.pm
cp Bio/Tools/Run/PiseApplication/Puzzle.pm blib/lib/Bio/Tools/Run/PiseApplication/Puzzle.pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::stssearch.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::filtersites.3
Manifying blib/man3/Bio::Tools::Run::EMBOSSacd.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::protal2dna.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::confmat.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::sam2hmmer.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::primo.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::domainer.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnainverse.3
Manifying blib/man3/Bio::Tools::Run::Alignment::StandAloneFasta.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::wordmatch.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::fuzzpro.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::distquart.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::whichdb.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::fmtseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::newcpgreport.3
Manifying blib/man3/Bio::Tools::Run::AnalysisFactory.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::blimps_matrix.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::redata.3
Manifying blib/man3/Bio::Tools::Run::AnalysisFactory::Pise.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pscan.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::predator.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::tipdate.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::extractfeat.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::most.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepinfo.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::golden.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dotmatcher.3
Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::Neighbor.3
Manifying blib/man3/Bio::Tools::Run::AnalysisFactory::soap.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::wobble.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::silent.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::abiview.3
Manifying blib/man3/Bio::Tools::Run::Hmmer.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::maskseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::btwisted.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::restover.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::assp.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::supermatcher.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::iep.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::showalign.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::repeats.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::xblast.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::lassap.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::interface.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::emowse.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::con_filter.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::grailclnt.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::fitch.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::emma.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::unroot.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::splitter.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::sigcleave.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::environ.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::newseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::xpound.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::prophecy.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dotpath.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::chips.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::map.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::maskfeat.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::weighbor.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::showfeat.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::lvb.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::kitsch.3
Manifying blib/man3/Bio::Tools::Run::Alignment::Lagan.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::msbar.3
Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::DrawGram.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::seqgen.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::bl2seq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pasteseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dan.3
Manifying blib/man3/Bio::Tools::Run::Seg.3
Manifying blib/man3/Bio::Tools::Run::RepeatMasker.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::listor.3
Manifying blib/man3/Bio::Tools::Run::Genewise.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::tacg.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::polydot.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmalign.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::sreformat.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::wordcount.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::prettyplot.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::siggen.3
Manifying blib/man3/Bio::Tools::Run::Primer3.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::needle.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::cutseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::findkm.3
Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pam.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::prettyseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::transeq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::combat.3
Manifying blib/man3/Bio::Tools::Run::PiseJobParser.3
Manifying blib/man3/Bio::Tools::Run::PiseWorkflow.3
Manifying blib/man3/Bio::Tools::Run::Alignment::DBA.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::restrict.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::patser.3
Manifying blib/man3/Bio::Tools::Run::Primate.3
Manifying blib/man3/Bio::Tools::Run::Alignment::Blat.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmsearch.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::mreps.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmpfam.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::revseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnaga.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::blimps.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::gruppi.3
Manifying blib/man3/Bio::Tools::Run::Analysis.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::lindna.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnaeval.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::palindrome.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dnadist.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::stride.3
Manifying blib/man3/Bio::Tools::Run::Hmmpfam.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepcoil.3
Manifying blib/man3/Bio::Tools::Run::Alignment::Clustalw.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::clustalw.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::gibbs_scan.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::sigscan.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::modelfromalign.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmemit.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::treealign.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::toppred.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::wise2.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::fastdnaml.3
Manifying blib/man3/Bio::Tools::Run::TribeMCL.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dca.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::vectorstrip.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::prodom.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::tranalign.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::njdist.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::charge.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmscore.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmfetch.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::etandem.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::backtranseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmconvert.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::est2genome.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::prot_nucml.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnaheat.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::gibbs.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::codcmp.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::bionj.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::comalign.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnasubopt.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::qstar.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::preg.3
Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::Base.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::mview_blast.3
Manifying blib/man3/Bio::Tools::Run::Phylo::PAML::Yn00.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmoment.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::nnssp.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::trimseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::matcher.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::CSR.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::boxshade.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::consense.3
Manifying blib/man3/Bio::Tools::Run::PiseJob.3
Manifying blib/man3/Bio::Tools::Run::Phylo::Molphy::ProtML.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dsc.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::einverted.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::newcpgseek.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::clustalw_convert.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::drawtree.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::nrscope.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::octanol.3
Manifying blib/man3/Bio::Tools::Run::Alignment::Sim4.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::bambe.3
Manifying blib/man3/Bio::Tools::Run::FootPrinter.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::syco.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pratt.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::gff2ps.3
Manifying blib/man3/Bio::Tools::Run::Phylo::PAML::Codeml.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::tmap.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepwindow.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::checktrans.3
Manifying blib/man3/Bio::Tools::Run::Genscan.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::protpars.3
Manifying blib/man3/Bio::Tools::Run::Analysis::soap.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::notseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::blimps_block.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::protdist.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::seqstat.3
Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::PhylipConf.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::equicktandem.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::infoalign.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::trimest.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pyreval.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::trnascan.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::recoder.3
Manifying blib/man3/Bio::Tools::Run::Coil.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::seqsblast.3
Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::ProtPars.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::patmatmotifs.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::geecee.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::druid.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::patmatdb.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::seqboot.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dnapars.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::cpgreport.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::plsearch.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::biosed.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmcalibrate.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::neighbor.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::wublast2.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dollop.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::gb2xml.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pdbsearch.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepstats.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::loadseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::prettyalign.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::cusp.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::mix.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::banana.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dottup.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::scopparse.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::alistat.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::msa.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::drawgram.3
Manifying blib/man3/Bio::Tools::Run::Alignment::TCoffee.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::coderet.3
Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::ProtDist.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::codnocod.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::oddcomp.3
Manifying blib/man3/Bio::Tools::Run::EMBOSSApplication.3
Manifying blib/man3/Bio::Tools::Run::Signalp.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::cirdna.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::lgicsearch.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::consensus.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::helixturnhelix.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::getblock.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::diffseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::sampleseqs.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::codontree.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepnet.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::scope.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnapdist.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::water.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::parciquart.3
Manifying blib/man3/Bio::Tools::Run::Mdust.3
Manifying blib/man3/Bio::Factory::EMBOSS.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmbuild.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::align2model.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::cons.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnadistance.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::marscan.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pars.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::homology.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pima.3
Manifying blib/man3/Bio::Tools::Run::Profile.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::tfscan.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::mfold.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::antigenic.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::sirna.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmer2sam.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::plotorf.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::descseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::codonw.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::html4blast.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::megamerger.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::phiblast.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::nthseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dreg.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::fuzznuc.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::fasta.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::melting.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::distmat.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::drawpyr.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::showorf.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::cai.3
Manifying blib/man3/Bio::Tools::Run::Pseudowise.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::fuzztran.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepwindowall.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::degapseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::readseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::freak.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::primersearch.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::scan_for_matches.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pftools.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dialign2.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::seqmatchall.3
Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::DrawTree.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::quicktree.3
Manifying blib/man3/Bio::Tools::Run::Prints.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pestfind.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::cds.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::extractseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::fastrna.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::genscan.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::getorf.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dssp.3
Manifying blib/man3/Bio::Tools::Run::Vista.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::psiblast.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::mwfilter.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::showseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::eprimer3.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::infoseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::prose.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pyramids.3
Manifying blib/man3/Bio::Tools::Run::Eponine.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::twofeat.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnafold.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::clique.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::addquart.3
Manifying blib/man3/Bio::Tools::Run::Promoterwise.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::blast2.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::satellites.3
Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::Consense.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::profit.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::plotcon.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::stretcher.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::makehist.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::digest.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::decorate.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::merger.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::psort2.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::saps.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::prophet.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::cap.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::mview_alig.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::readnexus.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::cpgplot.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::chaos.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::mspcrunch.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::remap.3
Manifying blib/man3/Bio::Tools::Run::Tmhmm.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::compseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepwheel.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::shuffleseq.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::isochore.3
Manifying blib/man3/Bio::Tools::Run::PiseApplication::Puzzle.3

[ERROR] [Fri Apr 18 12:09:22 2008] MAKE TEST failed:  PERL_DL_NONLAZY=1 /home/cpan/perl586/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/Analysis_soap...........SOAP::Lite not installed. Skipping some tests.
ok
        16/17 skipped: various reasons
t/AnalysisFactory_soap....SOAP::Lite not installed. Skipping some tests.
ok
        7/8 skipped: various reasons
t/Blat....................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Alignment/Blat.pm line 60.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Alignment/Blat.pm line 60.
Compilation failed in require at t/Blat.t line 24.
BEGIN failed--compilation aborted at t/Blat.t line 24.
dubious
	Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-11
	Failed 11/11 tests, 0.00% okay
t/Clustalw................Can't locate Bio/Seq.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Alignment/Clustalw.pm line 321.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Alignment/Clustalw.pm line 321.
Compilation failed in require at t/Clustalw.t line 17.
BEGIN failed--compilation aborted at t/Clustalw.t line 17.
dubious
	Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-9
	Failed 9/9 tests, 0.00% okay
t/Coil....................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Coil.pm line 69.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Coil.pm line 69.
Compilation failed in require at t/Coil.t line 22.
BEGIN failed--compilation aborted at t/Coil.t line 22.
dubious
	Test returned status 2 (wstat 512, 0x200)
	after all the subtests completed successfully
t/Consense................IO::String not installed. Skipping tests 1 to 7.
ok
        7/7 skipped: various reasons
t/DBA.....................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Alignment/DBA.pm line 81.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Alignment/DBA.pm line 81.
Compilation failed in require at t/DBA.t line 16.
BEGIN failed--compilation aborted at t/DBA.t line 16.
dubious
	Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-15
	Failed 15/15 tests, 0.00% okay
t/DrawGram................Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm line 85.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm line 85.
Compilation failed in require at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm line 76.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm line 76.
Compilation failed in require at t/DrawGram.t line 20.
BEGIN failed--compilation aborted at t/DrawGram.t line 20.
dubious
	Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-4
	Failed 4/4 tests, 0.00% okay
t/DrawTree................Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm line 85.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm line 85.
Compilation failed in require at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm line 76.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm line 76.
Compilation failed in require at t/DrawTree.t line 20.
BEGIN failed--compilation aborted at t/DrawTree.t line 20.
dubious
	Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-4
	Failed 4/4 tests, 0.00% okay
t/EMBOSS..................Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Factory/EMBOSS.pm line 102.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Factory/EMBOSS.pm line 102.
Compilation failed in require at t/EMBOSS.t line 23.
BEGIN failed--compilation aborted at t/EMBOSS.t line 23.
dubious
	Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-30
	Failed 30/30 tests, 0.00% okay
t/Eponine.................Can't locate Bio/Tools/Eponine.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Eponine.pm line 91.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Eponine.pm line 91.
Compilation failed in require at t/Eponine.t line 25.
BEGIN failed--compilation aborted at t/Eponine.t line 25.
dubious
	Test returned status 2 (wstat 512, 0x200)
	after all the subtests completed successfully
t/FootPrinter.............Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/FootPrinter.pm line 164.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/FootPrinter.pm line 164.
Compilation failed in require at t/FootPrinter.t line 16.
BEGIN failed--compilation aborted at t/FootPrinter.t line 16.
dubious
	Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-18
	Failed 18/18 tests, 0.00% okay
t/Genewise................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Genewise.pm line 92.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Genewise.pm line 92.
Compilation failed in require at t/Genewise.t line 16.
BEGIN failed--compilation aborted at t/Genewise.t line 16.
dubious
	Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-13
	Failed 13/13 tests, 0.00% okay
t/Genscan.................Can't locate Bio/Seq.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Genscan.pm line 66.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Genscan.pm line 66.
Compilation failed in require at t/Genscan.t line 23.
BEGIN failed--compilation aborted at t/Genscan.t line 23.
dubious
	Test returned status 2 (wstat 512, 0x200)
	after all the subtests completed successfully
t/Hmmer...................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Hmmer.pm line 91.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Hmmer.pm line 91.
Compilation failed in require at t/Hmmer.t line 24.
BEGIN failed--compilation aborted at t/Hmmer.t line 24.
dubious
	Test returned status 2 (wstat 512, 0x200)
	after all the subtests completed successfully
t/Hmmpfam.................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Hmmpfam.pm line 85.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Hmmpfam.pm line 85.
Compilation failed in require at t/Hmmpfam.t line 23.
BEGIN failed--compilation aborted at t/Hmmpfam.t line 23.
dubious
	Test returned status 2 (wstat 512, 0x200)
	after all the subtests completed successfully
t/Lagan...................Can't locate Bio/AlignIO.pm in @INC (@INC contains: /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl . /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at t/Lagan.t line 6.
BEGIN failed--compilation aborted at t/Lagan.t line 6.
dubious
	Test returned status 2 (wstat 512, 0x200)
t/Mdust...................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Mdust.pm line 87.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Mdust.pm line 87.
Compilation failed in require at t/Mdust.t line 17.
BEGIN failed--compilation aborted at t/Mdust.t line 17.
dubious
	Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-2
	Failed 2/2 tests, 0.00% okay
t/Molphy..................IO::String not installed. Skipping tests 1 to 7.
ok
        7/7 skipped: various reasons
t/Neighbor................Can't locate Bio/SimpleAlign.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm line 211.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm line 211.
Compilation failed in require at t/Neighbor.t line 19.
BEGIN failed--compilation aborted at t/Neighbor.t line 19.
dubious
	Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-14
	Failed 14/14 tests, 0.00% okay
t/PAML....................IO::String not installed. Skipping tests 1 to 17.
ok
        17/17 skipped: various reasons
t/Pise....................Need XML::Parser::PerlSA to run test, skipping test
ok
        10/10 skipped: various reasons
t/Primate.................Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Primate.pm line 73.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Primate.pm line 73.
Compilation failed in require at t/Primate.t line 43.
BEGIN failed--compilation aborted at t/Primate.t line 43.
dubious
	Test returned status 2 (wstat 512, 0x200)
	after all the subtests completed successfully
t/Primer3.................Can't locate Bio/Root/Root.pm in @INC (@INC contains: t .. /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Primer3.pm line 132.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Primer3.pm line 132.
Compilation failed in require at t/Primer3.t line 27.
BEGIN failed--compilation aborted at t/Primer3.t line 27.
dubious
	Test returned status 2 (wstat 512, 0x200)
	after all the subtests completed successfully
t/Prints..................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Prints.pm line 63.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Prints.pm line 63.
Compilation failed in require at t/Prints.t line 23.
BEGIN failed--compilation aborted at t/Prints.t line 23.
dubious
	Test returned status 2 (wstat 512, 0x200)
	after all the subtests completed successfully
t/Profile.................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Profile.pm line 65.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Profile.pm line 65.
Compilation failed in require at t/Profile.t line 23.
BEGIN failed--compilation aborted at t/Profile.t line 23.
dubious
	Test returned status 2 (wstat 512, 0x200)
	after all the subtests completed successfully
t/Promoterwise............Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Promoterwise.pm line 87.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Promoterwise.pm line 87.
Compilation failed in require at t/Promoterwise.t line 16.
BEGIN failed--compilation aborted at t/Promoterwise.t line 16.
dubious
	Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-8
	Failed 8/8 tests, 0.00% okay
t/ProtDist................Can't locate Bio/SimpleAlign.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm line 211.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm line 211.
Compilation failed in require at t/ProtDist.t line 20.
BEGIN failed--compilation aborted at t/ProtDist.t line 20.
dubious
	Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-11
	Failed 11/11 tests, 0.00% okay
t/ProtPars................Can't locate Bio/SimpleAlign.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm line 130.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm line 130.
Compilation failed in require at t/ProtPars.t line 20.
BEGIN failed--compilation aborted at t/ProtPars.t line 20.
dubious
	Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-7
	Failed 7/7 tests, 0.00% okay
t/Pseudowise..............Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Pseudowise.pm line 67.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Pseudowise.pm line 67.
Compilation failed in require at t/Pseudowise.t line 23.
BEGIN failed--compilation aborted at t/Pseudowise.t line 23.
dubious
	Test returned status 2 (wstat 512, 0x200)
	after all the subtests completed successfully
t/RepeatMasker............Can't locate Bio/SeqFeature/Generic.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/5.8.6 /home/cpan/perl586/lib/site_perl/5.8.6/i386-netbsd-thread-multi-64int /home/cpan/perl586/lib/site_perl/5.8.6 /home/cpan/perl586/lib/site_perl .) at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/RepeatMasker.pm line 85.
BEGIN failed--compilation aborted at /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/RepeatMasker.pm line 85.
Compilation failed in require at t/RepeatMasker.t line 16.
BEGIN failed--compilation aborted at t/RepeatMasker.t line 16.
dubious
	Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-8
	Failed 8/8 tests, 0.00% okay
t/Seg.....................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/lib /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib/arch /home/cpan/perl586/.cpanplus/5.8.6/build/bioperl-run-1.4/blib /home/cpan/perl586/lib/5.8.6/i386-netbsd-thread-multi-64i