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Postings from April 2008
FAIL bioperl-run-1.4 OpenBSD.i386-openbsd-thread-multi-64int 4.1
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From:
chris
Date:
April 22, 2008 09:05
Subject:
FAIL bioperl-run-1.4 OpenBSD.i386-openbsd-thread-multi-64int 4.1
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 0.84. Testers personal comments may appear
at the end of this report.
Thank you for uploading your work to CPAN. However, it appears that
there were some problems testing your distribution.
TEST RESULTS:
Below is the error stack from stage 'make test':
[MSG] [Tue Apr 22 17:02:49 2008] Trying to get 'http://www.cpan.org/authors/id/L/LI/LIMAONE/CHECKSUMS'
[MSG] [Tue Apr 22 17:02:50 2008] Checksum matches for 'Bio-Grep-0.10.3.tar.gz'
[MSG] [Tue Apr 22 17:02:52 2008] Extracted 'Bio-Grep-0.10.3/'
[MSG] [Tue Apr 22 17:02:52 2008] Extracted 'Bio-Grep-0.10.3/README'
[MSG] [Tue Apr 22 17:02:52 2008] Extracted 'Bio-Grep-0.10.3/TODO'
[MSG] [Tue Apr 22 17:02:52 2008] Extracted 'Bio-Grep-0.10.3/examples/'
[MSG] [Tue Apr 22 17:02:52 2008] Extracted 'Bio-Grep-0.10.3/examples/bgrep'
[MSG] [Tue Apr 22 17:02:52 2008] Extracted 'Bio-Grep-0.10.3/examples/Benchmarks.tt'
[MSG] [Tue Apr 22 17:02:52 2008] Extracted 'Bio-Grep-0.10.3/examples/benchmark.pl'
[MSG] [Tue Apr 22 17:02:52 2008] Extracted 'Bio-Grep-0.10.3/lib/'
[MSG] [Tue Apr 22 17:02:52 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/'
[MSG] [Tue Apr 22 17:02:52 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/'
[MSG] [Tue Apr 22 17:02:52 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Backend/'
[MSG] [Tue Apr 22 17:02:52 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Backend/Vmatch.pm'
[MSG] [Tue Apr 22 17:02:52 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Backend/RE.pm'
[MSG] [Tue Apr 22 17:02:52 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Backend/GUUGle.pm'
[MSG] [Tue Apr 22 17:02:52 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Backend/Agrep.pm'
[MSG] [Tue Apr 22 17:02:52 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Backend/BackendI.pm'
[MSG] [Tue Apr 22 17:02:52 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Benchmarks.pod'
[MSG] [Tue Apr 22 17:02:52 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Cookbook.pod'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Root.pm'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Filter/'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Filter/FilterI.pm'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/Filter/FilterRemoveDuplicates.pm'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/SearchSettings.pm'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep/SearchResult.pm'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/lib/Bio/Grep.pm'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/META.yml'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/Makefile.PL'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/Build.PL'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/t/'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/t/Test_DB_Extend.fasta'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/t/pod-coverage.t'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/t/perlcriticrc'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/t/pod.t'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/t/TestFilter.pm'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/t/00.checkprereq.t'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/t/Test_DB_RevCom.fasta'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/t/Test_DB_Big.fasta'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/t/00.load.t'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/t/50.synopsis.t'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/t/perlcritic.t'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/t/Test_DB_Small.fasta'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/t/Test_DB_Protein.fasta'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/t/11.backends.guugle.t'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/t/40.utils.t'
[MSG] [Tue Apr 22 17:02:53 2008] Extracted 'Bio-Grep-0.10.3/t/Test_query_revcom.fasta'
[MSG] [Tue Apr 22 17:02:54 2008] Extracted 'Bio-Grep-0.10.3/t/11.backends.re.t'
[MSG] [Tue Apr 22 17:02:54 2008] Extracted 'Bio-Grep-0.10.3/t/BioGrepTest.pm'
[MSG] [Tue Apr 22 17:02:54 2008] Extracted 'Bio-Grep-0.10.3/t/10.backends.all.t'
[MSG] [Tue Apr 22 17:02:54 2008] Extracted 'Bio-Grep-0.10.3/t/30.features.alignments.t'
[MSG] [Tue Apr 22 17:02:54 2008] Extracted 'Bio-Grep-0.10.3/t/20.filter.t'
[MSG] [Tue Apr 22 17:02:54 2008] Extracted 'Bio-Grep-0.10.3/t/BioGrepSkip.pm'
[MSG] [Tue Apr 22 17:02:54 2008] Extracted 'Bio-Grep-0.10.3/t/Test_query.fasta'
[MSG] [Tue Apr 22 17:02:54 2008] Extracted 'Bio-Grep-0.10.3/t/30.features.updownstream.t'
[MSG] [Tue Apr 22 17:02:54 2008] Extracted 'Bio-Grep-0.10.3/Changes'
[MSG] [Tue Apr 22 17:02:54 2008] Extracted 'Bio-Grep-0.10.3/MANIFEST'
[MSG] [Tue Apr 22 17:02:54 2008] Extracted 'Bio-Grep-0.10.3/LICENSE'
[MSG] [Tue Apr 22 17:02:54 2008] Extracted 'Bio::Grep' to '/home/chris/perl5.10.0/.cpanplus/5.10.0/build/Bio-Grep-0.10.3'
[MSG] [Tue Apr 22 17:02:58 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.
Warning: prerequisite UNIVERSAL::require 0.11 not found.
Writing Makefile for Bio::Grep
[MSG] [Tue Apr 22 17:02:58 2008] DEFAULT 'filter_prereqs' HANDLER RETURNING 'sub return value'
[ERROR] [Tue Apr 22 17:02:58 2008] No such module 'Bio::AlignIO' found on CPAN
[MSG] [Tue Apr 22 17:02:58 2008] Module 'Bio::Grep' requires 'Bio::Factory::EMBOSS' version '0' to be installed
[ERROR] [Tue Apr 22 17:02:58 2008] No such module 'Bio::Index::Fasta' found on CPAN
[ERROR] [Tue Apr 22 17:02:58 2008] No such module 'Bio::Root::Root' found on CPAN
[MSG] [Tue Apr 22 17:02:58 2008] Module 'Bio::Grep' requires 'Bio::Root::Version' version '0' to be installed
[MSG] [Tue Apr 22 17:02:58 2008] Module 'Bio::Grep' requires 'Bio::Seq' version '0' to be installed
[ERROR] [Tue Apr 22 17:02:58 2008] No such module 'Bio::SeqIO' found on CPAN
[MSG] [Tue Apr 22 17:02:58 2008] Module 'Bio::Grep' requires 'Carp::Assert' version '0' to be installed
[MSG] [Tue Apr 22 17:02:58 2008] Module 'Bio::Grep' requires 'Class::MethodMaker' version '2.02' to be installed
[MSG] [Tue Apr 22 17:02:58 2008] Module 'Bio::Grep' requires 'IO::String' version '1' to be installed
[MSG] [Tue Apr 22 17:02:58 2008] Module 'Bio::Grep' requires 'ToolSet' version '0.13' to be installed
[MSG] [Tue Apr 22 17:02:58 2008] Module 'Bio::Grep' requires 'UNIVERSAL::require' version '0.11' to be installed
[MSG] [Tue Apr 22 17:03:03 2008] Trying to get 'http://www.cpan.org/authors/id/B/BI/BIRNEY/CHECKSUMS'
[MSG] [Tue Apr 22 17:03:04 2008] Checksum matches for 'bioperl-run-1.4.tar.gz'
[MSG] [Tue Apr 22 17:03:13 2008] Extracted 'bioperl-run-1.4/'
[MSG] [Tue Apr 22 17:03:13 2008] Extracted 'bioperl-run-1.4/Makefile.PL'
[MSG] [Tue Apr 22 17:03:13 2008] Extracted 'bioperl-run-1.4/AUTHORS'
[MSG] [Tue Apr 22 17:03:13 2008] Extracted 'bioperl-run-1.4/Changes'
[MSG] [Tue Apr 22 17:03:13 2008] Extracted 'bioperl-run-1.4/Bio/'
[MSG] [Tue Apr 22 17:03:13 2008] Extracted 'bioperl-run-1.4/Bio/Factory/'
[MSG] [Tue Apr 22 17:03:13 2008] Extracted 'bioperl-run-1.4/Bio/Factory/EMBOSS.pm'
[MSG] [Tue Apr 22 17:03:13 2008] Extracted 'bioperl-run-1.4/Bio/Tools/'
[MSG] [Tue Apr 22 17:03:13 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/'
[MSG] [Tue Apr 22 17:03:13 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Alignment/'
[MSG] [Tue Apr 22 17:03:13 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Alignment/Clustalw.pm'
[MSG] [Tue Apr 22 17:03:13 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Alignment/Blat.pm'
[MSG] [Tue Apr 22 17:03:13 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Alignment/Lagan.pm'
[MSG] [Tue Apr 22 17:03:13 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Alignment/DBA.pm'
[MSG] [Tue Apr 22 17:03:13 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Alignment/TCoffee.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Alignment/Sim4.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Alignment/StandAloneFasta.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Analysis.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/AnalysisFactory.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Coil.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/EMBOSSApplication.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/EMBOSSacd.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Eponine.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/FootPrinter.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Genewise.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Genscan.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Hmmer.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Hmmpfam.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Mdust.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseJob.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseJobParser.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseWorkflow.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Primate.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Primer3.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Prints.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Profile.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Promoterwise.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Pseudowise.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/RepeatMasker.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Seg.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Signalp.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Tmhmm.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/TribeMCL.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Vista.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Analysis/'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Analysis/soap.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/AnalysisFactory/'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/AnalysisFactory/Pise.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/AnalysisFactory/soap.pm'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Molphy/'
[MSG] [Tue Apr 22 17:03:14 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Molphy/ProtML.pm'
[MSG] [Tue Apr 22 17:03:15 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/PAML/'
[MSG] [Tue Apr 22 17:03:15 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/PAML/Codeml.pm'
[MSG] [Tue Apr 22 17:03:15 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/PAML/Yn00.pm'
[MSG] [Tue Apr 22 17:03:15 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/'
[MSG] [Tue Apr 22 17:03:15 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/Consense.pm'
[MSG] [Tue Apr 22 17:03:15 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/Base.pm'
[MSG] [Tue Apr 22 17:03:15 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm'
[MSG] [Tue Apr 22 17:03:15 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm'
[MSG] [Tue Apr 22 17:03:15 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm'
[MSG] [Tue Apr 22 17:03:15 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm'
[MSG] [Tue Apr 22 17:03:15 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm'
[MSG] [Tue Apr 22 17:03:15 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm'
[MSG] [Tue Apr 22 17:03:15 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm'
[MSG] [Tue Apr 22 17:03:15 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/'
[MSG] [Tue Apr 22 17:03:15 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/Puzzle.pm'
[MSG] [Tue Apr 22 17:03:15 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/CSR.pm'
[MSG] [Tue Apr 22 17:03:15 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/abiview.pm'
[MSG] [Tue Apr 22 17:03:15 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/addquart.pm'
[MSG] [Tue Apr 22 17:03:16 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/align2model.pm'
[MSG] [Tue Apr 22 17:03:16 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/alistat.pm'
[MSG] [Tue Apr 22 17:03:16 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/antigenic.pm'
[MSG] [Tue Apr 22 17:03:16 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/assp.pm'
[MSG] [Tue Apr 22 17:03:16 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/backtranseq.pm'
[MSG] [Tue Apr 22 17:03:16 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/bambe.pm'
[MSG] [Tue Apr 22 17:03:16 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/banana.pm'
[MSG] [Tue Apr 22 17:03:16 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/bionj.pm'
[MSG] [Tue Apr 22 17:03:16 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/biosed.pm'
[MSG] [Tue Apr 22 17:03:16 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/bl2seq.pm'
[MSG] [Tue Apr 22 17:03:16 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/blast2.pm'
[MSG] [Tue Apr 22 17:03:16 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/blimps.pm'
[MSG] [Tue Apr 22 17:03:16 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/blimps_block.pm'
[MSG] [Tue Apr 22 17:03:17 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/blimps_matrix.pm'
[MSG] [Tue Apr 22 17:03:17 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/boxshade.pm'
[MSG] [Tue Apr 22 17:03:17 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/btwisted.pm'
[MSG] [Tue Apr 22 17:03:17 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/cai.pm'
[MSG] [Tue Apr 22 17:03:17 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/cap.pm'
[MSG] [Tue Apr 22 17:03:17 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/cds.pm'
[MSG] [Tue Apr 22 17:03:17 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/chaos.pm'
[MSG] [Tue Apr 22 17:03:17 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/charge.pm'
[MSG] [Tue Apr 22 17:03:17 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/checktrans.pm'
[MSG] [Tue Apr 22 17:03:17 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/chips.pm'
[MSG] [Tue Apr 22 17:03:17 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/cirdna.pm'
[MSG] [Tue Apr 22 17:03:17 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/clique.pm'
[MSG] [Tue Apr 22 17:03:17 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/clustalw.pm'
[MSG] [Tue Apr 22 17:03:17 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/clustalw_convert.pm'
[MSG] [Tue Apr 22 17:03:17 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/codcmp.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/coderet.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/codnocod.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/codontree.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/codonw.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/comalign.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/combat.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/compseq.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/con_filter.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/confmat.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/cons.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/consense.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/consensus.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/cpgplot.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/cpgreport.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/cusp.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/cutseq.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dan.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dca.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/decorate.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/degapseq.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/descseq.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dialign2.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/diffseq.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/digest.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/distmat.pm'
[MSG] [Tue Apr 22 17:03:18 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/distquart.pm'
[MSG] [Tue Apr 22 17:03:19 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dnadist.pm'
[MSG] [Tue Apr 22 17:03:19 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dnapars.pm'
[MSG] [Tue Apr 22 17:03:19 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dollop.pm'
[MSG] [Tue Apr 22 17:03:19 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/domainer.pm'
[MSG] [Tue Apr 22 17:03:19 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dotmatcher.pm'
[MSG] [Tue Apr 22 17:03:19 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dotpath.pm'
[MSG] [Tue Apr 22 17:03:19 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dottup.pm'
[MSG] [Tue Apr 22 17:03:19 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/drawgram.pm'
[MSG] [Tue Apr 22 17:03:19 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/drawpyr.pm'
[MSG] [Tue Apr 22 17:03:19 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/drawtree.pm'
[MSG] [Tue Apr 22 17:03:19 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dreg.pm'
[MSG] [Tue Apr 22 17:03:19 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/druid.pm'
[MSG] [Tue Apr 22 17:03:19 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dsc.pm'
[MSG] [Tue Apr 22 17:03:19 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/dssp.pm'
[MSG] [Tue Apr 22 17:03:19 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/einverted.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/emma.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/emowse.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/environ.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/eprimer3.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/equicktandem.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/est2genome.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/etandem.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/extractfeat.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/extractseq.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/fasta.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/fastdnaml.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/fastrna.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/filtersites.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/findkm.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/fitch.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/fmtseq.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/freak.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/fuzznuc.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/fuzzpro.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/fuzztran.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/gb2xml.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/geecee.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/genscan.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/getblock.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/getorf.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/gff2ps.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/gibbs.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/gibbs_scan.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/golden.pm'
[MSG] [Tue Apr 22 17:03:20 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/grailclnt.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/gruppi.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/helixturnhelix.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmalign.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmbuild.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmcalibrate.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmconvert.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmemit.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmer2sam.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmfetch.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmpfam.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmscore.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmmsearch.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/hmoment.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/homology.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/html4blast.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/iep.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/infoalign.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/infoseq.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/interface.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/isochore.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/kitsch.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/lassap.pm'
[MSG] [Tue Apr 22 17:03:21 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/lgicsearch.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/lindna.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/listor.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/loadseq.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/lvb.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/makehist.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/map.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/marscan.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/maskfeat.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/maskseq.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/matcher.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/megamerger.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/melting.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/merger.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/mfold.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/mix.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/modelfromalign.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/most.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/mreps.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/msa.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/msbar.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/mspcrunch.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/mview_alig.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/mview_blast.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/mwfilter.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/needle.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/neighbor.pm'
[MSG] [Tue Apr 22 17:03:22 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/newcpgreport.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/newcpgseek.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/newseq.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/njdist.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/nnssp.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/notseq.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/nrscope.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/nthseq.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/octanol.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/oddcomp.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/palindrome.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pam.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/parciquart.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pars.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pasteseq.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/patmatdb.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/patmatmotifs.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/patser.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pdbsearch.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pepcoil.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pepinfo.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pepnet.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pepstats.pm'
[MSG] [Tue Apr 22 17:03:23 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pepwheel.pm'
[MSG] [Tue Apr 22 17:03:24 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pepwindow.pm'
[MSG] [Tue Apr 22 17:03:24 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pepwindowall.pm'
[MSG] [Tue Apr 22 17:03:24 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pestfind.pm'
[MSG] [Tue Apr 22 17:03:24 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pftools.pm'
[MSG] [Tue Apr 22 17:03:24 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/phiblast.pm'
[MSG] [Tue Apr 22 17:03:24 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pima.pm'
[MSG] [Tue Apr 22 17:03:24 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/plotcon.pm'
[MSG] [Tue Apr 22 17:03:24 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/plotorf.pm'
[MSG] [Tue Apr 22 17:03:24 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/plsearch.pm'
[MSG] [Tue Apr 22 17:03:24 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/polydot.pm'
[MSG] [Tue Apr 22 17:03:24 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pratt.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/predator.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/preg.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/prettyalign.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/prettyplot.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/prettyseq.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/primersearch.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/primo.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/prodom.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/profit.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/prophecy.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/prophet.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/prose.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/prot_nucml.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/protal2dna.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/protdist.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pscan.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/protpars.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/psiblast.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/psort2.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pyramids.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/pyreval.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/qstar.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/quicktree.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/readnexus.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/readseq.pm'
[MSG] [Tue Apr 22 17:03:25 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/recoder.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/redata.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/remap.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/repeats.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/restover.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/restrict.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/revseq.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/rnadistance.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/rnaeval.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/rnafold.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/rnaga.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/rnaheat.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/rnainverse.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/rnapdist.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/rnasubopt.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/sam2hmmer.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/sampleseqs.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/saps.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/satellites.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/scan_for_matches.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/scope.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/scopparse.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/seqboot.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/seqgen.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/seqmatchall.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/seqsblast.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/seqstat.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/showalign.pm'
[MSG] [Tue Apr 22 17:03:26 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/showfeat.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/showorf.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/showseq.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/shuffleseq.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/sigcleave.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/siggen.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/sigscan.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/silent.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/sirna.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/splitter.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/sreformat.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/stretcher.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/stride.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/stssearch.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/supermatcher.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/syco.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/tacg.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/tfscan.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/tipdate.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/tmap.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/toppred.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/tranalign.pm'
[MSG] [Tue Apr 22 17:03:27 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/transeq.pm'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/treealign.pm'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/trimest.pm'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/trimseq.pm'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/trnascan.pm'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/twofeat.pm'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/unroot.pm'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/vectorstrip.pm'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/water.pm'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/weighbor.pm'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/whichdb.pm'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/wise2.pm'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/wobble.pm'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/wordcount.pm'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/wordmatch.pm'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/wublast2.pm'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/xblast.pm'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/Bio/Tools/Run/PiseApplication/xpound.pm'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/t/'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/t/data/'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/t/data/FootPrinter.seq.fa'
[MSG] [Tue Apr 22 17:03:28 2008] Extracted 'bioperl-run-1.4/t/data/Genscan.FastA'
[MSG] [Tue Apr 22 17:03:29 2008] Extracted 'bioperl-run-1.4/t/data/NM_002254.gb'
[MSG] [Tue Apr 22 17:03:29 2008] Extracted 'bioperl-run-1.4/t/data/Primer3.fa'
[MSG] [Tue Apr 22 17:03:29 2008] Extracted 'bioperl-run-1.4/t/data/Prints_prot.FastA'
[MSG] [Tue Apr 22 17:03:29 2008] Extracted 'bioperl-run-1.4/t/data/TribeMCL.bls'
[MSG] [Tue Apr 22 17:03:29 2008] Extracted 'bioperl-run-1.4/t/data/TribeMCL.desc'
[MSG] [Tue Apr 22 17:03:29 2008] Extracted 'bioperl-run-1.4/t/data/amino.fa'
[MSG] [Tue Apr 22 17:03:29 2008] Extracted 'bioperl-run-1.4/t/data/blat_dna.fa'
[MSG] [Tue Apr 22 17:03:29 2008] Extracted 'bioperl-run-1.4/t/data/cel-cbr-fam.aln'
[MSG] [Tue Apr 22 17:03:29 2008] Extracted 'bioperl-run-1.4/t/data/codeml.mlc'
[MSG] [Tue Apr 22 17:03:29 2008] Extracted 'bioperl-run-1.4/t/data/coil_protein_input'
[MSG] [Tue Apr 22 17:03:29 2008] Extracted 'bioperl-run-1.4/t/data/consense.treefile'
[MSG] [Tue Apr 22 17:03:29 2008] Extracted 'bioperl-run-1.4/t/data/cysprot.fa'
[MSG] [Tue Apr 22 17:03:29 2008] Extracted 'bioperl-run-1.4/t/data/cysprot.msf'
[MSG] [Tue Apr 22 17:03:29 2008] Extracted 'bioperl-run-1.4/t/data/cysprot1a.fa'
[MSG] [Tue Apr 22 17:03:29 2008] Extracted 'bioperl-run-1.4/t/data/cysprot1a.msf'
[MSG] [Tue Apr 22 17:03:29 2008] Extracted 'bioperl-run-1.4/t/data/cysprot1b.fa'
[MSG] [Tue Apr 22 17:03:29 2008] Extracted 'bioperl-run-1.4/t/data/cysprot1b.msf'
[MSG] [Tue Apr 22 17:03:29 2008] Extracted 'bioperl-run-1.4/t/data/dba1a.fa'
[MSG] [Tue Apr 22 17:03:29 2008] Extracted 'bioperl-run-1.4/t/data/dba1b.fa'
[MSG] [Tue Apr 22 17:03:30 2008] Extracted 'bioperl-run-1.4/t/data/dba2.fa'
[MSG] [Tue Apr 22 17:03:30 2008] Extracted 'bioperl-run-1.4/t/data/dna1.fa'
[MSG] [Tue Apr 22 17:03:30 2008] Extracted 'bioperl-run-1.4/t/data/dna2.fa'
[MSG] [Tue Apr 22 17:03:30 2008] Extracted 'bioperl-run-1.4/t/data/ecolitst.fa'
[MSG] [Tue Apr 22 17:03:30 2008] Extracted 'bioperl-run-1.4/t/data/eponine.fa'
[MSG] [Tue Apr 22 17:03:30 2008] Extracted 'bioperl-run-1.4/t/data/fasta.fa'
[MSG] [Tue Apr 22 17:03:30 2008] Extracted 'bioperl-run-1.4/t/data/fastalib.fa'
[MSG] [Tue Apr 22 17:03:30 2008] Extracted 'bioperl-run-1.4/t/data/fastaprot.fa'
[MSG] [Tue Apr 22 17:03:30 2008] Extracted 'bioperl-run-1.4/t/data/fontfile'
[MSG] [Tue Apr 22 17:03:30 2008] Extracted 'bioperl-run-1.4/t/data/gf-s85.phylip'
[MSG] [Tue Apr 22 17:03:30 2008] Extracted 'bioperl-run-1.4/t/data/hmmpfam_protein_input'
[MSG] [Tue Apr 22 17:03:30 2008] Extracted 'bioperl-run-1.4/t/data/lagan_dna.fa'
[MSG] [Tue Apr 22 17:03:30 2008] Extracted 'bioperl-run-1.4/t/data/neighbor.dist'
[MSG] [Tue Apr 22 17:03:30 2008] Extracted 'bioperl-run-1.4/t/data/new_dna.fa'
[MSG] [Tue Apr 22 17:03:30 2008] Extracted 'bioperl-run-1.4/t/data/new_pep.fa'
[MSG] [Tue Apr 22 17:03:30 2008] Extracted 'bioperl-run-1.4/t/data/pfam_sample_R11'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/data/primate_query.fa'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/data/primate_target.fa'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/data/prints.dat'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/data/profile_prot.FastA'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/data/prosite.dat'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/data/protpars.phy'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/data/ps1.fa'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/data/repeatmasker.fa'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/data/repeatmasker.fa.out'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/data/signalp_input_protein'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/data/sim4_cdna.fa'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/data/sim4_database.fa'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/data/sim4_genomic.fa'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/data/test.txt'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/data/test_prot.FastA'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/data/tree_of_life'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/data/treefile.example'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/data/vista.cls'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/data/vista.gff'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/AnalysisFactory_soap.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/Analysis_soap.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/Blat.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/Clustalw.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/Coil.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/Consense.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/DBA.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/DrawGram.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/DrawTree.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/EMBOSS.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/Eponine.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/FootPrinter.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/Genewise.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/Genscan.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/Hmmer.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/Hmmpfam.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/Lagan.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/Mdust.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/Molphy.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/Neighbor.t'
[MSG] [Tue Apr 22 17:03:31 2008] Extracted 'bioperl-run-1.4/t/PAML.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/t/Pise.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/t/Primate.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/t/Primer3.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/t/Prints.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/t/Profile.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/t/Promoterwise.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/t/ProtDist.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/t/ProtPars.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/t/Pseudowise.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/t/RepeatMasker.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/t/Seg.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/t/SeqBoot.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/t/Signalp.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/t/Sim4.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/t/StandAloneFasta.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/t/TCoffee.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/t/Tmhmm.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/t/TribeMCL.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/t/Vista.t'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/INSTALL.PROGRAMS'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/MANIFEST.SKIP'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/README'
[MSG] [Tue Apr 22 17:03:32 2008] Extracted 'bioperl-run-1.4/examples/'
[MSG] [Tue Apr 22 17:03:33 2008] Extracted 'bioperl-run-1.4/examples/pise/'
[MSG] [Tue Apr 22 17:03:33 2008] Extracted 'bioperl-run-1.4/examples/pise/blast-kun.pl'
[MSG] [Tue Apr 22 17:03:33 2008] Extracted 'bioperl-run-1.4/examples/pise/blast2.pl'
[MSG] [Tue Apr 22 17:03:33 2008] Extracted 'bioperl-run-1.4/examples/pise/clustalw.pl'
[MSG] [Tue Apr 22 17:03:33 2008] Extracted 'bioperl-run-1.4/examples/pise/dnadist.data'
[MSG] [Tue Apr 22 17:03:33 2008] Extracted 'bioperl-run-1.4/examples/pise/dnadist.pl'
[MSG] [Tue Apr 22 17:03:33 2008] Extracted 'bioperl-run-1.4/examples/pise/genscan.pl'
[MSG] [Tue Apr 22 17:03:33 2008] Extracted 'bioperl-run-1.4/examples/pise/needle.pl'
[MSG] [Tue Apr 22 17:03:33 2008] Extracted 'bioperl-run-1.4/examples/pise/phylo-kun.pl'
[MSG] [Tue Apr 22 17:03:33 2008] Extracted 'bioperl-run-1.4/examples/pise/toppred.pl'
[MSG] [Tue Apr 22 17:03:33 2008] Extracted 'bioperl-run-1.4/scripts/'
[MSG] [Tue Apr 22 17:03:33 2008] Extracted 'bioperl-run-1.4/scripts/panalysis.PLS'
[MSG] [Tue Apr 22 17:03:33 2008] Extracted 'bioperl-run-1.4/scripts/papplmaker.PLS'
[MSG] [Tue Apr 22 17:03:33 2008] Extracted 'bioperl-run-1.4/scripts/run_neighbor.PLS'
[MSG] [Tue Apr 22 17:03:33 2008] Extracted 'bioperl-run-1.4/scripts/run_protdist.PLS'
[MSG] [Tue Apr 22 17:03:33 2008] Extracted 'bioperl-run-1.4/MANIFEST'
[MSG] [Tue Apr 22 17:03:34 2008] Extracted 'Bio::Factory::EMBOSS' to '/home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4'
[MSG] [Tue Apr 22 17:03:39 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 HTML::Parser, HTML Parser,
is not installed on this computer.
The Pise::Job module in bioperl-run needs it for Pise Applications
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] [Tue Apr 22 17:03:39 2008] DEFAULT 'filter_prereqs' HANDLER RETURNING 'sub return value'
[MSG] [Tue Apr 22 17:04:33 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] [Tue Apr 22 17:04:53 2008] MAKE TEST failed: Illegal seek PERL_DL_NONLAZY=1 /home/chris/perl5.10.0/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
t/AnalysisFactory_soap......SOAP::Lite not installed. Skipping some tests.
ok
t/Blat......................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Alignment/Blat.pm line 60.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
Failed 11/11 subtests
t/Clustalw..................Can't locate Bio/Seq.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Alignment/Clustalw.pm line 321.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
Failed 9/9 subtests
t/Coil......................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Coil.pm line 69.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
All 4 subtests passed
(less 4 skipped subtests: 0 okay)
t/Consense..................IO::String not installed. Skipping tests 1 to 7.
ok
t/DBA.......................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Alignment/DBA.pm line 81.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
Failed 15/15 subtests
t/DrawGram..................Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm line 85.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm line 85.
Compilation failed in require at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm line 76.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
Failed 4/4 subtests
t/DrawTree..................Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm line 85.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm line 85.
Compilation failed in require at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm line 76.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
Failed 4/4 subtests
t/EMBOSS....................Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Factory/EMBOSS.pm line 102.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
Failed 30/30 subtests
t/Eponine...................Can't locate Bio/Tools/Eponine.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Eponine.pm line 91.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
All 5 subtests passed
t/FootPrinter...............Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/FootPrinter.pm line 164.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
Failed 18/18 subtests
t/Genewise..................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Genewise.pm line 92.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
Failed 13/13 subtests
t/Genscan...................Can't locate Bio/Seq.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Genscan.pm line 66.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
All 4 subtests passed
(less 4 skipped subtests: 0 okay)
t/Hmmer.....................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Hmmer.pm line 91.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
All 17 subtests passed
(less 17 skipped subtests: 0 okay)
t/Hmmpfam...................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Hmmpfam.pm line 85.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
All 8 subtests passed
(less 8 skipped subtests: 0 okay)
t/Lagan.....................Can't locate Bio/AlignIO.pm in @INC (@INC contains: /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at t/Lagan.t line 6.
BEGIN failed--compilation aborted at t/Lagan.t line 6.
Dubious, test returned 2 (wstat 512, 0x200)
No subtests run
t/Mdust.....................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Mdust.pm line 87.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
Failed 2/2 subtests
t/Molphy....................IO::String not installed. Skipping tests 1 to 7.
ok
t/Neighbor..................Can't locate Bio/SimpleAlign.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm line 211.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
Failed 14/14 subtests
t/PAML......................IO::String not installed. Skipping tests 1 to 17.
ok
t/Pise......................Need XML::Parser::PerlSA to run test, skipping test
ok
t/Primate...................Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Primate.pm line 73.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
All 6 subtests passed
(less 6 skipped subtests: 0 okay)
t/Primer3...................Can't locate Bio/Root/Root.pm in @INC (@INC contains: t .. /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Primer3.pm line 132.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
All 7 subtests passed
(less 7 skipped subtests: 0 okay)
t/Prints....................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Prints.pm line 63.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
All 5 subtests passed
(less 5 skipped subtests: 0 okay)
t/Profile...................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Profile.pm line 65.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
All 5 subtests passed
(less 5 skipped subtests: 0 okay)
t/Promoterwise..............Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Promoterwise.pm line 87.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
Failed 8/8 subtests
t/ProtDist..................Can't locate Bio/SimpleAlign.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm line 211.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
Failed 11/11 subtests
t/ProtPars..................Can't locate Bio/SimpleAlign.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm line 130.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
Failed 7/7 subtests
t/Pseudowise................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/Pseudowise.pm line 67.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
All 13 subtests passed
(less 13 skipped subtests: 0 okay)
t/RepeatMasker..............Can't locate Bio/SeqFeature/Generic.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /home/chris/perl5.10.0/lib/site_perl/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/site_perl/5.10.0 .) at /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib/Bio/Tools/Run/RepeatMasker.pm line 85.
BEGIN failed--compilation aborted at /home/chris/perl5.10.0/.cpanplus/5.10.0/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 2 (wstat 512, 0x200)
Failed 8/8 subtests
t/Seg.......................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/lib /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib/arch /home/chris/perl5.10.0/.cpanplus/5.10.0/build/bioperl-run-1.4/blib /home/chris/perl5.10.0/lib/5.10.0/OpenBSD.i386-openbsd-thread-multi-64int /home/chris/perl5.10.0/lib/5.10.0 /ho