CPAN: File::HomeDir loaded ok (v0.67)
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Going to read /var/root/.cpan/Metadata
  Database was generated on Tue, 12 Feb 2008 19:30:55 GMT
CPAN: LWP::UserAgent loaded ok (v2.036)
CPAN: Time::HiRes loaded ok (v1.65)

I would like to connect to one of the following sites to get 'authors/01mailrc.txt.gz':

 http://www.perl.org/CPAN/
 ftp://ftp.perl.org/pub/CPAN/

Is it OK to try to connect to the Internet? [yes] y
Fetching with LWP:
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  Database was generated on Mon, 03 Mar 2008 15:30:54 GMT
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Running install for module 'Bio::Factory::EMBOSS'
Running make for B/BI/BIRNEY/bioperl-run-1.4.tar.gz
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CPAN: Digest::SHA loaded ok (v5.45)
Fetching with LWP:
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Checksum for /var/root/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-run-1.4.tar.gz ok
bioperl-run-1.4/
bioperl-run-1.4/Makefile.PL
bioperl-run-1.4/AUTHORS
bioperl-run-1.4/Changes
bioperl-run-1.4/Bio/
bioperl-run-1.4/Bio/Factory/
bioperl-run-1.4/Bio/Factory/EMBOSS.pm
bioperl-run-1.4/Bio/Tools/
bioperl-run-1.4/Bio/Tools/Run/
bioperl-run-1.4/Bio/Tools/Run/Alignment/
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bioperl-run-1.4/Bio/Tools/Run/Alignment/Blat.pm
bioperl-run-1.4/Bio/Tools/Run/Alignment/Lagan.pm
bioperl-run-1.4/Bio/Tools/Run/Alignment/DBA.pm
bioperl-run-1.4/Bio/Tools/Run/Alignment/TCoffee.pm
bioperl-run-1.4/Bio/Tools/Run/Alignment/Sim4.pm
bioperl-run-1.4/Bio/Tools/Run/Alignment/StandAloneFasta.pm
bioperl-run-1.4/Bio/Tools/Run/Analysis.pm
bioperl-run-1.4/Bio/Tools/Run/AnalysisFactory.pm
bioperl-run-1.4/Bio/Tools/Run/Coil.pm
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bioperl-run-1.4/Bio/Tools/Run/EMBOSSacd.pm
bioperl-run-1.4/Bio/Tools/Run/Eponine.pm
bioperl-run-1.4/Bio/Tools/Run/FootPrinter.pm
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bioperl-run-1.4/Bio/Tools/Run/Genscan.pm
bioperl-run-1.4/Bio/Tools/Run/Hmmer.pm
bioperl-run-1.4/Bio/Tools/Run/Hmmpfam.pm
bioperl-run-1.4/Bio/Tools/Run/Mdust.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication.pm
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bioperl-run-1.4/Bio/Tools/Run/Analysis/
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bioperl-run-1.4/Bio/Tools/Run/AnalysisFactory/
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bioperl-run-1.4/Bio/Tools/Run/PiseApplication/rnainverse.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/rnapdist.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/rnasubopt.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/sam2hmmer.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/sampleseqs.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/saps.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/satellites.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/scan_for_matches.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/scope.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/scopparse.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/seqboot.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/seqgen.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/seqmatchall.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/seqsblast.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/seqstat.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/showalign.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/showfeat.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/showorf.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/showseq.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/shuffleseq.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/sigcleave.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/siggen.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/sigscan.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/silent.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/sirna.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/splitter.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/sreformat.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/stretcher.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/stride.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/stssearch.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/supermatcher.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/syco.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/tacg.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/tfscan.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/tipdate.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/tmap.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/toppred.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/tranalign.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/transeq.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/treealign.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/trimest.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/trimseq.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/trnascan.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/twofeat.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/unroot.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/vectorstrip.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/water.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/weighbor.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/whichdb.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/wise2.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/wobble.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/wordcount.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/wordmatch.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/wublast2.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/xblast.pm
bioperl-run-1.4/Bio/Tools/Run/PiseApplication/xpound.pm
bioperl-run-1.4/t/
bioperl-run-1.4/t/data/
bioperl-run-1.4/t/data/FootPrinter.seq.fa
bioperl-run-1.4/t/data/Genscan.FastA
bioperl-run-1.4/t/data/NM_002254.gb
bioperl-run-1.4/t/data/Primer3.fa
bioperl-run-1.4/t/data/Prints_prot.FastA
bioperl-run-1.4/t/data/TribeMCL.bls
bioperl-run-1.4/t/data/TribeMCL.desc
bioperl-run-1.4/t/data/amino.fa
bioperl-run-1.4/t/data/blat_dna.fa
bioperl-run-1.4/t/data/cel-cbr-fam.aln
bioperl-run-1.4/t/data/codeml.mlc
bioperl-run-1.4/t/data/coil_protein_input
bioperl-run-1.4/t/data/consense.treefile
bioperl-run-1.4/t/data/cysprot.fa
bioperl-run-1.4/t/data/cysprot.msf
bioperl-run-1.4/t/data/cysprot1a.fa
bioperl-run-1.4/t/data/cysprot1a.msf
bioperl-run-1.4/t/data/cysprot1b.fa
bioperl-run-1.4/t/data/cysprot1b.msf
bioperl-run-1.4/t/data/dba1a.fa
bioperl-run-1.4/t/data/dba1b.fa
bioperl-run-1.4/t/data/dba2.fa
bioperl-run-1.4/t/data/dna1.fa
bioperl-run-1.4/t/data/dna2.fa
bioperl-run-1.4/t/data/ecolitst.fa
bioperl-run-1.4/t/data/eponine.fa
bioperl-run-1.4/t/data/fasta.fa
bioperl-run-1.4/t/data/fastalib.fa
bioperl-run-1.4/t/data/fastaprot.fa
bioperl-run-1.4/t/data/fontfile
bioperl-run-1.4/t/data/gf-s85.phylip
bioperl-run-1.4/t/data/hmmpfam_protein_input
bioperl-run-1.4/t/data/lagan_dna.fa
bioperl-run-1.4/t/data/neighbor.dist
bioperl-run-1.4/t/data/new_dna.fa
bioperl-run-1.4/t/data/new_pep.fa
bioperl-run-1.4/t/data/pfam_sample_R11
bioperl-run-1.4/t/data/primate_query.fa
bioperl-run-1.4/t/data/primate_target.fa
bioperl-run-1.4/t/data/prints.dat
bioperl-run-1.4/t/data/profile_prot.FastA
bioperl-run-1.4/t/data/prosite.dat
bioperl-run-1.4/t/data/protpars.phy
bioperl-run-1.4/t/data/ps1.fa
bioperl-run-1.4/t/data/repeatmasker.fa
bioperl-run-1.4/t/data/repeatmasker.fa.out
bioperl-run-1.4/t/data/signalp_input_protein
bioperl-run-1.4/t/data/sim4_cdna.fa
bioperl-run-1.4/t/data/sim4_database.fa
bioperl-run-1.4/t/data/sim4_genomic.fa
bioperl-run-1.4/t/data/test.txt
bioperl-run-1.4/t/data/test_prot.FastA
bioperl-run-1.4/t/data/tree_of_life
bioperl-run-1.4/t/data/treefile.example
bioperl-run-1.4/t/data/vista.cls
bioperl-run-1.4/t/data/vista.gff
bioperl-run-1.4/t/AnalysisFactory_soap.t
bioperl-run-1.4/t/Analysis_soap.t
bioperl-run-1.4/t/Blat.t
bioperl-run-1.4/t/Clustalw.t
bioperl-run-1.4/t/Coil.t
bioperl-run-1.4/t/Consense.t
bioperl-run-1.4/t/DBA.t
bioperl-run-1.4/t/DrawGram.t
bioperl-run-1.4/t/DrawTree.t
bioperl-run-1.4/t/EMBOSS.t
bioperl-run-1.4/t/Eponine.t
bioperl-run-1.4/t/FootPrinter.t
bioperl-run-1.4/t/Genewise.t
bioperl-run-1.4/t/Genscan.t
bioperl-run-1.4/t/Hmmer.t
bioperl-run-1.4/t/Hmmpfam.t
bioperl-run-1.4/t/Lagan.t
bioperl-run-1.4/t/Mdust.t
bioperl-run-1.4/t/Molphy.t
bioperl-run-1.4/t/Neighbor.t
bioperl-run-1.4/t/PAML.t
bioperl-run-1.4/t/Pise.t
bioperl-run-1.4/t/Primate.t
bioperl-run-1.4/t/Primer3.t
bioperl-run-1.4/t/Prints.t
bioperl-run-1.4/t/Profile.t
bioperl-run-1.4/t/Promoterwise.t
bioperl-run-1.4/t/ProtDist.t
bioperl-run-1.4/t/ProtPars.t
bioperl-run-1.4/t/Pseudowise.t
bioperl-run-1.4/t/RepeatMasker.t
bioperl-run-1.4/t/Seg.t
bioperl-run-1.4/t/SeqBoot.t
bioperl-run-1.4/t/Signalp.t
bioperl-run-1.4/t/Sim4.t
bioperl-run-1.4/t/StandAloneFasta.t
bioperl-run-1.4/t/TCoffee.t
bioperl-run-1.4/t/Tmhmm.t
bioperl-run-1.4/t/TribeMCL.t
bioperl-run-1.4/t/Vista.t
bioperl-run-1.4/INSTALL.PROGRAMS
bioperl-run-1.4/MANIFEST.SKIP
bioperl-run-1.4/README
bioperl-run-1.4/examples/
bioperl-run-1.4/examples/pise/
bioperl-run-1.4/examples/pise/blast-kun.pl
bioperl-run-1.4/examples/pise/blast2.pl
bioperl-run-1.4/examples/pise/clustalw.pl
bioperl-run-1.4/examples/pise/dnadist.data
bioperl-run-1.4/examples/pise/dnadist.pl
bioperl-run-1.4/examples/pise/genscan.pl
bioperl-run-1.4/examples/pise/needle.pl
bioperl-run-1.4/examples/pise/phylo-kun.pl
bioperl-run-1.4/examples/pise/toppred.pl
bioperl-run-1.4/scripts/
bioperl-run-1.4/scripts/panalysis.PLS
bioperl-run-1.4/scripts/papplmaker.PLS
bioperl-run-1.4/scripts/run_neighbor.PLS
bioperl-run-1.4/scripts/run_protdist.PLS
bioperl-run-1.4/MANIFEST
CPAN: File::Temp loaded ok (v0.20)

  CPAN.pm: Going to build B/BI/BIRNEY/bioperl-run-1.4.tar.gz

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 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
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/CSR.pm blib/lib/Bio/Tools/Run/PiseApplication/CSR.pm
cp Bio/Tools/Run/PiseApplication.pm blib/lib/Bio/Tools/Run/PiseApplication.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/psiblast.pm blib/lib/Bio/Tools/Run/PiseApplication/psiblast.pm
cp Bio/Tools/Run/PiseApplication/mwfilter.pm blib/lib/Bio/Tools/Run/PiseApplication/mwfilter.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.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::filtersites.3pm
Manifying blib/man3/Bio::Tools::Run::EMBOSSacd.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::protal2dna.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::confmat.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::sam2hmmer.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::primo.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::domainer.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnainverse.3pm
Manifying blib/man3/Bio::Tools::Run::Alignment::StandAloneFasta.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::wordmatch.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::fuzzpro.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::distquart.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::whichdb.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::fmtseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::newcpgreport.3pm
Manifying blib/man3/Bio::Tools::Run::AnalysisFactory.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::blimps_matrix.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::redata.3pm
Manifying blib/man3/Bio::Tools::Run::AnalysisFactory::Pise.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pscan.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::predator.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::tipdate.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::extractfeat.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::most.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepinfo.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::golden.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dotmatcher.3pm
Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::Neighbor.3pm
Manifying blib/man3/Bio::Tools::Run::AnalysisFactory::soap.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::wobble.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::silent.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::abiview.3pm
Manifying blib/man3/Bio::Tools::Run::Hmmer.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::maskseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::btwisted.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::restover.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::assp.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::supermatcher.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::iep.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::showalign.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::repeats.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::xblast.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::lassap.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::interface.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::emowse.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::con_filter.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::grailclnt.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::fitch.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::emma.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::unroot.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::splitter.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::sigcleave.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::environ.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::newseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::xpound.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::prophecy.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dotpath.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::chips.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::map.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::maskfeat.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::weighbor.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::showfeat.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::lvb.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::kitsch.3pm
Manifying blib/man3/Bio::Tools::Run::Alignment::Lagan.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::msbar.3pm
Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::DrawGram.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::seqgen.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::bl2seq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pasteseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dan.3pm
Manifying blib/man3/Bio::Tools::Run::Seg.3pm
Manifying blib/man3/Bio::Tools::Run::RepeatMasker.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::listor.3pm
Manifying blib/man3/Bio::Tools::Run::Genewise.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::tacg.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::polydot.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmalign.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::sreformat.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::wordcount.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::prettyplot.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::siggen.3pm
Manifying blib/man3/Bio::Tools::Run::Primer3.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::needle.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::cutseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::findkm.3pm
Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pam.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::prettyseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::transeq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::combat.3pm
Manifying blib/man3/Bio::Tools::Run::PiseJobParser.3pm
Manifying blib/man3/Bio::Tools::Run::PiseWorkflow.3pm
Manifying blib/man3/Bio::Tools::Run::Alignment::DBA.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::restrict.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::patser.3pm
Manifying blib/man3/Bio::Tools::Run::Primate.3pm
Manifying blib/man3/Bio::Tools::Run::Alignment::Blat.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmsearch.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::mreps.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmpfam.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::revseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnaga.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::blimps.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::gruppi.3pm
Manifying blib/man3/Bio::Tools::Run::Analysis.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::lindna.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnaeval.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::palindrome.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dnadist.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::stride.3pm
Manifying blib/man3/Bio::Tools::Run::Hmmpfam.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepcoil.3pm
Manifying blib/man3/Bio::Tools::Run::Alignment::Clustalw.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::clustalw.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::gibbs_scan.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::sigscan.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::modelfromalign.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmemit.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::treealign.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::toppred.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::wise2.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::fastdnaml.3pm
Manifying blib/man3/Bio::Tools::Run::TribeMCL.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dca.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::vectorstrip.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::prodom.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::tranalign.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::njdist.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::charge.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmscore.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmfetch.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::etandem.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::backtranseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmconvert.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::est2genome.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::prot_nucml.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnaheat.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::gibbs.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::codcmp.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::bionj.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::comalign.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnasubopt.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::qstar.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::preg.3pm
Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::Base.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::mview_blast.3pm
Manifying blib/man3/Bio::Tools::Run::Phylo::PAML::Yn00.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmoment.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::nnssp.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::trimseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::matcher.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::CSR.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::boxshade.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::consense.3pm
Manifying blib/man3/Bio::Tools::Run::PiseJob.3pm
Manifying blib/man3/Bio::Tools::Run::Phylo::Molphy::ProtML.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dsc.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::einverted.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::newcpgseek.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::clustalw_convert.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::drawtree.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::nrscope.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::octanol.3pm
Manifying blib/man3/Bio::Tools::Run::Alignment::Sim4.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::bambe.3pm
Manifying blib/man3/Bio::Tools::Run::FootPrinter.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::syco.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pratt.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::gff2ps.3pm
Manifying blib/man3/Bio::Tools::Run::Phylo::PAML::Codeml.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::tmap.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepwindow.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::checktrans.3pm
Manifying blib/man3/Bio::Tools::Run::Genscan.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::protpars.3pm
Manifying blib/man3/Bio::Tools::Run::Analysis::soap.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::notseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::blimps_block.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::protdist.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::seqstat.3pm
Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::PhylipConf.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::equicktandem.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::infoalign.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::trimest.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pyreval.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::trnascan.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::recoder.3pm
Manifying blib/man3/Bio::Tools::Run::Coil.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::seqsblast.3pm
Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::ProtPars.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::patmatmotifs.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::geecee.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::druid.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::patmatdb.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::seqboot.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dnapars.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::cpgreport.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::plsearch.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::biosed.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmcalibrate.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::neighbor.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::wublast2.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dollop.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::gb2xml.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pdbsearch.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepstats.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::loadseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::prettyalign.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::cusp.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::mix.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::banana.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dottup.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::scopparse.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::alistat.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::msa.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::drawgram.3pm
Manifying blib/man3/Bio::Tools::Run::Alignment::TCoffee.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::coderet.3pm
Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::ProtDist.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::codnocod.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::oddcomp.3pm
Manifying blib/man3/Bio::Tools::Run::EMBOSSApplication.3pm
Manifying blib/man3/Bio::Tools::Run::Signalp.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::cirdna.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::lgicsearch.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::consensus.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::helixturnhelix.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::getblock.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::diffseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::sampleseqs.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::codontree.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepnet.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::scope.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnapdist.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::water.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::parciquart.3pm
Manifying blib/man3/Bio::Tools::Run::Mdust.3pm
Manifying blib/man3/Bio::Factory::EMBOSS.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmbuild.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::align2model.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::cons.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnadistance.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::marscan.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pars.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::homology.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pima.3pm
Manifying blib/man3/Bio::Tools::Run::Profile.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::tfscan.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::mfold.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::antigenic.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::sirna.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmer2sam.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::plotorf.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::descseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::codonw.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::html4blast.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::megamerger.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::phiblast.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::nthseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dreg.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::fuzznuc.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::fasta.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::melting.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::distmat.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::drawpyr.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::showorf.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::cai.3pm
Manifying blib/man3/Bio::Tools::Run::Pseudowise.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::fuzztran.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepwindowall.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::degapseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::readseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::freak.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::primersearch.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::scan_for_matches.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pftools.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dialign2.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::seqmatchall.3pm
Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::DrawTree.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::quicktree.3pm
Manifying blib/man3/Bio::Tools::Run::Prints.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pestfind.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::cds.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::extractseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::fastrna.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::genscan.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::getorf.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::dssp.3pm
Manifying blib/man3/Bio::Tools::Run::Vista.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::mwfilter.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::psiblast.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::showseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::eprimer3.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::infoseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::prose.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pyramids.3pm
Manifying blib/man3/Bio::Tools::Run::Eponine.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::twofeat.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnafold.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::clique.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::addquart.3pm
Manifying blib/man3/Bio::Tools::Run::Promoterwise.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::blast2.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::satellites.3pm
Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::Consense.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::profit.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::plotcon.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::stretcher.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::makehist.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::digest.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::decorate.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::merger.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::psort2.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::saps.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::prophet.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::cap.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::mview_alig.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::readnexus.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::cpgplot.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::chaos.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::mspcrunch.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::remap.3pm
Manifying blib/man3/Bio::Tools::Run::Tmhmm.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::compseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepwheel.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::shuffleseq.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::isochore.3pm
Manifying blib/man3/Bio::Tools::Run::PiseApplication::Puzzle.3pm
  BIRNEY/bioperl-run-1.4.tar.gz
  /usr/bin/make -- OK
Running make test
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/Analysis_soap.............1/17 SOAP::Lite not installed. Skipping some tests.
t/Analysis_soap.............ok     
t/AnalysisFactory_soap......1/8 SOAP::Lite not installed. Skipping some tests.
t/AnalysisFactory_soap......ok   
t/Blat......................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Alignment/Blat.pm line 60.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/Blat...................... Dubious, test returned 2 (wstat 512, 0x200)
 Failed 11/11 subtests 
t/Clustalw..................Can't locate Bio/Seq.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Alignment/Clustalw.pm line 321.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/Clustalw.................. Dubious, test returned 2 (wstat 512, 0x200)
 Failed 9/9 subtests 
t/Coil......................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Coil.pm line 69.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/Coil...................... Dubious, test returned 2 (wstat 512, 0x200)
 All 4 subtests passed 
        (less 4 skipped subtests: 0 okay)
t/Consense..................Can't locate Bio/SimpleAlign.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm line 183.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm line 183.
Compilation failed in require at t/Consense.t line 27.
BEGIN failed--compilation aborted at t/Consense.t line 27.
t/Consense.................. Dubious, test returned 2 (wstat 512, 0x200)
 Failed 7/7 subtests 
t/DBA.......................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Alignment/DBA.pm line 81.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/DBA....................... 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 /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm line 85.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm line 85.
Compilation failed in require at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm line 76.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/DrawGram.................. 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 /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm line 85.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm line 85.
Compilation failed in require at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm line 76.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/DrawTree.................. 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 /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Factory/EMBOSS.pm line 102.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/EMBOSS.................... 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 /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Eponine.pm line 91.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/Eponine................... 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 /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/FootPrinter.pm line 164.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/FootPrinter............... Dubious, test returned 2 (wstat 512, 0x200)
 Failed 18/18 subtests 
t/Genewise..................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Genewise.pm line 92.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/Genewise.................. Dubious, test returned 2 (wstat 512, 0x200)
 Failed 13/13 subtests 
t/Genscan...................1/4 Can't locate Bio/Seq.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Genscan.pm line 66.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/Genscan................... Dubious, test returned 2 (wstat 512, 0x200)
 All 4 subtests passed 
        (less 4 skipped subtests: 0 okay)
t/Hmmer.....................1/17 Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Hmmer.pm line 91.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/Hmmer..................... Dubious, test returned 2 (wstat 512, 0x200)
 All 17 subtests passed 
        (less 17 skipped subtests: 0 okay)
t/Hmmpfam...................1/8 Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Hmmpfam.pm line 85.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/Hmmpfam................... 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: /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at t/Lagan.t line 6.
BEGIN failed--compilation aborted at t/Lagan.t line 6.
t/Lagan..................... Dubious, test returned 2 (wstat 512, 0x200)
 No subtests run 
t/Mdust.....................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Mdust.pm line 87.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/Mdust..................... Dubious, test returned 2 (wstat 512, 0x200)
 Failed 2/2 subtests 
t/Molphy....................Can't locate Bio/Tools/Phylo/Molphy.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at t/Molphy.t line 46.
BEGIN failed--compilation aborted at t/Molphy.t line 46.
t/Molphy.................... Dubious, test returned 2 (wstat 512, 0x200)
 Failed 7/7 subtests 
t/Neighbor..................Can't locate Bio/SimpleAlign.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm line 211.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/Neighbor.................. Dubious, test returned 2 (wstat 512, 0x200)
 Failed 14/14 subtests 
t/PAML......................Can't locate Bio/Tools/Phylo/PAML.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at t/PAML.t line 54.
BEGIN failed--compilation aborted at t/PAML.t line 54.
t/PAML...................... Dubious, test returned 2 (wstat 512, 0x200)
 All 17 subtests passed 
        (less 17 skipped subtests: 0 okay)
t/Pise......................1/10 Need XML::Parser::PerlSA to run test, skipping test
t/Pise......................ok     
t/Primate...................1/6 Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Primate.pm line 73.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/Primate................... 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 .. /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Primer3.pm line 132.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/Primer3................... Dubious, test returned 2 (wstat 512, 0x200)
 All 7 subtests passed 
        (less 7 skipped subtests: 0 okay)
t/Prints....................1/5 Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Prints.pm line 63.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/Prints.................... 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 /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Profile.pm line 65.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/Profile................... 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 /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Promoterwise.pm line 87.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/Promoterwise.............. Dubious, test returned 2 (wstat 512, 0x200)
 Failed 8/8 subtests 
t/ProtDist..................Can't locate Bio/SimpleAlign.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm line 211.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/ProtDist.................. Dubious, test returned 2 (wstat 512, 0x200)
 Failed 11/11 subtests 
t/ProtPars..................Can't locate Bio/SimpleAlign.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm line 130.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/ProtPars.................. Dubious, test returned 2 (wstat 512, 0x200)
 Failed 7/7 subtests 
t/Pseudowise................1/13 Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Pseudowise.pm line 67.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/Pseudowise................ 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 /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/RepeatMasker.pm line 85.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/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.
t/RepeatMasker.............. Dubious, test returned 2 (wstat 512, 0x200)
 Failed 8/8 subtests 
t/Seg.......................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Seg.pm line 65.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Seg.pm line 65.
Compilation failed in require at t/Seg.t line 23.
BEGIN failed--compilation aborted at t/Seg.t line 23.
t/Seg....................... Dubious, test returned 2 (wstat 512, 0x200)
 All 6 subtests passed 
        (less 6 skipped subtests: 0 okay)
t/SeqBoot...................Can't locate Bio/SimpleAlign.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm line 156.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm line 156.
Compilation failed in require at t/SeqBoot.t line 20.
BEGIN failed--compilation aborted at t/SeqBoot.t line 20.
t/SeqBoot................... Dubious, test returned 2 (wstat 512, 0x200)
 Failed 6/6 subtests 
t/Signalp...................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Signalp.pm line 66.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Signalp.pm line 66.
Compilation failed in require at t/Signalp.t line 23.
BEGIN failed--compilation aborted at t/Signalp.t line 23.
t/Signalp................... Dubious, test returned 2 (wstat 512, 0x200)
 All 5 subtests passed 
        (less 5 skipped subtests: 0 okay)
t/Sim4......................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Alignment/Sim4.pm line 89.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Alignment/Sim4.pm line 89.
Compilation failed in require at t/Sim4.t line 16.
BEGIN failed--compilation aborted at t/Sim4.t line 16.
t/Sim4...................... Dubious, test returned 2 (wstat 512, 0x200)
 Failed 20/20 subtests 
t/StandAloneFasta...........Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm line 116.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm line 116.
Compilation failed in require at t/StandAloneFasta.t line 24.
BEGIN failed--compilation aborted at t/StandAloneFasta.t line 24.
t/StandAloneFasta........... Dubious, test returned 2 (wstat 512, 0x200)
 All 15 subtests passed 
        (less 15 skipped subtests: 0 okay)
t/TCoffee...................Can't locate Bio/Seq.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm line 500.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm line 500.
Compilation failed in require at t/TCoffee.t line 20.
BEGIN failed--compilation aborted at t/TCoffee.t line 20.
t/TCoffee................... Dubious, test returned 2 (wstat 512, 0x200)
 Failed 22/22 subtests 
t/Tmhmm.....................1/5 Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Tmhmm.pm line 69.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Tmhmm.pm line 69.
Compilation failed in require at t/Tmhmm.t line 23.
BEGIN failed--compilation aborted at t/Tmhmm.t line 23.
t/Tmhmm..................... Dubious, test returned 2 (wstat 512, 0x200)
 All 5 subtests passed 
        (less 5 skipped subtests: 0 okay)
t/TribeMCL..................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/TribeMCL.pm line 153.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/TribeMCL.pm line 153.
Compilation failed in require at t/TribeMCL.t line 17.
BEGIN failed--compilation aborted at t/TribeMCL.t line 17.
t/TribeMCL.................. Dubious, test returned 2 (wstat 512, 0x200)
 Failed 22/22 subtests 
t/Vista.....................Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/arch /System/Library/Perl/5.8.6/darwin-thread-multi-2level /System/Library/Perl/5.8.6 /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 /Library/Perl /Network/Library/Perl/5.8.6/darwin-thread-multi-2level /Network/Library/Perl/5.8.6 /Network/Library/Perl /System/Library/Perl/Extras/5.8.6/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.6 /Library/Perl/5.8.1 .) at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Vista.pm line 125.
BEGIN failed--compilation aborted at /private/var/root/.cpan/build/bioperl-run-1.4-hNJE01/blib/lib/Bio/Tools/Run/Vista.pm line 125.
Compilation failed in require at t/Vista.t line 26.
BEGIN failed--compilation aborted at t/Vista.t line 26.
t/Vista..................... Dubious, test returned 2 (wstat 512, 0x200)
 All 5 subtests passed 

Test Summary Report
-------------------
t/Blat.t                (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 11 tests but ran 0.
t/Clustalw.t            (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 9 tests but ran 0.
t/Coil.t                (Wstat: 512 Tests: 4 Failed: 0)
  Non-zero exit status: 2
t/Consense.t            (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 7 tests but ran 0.
t/DBA.t                 (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 15 tests but ran 0.
t/DrawGram.t            (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 4 tests but ran 0.
t/DrawTree.t            (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 4 tests but ran 0.
t/EMBOSS.t              (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 30 tests but ran 0.
t/Eponine.t             (Wstat: 512 Tests: 5 Failed: 0)
  Non-zero exit status: 2
t/FootPrinter.t         (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 18 tests but ran 0.
t/Genewise.t            (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 13 tests but ran 0.
t/Genscan.t             (Wstat: 512 Tests: 4 Failed: 0)
  Non-zero exit status: 2
t/Hmmer.t               (Wstat: 512 Tests: 17 Failed: 0)
  Non-zero exit status: 2
t/Hmmpfam.t             (Wstat: 512 Tests: 8 Failed: 0)
  Non-zero exit status: 2
t/Lagan.t               (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: No plan found in TAP output
t/Mdust.t               (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 2 tests but ran 0.
t/Molphy.t              (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 7 tests but ran 0.
t/Neighbor.t            (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 14 tests but ran 0.
t/PAML.t                (Wstat: 512 Tests: 17 Failed: 0)
  Non-zero exit status: 2
t/Primate.t             (Wstat: 512 Tests: 6 Failed: 0)
  Non-zero exit status: 2
t/Primer3.t             (Wstat: 512 Tests: 7 Failed: 0)
  Non-zero exit status: 2
t/Prints.t              (Wstat: 512 Tests: 5 Failed: 0)
  Non-zero exit status: 2
t/Profile.t             (Wstat: 512 Tests: 5 Failed: 0)
  Non-zero exit status: 2
t/Promoterwise.t        (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 8 tests but ran 0.
t/ProtDist.t            (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 11 tests but ran 0.
t/ProtPars.t            (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 7 tests but ran 0.
t/Pseudowise.t          (Wstat: 512 Tests: 13 Failed: 0)
  Non-zero exit status: 2
t/RepeatMasker.t        (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 8 tests but ran 0.
t/Seg.t                 (Wstat: 512 Tests: 6 Failed: 0)
  Non-zero exit status: 2
t/SeqBoot.t             (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 6 tests but ran 0.
t/Signalp.t             (Wstat: 512 Tests: 5 Failed: 0)
  Non-zero exit status: 2
t/Sim4.t                (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 20 tests but ran 0.
t/StandAloneFasta.t     (Wstat: 512 Tests: 15 Failed: 0)
  Non-zero exit status: 2
t/TCoffee.t             (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 22 tests but ran 0.
t/Tmhmm.t               (Wstat: 512 Tests: 5 Failed: 0)
  Non-zero exit status: 2
t/TribeMCL.t            (Wstat: 512 Tests: 0 Failed: 0)
  Non-zero exit status: 2
  Parse errors: Bad plan.  You planned 22 tests but ran 0.
t/Vista.t               (Wstat: 512 Tests: 5 Failed: 0)
  Non-zero exit status: 2
Files=40, Tests=162,  5 wallclock secs ( 0.36 usr  0.26 sys +  1.44 cusr  0.52 csys =  2.58 CPU)
Result: FAIL
Failed 37/40 test programs. 0/162 subtests failed.
make: *** [test_dynamic] Error 2
  BIRNEY/bioperl-run-1.4.tar.gz
  /usr/bin/make test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports BIRNEY/bioperl-run-1.4.tar.gz
Running make install
  make test had returned bad status, won't install without force