Generated sub tests. go make show_tests to see available subtests 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.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::filtersites.3 Manifying blib/man3/Bio::Tools::Run::EMBOSSacd.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::protal2dna.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::confmat.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::sam2hmmer.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::primo.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::domainer.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnainverse.3 Manifying blib/man3/Bio::Tools::Run::Alignment::StandAloneFasta.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::wordmatch.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::fuzzpro.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::distquart.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::whichdb.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::fmtseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::newcpgreport.3 Manifying blib/man3/Bio::Tools::Run::AnalysisFactory.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::blimps_matrix.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::redata.3 Manifying blib/man3/Bio::Tools::Run::AnalysisFactory::Pise.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::pscan.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::predator.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::tipdate.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::extractfeat.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::most.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepinfo.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::golden.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::dotmatcher.3 Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::Neighbor.3 Manifying blib/man3/Bio::Tools::Run::AnalysisFactory::soap.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::wobble.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::silent.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::abiview.3 Manifying blib/man3/Bio::Tools::Run::Hmmer.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::maskseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::btwisted.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::restover.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::assp.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::supermatcher.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::iep.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::showalign.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::repeats.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::xblast.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::lassap.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::interface.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::emowse.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::con_filter.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::grailclnt.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::fitch.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::emma.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::unroot.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::splitter.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::sigcleave.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::environ.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::newseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::xpound.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::prophecy.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::dotpath.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::chips.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::map.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::maskfeat.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::weighbor.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::showfeat.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::lvb.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::kitsch.3 Manifying blib/man3/Bio::Tools::Run::Alignment::Lagan.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::msbar.3 Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::DrawGram.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::seqgen.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::bl2seq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::pasteseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::dan.3 Manifying blib/man3/Bio::Tools::Run::Seg.3 Manifying blib/man3/Bio::Tools::Run::RepeatMasker.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::listor.3 Manifying blib/man3/Bio::Tools::Run::Genewise.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::tacg.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::polydot.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmalign.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::sreformat.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::wordcount.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::prettyplot.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::siggen.3 Manifying blib/man3/Bio::Tools::Run::Primer3.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::needle.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::cutseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::findkm.3 Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::pam.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::prettyseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::transeq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::combat.3 Manifying blib/man3/Bio::Tools::Run::PiseJobParser.3 Manifying blib/man3/Bio::Tools::Run::PiseWorkflow.3 Manifying blib/man3/Bio::Tools::Run::Alignment::DBA.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::restrict.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::patser.3 Manifying blib/man3/Bio::Tools::Run::Primate.3 Manifying blib/man3/Bio::Tools::Run::Alignment::Blat.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmsearch.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::mreps.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmpfam.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::revseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnaga.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::blimps.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::gruppi.3 Manifying blib/man3/Bio::Tools::Run::Analysis.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::lindna.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnaeval.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::palindrome.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::dnadist.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::stride.3 Manifying blib/man3/Bio::Tools::Run::Hmmpfam.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepcoil.3 Manifying blib/man3/Bio::Tools::Run::Alignment::Clustalw.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::clustalw.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::gibbs_scan.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::sigscan.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::modelfromalign.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmemit.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::treealign.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::toppred.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::wise2.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::fastdnaml.3 Manifying blib/man3/Bio::Tools::Run::TribeMCL.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::dca.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::vectorstrip.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::prodom.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::tranalign.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::njdist.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::charge.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmscore.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmfetch.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::etandem.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::backtranseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmconvert.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::est2genome.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::prot_nucml.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnaheat.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::gibbs.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::codcmp.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::bionj.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::comalign.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnasubopt.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::qstar.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::preg.3 Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::Base.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::mview_blast.3 Manifying blib/man3/Bio::Tools::Run::Phylo::PAML::Yn00.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmoment.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::nnssp.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::trimseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::matcher.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::CSR.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::boxshade.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::consense.3 Manifying blib/man3/Bio::Tools::Run::PiseJob.3 Manifying blib/man3/Bio::Tools::Run::Phylo::Molphy::ProtML.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::dsc.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::einverted.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::newcpgseek.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::clustalw_convert.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::drawtree.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::nrscope.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::octanol.3 Manifying blib/man3/Bio::Tools::Run::Alignment::Sim4.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::bambe.3 Manifying blib/man3/Bio::Tools::Run::FootPrinter.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::syco.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::pratt.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::gff2ps.3 Manifying blib/man3/Bio::Tools::Run::Phylo::PAML::Codeml.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::tmap.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepwindow.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::checktrans.3 Manifying blib/man3/Bio::Tools::Run::Genscan.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::protpars.3 Manifying blib/man3/Bio::Tools::Run::Analysis::soap.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::notseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::blimps_block.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::protdist.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::seqstat.3 Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::PhylipConf.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::equicktandem.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::infoalign.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::trimest.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::pyreval.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::trnascan.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::recoder.3 Manifying blib/man3/Bio::Tools::Run::Coil.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::seqsblast.3 Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::ProtPars.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::patmatmotifs.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::geecee.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::druid.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::patmatdb.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::seqboot.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::dnapars.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::cpgreport.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::plsearch.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::biosed.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmcalibrate.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::neighbor.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::wublast2.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::dollop.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::gb2xml.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::pdbsearch.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepstats.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::loadseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::prettyalign.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::cusp.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::mix.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::banana.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::dottup.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::scopparse.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::alistat.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::msa.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::drawgram.3 Manifying blib/man3/Bio::Tools::Run::Alignment::TCoffee.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::coderet.3 Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::ProtDist.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::codnocod.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::oddcomp.3 Manifying blib/man3/Bio::Tools::Run::EMBOSSApplication.3 Manifying blib/man3/Bio::Tools::Run::Signalp.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::cirdna.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::lgicsearch.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::consensus.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::helixturnhelix.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::getblock.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::diffseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::sampleseqs.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::codontree.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepnet.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::scope.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnapdist.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::water.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::parciquart.3 Manifying blib/man3/Bio::Tools::Run::Mdust.3 Manifying blib/man3/Bio::Factory::EMBOSS.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmbuild.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::align2model.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::cons.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnadistance.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::marscan.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::pars.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::homology.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::pima.3 Manifying blib/man3/Bio::Tools::Run::Profile.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::tfscan.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::mfold.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::antigenic.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::sirna.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::hmmer2sam.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::plotorf.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::descseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::codonw.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::html4blast.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::megamerger.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::phiblast.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::nthseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::dreg.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::fuzznuc.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::fasta.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::melting.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::distmat.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::drawpyr.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::showorf.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::cai.3 Manifying blib/man3/Bio::Tools::Run::Pseudowise.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::fuzztran.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepwindowall.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::degapseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::readseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::freak.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::primersearch.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::scan_for_matches.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::pftools.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::dialign2.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::seqmatchall.3 Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::DrawTree.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::quicktree.3 Manifying blib/man3/Bio::Tools::Run::Prints.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::pestfind.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::cds.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::extractseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::fastrna.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::genscan.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::getorf.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::dssp.3 Manifying blib/man3/Bio::Tools::Run::Vista.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::mwfilter.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::psiblast.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::showseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::eprimer3.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::infoseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::prose.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::pyramids.3 Manifying blib/man3/Bio::Tools::Run::Eponine.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::twofeat.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::rnafold.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::clique.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::addquart.3 Manifying blib/man3/Bio::Tools::Run::Promoterwise.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::blast2.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::satellites.3 Manifying blib/man3/Bio::Tools::Run::Phylo::Phylip::Consense.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::profit.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::plotcon.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::stretcher.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::makehist.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::digest.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::decorate.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::merger.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::psort2.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::saps.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::prophet.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::cap.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::mview_alig.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::readnexus.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::cpgplot.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::chaos.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::mspcrunch.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::remap.3 Manifying blib/man3/Bio::Tools::Run::Tmhmm.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::compseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::pepwheel.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::shuffleseq.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::isochore.3 Manifying blib/man3/Bio::Tools::Run::PiseApplication::Puzzle.3 PERL_DL_NONLAZY=1 /Users/cpanrun/pristine/5.8.7/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/Analysis_soap...........# Failed test 2 in t/Analysis_soap.t at line 66 # t/Analysis_soap.t line 66 is: print sprintf ($format, 'new ...Analysis (-name=>seqret) '); skip ($serror, defined $seqret); FAILED test 2 Failed 1/17 tests, 94.12% okay (less 15 skipped tests: 1 okay, 5.88%) t/AnalysisFactory_soap....# Failed test 2 in t/AnalysisFactory_soap.t at line 55 # t/AnalysisFactory_soap.t line 55 is: print sprintf ($format, 'new Bio::Tools::Run::AnalysisFactory '); skip ($serror, defined $factory); # Failed test 3 in t/AnalysisFactory_soap.t at line 61 # t/AnalysisFactory_soap.t line 61 is: print sprintf ($format, 'new with an explicit access '); skip ($serror, defined $factory_tmp); Use of uninitialized value in concatenation (.) or string at t/AnalysisFactory_soap.t line 93. Warning: (Probably) couldn't connect to . Can't call method "available_categories" on an undefined value at t/AnalysisFactory_soap.t line 80. FAILED tests 2-3 Failed 2/8 tests, 75.00% okay (less 4 skipped tests: 2 okay, 25.00%) t/Blat....................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Alignment/Blat.pm line 60. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Alignment/Blat.pm line 60. Compilation failed in require at t/Blat.t line 24. BEGIN failed--compilation aborted at t/Blat.t line 24. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-11 Failed 11/11 tests, 0.00% okay t/Clustalw................Can't locate Bio/Seq.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Alignment/Clustalw.pm line 321. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Alignment/Clustalw.pm line 321. Compilation failed in require at t/Clustalw.t line 17. BEGIN failed--compilation aborted at t/Clustalw.t line 17. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-9 Failed 9/9 tests, 0.00% okay t/Coil....................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Coil.pm line 69. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Coil.pm line 69. Compilation failed in require at t/Coil.t line 22. BEGIN failed--compilation aborted at t/Coil.t line 22. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/Consense................Can't locate Bio/SimpleAlign.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm line 183. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/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. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-7 Failed 7/7 tests, 0.00% okay t/DBA.....................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Alignment/DBA.pm line 81. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Alignment/DBA.pm line 81. Compilation failed in require at t/DBA.t line 16. BEGIN failed--compilation aborted at t/DBA.t line 16. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-15 Failed 15/15 tests, 0.00% okay t/DrawGram................Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm line 85. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm line 85. Compilation failed in require at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm line 76. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm line 76. Compilation failed in require at t/DrawGram.t line 20. BEGIN failed--compilation aborted at t/DrawGram.t line 20. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-4 Failed 4/4 tests, 0.00% okay t/DrawTree................Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm line 85. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm line 85. Compilation failed in require at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm line 76. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm line 76. Compilation failed in require at t/DrawTree.t line 20. BEGIN failed--compilation aborted at t/DrawTree.t line 20. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-4 Failed 4/4 tests, 0.00% okay t/EMBOSS..................Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Factory/EMBOSS.pm line 102. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Factory/EMBOSS.pm line 102. Compilation failed in require at t/EMBOSS.t line 23. BEGIN failed--compilation aborted at t/EMBOSS.t line 23. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-30 Failed 30/30 tests, 0.00% okay t/Eponine.................Can't locate Bio/Tools/Eponine.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Eponine.pm line 91. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Eponine.pm line 91. Compilation failed in require at t/Eponine.t line 25. BEGIN failed--compilation aborted at t/Eponine.t line 25. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/FootPrinter.............Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/FootPrinter.pm line 164. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/FootPrinter.pm line 164. Compilation failed in require at t/FootPrinter.t line 16. BEGIN failed--compilation aborted at t/FootPrinter.t line 16. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-18 Failed 18/18 tests, 0.00% okay t/Genewise................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Genewise.pm line 92. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Genewise.pm line 92. Compilation failed in require at t/Genewise.t line 16. BEGIN failed--compilation aborted at t/Genewise.t line 16. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-13 Failed 13/13 tests, 0.00% okay t/Genscan.................Can't locate Bio/Seq.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Genscan.pm line 66. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Genscan.pm line 66. Compilation failed in require at t/Genscan.t line 23. BEGIN failed--compilation aborted at t/Genscan.t line 23. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/Hmmer...................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Hmmer.pm line 91. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Hmmer.pm line 91. Compilation failed in require at t/Hmmer.t line 24. BEGIN failed--compilation aborted at t/Hmmer.t line 24. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/Hmmpfam.................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Hmmpfam.pm line 85. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Hmmpfam.pm line 85. Compilation failed in require at t/Hmmpfam.t line 23. BEGIN failed--compilation aborted at t/Hmmpfam.t line 23. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/Lagan...................Can't locate Bio/AlignIO.pm in @INC (@INC contains: /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at t/Lagan.t line 6. BEGIN failed--compilation aborted at t/Lagan.t line 6. dubious Test returned status 2 (wstat 512, 0x200) t/Mdust...................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Mdust.pm line 87. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Mdust.pm line 87. Compilation failed in require at t/Mdust.t line 17. BEGIN failed--compilation aborted at t/Mdust.t line 17. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-2 Failed 2/2 tests, 0.00% okay t/Molphy..................Can't locate Bio/Tools/Phylo/Molphy.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at t/Molphy.t line 46. BEGIN failed--compilation aborted at t/Molphy.t line 46. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-7 Failed 7/7 tests, 0.00% okay t/Neighbor................Can't locate Bio/SimpleAlign.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm line 211. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm line 211. Compilation failed in require at t/Neighbor.t line 19. BEGIN failed--compilation aborted at t/Neighbor.t line 19. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-14 Failed 14/14 tests, 0.00% okay t/PAML....................Can't locate Bio/Tools/Phylo/PAML.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at t/PAML.t line 54. BEGIN failed--compilation aborted at t/PAML.t line 54. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/Pise....................Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/AnalysisFactory/Pise.pm line 148. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/AnalysisFactory/Pise.pm line 148. Compilation failed in require at t/Pise.t line 34. BEGIN failed--compilation aborted at t/Pise.t line 34. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/Primate.................Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Primate.pm line 73. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Primate.pm line 73. Compilation failed in require at t/Primate.t line 43. BEGIN failed--compilation aborted at t/Primate.t line 43. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/Primer3.................Can't locate Bio/Root/Root.pm in @INC (@INC contains: t .. /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Primer3.pm line 132. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Primer3.pm line 132. Compilation failed in require at t/Primer3.t line 27. BEGIN failed--compilation aborted at t/Primer3.t line 27. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/Prints..................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Prints.pm line 63. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Prints.pm line 63. Compilation failed in require at t/Prints.t line 23. BEGIN failed--compilation aborted at t/Prints.t line 23. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/Profile.................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Profile.pm line 65. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Profile.pm line 65. Compilation failed in require at t/Profile.t line 23. BEGIN failed--compilation aborted at t/Profile.t line 23. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/Promoterwise............Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Promoterwise.pm line 87. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Promoterwise.pm line 87. Compilation failed in require at t/Promoterwise.t line 16. BEGIN failed--compilation aborted at t/Promoterwise.t line 16. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-8 Failed 8/8 tests, 0.00% okay t/ProtDist................Can't locate Bio/SimpleAlign.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm line 211. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm line 211. Compilation failed in require at t/ProtDist.t line 20. BEGIN failed--compilation aborted at t/ProtDist.t line 20. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-11 Failed 11/11 tests, 0.00% okay t/ProtPars................Can't locate Bio/SimpleAlign.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm line 130. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm line 130. Compilation failed in require at t/ProtPars.t line 20. BEGIN failed--compilation aborted at t/ProtPars.t line 20. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-7 Failed 7/7 tests, 0.00% okay t/Pseudowise..............Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Pseudowise.pm line 67. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Pseudowise.pm line 67. Compilation failed in require at t/Pseudowise.t line 23. BEGIN failed--compilation aborted at t/Pseudowise.t line 23. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/RepeatMasker............Can't locate Bio/SeqFeature/Generic.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/RepeatMasker.pm line 85. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/RepeatMasker.pm line 85. Compilation failed in require at t/RepeatMasker.t line 16. BEGIN failed--compilation aborted at t/RepeatMasker.t line 16. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-8 Failed 8/8 tests, 0.00% okay t/Seg.....................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Seg.pm line 65. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/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. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/SeqBoot.................Can't locate Bio/SimpleAlign.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm line 156. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/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. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-6 Failed 6/6 tests, 0.00% okay t/Signalp.................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Signalp.pm line 66. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/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. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/Sim4....................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Alignment/Sim4.pm line 89. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/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. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-20 Failed 20/20 tests, 0.00% okay t/StandAloneFasta.........Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm line 116. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/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. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/TCoffee.................Can't locate Bio/Seq.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Alignment/TCoffee.pm line 500. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/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. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-22 Failed 22/22 tests, 0.00% okay t/Tmhmm...................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Tmhmm.pm line 69. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/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. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully t/TribeMCL................Can't locate Bio/SeqIO.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/TribeMCL.pm line 153. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/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. dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-22 Failed 22/22 tests, 0.00% okay t/Vista...................Can't locate Bio/Root/Root.pm in @INC (@INC contains: t /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/arch /Users/cpanrun/depot/main/Apps/CPAN_Run/lib /Users/cpanrun/pristine/5.8.7/lib/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7/darwin-thread-multi-2level /Users/cpanrun/pristine/5.8.7/lib/site_perl/5.8.7 /Users/cpanrun/pristine/5.8.7/lib/site_perl .) at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/blib/lib/Bio/Tools/Run/Vista.pm line 125. BEGIN failed--compilation aborted at /Users/cpanrun/depot/main/contrib-patched/perl/CPAN/src/bioperl-run/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. dubious Test returned status 2 (wstat 512, 0x200) after all the subtests completed successfully Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/AnalysisFactory_soap.t 8 2 25.00% 2-3 t/Analysis_soap.t 17 1 5.88% 2 t/Blat.t 2 512 11 22 200.00% 1-11 t/Clustalw.t 2 512 9 18 200.00% 1-9 t/Coil.t 2 512 4 0 0.00% ?? t/Consense.t 2 512 7 14 200.00% 1-7 t/DBA.t 2 512 15 30 200.00% 1-15 t/DrawGram.t 2 512 4 8 200.00% 1-4 t/DrawTree.t 2 512 4 8 200.00% 1-4 t/EMBOSS.t 2 512 30 60 200.00% 1-30 t/Eponine.t 2 512 5 0 0.00% ?? t/FootPrinter.t 2 512 18 36 200.00% 1-18 t/Genewise.t 2 512 13 26 200.00% 1-13 t/Genscan.t 2 512 4 0 0.00% ?? t/Hmmer.t 2 512 17 0 0.00% ?? t/Hmmpfam.t 2 512 8 0 0.00% ?? t/Lagan.t 2 512 ?? ?? % ?? t/Mdust.t 2 512 2 4 200.00% 1-2 t/Molphy.t 2 512 7 14 200.00% 1-7 t/Neighbor.t 2 512 14 28 200.00% 1-14 t/PAML.t 2 512 17 0 0.00% ?? t/Pise.t 2 512 10 0 0.00% ?? t/Primate.t 2 512 6 0 0.00% ?? t/Primer3.t 2 512 7 0 0.00% ?? t/Prints.t 2 512 5 0 0.00% ?? t/Profile.t 2 512 5 0 0.00% ?? t/Promoterwise.t 2 512 8 16 200.00% 1-8 t/ProtDist.t 2 512 11 22 200.00% 1-11 t/ProtPars.t 2 512 7 14 200.00% 1-7 t/Pseudowise.t 2 512 13 0 0.00% ?? t/RepeatMasker.t 2 512 8 16 200.00% 1-8 t/Seg.t 2 512 6 0 0.00% ?? t/SeqBoot.t 2 512 6 12 200.00% 1-6 t/Signalp.t 2 512 5 0 0.00% ?? t/Sim4.t 2 512 20 40 200.00% 1-20 t/StandAloneFasta.t 2 512 15 0 0.00% ?? t/TCoffee.t 2 512 22 44 200.00% 1-22 t/Tmhmm.t 2 512 5 0 0.00% ?? t/TribeMCL.t 2 512 22 44 200.00% 1-22 t/Vista.t 2 512 5 0 0.00% ?? 146 subtests skipped. Failed 40/40 test scripts, 0.00% okay. 241/400 subtests failed, 39.75% okay. make: *** [test_dynamic] Error 2