Errors

configure_prereq_matches_use

• Bio::Root::Build

extracts_nicely

expected BioPerl-run-1.6.1 but BioPerl-run-1.6.0 is found

no_pod_errors

BioPerl-run-1.6.0/Bio/Tools/Run/ERPIN.pm -- Around line 35: Non-ASCII character seen before =encoding in ''Ðumask'. Assuming CP1252

prereq_matches_use

• Bio::AlignIO
• Bio::AnalysisI
• Bio::Annotation::DBLink
• Bio::Annotation::SimpleValue
• Bio::Assembly::IO
• Bio::Cluster::SequenceFamily
• Bio::DB::EUtilities
• Bio::Factory::AnalysisI
• Bio::Factory::ApplicationFactoryI
• Bio::FeatureIO
• Bio::Map::Position
• Bio::Map::Prediction
• Bio::Matrix::IO
• Bio::Matrix::PhylipDist
• Bio::Root::IO
• Bio::Root::Root
• Bio::Search::HSP::GenericHSP
• Bio::SearchIO
• Bio::Seq
• Bio::SeqFeature::FeaturePair
• Bio::SeqFeature::Gene::Exon
• Bio::SeqFeature::Gene::GeneStructure
• Bio::SeqFeature::Gene::Transcript
• Bio::SeqFeature::Generic
• Bio::SeqIO
• Bio::SimpleAlign
• Bio::Species
• Bio::Tools::AnalysisResult
• Bio::Tools::Coil
• Bio::Tools::Eponine
• Bio::Tools::FootPrinter
• Bio::Tools::GFF
• Bio::Tools::Genemark
• Bio::Tools::Genewise
• Bio::Tools::Genscan
• Bio::Tools::Glimmer
• Bio::Tools::Match
• Bio::Tools::Phylo::Gerp
• Bio::Tools::Phylo::Gumby
• Bio::Tools::Phylo::Molphy
• Bio::Tools::Phylo::PAML
• Bio::Tools::Phylo::Phylip::ProtDist
• Bio::Tools::Primer3
• Bio::Tools::Prints
• Bio::Tools::Profile
• Bio::Tools::Promoterwise
• Bio::Tools::Pseudowise
• Bio::Tools::RepeatMasker
• Bio::Tools::Run::WrapperBase
• Bio::Tools::Seg
• Bio::Tools::Signalp
• Bio::Tools::Sim4::Results
• Bio::Tools::Tmhmm
• Bio::Tools::tRNAscanSE
• Bio::TreeIO
• Bio::WebAgent
• Clone
• HTTP::Request::Common
• IO::String
• IPC::Run
• LWP
• SOAP::Lite

proper_libs

Bio/Factory/EMBOSS.pm, Bio/Installer/Clustalw.pm, Bio/Installer/EMBOSS.pm, Bio/Installer/Generic.pm, Bio/Installer/Hyphy.pm, Bio/Installer/Muscle.pm, Bio/Installer/PAML.pm, Bio/Installer/Probcons.pm, Bio/Installer/SLR.pm, Bio/Installer/TCoffee.pm, Bio/Tools/Run/Alignment/Amap.pm, Bio/Tools/Run/Alignment/Blat.pm, Bio/Tools/Run/Alignment/Clustalw.pm, Bio/Tools/Run/Alignment/DBA.pm, Bio/Tools/Run/Alignment/Exonerate.pm, Bio/Tools/Run/Alignment/Kalign.pm, Bio/Tools/Run/Alignment/Lagan.pm, Bio/Tools/Run/Alignment/MAFFT.pm, Bio/Tools/Run/Alignment/Muscle.pm, Bio/Tools/Run/Alignment/Pal2Nal.pm, Bio/Tools/Run/Alignment/Probalign.pm, Bio/Tools/Run/Alignment/Probcons.pm, Bio/Tools/Run/Alignment/Proda.pm, Bio/Tools/Run/Alignment/Sim4.pm, Bio/Tools/Run/Alignment/StandAloneFasta.pm, Bio/Tools/Run/Alignment/TCoffee.pm, Bio/Tools/Run/Analysis.pm, Bio/Tools/Run/Analysis.pm, Bio/Tools/Run/Analysis/soap.pm, Bio/Tools/Run/Analysis.pm, Bio/Tools/Run/Analysis/soap.pm, Bio/Tools/Run/AnalysisFactory.pm, Bio/Tools/Run/AnalysisFactory/soap.pm, Bio/Tools/Run/Cap3.pm, Bio/Tools/Run/Coil.pm, Bio/Tools/Run/EMBOSSApplication.pm, Bio/Tools/Run/EMBOSSacd.pm, Bio/Tools/Run/ERPIN.pm, Bio/Tools/Run/Ensembl.pm, Bio/Tools/Run/Eponine.pm, Bio/Tools/Run/FootPrinter.pm, Bio/Tools/Run/Genemark.pm, Bio/Tools/Run/Genewise.pm, Bio/Tools/Run/Genscan.pm, Bio/Tools/Run/Glimmer.pm, Bio/Tools/Run/Hmmer.pm, Bio/Tools/Run/Infernal.pm, Bio/Tools/Run/MCS.pm, Bio/Tools/Run/Match.pm, Bio/Tools/Run/Mdust.pm, Bio/Tools/Run/Meme.pm, Bio/Tools/Run/Phrap.pm, Bio/Tools/Run/Phylo/Gerp.pm, Bio/Tools/Run/Phylo/Gumby.pm, Bio/Tools/Run/Phylo/Hyphy/Base.pm, Bio/Tools/Run/Phylo/Hyphy/FEL.pm, Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm, Bio/Tools/Run/Phylo/Hyphy/REL.pm, Bio/Tools/Run/Phylo/Hyphy/SLAC.pm, Bio/Tools/Run/Phylo/LVB.pm, Bio/Tools/Run/Phylo/Molphy/ProtML.pm, Bio/Tools/Run/Phylo/Njtree/Best.pm, Bio/Tools/Run/Phylo/PAML/Baseml.pm, Bio/Tools/Run/Phylo/PAML/Codeml.pm, Bio/Tools/Run/Phylo/PAML/Evolver.pm, Bio/Tools/Run/Phylo/PAML/Yn00.pm, Bio/Tools/Run/Phylo/Phast/PhastCons.pm, Bio/Tools/Run/Phylo/Phast/PhyloFit.pm, Bio/Tools/Run/Phylo/Phylip/Base.pm, Bio/Tools/Run/Phylo/Phylip/Consense.pm, Bio/Tools/Run/Phylo/Phylip/DrawGram.pm, Bio/Tools/Run/Phylo/Phylip/DrawTree.pm, Bio/Tools/Run/Phylo/Phylip/Neighbor.pm, Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm, Bio/Tools/Run/Phylo/Phylip/ProtDist.pm, Bio/Tools/Run/Phylo/Phylip/ProtPars.pm, Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm, Bio/Tools/Run/Phylo/PhyloBase.pm, Bio/Tools/Run/Phylo/Phyml.pm, Bio/Tools/Run/Phylo/QuickTree.pm, Bio/Tools/Run/Phylo/SLR.pm, Bio/Tools/Run/Phylo/Semphy.pm, Bio/Tools/Run/Primate.pm, Bio/Tools/Run/Primer3.pm, Bio/Tools/Run/Prints.pm, Bio/Tools/Run/Profile.pm, Bio/Tools/Run/Promoterwise.pm, Bio/Tools/Run/Pseudowise.pm, Bio/Tools/Run/RNAMotif.pm, Bio/Tools/Run/RepeatMasker.pm, Bio/Tools/Run/Seg.pm, Bio/Tools/Run/Signalp.pm, Bio/Tools/Run/Simprot.pm, Bio/Tools/Run/TigrAssembler.pm, Bio/Tools/Run/Tmhmm.pm, Bio/Tools/Run/TribeMCL.pm, Bio/Tools/Run/Vista.pm, Bio/Tools/Run/tRNAscanSE.pm

test_prereq_matches_use

• Bio::Root::Test

use_warnings

Bio::Factory::EMBOSS, Bio::Installer::Clustalw, Bio::Installer::EMBOSS, Bio::Installer::Generic, Bio::Installer::Hyphy, Bio::Installer::Muscle, Bio::Installer::PAML, Bio::Installer::Probcons, Bio::Installer::SLR, Bio::Installer::TCoffee, Bio::Tools::Run::Alignment::Amap, Bio::Tools::Run::Alignment::Blat, Bio::Tools::Run::Alignment::Clustalw, Bio::Tools::Run::Alignment::DBA, Bio::Tools::Run::Alignment::Exonerate, Bio::Tools::Run::Alignment::Kalign, Bio::Tools::Run::Alignment::Lagan, Bio::Tools::Run::Alignment::MAFFT, Bio::Tools::Run::Alignment::Muscle, Bio::Tools::Run::Alignment::Pal2Nal, Bio::Tools::Run::Alignment::Probalign, Bio::Tools::Run::Alignment::Probcons, Bio::Tools::Run::Alignment::Proda, Bio::Tools::Run::Alignment::Sim4, Bio::Tools::Run::Alignment::StandAloneFasta, Bio::Tools::Run::Alignment::TCoffee, Bio::Tools::Run::Analysis, Bio::Tools::Run::Analysis::soap, Bio::Tools::Run::AnalysisFactory, Bio::Tools::Run::AnalysisFactory::soap, Bio::Tools::Run::Cap3, Bio::Tools::Run::Coil, Bio::Tools::Run::EMBOSSApplication, Bio::Tools::Run::EMBOSSacd, Bio::Tools::Run::ERPIN, Bio::Tools::Run::Ensembl, Bio::Tools::Run::Eponine, Bio::Tools::Run::FootPrinter, Bio::Tools::Run::Genewise, Bio::Tools::Run::Genscan, Bio::Tools::Run::Hmmer, Bio::Tools::Run::Infernal, Bio::Tools::Run::MCS, Bio::Tools::Run::Match, Bio::Tools::Run::Mdust, Bio::Tools::Run::Meme, Bio::Tools::Run::Phrap, Bio::Tools::Run::Phylo::Gerp, Bio::Tools::Run::Phylo::Gumby, Bio::Tools::Run::Phylo::Hyphy::Base, Bio::Tools::Run::Phylo::Hyphy::FEL, Bio::Tools::Run::Phylo::Hyphy::Modeltest, Bio::Tools::Run::Phylo::Hyphy::REL, Bio::Tools::Run::Phylo::Hyphy::SLAC, Bio::Tools::Run::Phylo::LVB, Bio::Tools::Run::Phylo::Molphy::ProtML, Bio::Tools::Run::Phylo::Njtree::Best, Bio::Tools::Run::Phylo::PAML::Baseml, Bio::Tools::Run::Phylo::PAML::Codeml, Bio::Tools::Run::Phylo::PAML::Evolver, Bio::Tools::Run::Phylo::PAML::Yn00, Bio::Tools::Run::Phylo::Phast::PhastCons, Bio::Tools::Run::Phylo::Phast::PhyloFit, Bio::Tools::Run::Phylo::Phylip::Base, Bio::Tools::Run::Phylo::Phylip::Consense, Bio::Tools::Run::Phylo::Phylip::DrawGram, Bio::Tools::Run::Phylo::Phylip::DrawTree, Bio::Tools::Run::Phylo::Phylip::Neighbor, Bio::Tools::Run::Phylo::Phylip::PhylipConf, Bio::Tools::Run::Phylo::Phylip::ProtDist, Bio::Tools::Run::Phylo::Phylip::ProtPars, Bio::Tools::Run::Phylo::Phylip::SeqBoot, Bio::Tools::Run::Phylo::PhyloBase, Bio::Tools::Run::Phylo::Phyml, Bio::Tools::Run::Phylo::QuickTree, Bio::Tools::Run::Phylo::SLR, Bio::Tools::Run::Phylo::Semphy, Bio::Tools::Run::Primate, Bio::Tools::Run::Primer3, Bio::Tools::Run::Prints, Bio::Tools::Run::Profile, Bio::Tools::Run::Promoterwise, Bio::Tools::Run::Pseudowise, Bio::Tools::Run::RNAMotif, Bio::Tools::Run::RepeatMasker, Bio::Tools::Run::Seg, Bio::Tools::Run::Signalp, Bio::Tools::Run::Simprot, Bio::Tools::Run::TigrAssembler, Bio::Tools::Run::Tmhmm, Bio::Tools::Run::TribeMCL, Bio::Tools::Run::Vista