[Bioperl-l] BioPerl-Run install on Mac OS X
galeb abu-ali
abualiga2 at gmail.com
Sun Oct 13 21:37:23 UTC 2013
Hi Chris,
did you have any luck with these failures?
thanks!
galeb
On Mon, Oct 7, 2013 at 4:28 PM, Fields, Christopher J <cjfields at illinois.edu
> wrote:
> Not sure, to tell the truth. I can have a look; the failures you are
> getting are a bit troubling, but may be due to version changes.
>
> chris
>
> On Oct 7, 2013, at 12:28 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:
>
> > Hi All,
> >
> > I would like to install Bio::Grep to do fuzzy-matching with Vmatch. To
> > install Bio::Grep, I first need to install BioPerl-Run, and this is
> where I
> > have a problem. While I don't have most executables, I do have samtools,
> > Bio-SamTools, and bedtools installed. I do not understand the below
> > exception, probably referring to bedtools, given I have bedtools in
> > /usr/local/bin. Below is cpan output. At your convenience, please
> advise.
> >
> > many thanks
> >
> > galeb
> >
> > p/s - I have the BioPerl core package, of course.
> >
> >
> > cpan[4]> d /bioperl-run/
> > Distribution id = C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz
> > CPAN_USERID CJFIELDS (Christopher Fields <cjfields at bioperl.org>)
> > CALLED_FOR C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz
> > CHECKSUM_STATUS OK
> > CONTAINSMODS Bio::DB::ESoap Bio::DB::ESoap::WSDL
> > Bio::DB::SoapEUtilities Bio::DB::SoapEUtilities::DocSumAdaptor
> > Bio::DB::SoapEUtilities::DocSumAdaptor::docsum
> > Bio::DB::SoapEUtilities::FetchAdaptor
> > Bio::DB::SoapEUtilities::FetchAdaptor::seq
> > Bio::DB::SoapEUtilities::FetchAdaptor::species
> > Bio::DB::SoapEUtilities::GQueryAdaptor
> > Bio::DB::SoapEUtilities::GQueryAdaptor::gquery
> > Bio::DB::SoapEUtilities::LinkAdaptor
> > Bio::DB::SoapEUtilities::LinkAdaptor::linkset
> > Bio::DB::SoapEUtilities::Result 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::Gmap
> > 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::Job Bio::Tools::Run::Analysis::Job::soap
> > Bio::Tools::Run::Analysis::Utils Bio::Tools::Run::Analysis::soap
> > Bio::Tools::Run::AnalysisFactory Bio::Tools::Run::AnalysisFactory::soap
> > Bio::Tools::Run::AssemblerBase Bio::Tools::Run::BEDTools
> > Bio::Tools::Run::BEDTools::Config Bio::Tools::Run::BWA
> > Bio::Tools::Run::BWA::Config Bio::Tools::Run::BlastPlus
> > Bio::Tools::Run::BlastPlus::Config Bio::Tools::Run::Bowtie
> > Bio::Tools::Run::Bowtie::Config 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::Genemark
> > Bio::Tools::Run::Genewise Bio::Tools::Run::Genscan
> Bio::Tools::Run::Glimmer
> > Bio::Tools::Run::Hmmer Bio::Tools::Run::Infernal Bio::Tools::Run::MCS
> > Bio::Tools::Run::Maq Bio::Tools::Run::Maq::Config Bio::Tools::Run::Match
> > Bio::Tools::Run::Mdust Bio::Tools::Run::Meme Bio::Tools::Run::Minimo
> > Bio::Tools::Run::Newbler 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::Samtools
> > Bio::Tools::Run::Samtools::Config Bio::Tools::Run::Seg
> > Bio::Tools::Run::Signalp Bio::Tools::Run::Simprot
> > Bio::Tools::Run::StandAloneBlastPlus Bio::Tools::Run::TigrAssembler
> > Bio::Tools::Run::Tmhmm Bio::Tools::Run::TribeMCL Bio::Tools::Run::Vista
> > Bio::Tools::Run::tRNAscanSE
> > UPLOAD_DATE 2011-04-21
> > archived tar
> > build_dir /var/root/.cpan/build/BioPerl-Run-1.006900-hgSg0B
> > incommandcolor 0
> > localfile
> >
> /var/root/.cpan/sources/authors/id/C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz
> > make YES
> > make_test NO
> > modulebuild 1
> > negative_prefs_cache 2
> > prefs HASH(0x7f9e0d2e9828)
> > prereq_pm requires:Bio::Root::Version=>1.006900,perl=>v5.6.1
> > reqtype c
> > unwrapped YES
> > writemakefile YES
> >
> >
> > cpan[5]> install C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz
> > Running Build for C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz
> > Has already been unwrapped into directory
> > /var/root/.cpan/build/BioPerl-Run-1.006900-hgSg0B
> > Has already been made
> > Running Build test
> > t/Amap.t ...................... 1/18 # Required executable for
> > Bio::Tools::Run::Alignment::Amap is not present
> > t/Amap.t ...................... ok
> > t/AnalysisFactory_soap.t ...... skipped: Network tests have not been
> > requested
> > t/Analysis_soap.t ............. skipped: Network tests have not been
> > requested
> > t/BEDTools.t .................. 1/423
> > # Failed test 'get version for 'annotate''
> > # at t/BEDTools.t line 189.
> > t/BEDTools.t .................. 20/423
> > # Failed test 'get version for 'fasta_from_bed''
> > # at t/BEDTools.t line 189.
> >
> > # Failed test 'get version for 'overlap''
> > # at t/BEDTools.t line 189.
> >
> > ------------- EXCEPTION: Bio::Root::Exception -------------
> > MSG: No executable!
> > STACK: Error::throw
> > STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:472
> > STACK: Bio::Tools::Run::BEDTools::run
> >
> /var/root/.cpan/build/BioPerl-Run-1.006900-hgSg0B/blib/lib/Bio/Tools/Run/BEDTools.pm:279
> > STACK: t/BEDTools.t:252
> > -----------------------------------------------------------
> > # Looks like you planned 423 tests but ran 45.
> > # Looks like you failed 3 tests of 45 run.
> > # Looks like your test exited with 2 just after 45.
> > t/BEDTools.t .................. Dubious, test returned 2 (wstat 512,
> 0x200)
> > Failed 381/423 subtests
> > t/BWA.t ....................... 1/36 # Required executable for
> > Bio::Tools::Run::BWA is not present
> > t/BWA.t ....................... ok
> > t/Blat.t ...................... 1/33 # Required executable for
> > Bio::Tools::Run::Alignment::Blat is not present
> > # Looks like you planned 33 tests but ran 20.
> > t/Blat.t ...................... Dubious, test returned 255 (wstat 65280,
> > 0xff00)
> > Failed 13/33 subtests
> > (less 15 skipped subtests: 5 okay)
> > t/Bowtie.t .................... 1/73 # Required executable for
> > Bio::Tools::Run::Bowtie is not present
> > t/Bowtie.t .................... ok
> > t/Cap3.t ...................... 1/91 # Required executable for
> > Bio::Tools::Run::Cap3 is not present
> > t/Cap3.t ...................... ok
> > t/Clustalw.t .................. 1/45 # Required executable for
> > Bio::Tools::Run::Alignment::Clustalw is not present
> > t/Clustalw.t .................. ok
> > t/Coil.t ...................... 1/6 # Required executable for
> > Bio::Tools::Run::Coil is not present
> > t/Coil.t ...................... ok
> > t/Consense.t .................. 1/9 # Required executable for
> > Bio::Tools::Run::Phylo::Phylip::Consense is not present
> > t/Consense.t .................. ok
> > t/DBA.t ....................... 1/18 # Required executable for
> > Bio::Tools::Run::Alignment::DBA is not present
> > t/DBA.t ....................... ok
> > t/DrawGram.t .................. 2/6 # Required executable for
> > Bio::Tools::Run::Phylo::Phylip::DrawGram is not present
> > t/DrawGram.t .................. ok
> > t/DrawTree.t .................. 1/6 # Required executable for
> > Bio::Tools::Run::Phylo::Phylip::DrawTree is not present
> > t/DrawTree.t .................. ok
> > t/EMBOSS.t .................... ok
> > t/Ensembl.t ................... skipped: Network tests have not been
> > requested
> > t/Eponine.t ................... 1/7 # Required environment variable
> > $EPONINEDIR is not set
> > t/Eponine.t ................... ok
> > t/Exonerate.t ................. 1/89 # Required executable for
> > Bio::Tools::Run::Alignment::Exonerate is not present
> > t/Exonerate.t ................. ok
> > t/FootPrinter.t ............... 1/24 # Required executable for
> > Bio::Tools::Run::FootPrinter is not present
> > t/FootPrinter.t ............... ok
> > t/Genemark.hmm.prokaryotic.t .. 1/99 # Required environment variable
> > $GENEMARK_MODELS is not set
> > t/Genemark.hmm.prokaryotic.t .. ok
> > t/Genewise.t .................. 1/20 # Required executable for
> > Bio::Tools::Run::Genewise is not present
> > t/Genewise.t .................. ok
> > t/Genscan.t ................... 1/6 # Required environment variable
> > $GENSCANDIR is not set
> > t/Genscan.t ................... ok
> > t/Gerp.t ...................... 1/33 # Required executable for
> > Bio::Tools::Run::Phylo::Gerp is not present
> > t/Gerp.t ...................... ok
> > t/Glimmer2.t .................. 1/217 # Required executable for
> > Bio::Tools::Run::Glimmer is not present
> > t/Glimmer2.t .................. ok
> > t/Glimmer3.t .................. 1/111 # Required executable for
> > Bio::Tools::Run::Glimmer is not present
> > t/Glimmer3.t .................. ok
> > t/Gumby.t ..................... 1/124 # Required executable for
> > Bio::Tools::Run::Phylo::Gumby is not present
> > t/Gumby.t ..................... ok
> > t/Hmmer.t ..................... 1/27 # Required executable for
> > Bio::Tools::Run::Hmmer is not present
> > t/Hmmer.t ..................... ok
> > t/Hyphy.t ..................... 1/15 # Required executable for
> > Bio::Tools::Run::Phylo::Hyphy::SLAC is not present
> > t/Hyphy.t ..................... ok
> > t/Infernal.t .................. 1/43 # Required executable for
> > Bio::Tools::Run::Infernal is not present
> > t/Infernal.t .................. ok
> > t/Kalign.t .................... 1/8 # Required executable for
> > Bio::Tools::Run::Alignment::Kalign is not present
> > t/Kalign.t .................... ok
> > t/LVB.t ....................... 1/19 # Required executable for
> > Bio::Tools::Run::Phylo::LVB is not present
> > t/LVB.t ....................... ok
> > t/Lagan.t ..................... 2/12 # Required executable for
> > Bio::Tools::Run::Alignment::Lagan is not present
> > t/Lagan.t ..................... ok
> > t/MAFFT.t ..................... 1/17 # Required executable for
> > Bio::Tools::Run::Alignment::MAFFT is not present
> > t/MAFFT.t ..................... ok
> > t/MCS.t ....................... 1/24 # Required executable for
> > Bio::Tools::Run::MCS is not present
> > t/MCS.t ....................... ok
> > t/Maq.t ....................... 1/51 # Required executable for
> > Bio::Tools::Run::Maq is not present
> > t/Maq.t ....................... ok
> > t/Match.t ..................... 1/7 # Required executable for
> > Bio::Tools::Run::Match is not present
> > t/Match.t ..................... ok
> > t/Mdust.t ..................... 1/5 # Required executable for
> > Bio::Tools::Run::Mdust is not present
> > t/Mdust.t ..................... ok
> > t/Meme.t ...................... 1/25 # Required executable for
> > Bio::Tools::Run::Meme is not present
> > t/Meme.t ...................... ok
> > t/Minimo.t .................... 1/72 # Required executable for
> > Bio::Tools::Run::Minimo is not present
> > t/Minimo.t .................... ok
> > t/Molphy.t .................... 1/10 # Required executable for
> > Bio::Tools::Run::Phylo::Molphy::ProtML is not present
> > t/Molphy.t .................... ok
> > t/Muscle.t .................... 1/16 # Required executable for
> > Bio::Tools::Run::Alignment::Muscle is not present
> > t/Muscle.t .................... ok
> > t/Neighbor.t .................. 1/17 # Required executable for
> > Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
> > t/Neighbor.t .................. ok
> > t/Newbler.t ................... 1/98 # Required executable for
> > Bio::Tools::Run::Newbler is not present
> > t/Newbler.t ................... ok
> > t/Njtree.t .................... 1/6 # Required executable for
> > Bio::Tools::Run::Phylo::Njtree::Best is not present
> > t/Njtree.t .................... ok
> > t/PAML.t ...................... 1/28 # Required executable for
> > Bio::Tools::Run::Phylo::PAML::Codeml is not present
> > t/PAML.t ...................... ok
> > t/Pal2Nal.t ................... 1/9 # Required executable for
> > Bio::Tools::Run::Alignment::Pal2Nal is not present
> > t/Pal2Nal.t ................... ok
> > t/PhastCons.t ................. 1/181 # Required executable for
> > Bio::Tools::Run::Phylo::Phast::PhastCons is not present
> > t/PhastCons.t ................. ok
> > t/Phrap.t ..................... 1/127 # Required executable for
> > Bio::Tools::Run::Phrap is not present
> > t/Phrap.t ..................... ok
> > t/Phyml.t ..................... 1/47 # Required executable for
> > Bio::Tools::Run::Phylo::Phyml is not present
> > t/Phyml.t ..................... ok
> > t/Primate.t ................... 1/8 # Required executable for
> > Bio::Tools::Run::Primate is not present
> > t/Primate.t ................... ok
> > t/Primer3.t ................... 1/9 # Required executable for
> > Bio::Tools::Run::Primer3 is not present
> > t/Primer3.t ................... ok
> > t/Prints.t .................... 1/7 # Required executable for
> > Bio::Tools::Run::Prints is not present
> > t/Prints.t .................... ok
> > t/Probalign.t ................. 1/13 # Required executable for
> > Bio::Tools::Run::Alignment::Probalign is not present
> > t/Probalign.t ................. ok
> > t/Probcons.t .................. 1/11 # Required executable for
> > Bio::Tools::Run::Alignment::Probcons is not present
> > t/Probcons.t .................. ok
> > t/Profile.t ................... 1/7 # Required executable for
> > Bio::Tools::Run::Profile is not present
> > t/Profile.t ................... ok
> > t/Promoterwise.t .............. 1/9 # Required executable for
> > Bio::Tools::Run::Promoterwise is not present
> > t/Promoterwise.t .............. ok
> > t/ProtDist.t .................. 1/14 # Required executable for
> > Bio::Tools::Run::Phylo::Phylip::ProtDist is not present
> > t/ProtDist.t .................. ok
> > t/ProtPars.t .................. 1/11 # Required executable for
> > Bio::Tools::Run::Phylo::Phylip::ProtPars is not present
> > t/ProtPars.t .................. ok
> > t/Pseudowise.t ................ 1/18 # Required executable for
> > Bio::Tools::Run::Pseudowise is not present
> > t/Pseudowise.t ................ ok
> > t/QuickTree.t ................. 1/13 # Required executable for
> > Bio::Tools::Run::Phylo::QuickTree is not present
> > t/QuickTree.t ................. ok
> > t/RepeatMasker.t .............. 1/12 RepeatMasker program not found as
> or
> > not executable.
> > # Required executable for Bio::Tools::Run::RepeatMasker is not present
> > t/RepeatMasker.t .............. ok
> > t/SABlastPlus.t ............... 1/65 # Required executable for
> > Bio::Tools::Run::BlastPlus is not present
> > # Looks like you planned 65 tests but ran 63.
> > t/SABlastPlus.t ............... Dubious, test returned 255 (wstat 65280,
> > 0xff00)
> > Failed 2/65 subtests
> > (less 59 skipped subtests: 4 okay)
> > t/SLR.t ....................... 1/7 # Required executable for
> > Bio::Tools::Run::Phylo::SLR is not present
> > t/SLR.t ....................... ok
> > t/Samtools.t .................. ok
> > t/Seg.t ....................... 1/8 # Required executable for
> > Bio::Tools::Run::Seg is not present
> > t/Seg.t ....................... ok
> > t/Semphy.t .................... 1/19 # Required executable for
> > Bio::Tools::Run::Phylo::Semphy is not present
> > t/Semphy.t .................... ok
> > t/SeqBoot.t ................... 1/9 # Required executable for
> > Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present
> > t/SeqBoot.t ................... ok
> > t/Signalp.t ................... 1/7 # Required executable for
> > Bio::Tools::Run::Signalp is not present
> > t/Signalp.t ................... ok
> > t/Sim4.t ...................... 1/23 # Required executable for
> > Bio::Tools::Run::Alignment::Sim4 is not present
> > t/Sim4.t ...................... ok
> > t/Simprot.t ................... 1/6 # Required executable for
> > Bio::Tools::Run::Simprot is not present
> > t/Simprot.t ................... ok
> > t/SoapEU-function.t ........... skipped: Valid email not provided;
> required
> > for tests
> > t/SoapEU-unit.t ............... # NOTE: No network access required for
> > these tests; all are local file-based.
> > t/SoapEU-unit.t ............... ok
> > t/StandAloneFasta.t ........... 1/15 # Required executable for
> > Bio::Tools::Run::Alignment::StandAloneFasta is not present
> > t/StandAloneFasta.t ........... ok
> > t/TCoffee.t ................... 1/27 # Required executable for
> > Bio::Tools::Run::Alignment::TCoffee is not present
> > t/TCoffee.t ................... ok
> > t/TigrAssembler.t ............. 1/88 # Required executable for
> > Bio::Tools::Run::TigrAssembler is not present
> > # Required executable for Bio::Tools::Run::TigrAssembler is not present
> > t/TigrAssembler.t ............. ok
> > t/Tmhmm.t ..................... 1/9 # Required executable for
> > Bio::Tools::Run::Tmhmm is not present
> > t/Tmhmm.t ..................... ok
> > t/TribeMCL.t .................. ok
> > t/Vista.t ..................... 1/7 # Vista.jar is not in your class
> > path:Exception in thread "main" java.lang.NoClassDefFoundError: Vista
> > t/Vista.t ..................... ok
> > t/gmap-run.t .................. 1/8 # Required executable for
> > Bio::Tools::Run::Alignment::Gmap is not present
> > t/gmap-run.t .................. ok
> > t/tRNAscanSE.t ................ 1/12 # Required executable for
> > Bio::Tools::Run::tRNAscanSE is not present
> > t/tRNAscanSE.t ................ ok
> >
> > Test Summary Report
> > -------------------
> > t/BEDTools.t (Wstat: 512 Tests: 45 Failed: 3)
> > Failed tests: 8, 26, 44
> > Non-zero exit status: 2
> > Parse errors: Bad plan. You planned 423 tests but ran 45.
> > t/Blat.t (Wstat: 65280 Tests: 20 Failed: 0)
> > Non-zero exit status: 255
> > Parse errors: Bad plan. You planned 33 tests but ran 20.
> > t/SABlastPlus.t (Wstat: 65280 Tests: 63 Failed: 0)
> > Non-zero exit status: 255
> > Parse errors: Bad plan. You planned 65 tests but ran 63.
> > Files=80, Tests=2642, 22 wallclock secs ( 0.44 usr 0.19 sys + 18.10 cusr
> > 1.84 csys = 20.57 CPU)
> > Result: FAIL
> > Failed 3/80 test programs. 3/2642 subtests failed.
> > CJFIELDS/BioPerl-Run-1.006900.tar.gz
> > ./Build test -- NOT OK
> > //hint// to see the cpan-testers results for installing this module, try:
> > reports CJFIELDS/BioPerl-Run-1.006900.tar.gz
> > Running Build install
> > make test had returned bad status, won't install without force
> > Failed during this command:
> > CJFIELDS/BioPerl-Run-1.006900.tar.gz : make_test NO
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
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