Fields, Christopher J | 7 Oct 22:28 2013

Re: BioPerl-Run install on Mac OS X

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
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Gmane