[Bioperl-l] failed to install Bio::Tools::Run::StandAloneBlastPlus - full test output
Chris Fields
cjfields at illinois.edu
Thu May 19 13:40:23 UTC 2011
Thanks for the full report. Looks as if the test suites for bwa and samtools aren't catching the lack of required executables or modules, I'll look into that. The tests for your module did pass (SABlast.t), however, so you could feasibly use 'force install' in this case if you don't plan on using the other modules.
chris
On May 19, 2011, at 8:29 AM, Galeb Abu-Ali wrote:
> Hi,
>
> I am not able to install Bio::Tools::Run::StandAloneBlastPlus. Pasted below
> is the full test output. At your convenience, I'd much appreciate your
> instruction.
>
> thanks
>
> galeb
>
>
>
>
> cpan[1]> install Bio::Tools::Run::StandAloneBlastPlus
> Going to read '/root/.cpan/Metadata'
> Database was generated on Wed, 18 May 2011 11:32:45 GMT
> Running install for module 'Bio::Tools::Run::StandAloneBlastPlus'
> Running make for C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz
> Checksum for
> /root/.cpan/sources/authors/id/C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz ok
> Scanning cache /root/.cpan/build for sizes
> .......................................................---------------------DONE
> DEL(1/12): /root/.cpan/build/BioPerl-1.6.900-gVKrU6
> DEL(2/12): /root/.cpan/build/BioPerl-1.6.900-gVKrU6.yml
> DEL(3/12): /root/.cpan/build/DB_File-1.822-Ys3EkN
> DEL(4/12): /root/.cpan/build/DB_File-1.822-Ys3EkN.yml
> DEL(5/12): /root/.cpan/build/Algorithm-Diff-1.1902-RIMxED
> DEL(6/12): /root/.cpan/build/Algorithm-Diff-1.1902-RIMxED.yml
> DEL(7/12): /root/.cpan/build/File-Sort-1.01-5wOvOP.yml
> DEL(8/12): /root/.cpan/build/File-Sort-1.01-5wOvOP
> DEL(9/12): /root/.cpan/build/IPC-Run-0.89-79rMje
> DEL(10/12): /root/.cpan/build/IPC-Run-0.89-79rMje.yml
> DEL(11/12): /root/.cpan/build/CPAN-DistnameInfo-0.12-4Etdsy
> DEL(12/12): /root/.cpan/build/CPAN-DistnameInfo-0.12-4Etdsy.yml
>
> CPAN.pm: Going to build C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz
>
> Install scripts? y/n [n ]y
> Do you want to run tests that require connection to servers across the
> internet
> (likely to cause some failures)? y/n [n ]n
> - will not run internet-requiring tests
> Created MYMETA.yml and MYMETA.json
> Creating new 'Build' script for 'BioPerl-Run' version '1.006900'
> Building BioPerl-Run
> CJFIELDS/BioPerl-Run-1.006900.tar.gz
> ./Build -- OK
> 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 # Required executable for
> Bio::Tools::Run::BEDTools is not present
> t/BEDTools.t .................. ok
> t/BWA.t .......................
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: __PACKAGE__ requires installation of samtools (libbam) and Bio::DB::Sam
> (available on CPAN; not part of BioPerl)
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/local/lib/perl5/site_perl/5.12.2/Bio/Root/Root.pm:472
> STACK: Bio::Assembly::IO::sam::BEGIN
> /usr/local/lib/perl5/site_perl/5.12.2/Bio/Assembly/IO/sam.pm:189
> STACK: main::BEGIN /usr/local/lib/perl5/site_perl/5.12.2/Bio/Assembly/IO/
> sam.pm:195
> STACK: /usr/local/lib/perl5/site_perl/5.12.2/Bio/Assembly/IO/sam.pm:195
> -----------------------------------------------------------
> BEGIN failed--compilation aborted at
> /usr/local/lib/perl5/site_perl/5.12.2/Bio/Assembly/IO/sam.pm line 195.
> Compilation failed in require at t/BWA.t line 21.
> BEGIN failed--compilation aborted at t/BWA.t line 21.
> # Looks like your test exited with 2 before it could output anything.
> t/BWA.t ....................... Dubious, test returned 2 (wstat 512, 0x200)
> Failed 36/36 subtests
> 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 .................. 1/6 # Required executable for
> Bio::Tools::Run::Phylo::Phylip::DrawGram is not present
> t/DrawGram.t .................. ok
> t/DrawTree.t .................. 2/6 # Required executable for
> Bio::Tools::Run::Phylo::Phylip::DrawTree is not present
> t/DrawTree.t .................. ok
> t/EMBOSS.t .................... skipped: The optional module XML::Twig (or
> dependencies thereof) was not installed
> 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 ..................... 1/12 # 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 ..................... 3/5 # 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 # DB and mask make tests
> t/SABlastPlus.t ............... 29/65 # run BLAST methods
> t/SABlastPlus.t ............... 62/65 Use of uninitialized value $hit_signif
> in numeric le (<=) at
> /usr/local/lib/perl5/site_perl/5.12.2/Bio/SearchIO/IteratedSearchResultEventBuilder.pm
> line 367, <GEN55> line 17.
> Use of uninitialized value $hit_signif in numeric le (<=) at
> /usr/local/lib/perl5/site_perl/5.12.2/Bio/SearchIO/IteratedSearchResultEventBuilder.pm
> line 315, <GEN55> line 17.
> t/SABlastPlus.t ............... ok
> t/SLR.t ....................... 1/7 # Required executable for
> Bio::Tools::Run::Phylo::SLR is not present
> t/SLR.t ....................... ok
> t/Samtools.t .................. 1/40
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Can't find executable for 'samtools'; can't continue
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/local/lib/perl5/site_perl/5.12.2/Bio/Root/Root.pm:472
> STACK: Bio::Tools::Run::WrapperBase::_run
> /usr/local/lib/perl5/site_perl/5.12.2/Bio/Tools/Run/WrapperBase/CommandExts.pm:974
> STACK: Bio::Tools::Run::Samtools::run
> /root/.cpan/build/BioPerl-Run-1.006900-8toBBs/blib/lib/Bio/Tools/Run/Samtools.pm:176
> STACK: t/Samtools.t:71
> -----------------------------------------------------------
> # Looks like you planned 40 tests but ran 24.
> # Looks like your test exited with 2 just after 24.
> t/Samtools.t .................. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 16/40 subtests
> 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: The optional module Bio::DB::ESoap
> (or dependencies thereof) was not installed
> t/SoapEU-unit.t ............... skipped: The optional module Bio::DB::ESoap
> (or dependencies thereof) was not installed
> 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/BWA.t (Wstat: 512 Tests: 0 Failed: 0)
> Non-zero exit status: 2
> Parse errors: Bad plan. You planned 36 tests but ran 0.
> 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/Samtools.t (Wstat: 512 Tests: 24 Failed: 0)
> Non-zero exit status: 2
> Parse errors: Bad plan. You planned 40 tests but ran 24.
> Files=80, Tests=2799, 95 wallclock secs ( 0.39 usr 0.04 sys + 30.85 cusr
> 4.08 csys = 35.36 CPU)
> Result: FAIL
> Failed 3/80 test programs. 0/2799 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
> cpan[2]>
>
>
> Hi Galeb,
>
> In your email, could you include the *full* test output? Just the
> summary isn't enough for us to diagnose what is happening.
>
> Rob
> _______________________________________________
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