[Bioperl-l] failed to install Bio::Tools::Run::StandAloneBlastPlus - full test output
Galeb Abu-Ali
abualiga at gmail.com
Thu May 19 13:29:08 UTC 2011
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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