[Bioperl-l] Problems installing Bio::Tools::Run:StandAloneBlastPlus
Tiago Hori
tiago.hori at gmail.com
Wed Feb 6 13:25:41 UTC 2013
Hi Guys,
I am trying to install the module Bio::Tools::Run:StandAloneBlastPlus, but
it has been hard so far.
I managed to install and compile samtools, after finding all the
dependencies, but I am still missing something! I posted the complete
report below!
Any help, would be great!
Cheers,
T.
cpan[1]> install Bio::Tools::Run::StandAloneBlastPlus
Reading '/home/tiagohori/.cpan/Metadata'
Database was generated on Tue, 05 Feb 2013 18:41:03 GMT
Running install for module 'Bio::Tools::Run::StandAloneBlastPlus'
Running make for C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz
Checksum for
/home/tiagohori/.cpan/sources/authors/id/C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz
ok
Scanning cache /home/tiagohori/.cpan/build for sizes
..................................------------------------------------------DONE
DEL(1/20): /home/tiagohori/.cpan/build/BioPerl-Run-1.006900-qpHfzz
DEL(2/20): /home/tiagohori/.cpan/build/BioPerl-Run-1.006900-qpHfzz.yml
DEL(3/20): /home/tiagohori/.cpan/build/BioPerl-Run-1.006900-nMOXgO
DEL(4/20): /home/tiagohori/.cpan/build/BioPerl-Run-1.006900-nMOXgO.yml
DEL(5/20): /home/tiagohori/.cpan/build/Bio-SamTools-1.37-bgBQyC
DEL(6/20): /home/tiagohori/.cpan/build/Bio-SamTools-1.37-bgBQyC.yml
DEL(7/20): /home/tiagohori/.cpan/build/Bio-SamTools-1.37-Ki3dbt
DEL(8/20): /home/tiagohori/.cpan/build/Bio-SamTools-1.37-Ki3dbt.yml
DEL(9/20): /home/tiagohori/.cpan/build/Bio-SamTools-1.37-ciM7U4
DEL(10/20): /home/tiagohori/.cpan/build/Bio-SamTools-1.37-ciM7U4.yml
DEL(11/20): /home/tiagohori/.cpan/build/Bio-SamTools-1.37-oDyi_5
DEL(12/20): /home/tiagohori/.cpan/build/Bio-SamTools-1.37-oDyi_5.yml
DEL(13/20): /home/tiagohori/.cpan/build/Bio-SamTools-1.37-AQiiAn
DEL(14/20): /home/tiagohori/.cpan/build/Bio-SamTools-1.37-AQiiAn.yml
DEL(15/20): /home/tiagohori/.cpan/build/Bio-SamTools-1.37-0H2Z9o
DEL(16/20): /home/tiagohori/.cpan/build/Bio-SamTools-1.37-0H2Z9o.yml
DEL(17/20): /home/tiagohori/.cpan/build/Bio-SamTools-1.37-c_8A_U
DEL(18/20): /home/tiagohori/.cpan/build/Bio-SamTools-1.37-c_8A_U.yml
DEL(19/20): /home/tiagohori/.cpan/build/Bio-SamTools-1.37-lWtV8v
DEL(20/20): /home/tiagohori/.cpan/build/Bio-SamTools-1.37-lWtV8v.yml
CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz
Install scripts? y/n [n ]
n
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 .................. 3/423 # Required executable for
Bio::Tools::Run::BEDTools is not present
t/BEDTools.t .................. ok
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 ...................... 2/6 # 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 .................. 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 # Looks like you planned 7 tests but
ran 2.
t/Eponine.t ................... Dubious, test returned 255 (wstat 65280,
0xff00)
Failed 5/7 subtests
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 ..................... 2/15 # 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 ..................... 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: 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 ..................... 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/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/Eponine.t (Wstat: 65280 Tests: 2 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 7 tests but ran 2.
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=2876, 39 wallclock secs ( 0.54 usr 0.23 sys + 32.54 cusr
4.94 csys = 38.25 CPU)
Result: FAIL
Failed 3/80 test programs. 0/2876 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
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