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From: metabase:user:314402c4-2aae-11df-837a-5e0a49663a4f
Subject: FAIL BioPerl-Run-1.006900 v5.22.0 RC2 GNU/Linux
Date: 2015-05-30T10:46:04Z
This distribution has been tested as part of the CPAN Testers
project, supporting the Perl programming language. See
http://wiki.cpantesters.org/ for more information or email
questions to cpan-testers-discuss@perl.org
--
Dear Christopher Fields,
This is a computer-generated report for BioPerl-Run-1.006900
on perl 5.22.0, created by CPAN-Reporter-1.2014.
Thank you for uploading your work to CPAN. However, there was a problem
testing your distribution.
If you think this report is invalid, please consult the CPAN Testers Wiki
for suggestions on how to avoid getting FAIL reports for missing library
or binary dependencies, unsupported operating systems, and so on:
http://wiki.cpantesters.org/wiki/CPANAuthorNotes
Sections of this report:
* Tester comments
* Program output
* Prerequisites
* Environment and other context
------------------------------
TESTER COMMENTS
------------------------------
Additional comments from tester:
none provided
------------------------------
PROGRAM OUTPUT
------------------------------
Output from './Build test':
# 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
# Required executable for Bio::Tools::Run::BEDTools is not present
t/BEDTools.t .................. ok
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Bio::Assembly::IO::sam requires installation of samtools (libbam) and Bio::DB::Sam (available on CPAN; not part of BioPerl)
STACK: Error::throw
STACK: Bio::Root::Root::throw /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/Bio/Root/Root.pm:449
STACK: Bio::Assembly::IO::sam::BEGIN /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/Bio/Assembly/IO/sam.pm:189
STACK: main::BEGIN /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/Bio/Assembly/IO/sam.pm:195
STACK: /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/Bio/Assembly/IO/sam.pm:195
-----------------------------------------------------------
BEGIN failed--compilation aborted at /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/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
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Cannot find executable for blat. path="blat"
STACK: Error::throw
STACK: Bio::Root::Root::throw /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/Bio/Root/Root.pm:449
STACK: Bio::Tools::Run::WrapperBase::executable /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/Bio/Tools/Run/WrapperBase.pm:340
STACK: t/Blat.t:23
-----------------------------------------------------------
# Looks like you planned 33 tests but ran 4.
# Looks like your test exited with 2 just after 4.
t/Blat.t ......................
Dubious, test returned 2 (wstat 512, 0x200)
Failed 29/33 subtests
1024
# Failed test 'translate params'
# at t/Bowtie.t line 111.
# got: '-v 4 -S -y --solexa-quals'
# expected: '-v 4 --solexa-quals -y -S'
# Required executable for Bio::Tools::Run::Bowtie is not present
# Looks like you failed 1 test of 73.
t/Bowtie.t ....................
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/73 subtests
(less 40 skipped subtests: 32 okay)
# Required executable for Bio::Tools::Run::Cap3 is not present
t/Cap3.t ...................... ok
# Required executable for Bio::Tools::Run::Alignment::Clustalw is not present
t/Clustalw.t .................. ok
# Required executable for Bio::Tools::Run::Coil is not present
t/Coil.t ...................... ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present
t/Consense.t .................. ok
# Required executable for Bio::Tools::Run::Alignment::DBA is not present
t/DBA.t ....................... ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present
t/DrawGram.t .................. ok
# 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
# You need at least version 1.2 of JDK to run eponine
t/Eponine.t ................... ok
# Required executable for Bio::Tools::Run::Alignment::Exonerate is not present
t/Exonerate.t ................. ok
# Required executable for Bio::Tools::Run::FootPrinter is not present
t/FootPrinter.t ............... ok
# Required environment variable $GENEMARK_MODELS is not set
t/Genemark.hmm.prokaryotic.t .. ok
# Required executable for Bio::Tools::Run::Genewise is not present
t/Genewise.t .................. ok
# Required environment variable $GENSCANDIR is not set
t/Genscan.t ................... ok
# Required executable for Bio::Tools::Run::Phylo::Gerp is not present
t/Gerp.t ...................... ok
# Required executable for Bio::Tools::Run::Glimmer is not present
t/Glimmer2.t .................. ok
# Required executable for Bio::Tools::Run::Glimmer is not present
t/Glimmer3.t .................. ok
# Failed test 'use Bio::Tools::Run::Phylo::Gumby;'
# at t/Gumby.t line 10.
# Tried to use 'Bio::Tools::Run::Phylo::Gumby'.
# Error: Can't locate Bio/SeqFeature/Annotated.pm in @INC (you may need to install the Bio::SeqFeature::Annotated module) (@INC contains: /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/lib /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/arch /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/x86_64-linux /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0 /opt/perl-5.22.0-RC2/lib/5.22.0/x86_64-linux /opt/perl-5.22.0-RC2/lib/5.22.0 .) at /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/Bio/Tools/Phylo/Gumby.pm line 83.
# BEGIN failed--compilation aborted at /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/Bio/Tools/Phylo/Gumby.pm line 83.
# Compilation failed in require at /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/lib/Bio/Tools/Run/Phylo/Gumby.pm line 143.
# BEGIN failed--compilation aborted at /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/lib/Bio/Tools/Run/Phylo/Gumby.pm line 143.
# Compilation failed in require at t/Gumby.t line 10.
# BEGIN failed--compilation aborted at t/Gumby.t line 10.
Can't locate object method "new" via package "Bio::Tools::Run::Phylo::Gumby" at t/Gumby.t line 25.
# Looks like you planned 124 tests but ran 8.
# Looks like you failed 1 test of 8 run.
# Looks like your test exited with 255 just after 8.
t/Gumby.t .....................
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 117/124 subtests
# Required executable for Bio::Tools::Run::Hmmer is not present
t/Hmmer.t ..................... ok
# Required executable for Bio::Tools::Run::Phylo::Hyphy::SLAC is not present
t/Hyphy.t ..................... ok
# Required executable for Bio::Tools::Run::Infernal is not present
t/Infernal.t .................. ok
# Required executable for Bio::Tools::Run::Alignment::Kalign is not present
t/Kalign.t .................... ok
# Required executable for Bio::Tools::Run::Phylo::LVB is not present
t/LVB.t ....................... ok
# Required executable for Bio::Tools::Run::Alignment::Lagan is not present
t/Lagan.t ..................... ok
# Required executable for Bio::Tools::Run::Alignment::MAFFT is not present
t/MAFFT.t ..................... ok
# Failed test 'use Bio::Tools::Run::MCS;'
# at t/MCS.t line 8.
# Tried to use 'Bio::Tools::Run::MCS'.
# Error: Can't locate Bio/FeatureIO.pm in @INC (you may need to install the Bio::FeatureIO module) (@INC contains: /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/lib /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/arch /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/x86_64-linux /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0 /opt/perl-5.22.0-RC2/lib/5.22.0/x86_64-linux /opt/perl-5.22.0-RC2/lib/5.22.0 .) at /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/lib/Bio/Tools/Run/MCS.pm line 132.
# BEGIN failed--compilation aborted at /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/lib/Bio/Tools/Run/MCS.pm line 132.
# Compilation failed in require at t/MCS.t line 8.
# BEGIN failed--compilation aborted at t/MCS.t line 8.
# Failed test 'use Bio::SeqFeature::Annotated;'
# at t/MCS.t line 9.
# Tried to use 'Bio::SeqFeature::Annotated'.
# Error: Can't locate Bio/SeqFeature/Annotated.pm in @INC (you may need to install the Bio::SeqFeature::Annotated module) (@INC contains: /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/lib /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/arch /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/x86_64-linux /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0 /opt/perl-5.22.0-RC2/lib/5.22.0/x86_64-linux /opt/perl-5.22.0-RC2/lib/5.22.0 .) at t/MCS.t line 9.
# BEGIN failed--compilation aborted at t/MCS.t line 9.
Can't locate object method "new" via package "Bio::Tools::Run::MCS" at t/MCS.t line 17.
# Looks like you planned 24 tests but ran 4.
# Looks like you failed 2 tests of 4 run.
# Looks like your test exited with 255 just after 4.
t/MCS.t .......................
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 22/24 subtests
# Failed test 'translate params'
# at t/Maq.t line 73.
# got: 'assemble -r 0.005 -m 4 -s'
# expected: 'assemble -m 4 -r 0.005 -s'
# Required executable for Bio::Tools::Run::Maq is not present
# Looks like you failed 1 test of 51.
t/Maq.t .......................
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/51 subtests
(less 27 skipped subtests: 23 okay)
# Failed test 'use Bio::Tools::Run::Match;'
# at t/Match.t line 9.
# Tried to use 'Bio::Tools::Run::Match'.
# Error: Can't locate Bio/FeatureIO.pm in @INC (you may need to install the Bio::FeatureIO module) (@INC contains: /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/lib /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/arch /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/x86_64-linux /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0 /opt/perl-5.22.0-RC2/lib/5.22.0/x86_64-linux /opt/perl-5.22.0-RC2/lib/5.22.0 .) at /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/lib/Bio/Tools/Run/Match.pm line 117.
# BEGIN failed--compilation aborted at /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/lib/Bio/Tools/Run/Match.pm line 117.
# Compilation failed in require at t/Match.t line 9.
# BEGIN failed--compilation aborted at t/Match.t line 9.
Can't locate object method "new" via package "Bio::Tools::Run::Match" at t/Match.t line 16.
# Looks like you planned 7 tests but ran 1.
# Looks like you failed 1 test of 1 run.
# Looks like your test exited with 255 just after 1.
t/Match.t .....................
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 7/7 subtests
# Required executable for Bio::Tools::Run::Mdust is not present
t/Mdust.t ..................... ok
# Required executable for Bio::Tools::Run::Meme is not present
t/Meme.t ...................... ok
# Required executable for Bio::Tools::Run::Minimo is not present
t/Minimo.t .................... ok
# Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
t/Molphy.t .................... ok
# Required executable for Bio::Tools::Run::Alignment::Muscle is not present
t/Muscle.t .................... ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
t/Neighbor.t .................. ok
# Required executable for Bio::Tools::Run::Newbler is not present
t/Newbler.t ................... ok
# Required executable for Bio::Tools::Run::Phylo::Njtree::Best is not present
t/Njtree.t .................... ok
# Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present
t/PAML.t ...................... ok
# Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present
t/Pal2Nal.t ................... ok
# Failed test 'use Bio::Tools::Run::Phylo::Phast::PhastCons;'
# at t/PhastCons.t line 10.
# Tried to use 'Bio::Tools::Run::Phylo::Phast::PhastCons'.
# Error: Can't locate Bio/FeatureIO.pm in @INC (you may need to install the Bio::FeatureIO module) (@INC contains: /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/lib /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/arch /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/x86_64-linux /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0 /opt/perl-5.22.0-RC2/lib/5.22.0/x86_64-linux /opt/perl-5.22.0-RC2/lib/5.22.0 .) at /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm line 140.
# BEGIN failed--compilation aborted at /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm line 140.
# Compilation failed in require at t/PhastCons.t line 10.
# BEGIN failed--compilation aborted at t/PhastCons.t line 10.
Can't locate object method "new" via package "Bio::Tools::Run::Phylo::Phast::PhastCons" at t/PhastCons.t line 23.
# Looks like you planned 181 tests but ran 6.
# Looks like you failed 1 test of 6 run.
# Looks like your test exited with 255 just after 6.
t/PhastCons.t .................
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 176/181 subtests
# Required executable for Bio::Tools::Run::Phrap is not present
t/Phrap.t ..................... ok
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Cannot find executable for phyml. path="phyml"
STACK: Error::throw
STACK: Bio::Root::Root::throw /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/Bio/Root/Root.pm:449
STACK: Bio::Tools::Run::WrapperBase::executable /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/Bio/Tools/Run/WrapperBase.pm:340
STACK: Bio::Tools::Run::Phylo::Phyml::version /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/lib/Bio/Tools/Run/Phylo/Phyml.pm:301
STACK: Bio::Tools::Run::Phylo::Phyml::model /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/lib/Bio/Tools/Run/Phylo/Phyml.pm:479
STACK: t/Phyml.t:31
-----------------------------------------------------------
# Looks like you planned 47 tests but ran 11.
# Looks like your test exited with 2 just after 11.
t/Phyml.t .....................
Dubious, test returned 2 (wstat 512, 0x200)
Failed 36/47 subtests
# Required executable for Bio::Tools::Run::Primate is not present
t/Primate.t ................... ok
# Required executable for Bio::Tools::Run::Primer3 is not present
t/Primer3.t ................... ok
# Required executable for Bio::Tools::Run::Prints is not present
t/Prints.t .................... ok
# Required executable for Bio::Tools::Run::Alignment::Probalign is not present
t/Probalign.t ................. ok
# Required executable for Bio::Tools::Run::Alignment::Probcons is not present
t/Probcons.t .................. ok
# Required executable for Bio::Tools::Run::Profile is not present
t/Profile.t ................... ok
# Required executable for Bio::Tools::Run::Promoterwise is not present
t/Promoterwise.t .............. ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present
t/ProtDist.t .................. ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present
t/ProtPars.t .................. ok
# Required executable for Bio::Tools::Run::Pseudowise is not present
t/Pseudowise.t ................ ok
# Required executable for Bio::Tools::Run::Phylo::QuickTree is not present
t/QuickTree.t ................. ok
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Cannot find executable for RepeatMasker. path="RepeatMasker"
STACK: Error::throw
STACK: Bio::Root::Root::throw /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/Bio/Root/Root.pm:449
STACK: Bio::Tools::Run::WrapperBase::executable /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/Bio/Tools/Run/WrapperBase.pm:340
STACK: Bio::Tools::Run::RepeatMasker::new /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/lib/Bio/Tools/Run/RepeatMasker.pm:207
STACK: t/RepeatMasker.t:18
-----------------------------------------------------------
# Looks like you planned 12 tests but ran 2.
# Looks like your test exited with 2 just after 2.
t/RepeatMasker.t ..............
Dubious, test returned 2 (wstat 512, 0x200)
Failed 10/12 subtests
# 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)
# Required executable for Bio::Tools::Run::Phylo::SLR is not present
t/SLR.t ....................... ok
# Failed test 'translate params'
# at t/Samtools.t line 68.
# got: 'pileup -f my.fas -T 0.05'
# expected: 'pileup -T 0.05 -f my.fas'
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Can't find executable for 'samtools'; can't continue
STACK: Error::throw
STACK: Bio::Root::Root::throw /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/Bio/Root/Root.pm:449
STACK: Bio::Tools::Run::WrapperBase::_run /opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/Bio/Tools/Run/WrapperBase/CommandExts.pm:974
STACK: Bio::Tools::Run::Samtools::run /tmpfs/.cpan-build/BioPerl-Run-1.006900-7VPSg3/blib/lib/Bio/Tools/Run/Samtools.pm:176
STACK: t/Samtools.t:71
-----------------------------------------------------------
# Looks like you planned 40 tests but ran 24.
# Looks like you failed 1 test of 24 run.
# Looks like your test exited with 2 just after 24.
t/Samtools.t ..................
Dubious, test returned 2 (wstat 512, 0x200)
Failed 17/40 subtests
# Required executable for Bio::Tools::Run::Seg is not present
t/Seg.t ....................... ok
# Required executable for Bio::Tools::Run::Phylo::Semphy is not present
t/Semphy.t .................... ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present
t/SeqBoot.t ................... ok
# Required executable for Bio::Tools::Run::Signalp is not present
t/Signalp.t ................... ok
# Required executable for Bio::Tools::Run::Alignment::Sim4 is not present
t/Sim4.t ...................... ok
# 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
# NOTE: No network access required for these tests; all are local file-based.
t/SoapEU-unit.t ............... ok
# Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present
t/StandAloneFasta.t ........... ok
# Required executable for Bio::Tools::Run::Alignment::TCoffee is not present
t/TCoffee.t ................... ok
# Required executable for Bio::Tools::Run::TigrAssembler is not present
# Required executable for Bio::Tools::Run::TigrAssembler is not present
t/TigrAssembler.t ............. ok
# Required executable for Bio::Tools::Run::Tmhmm is not present
t/Tmhmm.t ..................... ok
t/TribeMCL.t .................. ok
t/Vista.t ..................... ok
# Required executable for Bio::Tools::Run::Alignment::Gmap is not present
t/gmap-run.t .................. ok
# 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: 512 Tests: 4 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 33 tests but ran 4.
t/Bowtie.t (Wstat: 256 Tests: 73 Failed: 1)
Failed test: 33
Non-zero exit status: 1
t/Gumby.t (Wstat: 65280 Tests: 8 Failed: 1)
Failed test: 1
Non-zero exit status: 255
Parse errors: Bad plan. You planned 124 tests but ran 8.
t/MCS.t (Wstat: 65280 Tests: 4 Failed: 2)
Failed tests: 1-2
Non-zero exit status: 255
Parse errors: Bad plan. You planned 24 tests but ran 4.
t/Maq.t (Wstat: 256 Tests: 51 Failed: 1)
Failed test: 24
Non-zero exit status: 1
t/Match.t (Wstat: 65280 Tests: 1 Failed: 1)
Failed test: 1
Non-zero exit status: 255
Parse errors: Bad plan. You planned 7 tests but ran 1.
t/PhastCons.t (Wstat: 65280 Tests: 6 Failed: 1)
Failed test: 1
Non-zero exit status: 255
Parse errors: Bad plan. You planned 181 tests but ran 6.
t/Phyml.t (Wstat: 512 Tests: 11 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 47 tests but ran 11.
t/RepeatMasker.t (Wstat: 512 Tests: 2 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 12 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.
t/Samtools.t (Wstat: 512 Tests: 24 Failed: 1)
Failed test: 24
Non-zero exit status: 2
Parse errors: Bad plan. You planned 40 tests but ran 24.
Files=80, Tests=2589, 24 wallclock secs ( 0.29 usr 0.47 sys + 12.05 cusr 3.26 csys = 16.07 CPU)
Result: FAIL
Failed 12/80 test programs. 8/2589 subtests failed.
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------ -------- --------
Bio::Root::Version 1.006900 1.006924
perl v5.6.1 5.022000
configure_requires:
Module Need Have
------------------ -------- --------
Module::Build 0.38 0.4212
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
DBIC_NO_WARN_BAD_PERL = 1
LANG = C
LC_ALL = de_DE.UTF-8
PATH = /usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/eserte/bin/linux-gnu:/home/eserte/bin/sh:/home/eserte/bin:/usr/games:/home/eserte/devel:/home/eserte/src/srezic-misc/scripts
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 7041
PERL5_CPAN_IS_RUNNING = 7041
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 17529,7041
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1001/cpanreporter_022_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_HTML_DISPLAY_CLASS = HTML::Display::Mozilla
PERL_PARALLEL_SMOKER = yes
SHELL = /bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1001
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /opt/perl-5.22.0-RC2/bin/perl
$UID/$EUID = 1001 / 1001
$GID = 1001 109 1001
$EGID = 1001 109 1001
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.11
CPAN::Meta 2.150001
Cwd 3.56
ExtUtils::CBuilder 0.280221
ExtUtils::Command 1.20
ExtUtils::Install 2.04
ExtUtils::MakeMaker 7.04_01
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.28
File::Spec 3.56
JSON 2.90
JSON::PP 2.27300
Module::Build 0.4212
Module::Signature 0.79
Parse::CPAN::Meta 1.4414
Test::Harness 3.35
Test::More 1.001014
YAML 1.15
YAML::Syck 1.29
version 0.9909
--
Summary of my perl5 (revision 5 version 22 subversion 0) configuration:
Platform:
osname=linux, osvers=3.2.0-4-amd64, archname=x86_64-linux
uname='linux eserte 3.2.0-4-amd64 #1 smp debian 3.2.68-1+deb7u1 x86_64 gnulinux '
config_args='-ds -e -Dprefix=/opt/perl-5.22.0-RC2 -Dcf_email=srezic@cpan.org'
hint=recommended, useposix=true, d_sigaction=define
useithreads=undef, usemultiplicity=undef
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-fwrapv -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2',
optimize='-O2',
cppflags='-fwrapv -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='4.7.2', gccosandvers=''
intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678, doublekind=3
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16, longdblkind=3
ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=8, prototype=define
Linker and Libraries:
ld='cc', ldflags =' -fstack-protector -L/usr/local/lib'
libpth=/usr/local/lib /usr/lib/gcc/x86_64-linux-gnu/4.7/include-fixed /usr/include/x86_64-linux-gnu /usr/lib /lib/x86_64-linux-gnu /lib/../lib /usr/lib/x86_64-linux-gnu /usr/lib/../lib /lib
libs=-lpthread -lnsl -ldb -ldl -lm -lcrypt -lutil -lc
perllibs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
libc=libc-2.13.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.13'
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
cccdlflags='-fPIC', lddlflags='-shared -O2 -L/usr/local/lib -fstack-protector'
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES PERLIO_LAYERS PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD PERL_MALLOC_WRAP
PERL_NEW_COPY_ON_WRITE PERL_PRESERVE_IVUV
USE_64_BIT_ALL USE_64_BIT_INT USE_LARGE_FILES
USE_LOCALE USE_LOCALE_COLLATE USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC USE_LOCALE_TIME USE_PERLIO
USE_PERL_ATOF
Locally applied patches:
RC2
Built under linux
Compiled at May 27 2015 23:09:28
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="7041"
PERL5_CPAN_IS_RUNNING="7041"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="17529,7041"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1001/cpanreporter_022_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_HTML_DISPLAY_CLASS="HTML::Display::Mozilla"
PERL_PARALLEL_SMOKER="yes"
@INC:
/opt/perl-5.22.0-RC2/lib/site_perl/5.22.0/x86_64-linux
/opt/perl-5.22.0-RC2/lib/site_perl/5.22.0
/opt/perl-5.22.0-RC2/lib/5.22.0/x86_64-linux
/opt/perl-5.22.0-RC2/lib/5.22.0
.