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From: metabase:user:314402c4-2aae-11df-837a-5e0a49663a4f
Subject: FAIL BioPerl-Run-1.006900 v5.21.3 GNU/Linux
Date: 2014-08-31T06:56:52Z
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 5.21.3, created by CPAN-Reporter-1.2011.
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
t/BEDTools.t .................. skipped: The optional module Bio::Tools::Run::BEDTools (or dependencies thereof) was not installed
------------- 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-5.21.3/lib/site_perl/5.21.3/Bio/Root/Root.pm:449
STACK: Bio::Assembly::IO::sam::BEGIN /opt/perl-5.21.3/lib/site_perl/5.21.3/Bio/Assembly/IO/sam.pm:189
STACK: main::BEGIN /opt/perl-5.21.3/lib/site_perl/5.21.3/Bio/Assembly/IO/sam.pm:195
STACK: /opt/perl-5.21.3/lib/site_perl/5.21.3/Bio/Assembly/IO/sam.pm:195
-----------------------------------------------------------
BEGIN failed--compilation aborted at /opt/perl-5.21.3/lib/site_perl/5.21.3/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-5.21.3/lib/site_perl/5.21.3/Bio/Root/Root.pm:449
STACK: Bio::Tools::Run::WrapperBase::executable /opt/perl-5.21.3/lib/site_perl/5.21.3/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 -y --solexa-quals -S'
# 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
# Required executable for Bio::Tools::Run::Phylo::Gumby is not present
t/Gumby.t ..................... ok
# 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
# Required executable for Bio::Tools::Run::MCS is not present
t/MCS.t ....................... ok
# Failed test 'parameter really reset via arg'
# at t/Maq.t line 41.
# got: undef
# expected: '0.05'
# 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)
# Required executable for Bio::Tools::Run::Match is not present
t/Match.t ..................... ok
# 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
# Required executable for Bio::Tools::Run::Phylo::Phast::PhastCons is not present
t/PhastCons.t ................. ok
# 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-5.21.3/lib/site_perl/5.21.3/Bio/Root/Root.pm:449
STACK: Bio::Tools::Run::WrapperBase::executable /opt/perl-5.21.3/lib/site_perl/5.21.3/Bio/Tools/Run/WrapperBase.pm:340
STACK: Bio::Tools::Run::Phylo::Phyml::version /tmpfs/.cpan-build/BioPerl-Run-1.006900-gGO_a1/blib/lib/Bio/Tools/Run/Phylo/Phyml.pm:301
STACK: Bio::Tools::Run::Phylo::Phyml::model /tmpfs/.cpan-build/BioPerl-Run-1.006900-gGO_a1/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-5.21.3/lib/site_perl/5.21.3/Bio/Root/Root.pm:449
STACK: Bio::Tools::Run::WrapperBase::executable /opt/perl-5.21.3/lib/site_perl/5.21.3/Bio/Tools/Run/WrapperBase.pm:340
STACK: Bio::Tools::Run::RepeatMasker::new /tmpfs/.cpan-build/BioPerl-Run-1.006900-gGO_a1/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-5.21.3/lib/site_perl/5.21.3/Bio/Root/Root.pm:449
STACK: Bio::Tools::Run::WrapperBase::_run /opt/perl-5.21.3/lib/site_perl/5.21.3/Bio/Tools/Run/WrapperBase/CommandExts.pm:974
STACK: Bio::Tools::Run::Samtools::run /tmpfs/.cpan-build/BioPerl-Run-1.006900-gGO_a1/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/Maq.t (Wstat: 256 Tests: 51 Failed: 1)
Failed test: 14
Non-zero exit status: 1
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=2483, 25 wallclock secs ( 0.39 usr 0.76 sys + 17.61 cusr 3.37 csys = 22.13 CPU)
Result: FAIL
Failed 8/80 test programs. 3/2483 subtests failed.
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------ -------- --------
Bio::Root::Version 1.006900 1.006924
perl v5.6.1 5.021003
configure_requires:
Module Need Have
------------------ -------- --------
Module::Build 0.38 0.4208
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
DBIC_NO_WARN_BAD_PERL = 1
LANG = C
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 = /home/eserte/.cpan/build/Bio-FeatureIO-1.6.902-i4znIX/blib/arch:/home/eserte/.cpan/build/Bio-FeatureIO-1.6.902-i4znIX/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 32607
PERL5_CPAN_IS_RUNNING = 32607
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 32590,32607
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1001/ftzVNaGG_x_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_HTML_DISPLAY_CLASS = HTML::Display::Mozilla
SHELL = /bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1001
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /bbbike/perl-5.21.3/bin/perl5.21.3
$UID/$EUID = 1001 / 1001
$GID = 1001 109 1001
$EGID = 1001 109 1001
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.05
CPAN::Meta 2.142060
Cwd 3.49
ExtUtils::CBuilder 0.280217
ExtUtils::Command 1.18
ExtUtils::Install 1.68
ExtUtils::MakeMaker 6.98
ExtUtils::Manifest 1.65
ExtUtils::ParseXS 3.25
File::Spec 3.49
JSON 2.90
JSON::PP 2.27203
Module::Build 0.4208
Module::Signature 0.73
Parse::CPAN::Meta 1.4414
Test::Harness 3.33
Test::More 1.001003
YAML 1.11
YAML::Syck 1.27
version 0.9909
--
Summary of my perl5 (revision 5 version 21 subversion 3) 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 3.2.60-1+deb7u3 x86_64 gnulinux '
config_args='-ds -e -Dprefix=/opt/perl-5.21.3t -Dusedevel -Dusemallocwrap=no -Dusethreads'
hint=previous, 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 -fwrapv -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2'
ccversion='', gccversion='4.7.2', gccosandvers=''
intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678
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 /usr/local/lib /usr/lib/gcc/x86_64-linux-gnu/4.7/include-fixed /usr/include/x86_64-linux-gnu /usr/lib
libs=-lnsl -ldb -ldl -lm -lcrypt -lutil -lc
perllibs=-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_NEW_COPY_ON_WRITE PERL_PRESERVE_IVUV
PERL_USE_DEVEL 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
Built under linux
Compiled at Aug 21 2014 18:13:43
%ENV:
PERL5LIB="/home/eserte/.cpan/build/Bio-FeatureIO-1.6.902-i4znIX/blib/arch:/home/eserte/.cpan/build/Bio-FeatureIO-1.6.902-i4znIX/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="32607"
PERL5_CPAN_IS_RUNNING="32607"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="32590,32607"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1001/ftzVNaGG_x_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_HTML_DISPLAY_CLASS="HTML::Display::Mozilla"
@INC:
/home/eserte/.cpan/build/Bio-FeatureIO-1.6.902-i4znIX/blib/arch
/home/eserte/.cpan/build/Bio-FeatureIO-1.6.902-i4znIX/blib/lib
/opt/perl-5.21.3/lib/site_perl/5.21.3/x86_64-linux
/opt/perl-5.21.3/lib/site_perl/5.21.3
/opt/perl-5.21.3/lib/5.21.3/x86_64-linux
/opt/perl-5.21.3/lib/5.21.3
.