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From: metabase:user:9820532a-708b-1014-9a05-b18a96298da1
Subject: FAIL BioPerl-Run-1.006900 v5.8.9 FreeBSD
Date: 2011-12-09T20:07:01Z
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 5.8.9, created by CPAN-Reporter-1.2003.
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:
this report is from an automated smoke testing program
and was not reviewed by a human for accuracy
------------------------------
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: __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 /home/test/perl5/perlbrew/perls/perl-5.8.9/lib/site_perl/5.8.9/Bio/Root/Root.pm:472
STACK: Bio::Assembly::IO::sam::BEGIN /home/test/perl5/perlbrew/perls/perl-5.8.9/lib/site_perl/5.8.9/Bio/Assembly/IO/sam.pm:189
STACK: main::BEGIN /home/test/perl5/perlbrew/perls/perl-5.8.9/lib/site_perl/5.8.9/Bio/Assembly/IO/sam.pm:195
STACK: /home/test/perl5/perlbrew/perls/perl-5.8.9/lib/site_perl/5.8.9/Bio/Assembly/IO/sam.pm:195
-----------------------------------------------------------
BEGIN failed--compilation aborted at /home/test/perl5/perlbrew/perls/perl-5.8.9/lib/site_perl/5.8.9/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
# 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)
3: Bad file descriptor
# Required executable for Bio::Tools::Run::Bowtie is not present
t/Bowtie.t .................... ok
# 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
# Looks like you planned 7 tests but ran 2.
t/Eponine.t ...................
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 5/7 subtests
# 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
# Required executable for Bio::Tools::Run::Maq is not present
t/Maq.t ....................... ok
# 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
# Required executable for Bio::Tools::Run::Phylo::Phyml is not present
t/Phyml.t ..................... ok
# 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
RepeatMasker program not found as or not executable.
# Required executable for Bio::Tools::Run::RepeatMasker is not present
t/RepeatMasker.t .............. ok
# 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
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Can't find executable for 'samtools'; can't continue
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/test/perl5/perlbrew/perls/perl-5.8.9/lib/site_perl/5.8.9/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::WrapperBase::_run /home/test/perl5/perlbrew/perls/perl-5.8.9/lib/site_perl/5.8.9/Bio/Tools/Run/WrapperBase/CommandExts.pm:974
STACK: Bio::Tools::Run::Samtools::run /usr/home/test/.cpan/build/BioPerl-Run-1.006900-svGcvC/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
# 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
readline() on closed filehandle PIPE at t/Vista.t line 22.
Use of uninitialized value in numeric lt (<) at t/Vista.t line 36.
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: 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.
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=2540, 33 wallclock secs ( 0.95 usr 1.96 sys + 18.38 cusr 6.27 csys = 27.55 CPU)
Result: FAIL
Failed 5/80 test programs. 0/2540 subtests failed.
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------ -------- --------
Bio::Root::Version 1.006900 1.006901
perl v5.6.1 5.008009
configure_requires:
Module Need Have
------------------ -------- --------
Module::Build 0.38 0.39_01
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = C
LC_ALL = C
PATH = /home/test/perl5/perlbrew/bin:/home/test/perl5/perlbrew/perls/perl-5.8.9/bin:~/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/home/test/bin
PATH_WITHOUT_PERLBREW = ~/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/home/test/bin
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 27890
PERL5_CPAN_IS_RUNNING = 27890
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 1068,27890
PERLBREW_BASHRC_VERSION = 0.33
PERLBREW_HOME = /home/test/.perlbrew
PERLBREW_PATH = /home/test/perl5/perlbrew/bin:/home/test/perl5/perlbrew/perls/perl-5.8.9/bin
PERLBREW_PERL = perl-5.8.9
PERLBREW_ROOT = /home/test/perl5/perlbrew
PERLBREW_VERSION = 0.33
PERL_CPANM_OPT = --prompt --mirror http://172.16.1.3/cpan/
PERL_CR_SMOKER_CURRENT = BioPerl-Run-1.006900
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_MM_USE_DEFAULT = 1
SHELL = /usr/local/bin/bash
TERM = linux
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/test/perl5/perlbrew/perls/perl-5.8.9/bin/perl
$UID/$EUID = 1002 / 1002
$GID = 1002 1002
$EGID = 1002 1002
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 1.9800
CPAN::Meta 2.112621
Cwd 3.33
ExtUtils::CBuilder 0.280202
ExtUtils::Command 1.16
ExtUtils::Install 1.54
ExtUtils::MakeMaker 6.62
ExtUtils::Manifest 1.58
ExtUtils::ParseXS 3.07
File::Spec 3.33
JSON 2.53
JSON::PP 2.27200
Module::Build 0.39_01
Module::Signature n/a
Parse::CPAN::Meta 1.4401
Test::Harness 3.23
Test::More 0.98
YAML 0.77
YAML::Syck 1.19
version 0.95
--
Summary of my perl5 (revision 5 version 8 subversion 9) configuration:
Platform:
osname=freebsd, osvers=8.1-release, archname=amd64-freebsd
uname='freebsd fbsd.local 8.1-release freebsd 8.1-release #0: mon jul 19 02:36:49 utc 2010 root@mason.cse.buffalo.edu:usrobjusrsrcsysgeneric amd64 '
config_args='-de -Dprefix=/home/test/perl5/perlbrew/perls/perl-5.8.9'
hint=recommended, useposix=true, d_sigaction=define
usethreads=undef use5005threads=undef useithreads=undef usemultiplicity=undef
useperlio=define d_sfio=undef uselargefiles=define usesocks=undef
use64bitint=define use64bitall=define uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -I/usr/local/include',
optimize='-O',
cppflags='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -I/usr/local/include'
ccversion='', gccversion='4.2.1 20070719 [FreeBSD]', gccosandvers=''
intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=8, prototype=define
Linker and Libraries:
ld='cc', ldflags ='-Wl,-E -L/usr/local/lib'
libpth=/usr/lib /usr/local/lib
libs=-lm -lcrypt -lutil -lc
perllibs=-lm -lcrypt -lutil -lc
libc=, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags=' '
cccdlflags='-DPIC -fPIC', lddlflags='-shared -L/usr/local/lib'
Characteristics of this binary (from libperl):
Compile-time options: PERL_MALLOC_WRAP USE_64_BIT_ALL USE_64_BIT_INT
USE_FAST_STDIO USE_LARGE_FILES USE_PERLIO
Built under freebsd
Compiled at Dec 7 2011 10:40:29
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="27890"
PERL5_CPAN_IS_RUNNING="27890"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="1068,27890"
PERLBREW_BASHRC_VERSION="0.33"
PERLBREW_HOME="/home/test/.perlbrew"
PERLBREW_PATH="/home/test/perl5/perlbrew/bin:/home/test/perl5/perlbrew/perls/perl-5.8.9/bin"
PERLBREW_PERL="perl-5.8.9"
PERLBREW_ROOT="/home/test/perl5/perlbrew"
PERLBREW_VERSION="0.33"
PERL_CPANM_OPT="--prompt --mirror http://172.16.1.3/cpan/"
PERL_CR_SMOKER_CURRENT="BioPerl-Run-1.006900"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_MM_USE_DEFAULT="1"
@INC:
/home/test/perl5/perlbrew/perls/perl-5.8.9/lib/5.8.9/amd64-freebsd
/home/test/perl5/perlbrew/perls/perl-5.8.9/lib/5.8.9
/home/test/perl5/perlbrew/perls/perl-5.8.9/lib/site_perl/5.8.9/amd64-freebsd
/home/test/perl5/perlbrew/perls/perl-5.8.9/lib/site_perl/5.8.9
.