BioPerl-Run v1.007002 Perl 5 v5.22.3 x86_64-linux-ld
- Status
- Fail
- From
- Andreas J. König (ANDK)
- Dist
-
BioPerl-Run v1.007002
- Platform
- Perl 5 v5.22.3 x86_64-linux-ld
- Date
- 2017-12-08 04:58:33
- ID
- 70ccdf8a-dbd4-11e7-b03c-d88cad0c1d39
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-1.007002
on perl 5.22.3, created by CPAN-Reporter-1.2018.
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
t/BWA.t ....................... skipped: The optional module Bio::DB::Sam (or dependencies thereof) was not installed
# Required executable for Bio::Tools::Run::Alignment::Blat is not present
t/Blat.t ...................... ok
# 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::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::Phylo::FastTree is not present
t/FastTree.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
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::REL 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
t/MCS.t ....................... ok
# Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
t/MSAProbs.t .................. ok
# Required executable for Bio::Tools::Run::Maq is not present
t/Maq.t ....................... ok
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::Alignment::Pal2Nal is not present
t/Pal2Nal.t ................... ok
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
t/ProtDist.t .................. ok
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
# Required executable for Bio::Tools::Run::Phylo::Raxml is not present
t/Raxml.t ..................... ok
# Required executable for Bio::Tools::Run::RepeatMasker is not present
t/RepeatMasker.t .............. ok
# Required executable for Bio::Tools::Run::BlastPlus is not present
t/SABlastPlus.t ............... ok
# Required executable for Bio::Tools::Run::Phylo::SLR is not present
t/SLR.t ....................... ok
# Required executable for Bio::Tools::Run::Samtools is not present
t/Samtools.t .................. ok
# 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
# NCBI SOAP EUtilities API no longer supported as of 2015, modules are deprecated and will be removed in a future release
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::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/Eponine.t (Wstat: 65280 Tests: 2 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 7 tests but ran 2.
Files=80, Tests=2527, 49 wallclock secs ( 0.27 usr 0.59 sys + 13.28 cusr 3.12 csys = 17.26 CPU)
Result: FAIL
Failed 1/80 test programs. 0/2527 subtests failed.
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------ -------- --------
Bio::Root::Root 0 1.007002
Bio::Root::Version 1.007000 1.007002
perl v5.6.1 5.022003
build_requires:
Module Need Have
------------------ -------- --------
Bio::Root::Test 0 0
Bio::Root::Version 1.007000 1.007002
configure_requires:
Module Need Have
------------------ -------- --------
Module::Build 0.42 0.4224
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_US.UTF-8
PATH = /home/sand/bin:/usr/local/bin:/usr/bin:/bin:/usr/games:/usr/local/perl/bin:/usr/X11/bin:/sbin:/usr/sbin
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 15824
PERL5_CPAN_IS_RUNNING = 15824
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 1718,15824
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_MM_USE_DEFAULT = 1
PERL_USE_UNSAFE_INC = 1
SHELL = /usr/bin/zsh
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.22.3/2d7c/bin/perl
$UID/$EUID = 1005 / 1005
$GID = 1005 1005
$EGID = 1005 1005
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.20
CPAN::Meta 2.150010
Cwd 3.62
ExtUtils::CBuilder 0.280230
ExtUtils::Command 7.30
ExtUtils::Install 2.06
ExtUtils::MakeMaker 7.30
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.35
File::Spec 3.62
JSON 2.97000
JSON::PP 2.96
Module::Build 0.4224
Module::Signature 0.81
Parse::CPAN::Meta 2.150010
Test::Harness 3.39
Test::More 1.302120
YAML 1.24
YAML::Syck 1.30
version 0.9918
--
Summary of my perl5 (revision 5 version 22 subversion 3) configuration:
Derived from: 16b638b0a20de774856b3a21a75a5e373af5262c
Platform:
osname=linux, osvers=4.12.0-2-amd64, archname=x86_64-linux-ld
uname='linux k93msid 4.12.0-2-amd64 #1 smp debian 4.12.13-1 (2017-09-19) x86_64 gnulinux '
config_args='-Dprefix=/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.22.3/2d7c -Dmyhostname=k93msid -Dinstallusrbinperl=n -Uversiononly -Dusedevel -des -Ui_db -Dlibswanted=cl pthread socket inet nsl gdbm dbm malloc dl ld sun m crypt sec util c cposix posix ucb BSD gdbm_compat -Uuseithreads -Duselongdouble -DDEBUGGING=-g'
hint=recommended, useposix=true, d_sigaction=define
useithreads=undef, usemultiplicity=undef
use64bitint=define, use64bitall=define, uselongdouble=define
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2 -g',
cppflags='-fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
ccversion='', gccversion='7.2.0', 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='long double', nvsize=16, Off_t='off_t', lseeksize=8
alignbytes=16, prototype=define
Linker and Libraries:
ld='cc', ldflags =' -fstack-protector-strong -L/usr/local/lib'
libpth=/usr/local/lib /usr/lib/gcc/x86_64-linux-gnu/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 -ldl -lm -lcrypt -lutil -lc
perllibs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
libc=libc-2.24.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.24'
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
cccdlflags='-fPIC', lddlflags='-shared -O2 -g -L/usr/local/lib -fstack-protector-strong'
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
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_LONG_DOUBLE USE_PERLIO USE_PERL_ATOF
Locally applied patches:
uncommitted-changes
Built under linux
Compiled at Oct 2 2017 16:48:30
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="15824"
PERL5_CPAN_IS_RUNNING="15824"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="1718,15824"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_MM_USE_DEFAULT="1"
PERL_USE_UNSAFE_INC="1"
@INC:
/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.22.3/2d7c/lib/site_perl/5.22.3/x86_64-linux-ld
/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.22.3/2d7c/lib/site_perl/5.22.3
/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.22.3/2d7c/lib/5.22.3/x86_64-linux-ld
/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.22.3/2d7c/lib/5.22.3
.