BioPerl-Run v1.007002 Perl 5 v5.26.0 i86pc-solaris-thread-multi
- Status
- Pass
- From
- Serguei Trouchelle (STRO)
- Dist
-
BioPerl-Run v1.007002
- Platform
- Perl 5 v5.26.0 i86pc-solaris-thread-multi
- Date
- 2017-09-22 09:22:24
- ID
- 8b548cf2-9f77-11e7-ac3c-c4adf83032b5
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 5.26.0, created by CPAN-Reporter-1.2018.
Thank you for uploading your work to CPAN. Congratulations!
All tests were successful.
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
# 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::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: 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
# 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
All tests successful.
Files=80, Tests=2393, 31 wallclock secs ( 0.39 usr 0.21 sys + 14.91 cusr 3.12 csys = 18.63 CPU)
Result: PASS
------------------------------
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 5.026000
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
opt_requires:
Module Need Have
------------------ -------- --------
Algorithm::Diff 0 1.1903
! Bio::FeatureIO 0 n/a
Config::Any 0 0.32
! File::Sort 0 n/a
IO::String 0 1.08
IPC::Run 0 0.96
XML::Twig 0 3.52
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_US.UTF-8
PATH = /usr/gnu/bin:/usr/bin:/usr/sbin:/sbin:/usr/sfw/bin:
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 26289
PERL5_CPAN_IS_RUNNING = 26289
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 24236,26289
PERL_CR_SMOKER_CURRENT = Bio-Tools-Run-Alignment-Clustalw-1.7.2
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_MM_USE_DEFAULT = 1
PERL_USE_UNSAFE_INC = 1
SHELL = /bin/bash
TERM = xterm-256color
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/stro/perl/5.26.0t/bin/perl
$UID/$EUID = 101 / 101
$GID = 10 10
$EGID = 10 10
Perl module toolchain versions installed:
Module Have
------------------- ----------
CPAN 2.18
CPAN::Meta 2.150010
Cwd 3.67
ExtUtils::CBuilder 0.280225
ExtUtils::Command 7.24
ExtUtils::Install 2.04
ExtUtils::MakeMaker 7.24
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.34
File::Spec 3.67
JSON 2.94
JSON::PP 2.27400_02
Module::Build 0.4224
Module::Signature n/a
Parse::CPAN::Meta 2.150010
Test::Harness 3.38
Test::More 1.302096
YAML 1.23
YAML::Syck 1.30
version 0.9917
--
Summary of my perl5 (revision 5 version 26 subversion 0) configuration:
Platform:
osname=solaris
osvers=2.11
archname=i86pc-solaris-thread-multi
uname='sunos vm-openindiana-001 5.11 illumos-ed992b0aac i86pc i386 i86pc solaris '
config_args=''
hint=recommended
useposix=true
d_sigaction=define
useithreads=define
usemultiplicity=define
use64bitint=undef
use64bitall=undef
uselongdouble=undef
usemymalloc=n
default_inc_excludes_dot=define
bincompat5005=undef
Compiler:
cc='/opt/SUNWspro/bin/cc'
ccflags ='-D_REENTRANT -I/usr/gnu/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPERL_USE_SAFE_PUTENV'
optimize='-O'
cppflags='-D_REENTRANT -I/usr/gnu/include'
ccversion='Sun C 5.10 SunOS_i386 2009/06/03'
gccversion=''
gccosandvers=''
intsize=4
longsize=4
ptrsize=4
doublesize=8
byteorder=1234
doublekind=3
d_longlong=define
longlongsize=8
d_longdbl=define
longdblsize=12
longdblkind=3
ivtype='long'
ivsize=4
nvtype='double'
nvsize=8
Off_t='off_t'
lseeksize=8
alignbytes=4
prototype=define
Linker and Libraries:
ld='/opt/SUNWspro/bin/cc'
ldflags =' -L/usr/lib -L/usr/ccs/lib -L/opt/sunstudio12.1/prod/lib -L/lib -L/usr/gnu/lib '
libpth=/usr/lib /usr/ccs/lib /opt/sunstudio12.1/prod/lib /lib /usr/gnu/lib
libs=-lpthread -lsocket -lnsl -lgdbm -ldb -ldl -lm -lc
perllibs=-lpthread -lsocket -lnsl -ldl -lm -lc
libc=/lib/libc.so
so=so
useshrplib=true
libperl=libperl.so
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_dlopen.xs
dlext=so
d_dlsymun=undef
ccdlflags=' -R /home/stro/perl/5.26.0t/lib/5.26.0/i86pc-solaris-thread-multi/CORE'
cccdlflags='-KPIC'
lddlflags='-G -L/usr/lib -L/usr/ccs/lib -L/opt/sunstudio12.1/prod/lib -L/lib -L/usr/gnu/lib'
Characteristics of this binary (from libperl):
Compile-time options:
HAS_TIMES
MULTIPLICITY
PERLIO_LAYERS
PERL_COPY_ON_WRITE
PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
PERL_IMPLICIT_CONTEXT
PERL_MALLOC_WRAP
PERL_OP_PARENT
PERL_PRESERVE_IVUV
PERL_USE_SAFE_PUTENV
USE_ITHREADS
USE_LARGE_FILES
USE_LOCALE
USE_LOCALE_COLLATE
USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC
USE_LOCALE_TIME
USE_PERLIO
USE_PERL_ATOF
USE_REENTRANT_API
Built under solaris
Compiled at Sep 18 2017 00:57:02
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="26289"
PERL5_CPAN_IS_RUNNING="26289"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="24236,26289"
PERL_CR_SMOKER_CURRENT="Bio-Tools-Run-Alignment-Clustalw-1.7.2"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_MM_USE_DEFAULT="1"
PERL_USE_UNSAFE_INC="1"
@INC:
/home/stro/perl/5.26.0t/lib/site_perl/5.26.0/i86pc-solaris-thread-multi
/home/stro/perl/5.26.0t/lib/site_perl/5.26.0
/home/stro/perl/5.26.0t/lib/5.26.0/i86pc-solaris-thread-multi
/home/stro/perl/5.26.0t/lib/5.26.0
.