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From: metabase:user:30f4dfbe-2aae-11df-837a-5e0a49663a4f
Subject: FAIL BioPerl-Run-1.007000 v5.20.3 Mac OS X
Date: 2016-12-20T23:22:29Z
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-1.007000
on perl 5.20.3, 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 IPC::Run (or dependencies thereof) was not installed
t/BWA.t ....................... skipped: The optional module IPC::Run (or dependencies thereof) was not installed
# Required executable for Bio::Tools::Run::Alignment::Blat is not present
t/Blat.t ...................... ok
t/Bowtie.t .................... skipped: The optional module IPC::Run (or dependencies thereof) was not installed
# 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
-- namet is "-sequence" associated seqall qualifiers
-- namet is "-outfile" associated outfile qualifiers
t/EMBOSS.t .................... ok
t/Ensembl.t ................... skipped: Network tests have not been requested
# Required environment variable $EPONINEDIR is not set
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
t/Genemark.hmm.prokaryotic.t .. skipped: The optional module IPC::Run (or dependencies thereof) was not installed
# 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
t/Glimmer2.t .................. skipped: The optional module IPC::Run (or dependencies thereof) was not installed
t/Glimmer3.t .................. skipped: The optional module IPC::Run (or dependencies thereof) was not installed
# 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: /Users/hornenj/.cpan/build/BioPerl-Run-1.007000-2/blib/lib /Users/hornenj/.cpan/build/BioPerl-Run-1.007000-2/blib/arch /Users/hornenj/.cpan/build/BioPerl-1.007001-11/blib/arch /Users/hornenj/.cpan/build/BioPerl-1.007001-11/blib/lib /Users/hornenj/.cpan/build/Data-Stag-0.14-11/blib/arch /Users/hornenj/.cpan/build/Data-Stag-0.14-11/blib/lib /Users/hornenj/.cpan/build/BioPerl-1.007001-11/blib/arch /Users/hornenj/.cpan/build/BioPerl-1.007001-11/blib/lib /Users/hornenj/.cpan/build/Data-Stag-0.14-11/blib/arch /Users/hornenj/.cpan/build/Data-Stag-0.14-11/blib/lib /Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/site_perl/5.20.3/darwin-thread-multi-2level /Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/site_perl/5.20.3 /Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/5.20.3/darwin-thread-multi-2level /Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/5.20.3 .) at /Users/hornenj/.cpan/build/BioPerl-1.007001-11/blib/lib/Bio/Tools/Phylo/Gumby.pm line 83.
# BEGIN failed--compilation aborted at /Users/hornenj/.cpan/build/BioPerl-1.007001-11/blib/lib/Bio/Tools/Phylo/Gumby.pm line 83.
# Compilation failed in require at /Users/hornenj/.cpan/build/BioPerl-Run-1.007000-2/blib/lib/Bio/Tools/Run/Phylo/Gumby.pm line 142.
# BEGIN failed--compilation aborted at /Users/hornenj/.cpan/build/BioPerl-Run-1.007000-2/blib/lib/Bio/Tools/Run/Phylo/Gumby.pm line 142.
# 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 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::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 ....................... skipped: The optional module Config::Any (or dependencies thereof) was not installed
# Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
t/MSAProbs.t .................. ok
t/Maq.t ....................... skipped: The optional module IPC::Run (or dependencies thereof) was not installed
t/Match.t ..................... skipped: The optional module Config::Any (or dependencies thereof) was not installed
# 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
t/Minimo.t .................... skipped: The optional module IPC::Run (or dependencies thereof) was not installed
# 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
t/Newbler.t ................... skipped: The optional module IPC::Run (or dependencies thereof) was not installed
# 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: /Users/hornenj/.cpan/build/BioPerl-Run-1.007000-2/blib/lib /Users/hornenj/.cpan/build/BioPerl-Run-1.007000-2/blib/arch /Users/hornenj/.cpan/build/BioPerl-1.007001-11/blib/arch /Users/hornenj/.cpan/build/BioPerl-1.007001-11/blib/lib /Users/hornenj/.cpan/build/Data-Stag-0.14-11/blib/arch /Users/hornenj/.cpan/build/Data-Stag-0.14-11/blib/lib /Users/hornenj/.cpan/build/BioPerl-1.007001-11/blib/arch /Users/hornenj/.cpan/build/BioPerl-1.007001-11/blib/lib /Users/hornenj/.cpan/build/Data-Stag-0.14-11/blib/arch /Users/hornenj/.cpan/build/Data-Stag-0.14-11/blib/lib /Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/site_perl/5.20.3/darwin-thread-multi-2level /Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/site_perl/5.20.3 /Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/5.20.3/darwin-thread-multi-2level /Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/5.20.3 .) at /Users/hornenj/.cpan/build/BioPerl-Run-1.007000-2/blib/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm line 140.
# BEGIN failed--compilation aborted at /Users/hornenj/.cpan/build/BioPerl-Run-1.007000-2/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 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
# 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
# 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
# Failed test 'use Bio::Tools::Run::StandAloneBlastPlus;'
# at t/SABlastPlus.t line 15.
# Tried to use 'Bio::Tools::Run::StandAloneBlastPlus'.
# Error: Can't locate IPC/Run.pm in @INC (you may need to install the IPC::Run module) (@INC contains: ../../.. ../../../.. ../lib /Users/hornenj/.cpan/build/BioPerl-Run-1.007000-2/blib/lib /Users/hornenj/.cpan/build/BioPerl-Run-1.007000-2/blib/arch /Users/hornenj/.cpan/build/BioPerl-1.007001-11/blib/arch /Users/hornenj/.cpan/build/BioPerl-1.007001-11/blib/lib /Users/hornenj/.cpan/build/Data-Stag-0.14-11/blib/arch /Users/hornenj/.cpan/build/Data-Stag-0.14-11/blib/lib /Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/site_perl/5.20.3/darwin-thread-multi-2level /Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/site_perl/5.20.3 /Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/5.20.3/darwin-thread-multi-2level /Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/5.20.3 .) at /Users/hornenj/.cpan/build/BioPerl-Run-1.007000-2/blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm line 417.
# BEGIN failed--compilation aborted at /Users/hornenj/.cpan/build/BioPerl-Run-1.007000-2/blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm line 417.
# Compilation failed in require at /Users/hornenj/.cpan/build/BioPerl-Run-1.007000-2/blib/lib/Bio/Tools/Run/BlastPlus.pm line 84.
# BEGIN failed--compilation aborted at /Users/hornenj/.cpan/build/BioPerl-Run-1.007000-2/blib/lib/Bio/Tools/Run/BlastPlus.pm line 84.
# Compilation failed in require at /Users/hornenj/.cpan/build/BioPerl-Run-1.007000-2/blib/lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm line 174.
# BEGIN failed--compilation aborted at /Users/hornenj/.cpan/build/BioPerl-Run-1.007000-2/blib/lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm line 174.
# Compilation failed in require at /Users/hornenj/.cpan/build/BioPerl-Run-1.007000-2/blib/lib/Bio/Tools/Run/StandAloneBlastPlus.pm line 427.
# BEGIN failed--compilation aborted at /Users/hornenj/.cpan/build/BioPerl-Run-1.007000-2/blib/lib/Bio/Tools/Run/StandAloneBlastPlus.pm line 427.
# Compilation failed in require at t/SABlastPlus.t line 15.
# BEGIN failed--compilation aborted at t/SABlastPlus.t line 15.
# Failed test 'use Bio::Tools::Run::WrapperBase::CommandExts;'
# at t/SABlastPlus.t line 17.
# Tried to use 'Bio::Tools::Run::WrapperBase::CommandExts'.
# Error: Attempt to reload Bio/Tools/Run/WrapperBase/CommandExts.pm aborted.
# Compilation failed in require at t/SABlastPlus.t line 17.
# BEGIN failed--compilation aborted at t/SABlastPlus.t line 17.
Can't locate object method "new" via package "Bio::Tools::Run::BlastPlus" at t/SABlastPlus.t line 21.
# Looks like your test exited with 255 just after 3.
t/SABlastPlus.t ...............
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 72/73 subtests
# Required executable for Bio::Tools::Run::Phylo::SLR is not present
t/SLR.t ....................... ok
t/Samtools.t .................. skipped: The optional module IPC::Run (or dependencies thereof) was not installed
# 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::Alignment::TCoffee is not present
t/TCoffee.t ................... ok
t/TigrAssembler.t ............. skipped: The optional module IPC::Run (or dependencies thereof) was not installed
# Required executable for Bio::Tools::Run::Tmhmm is not present
t/Tmhmm.t ..................... ok
t/TribeMCL.t .................. ok
# Vista.jar is not in your class path: Error: Could not find or load main class Vista
t/Vista.t ..................... ok
# Required executable for Bio::Tools::Run::Alignment::Gmap is not present
t/gmap-run.t .................. ok
t/tRNAscanSE.t ................ skipped: The optional module IPC::Run (or dependencies thereof) was not installed
Test Summary Report
-------------------
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/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/SABlastPlus.t (Wstat: 65280 Tests: 3 Failed: 2)
Failed tests: 1, 3
Non-zero exit status: 255
Parse errors: Bad plan. You planned 73 tests but ran 3.
Files=83, Tests=1239, 11 wallclock secs ( 0.21 usr 0.13 sys + 7.40 cusr 1.32 csys = 9.06 CPU)
Result: FAIL
Failed 3/83 test programs. 4/1239 subtests failed.
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------ -------- --------
Bio::Root::Root 0 1.007001
Bio::Root::Version 1.007000 1.007001
perl v5.6.1 5.020003
build_requires:
Module Need Have
------------------ -------- --------
Bio::Root::Test 0 0
Bio::Root::Version 1.007000 1.007001
configure_requires:
Module Need Have
------------------ -------- --------
Module::Build 0.42 0.4220
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_US.UTF-8
LC_ALL = POSIX
LDFLAGS =
PATH = /Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/bin:/Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/bin:/sw/lib/perl5/ExtUtils:/sw/bin:/am/ncbiapdata/bin:/usr/bin:/bin:/usr/X11R6/bin:/netopt/ncbi_tools/bin:/usr/local/ncbi/blast/bin:/net/traces01.be-md.ncbi.nlm.nih.gov/trace_software/vdb/mac/release/x86_64/bin
PERL5LIB = /Users/hornenj/.cpan/build/BioPerl-1.007001-11/blib/arch:/Users/hornenj/.cpan/build/BioPerl-1.007001-11/blib/lib:/Users/hornenj/.cpan/build/Data-Stag-0.14-11/blib/arch:/Users/hornenj/.cpan/build/Data-Stag-0.14-11/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 97863
PERL5_CPAN_IS_RUNNING = 97863
PERL5_MINISMOKEBOX = 0.58
PERLBREW_BASHRC_VERSION = 0.77
PERLBREW_HOME = /Users/hornenj/.perlbrew
PERLBREW_LIB =
PERLBREW_MANPATH = /Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/man
PERLBREW_PATH = /Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/bin
PERLBREW_PERL = perl-5.20.3
PERLBREW_ROOT = /Users/hornenj/perl5/perlbrew
PERLBREW_VERSION = 0.77
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_LOCAL_LIB_ROOT =
PERL_MM_USE_DEFAULT = 1
SHELL = /bin/bash
TERM = xterm-256color
TMPDIR = /var/folders/pz/pd7y1qjs6s3cbk170cw50fjc000c61/T/
ac_cv_path_INTLTOOL_PERL = /usr/bin/perl
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/bin/perl5.20.3
$UID/$EUID = 12481 / 12481
$GID = 14 14 5344 37191 527 37223 241
$EGID = 14 14 5344 37191 527 37223 241
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.14
CPAN::Meta 2.150010
Cwd 3.62
ExtUtils::CBuilder 0.280224
ExtUtils::Command 7.24
ExtUtils::Install 2.04
ExtUtils::MakeMaker 7.24
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.30
File::Spec 3.62
JSON 2.90
JSON::PP 2.27400
Module::Build 0.4220
Module::Signature n/a
Parse::CPAN::Meta 2.150010
Test::Harness 3.36
Test::More 1.302062
YAML 1.19
YAML::Syck 1.29
version 0.9917
--
Summary of my perl5 (revision 5 version 20 subversion 3) configuration:
Platform:
osname=darwin, osvers=14.5.0, archname=darwin-thread-multi-2level
uname='darwin ncbimac2027.ncbi.nlm.nih.gov 14.5.0 darwin kernel version 14.5.0: wed jul 29 02:26:53 pdt 2015; root:xnu-2782.40.9~1release_x86_64 x86_64 '
config_args='-de -Dprefix=/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3 -Duseithreads -Dusemultiplicity -Dusedevel -Accflags=-O2 -W -Wformat=2 -Wswitch -Wshadow -Wwrite-strings -Wuninitialized -Wall -pipe -mtune=native -march=native -fomit-frame-pointer -msse2 -msse -mmmx -pedantic -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wstrict-prototypes -fstack-protector -Wstack-protector -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wdisabled-optimization -Wendif-labels -Wfloat-equal -Wformat-nonliteral -Winline -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wundef -Wformat-security -fassociative-math -Acc=cc -Aeval:scriptdir=/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/bin'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc=' cc', ccflags ='-fno-common -DPERL_DARWIN -O2 -W -Wformat=2 -Wswitch -Wshadow -Wwrite-strings -Wuninitialized -Wall -pipe -mtune=native -march=native -fomit-frame-pointer -msse2 -msse -mmmx -pedantic -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wstrict-prototypes -fstack-protector -Wstack-protector -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wdisabled-optimization -Wendif-labels -Wfloat-equal -Wformat-nonliteral -Winline -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wundef -Wformat-security -fassociative-math -fno-strict-aliasing -I/usr/local/include',
optimize='-O3',
cppflags='-fno-common -DPERL_DARWIN -O2 -W -Wformat=2 -Wswitch -Wshadow -Wwrite-strings -Wuninitialized -Wall -pipe -mtune=native -march=native -fomit-frame-pointer -msse2 -msse -mmmx -pedantic -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wstrict-prototypes -fstack-protector -Wstack-protector -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wdisabled-optimization -Wendif-labels -Wfloat-equal -Wformat-nonliteral -Winline -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wundef -Wformat-security -fassociative-math -fno-strict-aliasing -I/usr/local/include'
ccversion='', gccversion='4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)', 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='env MACOSX_DEPLOYMENT_TARGET=10.3 cc', ldflags =' -fstack-protector -L/usr/local/lib'
libpth=/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/lib /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib /usr/local/lib /usr/lib
libs=-lpthread -ldbm -ldl -lm -lutil -lc
perllibs=-lpthread -ldl -lm -lutil -lc
libc=, so=dylib, useshrplib=false, libperl=libperl.a
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=bundle, d_dlsymun=undef, ccdlflags=' '
cccdlflags=' ', lddlflags=' -bundle -undefined dynamic_lookup -L/usr/local/lib -fstack-protector'
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS
PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
PERL_NEW_COPY_ON_WRITE PERL_PRESERVE_IVUV
PERL_USE_DEVEL USE_64_BIT_ALL USE_64_BIT_INT
USE_ITHREADS USE_LARGE_FILES USE_LOCALE
USE_LOCALE_COLLATE USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC USE_PERLIO USE_PERL_ATOF
USE_REENTRANT_API
Locally applied patches:
Devel::PatchPerl 1.30
Built under darwin
Compiled at Sep 14 2015 07:51:22
%ENV:
PERL5LIB="/Users/hornenj/.cpan/build/BioPerl-1.007001-11/blib/arch:/Users/hornenj/.cpan/build/BioPerl-1.007001-11/blib/lib:/Users/hornenj/.cpan/build/Data-Stag-0.14-11/blib/arch:/Users/hornenj/.cpan/build/Data-Stag-0.14-11/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="97863"
PERL5_CPAN_IS_RUNNING="97863"
PERL5_MINISMOKEBOX="0.58"
PERLBREW_BASHRC_VERSION="0.77"
PERLBREW_HOME="/Users/hornenj/.perlbrew"
PERLBREW_LIB=""
PERLBREW_MANPATH="/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/man"
PERLBREW_PATH="/Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/bin"
PERLBREW_PERL="perl-5.20.3"
PERLBREW_ROOT="/Users/hornenj/perl5/perlbrew"
PERLBREW_VERSION="0.77"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_LOCAL_LIB_ROOT=""
PERL_MM_USE_DEFAULT="1"
@INC:
/Users/hornenj/.cpan/build/BioPerl-1.007001-11/blib/arch
/Users/hornenj/.cpan/build/BioPerl-1.007001-11/blib/lib
/Users/hornenj/.cpan/build/Data-Stag-0.14-11/blib/arch
/Users/hornenj/.cpan/build/Data-Stag-0.14-11/blib/lib
/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/site_perl/5.20.3/darwin-thread-multi-2level
/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/site_perl/5.20.3
/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/5.20.3/darwin-thread-multi-2level
/Users/hornenj/perl5/perlbrew/perls/perl-5.20.3/lib/5.20.3
.