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From: metabase:user:30f4dfbe-2aae-11df-837a-5e0a49663a4f
Subject: PASS Bio-VertRes-Config-1.133090 v5.14.3 Mac OS X
Date: 2013-11-08T02:35:06Z
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 Andrew Page,
This is a computer-generated report for Bio-VertRes-Config-1.133090
on perl 5.14.3, created by CPAN-Reporter-1.2010.
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 '/sw/bin/make test':
PERL_DL_NONLAZY=1 /Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/Bio/VertRes/Config/*.t t/Bio/VertRes/Config/CommandLine/*.t t/Bio/VertRes/Config/Pipelines/*.t t/Bio/VertRes/Config/Recipes/*.t t/bin/*.t
t/bin/bacteria_assembly_and_annotation.t ........................... ok
t/bin/bacteria_assembly_single_cell.t .............................. ok
t/bin/bacteria_mapping.t ........................................... ok
t/bin/bacteria_register_and_qc_study.t ............................. ok
t/bin/bacteria_rna_seq_expression.t ................................ ok
t/bin/bacteria_snp_calling.t ....................................... ok
t/bin/eukaryote_assembly.t ......................................... ok
t/bin/eukaryote_mapping.t .......................................... ok
t/bin/eukaryote_register_and_qc_study.t ............................ ok
t/bin/eukaryote_rna_seq_expression.t ............................... ok
t/bin/eukaryote_snp_calling.t ...................................... ok
t/bin/helminth_mapping.t ........................................... ok
t/bin/helminth_register_and_qc_study.t ............................. ok
t/bin/helminth_rna_seq_expression.t ................................ ok
t/bin/helminth_snp_calling.t ....................................... ok
t/bin/log_parameters.t ............................................. ok
t/bin/setup_global_configs.t ....................................... ok
t/bin/virus_assembly_and_annotation.t .............................. ok
t/bin/virus_mapping.t .............................................. ok
t/bin/virus_register_and_qc_study.t ................................ ok
t/bin/virus_rna_seq_expression.t ................................... ok
t/bin/virus_snp_calling.t .......................................... ok
t/Bio/VertRes/Config/CommandLine/Common.t .......................... ok
t/Bio/VertRes/Config/CommandLine/ConstructLimits.t ................. ok
t/Bio/VertRes/Config/CommandLine/LogParameters.t ................... ok
t/Bio/VertRes/Config/CommandLine/StudyNameSearch.t ................. ok
t/Bio/VertRes/Config/MultipleTopLevelFiles.t ....................... ok
t/Bio/VertRes/Config/Pipelines/AnnotateAssembly.t .................. ok
t/Bio/VertRes/Config/Pipelines/Assembly.t .......................... ok
t/Bio/VertRes/Config/Pipelines/BamImprovement.t .................... ok
t/Bio/VertRes/Config/Pipelines/Bowtie2Mapping.t .................... ok
t/Bio/VertRes/Config/Pipelines/BwaMapping.t ........................ ok
t/Bio/VertRes/Config/Pipelines/Common.t ............................ ok
t/Bio/VertRes/Config/Pipelines/Import.t ............................ ok
t/Bio/VertRes/Config/Pipelines/Mapping.t ........................... ok
t/Bio/VertRes/Config/Pipelines/QC.t ................................ ok
t/Bio/VertRes/Config/Pipelines/RnaSeqExpression.t .................. ok
t/Bio/VertRes/Config/Pipelines/SmaltMapping.t ...................... ok
t/Bio/VertRes/Config/Pipelines/SnpCalling.t ........................ ok
t/Bio/VertRes/Config/Pipelines/SpadesAssembly.t .................... ok
t/Bio/VertRes/Config/Pipelines/Ssaha2Mapping.t ..................... ok
t/Bio/VertRes/Config/Pipelines/StampyMapping.t ..................... ok
t/Bio/VertRes/Config/Pipelines/Store.t ............................. ok
t/Bio/VertRes/Config/Pipelines/Tradis.t ............................ ok
t/Bio/VertRes/Config/Pipelines/VelvetAssembly.t .................... ok
t/Bio/VertRes/Config/Recipes/BacteriaAssemblyAndAnnotation.t ....... ok
t/Bio/VertRes/Config/Recipes/BacteriaAssemblySingleCell.t .......... ok
t/Bio/VertRes/Config/Recipes/BacteriaRegisterAndQCStudy.t .......... ok
t/Bio/VertRes/Config/Recipes/BacteriaRnaSeqExpressionUsingBwa.t .... ok
t/Bio/VertRes/Config/Recipes/BacteriaRnaSeqExpressionUsingSmalt.t .. ok
t/Bio/VertRes/Config/Recipes/BacteriaSnpCallingUsingBwa.t .......... ok
t/Bio/VertRes/Config/Recipes/BacteriaSnpCallingUsingSmalt.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesAssembly.t .................. ok
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingBwa.t ........... ok
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingSmalt.t ......... ok
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingSsaha2.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingStampy.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesRegisterAndQCStudy.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesRnaSeqExpression.t .......... ok
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingBwa.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingSmalt.t ...... ok
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingSsaha2.t ..... ok
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingStampy.t ..... ok
t/Bio/VertRes/Config/Recipes/Global.t .............................. ok
t/Bio/VertRes/Config/Recipes/HelminthRegisterAndQCStudy.t .......... ok
t/Bio/VertRes/Config/Recipes/VirusAssemblyAndAnnotation.t .......... ok
t/Bio/VertRes/Config/Recipes/VirusRegisterAndQCStudy.t ............. ok
t/Bio/VertRes/Config/References.t .................................. ok
t/Bio/VertRes/Config/RegisterStudy.t ............................... ok
t/Bio/VertRes/Config/TopLevel.t .................................... ok
All tests successful.
Files=70, Tests=802, 54 wallclock secs ( 0.24 usr 0.10 sys + 50.44 cusr 2.76 csys = 53.54 CPU)
Result: PASS
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------------- ---- -------
Data::Dumper 0 2.145
DBI 0 1.628
Exception::Class 0 1.37
File::Basename 0 2.82
File::Path 0 2.09
File::Slurp 0 9999.19
Getopt::Long 0 2.41
Moose 0 2.1005
Moose::Role 0 2.1005
Moose::Util::TypeConstraints 0 2.1005
build_requires:
Module Need Have
---------------------------- ---- -------
File::Find 0 1.19
File::Temp 0 0.2301
strict 0 1.04
Test::Most 0 0.31
warnings 0 1.12
configure_requires:
Module Need Have
---------------------------- ---- -------
ExtUtils::MakeMaker 6.30 6.74
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LC_ALL = POSIX
LD_LIBRARY_PATH = :/net/traces01.be-md.ncbi.nlm.nih.gov/trace_software/vdb/mac/release/x86_64/lib
PATH = /Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/bin:/Users/hornenj/perl5/perlbrew/bin:/sw/lib/perl5/ExtUtils:/sw/bin:/sw/sbin:/am/ncbiapdata/bin:/usr/bin:/bin:/usr/X11R6/bin:/Users/hornenj/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 =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 73992
PERL5_CPAN_IS_RUNNING = 73992
PERL5_MINISMOKEBOX = 0.56
PERLBREW_BASHRC_VERSION = 0.66
PERLBREW_HOME = /Users/hornenj/.perlbrew
PERLBREW_MANPATH = /Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/man
PERLBREW_PATH = /Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/bin
PERLBREW_PERL = perl-5.14.3
PERLBREW_ROOT = /Users/hornenj/perl5/perlbrew
PERLBREW_VERSION = 0.66
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_MM_USE_DEFAULT = 1
SHELL = /bin/bash
TERM = xterm
TMPDIR = /var/folders/pz/pd7y1qjs6s3cbk170cw50fjc000c61/T/
VERSIONER_PERL_PREFER_32_BIT = no
VERSIONER_PERL_VERSION = 5.12
ac_cv_path_INTLTOOL_PERL = /usr/bin/perl
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/bin/perl
$UID/$EUID = 12481 / 12481
$GID = 14 14 5344 527 241 223 206 402 12 62 204
$EGID = 14 14 5344 527 241 223 206 402 12 62 204
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.00
CPAN::Meta 2.132140
Cwd 3.40
ExtUtils::CBuilder 0.280205
ExtUtils::Command 1.17
ExtUtils::Install 1.56
ExtUtils::MakeMaker 6.74
ExtUtils::Manifest 1.61
ExtUtils::ParseXS 3.22
File::Spec 3.40
JSON 2.59
JSON::PP 2.27202
Module::Build 0.4007
Module::Signature n/a
Parse::CPAN::Meta 1.4405
Test::Harness 3.28
Test::More 0.98
YAML 0.84
YAML::Syck 1.27
version 0.9904
--
Summary of my perl5 (revision 5 version 14 subversion 3) configuration:
Platform:
osname=darwin, osvers=12.2.1, archname=darwin-2level
uname='darwin ncbimac2008.ncbi.nlm.nih.gov 12.2.1 darwin kernel version 12.2.1: thu oct 18 12:13:47 pdt 2012; root:xnu-2050.20.9~1release_x86_64 x86_64 '
config_args='-de -Dprefix=/Users/hornenj/perl5/perlbrew/perls/perl-5.14.3'
hint=recommended, useposix=true, d_sigaction=define
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 ='-fno-common -DPERL_DARWIN -fno-strict-aliasing -pipe -fstack-protector',
optimize='-O3',
cppflags='-fno-common -DPERL_DARWIN -fno-strict-aliasing -pipe -fstack-protector'
ccversion='', gccversion='4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.24)', 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'
libpth=/usr/lib
libs=-ldbm -ldl -lm -lutil -lc
perllibs=-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 -fstack-protector'
Characteristics of this binary (from libperl):
Compile-time options: PERL_DONT_CREATE_GVSV PERL_MALLOC_WRAP
PERL_PRESERVE_IVUV USE_64_BIT_ALL USE_64_BIT_INT
USE_LARGE_FILES USE_PERLIO USE_PERL_ATOF
Built under darwin
Compiled at Mar 4 2013 17:42:44
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="73992"
PERL5_CPAN_IS_RUNNING="73992"
PERL5_MINISMOKEBOX="0.56"
PERLBREW_BASHRC_VERSION="0.66"
PERLBREW_HOME="/Users/hornenj/.perlbrew"
PERLBREW_MANPATH="/Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/man"
PERLBREW_PATH="/Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/bin"
PERLBREW_PERL="perl-5.14.3"
PERLBREW_ROOT="/Users/hornenj/perl5/perlbrew"
PERLBREW_VERSION="0.66"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_MM_USE_DEFAULT="1"
@INC:
/Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/lib/site_perl/5.14.3/darwin-2level
/Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/lib/site_perl/5.14.3
/Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/lib/5.14.3/darwin-2level
/Users/hornenj/perl5/perlbrew/perls/perl-5.14.3/lib/5.14.3
.