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From: metabase:user:30f4dfbe-2aae-11df-837a-5e0a49663a4f
Subject: PASS Bio_AssemblyImprovement-1.160490 v5.18.4 GNU/Linux
Date: 2016-02-18T12:53:01Z
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 Andrew Page,
This is a computer-generated report for Bio_AssemblyImprovement-1.160490
on perl 5.18.4, created by CPAN-Reporter-1.2015.
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 '/usr/bin/make test':
PERL_DL_NONLAZY=1 "/home/njh/perl5/perlbrew/perls/perl-5.18.4/bin/perl5.18.4" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/Abacas/*.t t/AdapterRemoval/Trimmomatic/*.t t/Assemble/SGA/*.t t/Circlator/*.t t/DigitalNormalisation/Khmer/*.t t/FillGaps/*.t t/IvaQC/*.t t/Overall/*.t t/PrepareForSubmission/*.t t/PrimerRemoval/*.t t/Quiver/*.t t/Scaffold/*.t t/Util/*.t t/Validate/*.t
t/Abacas/Iterative.t .................... ok
t/Abacas/Main.t ......................... ok
t/AdapterRemoval/Trimmomatic/Main.t ..... ok
t/Assemble/SGA/IndexAndCorrectReads.t ... ok
t/Assemble/SGA/Main.t ................... ok
t/Assemble/SGA/PreprocessReads.t ........ ok
t/Circlator/Main.t ...................... ok
t/DigitalNormalisation/Khmer/Main.t ..... ok
t/FillGaps/GapFillerConfig.t ............ ok
t/FillGaps/Iterative.t .................. ok
Traceback (most recent call last):
File "/home/njh/.cpan/build/Bio_AssemblyImprovement-1.160490-3Uu_Dm/t/dummy_iva_qc_script_raise_error.py", line 7, in <module>
raise Error ('Could not run iva_qc check - ignore error message')
__main__.Error: Could not run iva_qc check - ignore error message
Error running iva_qc with: /home/njh/.cpan/build/Bio_AssemblyImprovement-1.160490-3Uu_Dm/t/dummy_iva_qc_script_raise_error.py -f /home/njh/.cpan/build/Bio_AssemblyImprovement-1.160490-3Uu_Dm/t/data/forward.fastq -r /home/njh/.cpan/build/Bio_AssemblyImprovement-1.160490-3Uu_Dm/t/data/reverse.fastq --ref_db /home/njh/.cpan/build/Bio_AssemblyImprovement-1.160490-3Uu_Dm/t/data/database /home/njh/.cpan/build/Bio_AssemblyImprovement-1.160490-3Uu_Dm/t/data/contigs.fa test_iva_qc
test_iva_qc.gage for test_iva_qc.gage: No such file or directory at lib/Bio/AssemblyImprovement/IvaQC/Main.pm line 59.
t/IvaQC/Main.t .......................... ok
t/Overall/CheckAllModulesCompile.t ...... ok
t/PrepareForSubmission/RenameContigs.t .. ok
t/PrimerRemoval/Main.t .................. ok
t/Quiver/Main.t ......................... ok
t/requires_external.t ................... ok
t/Scaffold/Descaffold.t ................. ok
t/Scaffold/Iterative.t .................. ok
t/Scaffold/PreprocessInputFiles.t ....... ok
t/Scaffold/SSpaceConfig.t ............... ok
t/Util/FastaTools.t ..................... ok
t/Util/FastqTools.t ..................... ok
t/Util/OrderContigsByLength.t ........... ok
/home/njh/.cpan/build/Bio_AssemblyImprovement-1.160490-3Uu_Dm/t/does_not_exist.pl does not exist. Using default: /home/njh/.cpan/build/Bio_AssemblyImprovement-1.160490-3Uu_Dm/t/dummy_gap_filler_script.pl at lib/Bio/AssemblyImprovement/Validate/Executable.pm line 29.
t/Validate/Executable.t ................. ok
All tests successful.
Files=24, Tests=246, 6 wallclock secs ( 0.07 usr 0.02 sys + 5.42 cusr 0.46 csys = 5.97 CPU)
Result: PASS
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------- ---- -------
Bio::SeqIO 0 0
Cwd 0 3.47
File::Basename 0 2.84
File::Copy 0 2.26
File::Path 2.07 2.11
File::Spec 0 3.47
File::Temp 0 0.2304
File::Which 0 1.19
Getopt::Long 0 2.47
Getopt::Std 0 1.07
IO::Compress::Gzip 0 2.068
IO::Uncompress::Gunzip 0 2.068
lib 0 0.63
Moose 0 2.1404
Moose::Role 0 2.1404
POSIX 0 1.32
Statistics::Lite 0 3.62
strict 0 1.07
Switch 0 2.17
warnings 0 1.18
build_requires:
Module Need Have
---------------------- ---- -------
Env::Path 0 0.19
ExtUtils::MakeMaker 0 7.10
File::Slurp 0 9999.19
Test::File::Contents 0 0.21
Test::Most 0 0.34
configure_requires:
Module Need Have
---------------------- ---- -------
ExtUtils::MakeMaker 0 7.10
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_US.UTF-8
PATH = /home/njh/perl5/perlbrew/bin:/home/njh/perl5/perlbrew/perls/perl-5.18.4/bin:/home/njh/perl5/perlbrew/bin:/usr/bin:/bin
PERL5LIB = /home/njh/.cpan/build/Test-File-Contents-0.21-mQoh4z/blib/arch:/home/njh/.cpan/build/Test-File-Contents-0.21-mQoh4z/blib/lib:/home/njh/.cpan/build/Env-Path-0.19-Vo7gpH/blib/arch:/home/njh/.cpan/build/Env-Path-0.19-Vo7gpH/blib/lib:/home/njh/.cpan/build/Switch-2.17-nQecCf/blib/arch:/home/njh/.cpan/build/Switch-2.17-nQecCf/blib/lib:/home/njh/.cpan/build/Statistics-Lite-3.62-Hb47Bi/blib/arch:/home/njh/.cpan/build/Statistics-Lite-3.62-Hb47Bi/blib/lib:/home/njh/.cpan/build/BioPerl-1.6.924-vA4r6A/blib/arch:/home/njh/.cpan/build/BioPerl-1.6.924-vA4r6A/blib/lib:/home/njh/.cpan/build/Data-Stag-0.14-xcRRMH/blib/arch:/home/njh/.cpan/build/Data-Stag-0.14-xcRRMH/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 16549
PERL5_CPAN_IS_RUNNING = 16549
PERL5_MINISMOKEBOX = 0.58
PERLBREW_BASHRC_VERSION = 0.74
PERLBREW_LIB =
PERLBREW_MANPATH = /home/njh/perl5/perlbrew/perls/perl-5.18.4/man
PERLBREW_PATH = /home/njh/perl5/perlbrew/bin:/home/njh/perl5/perlbrew/perls/perl-5.18.4/bin
PERLBREW_PERL = perl-5.18.4
PERLBREW_ROOT = /home/njh/perl5/perlbrew
PERLBREW_VERSION = 0.74
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_LOCAL_LIB_ROOT =
PERL_MM_USE_DEFAULT = 1
SHELL = /bin/sh
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/njh/perl5/perlbrew/perls/perl-5.18.4/bin/perl5.18.4
$UID/$EUID = 1000 / 1000
$GID = 1000 4 24 25 29 30 44 46 103 104 107 110 1000
$EGID = 1000 4 24 25 29 30 44 46 103 104 107 110 1000
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 1.9800
CPAN::Meta 2.150005
Cwd 3.47
ExtUtils::CBuilder 0.280223
ExtUtils::Command 7.10
ExtUtils::Install 2.04
ExtUtils::MakeMaker 7.10
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.24
File::Spec 3.47
JSON 2.90
JSON::PP 2.27203
Module::Build 0.4214
Module::Signature n/a
Parse::CPAN::Meta 1.4414
Test::Harness 3.34
Test::More 1.001014
YAML 1.15
YAML::Syck 1.29
version 0.9902
--
Summary of my perl5 (revision 5 version 18 subversion 4) configuration:
Platform:
osname=linux, osvers=3.16.0-4-amd64, archname=x86_64-linux-thread-multi
uname='linux cyberpower2 3.16.0-4-amd64 #1 smp debian 3.16.7-2 (2014-11-06) x86_64 gnulinux '
config_args='-de -Dprefix=/home/njh/perl5/perlbrew/perls/perl-5.18.4 -Duseithreads -Dusemultiplicity -Dusedevel -Accflags= -Aeval:scriptdir=/home/njh/perl5/perlbrew/perls/perl-5.18.4/bin'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2',
cppflags='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='4.9.2', 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 =' -fstack-protector -L/usr/local/lib'
libpth=/usr/local/lib /lib/x86_64-linux-gnu /lib/../lib /usr/lib/x86_64-linux-gnu /usr/lib/../lib /lib /usr/lib
libs=-lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lpthread -lc -lgdbm_compat
perllibs=-lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
libc=libc-2.19.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.19'
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
cccdlflags='-fPIC', lddlflags='-shared -O2 -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_PRESERVE_IVUV PERL_SAWAMPERSAND 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
Built under linux
Compiled at Nov 16 2014 00:31:40
%ENV:
PERL5LIB="/home/njh/.cpan/build/Test-File-Contents-0.21-mQoh4z/blib/arch:/home/njh/.cpan/build/Test-File-Contents-0.21-mQoh4z/blib/lib:/home/njh/.cpan/build/Env-Path-0.19-Vo7gpH/blib/arch:/home/njh/.cpan/build/Env-Path-0.19-Vo7gpH/blib/lib:/home/njh/.cpan/build/Switch-2.17-nQecCf/blib/arch:/home/njh/.cpan/build/Switch-2.17-nQecCf/blib/lib:/home/njh/.cpan/build/Statistics-Lite-3.62-Hb47Bi/blib/arch:/home/njh/.cpan/build/Statistics-Lite-3.62-Hb47Bi/blib/lib:/home/njh/.cpan/build/BioPerl-1.6.924-vA4r6A/blib/arch:/home/njh/.cpan/build/BioPerl-1.6.924-vA4r6A/blib/lib:/home/njh/.cpan/build/Data-Stag-0.14-xcRRMH/blib/arch:/home/njh/.cpan/build/Data-Stag-0.14-xcRRMH/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="16549"
PERL5_CPAN_IS_RUNNING="16549"
PERL5_MINISMOKEBOX="0.58"
PERLBREW_BASHRC_VERSION="0.74"
PERLBREW_LIB=""
PERLBREW_MANPATH="/home/njh/perl5/perlbrew/perls/perl-5.18.4/man"
PERLBREW_PATH="/home/njh/perl5/perlbrew/bin:/home/njh/perl5/perlbrew/perls/perl-5.18.4/bin"
PERLBREW_PERL="perl-5.18.4"
PERLBREW_ROOT="/home/njh/perl5/perlbrew"
PERLBREW_VERSION="0.74"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_LOCAL_LIB_ROOT=""
PERL_MM_USE_DEFAULT="1"
@INC:
/home/njh/.cpan/build/Test-File-Contents-0.21-mQoh4z/blib/arch
/home/njh/.cpan/build/Test-File-Contents-0.21-mQoh4z/blib/lib
/home/njh/.cpan/build/Env-Path-0.19-Vo7gpH/blib/arch
/home/njh/.cpan/build/Env-Path-0.19-Vo7gpH/blib/lib
/home/njh/.cpan/build/Switch-2.17-nQecCf/blib/arch
/home/njh/.cpan/build/Switch-2.17-nQecCf/blib/lib
/home/njh/.cpan/build/Statistics-Lite-3.62-Hb47Bi/blib/arch
/home/njh/.cpan/build/Statistics-Lite-3.62-Hb47Bi/blib/lib
/home/njh/.cpan/build/BioPerl-1.6.924-vA4r6A/blib/arch
/home/njh/.cpan/build/BioPerl-1.6.924-vA4r6A/blib/lib
/home/njh/.cpan/build/Data-Stag-0.14-xcRRMH/blib/arch
/home/njh/.cpan/build/Data-Stag-0.14-xcRRMH/blib/lib
/home/njh/perl5/perlbrew/perls/perl-5.18.4/lib/site_perl/5.18.4/x86_64-linux-thread-multi
/home/njh/perl5/perlbrew/perls/perl-5.18.4/lib/site_perl/5.18.4
/home/njh/perl5/perlbrew/perls/perl-5.18.4/lib/5.18.4/x86_64-linux-thread-multi
/home/njh/perl5/perlbrew/perls/perl-5.18.4/lib/5.18.4
.