Bio_AssemblyImprovement v1.160490 Perl 5 v5.24.4 RC1 x86_64-linux
- Status
- Pass
- From
- Slaven Rezić (SREZIC)
- Dist
-
Bio_AssemblyImprovement v1.160490
- Platform
- Perl 5 v5.24.4 RC1 x86_64-linux
- Date
- 2018-03-26 20:31:08
- ID
- 9db5a2ba-3134-11e8-abf0-c93a1914d803
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 5.24.4, 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:
none provided
------------------------------
PROGRAM OUTPUT
------------------------------
Output from '/usr/bin/make test':
PERL_DL_NONLAZY=1 "/opt/perl-5.24.4-RC1/bin/perl" "-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/cpansand/.cpan/build/2018032606/Bio_AssemblyImprovement-1.160490-1/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/cpansand/.cpan/build/2018032606/Bio_AssemblyImprovement-1.160490-1/t/dummy_iva_qc_script_raise_error.py -f /home/cpansand/.cpan/build/2018032606/Bio_AssemblyImprovement-1.160490-1/t/data/forward.fastq -r /home/cpansand/.cpan/build/2018032606/Bio_AssemblyImprovement-1.160490-1/t/data/reverse.fastq --ref_db /home/cpansand/.cpan/build/2018032606/Bio_AssemblyImprovement-1.160490-1/t/data/database /home/cpansand/.cpan/build/2018032606/Bio_AssemblyImprovement-1.160490-1/t/data/contigs.fa test_iva_qc
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/cpansand/.cpan/build/2018032606/Bio_AssemblyImprovement-1.160490-1/t/does_not_exist.pl does not exist. Using default: /home/cpansand/.cpan/build/2018032606/Bio_AssemblyImprovement-1.160490-1/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, 7 wallclock secs ( 0.08 usr 0.07 sys + 4.52 cusr 1.25 csys = 5.92 CPU)
Result: PASS
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------- ---- --------
Bio::SeqIO 0 1.007002
Cwd 0 3.74
File::Basename 0 2.85
File::Copy 0 2.31
File::Path 2.07 2.15
File::Spec 0 3.74
File::Temp 0 0.2304
File::Which 0 1.22
Getopt::Long 0 2.5
Getopt::Std 0 1.11
IO::Compress::Gzip 0 2.074
IO::Uncompress::Gunzip 0 2.074
lib 0 0.63
Moose 0 2.2010
Moose::Role 0 2.2010
POSIX 0 1.65_01
Statistics::Lite 0 3.62
strict 0 1.11
Switch 0 2.17
warnings 0 1.36
build_requires:
Module Need Have
---------------------- ---- --------
Env::Path 0 0.19
ExtUtils::MakeMaker 0 7.34
File::Slurp 0 9999.19
Test::File::Contents 0 0.23
Test::Most 0 0.35
configure_requires:
Module Need Have
---------------------- ---- --------
ExtUtils::MakeMaker 0 7.34
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
LANG = en_US.UTF-8
LC_ALL = de_DE.UTF-8
PATH = /usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/cpansand/bin/linux-gnu:/home/cpansand/bin/sh:/home/cpansand/bin:/usr/games:/home/cpansand/devel:/home/eserte/src/srezic-misc/scripts
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 9762
PERL5_CPAN_IS_RUNNING = 9762
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 15283,9762
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2018032603/cpanreporter_001_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_PARALLEL_SMOKER = yes
SHELL = /usr/bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1023/2018032603
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /opt/perl-5.24.4-RC1/bin/perl
$UID/$EUID = 1023 / 1023
$GID = 1023 1023
$EGID = 1023 1023
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.16
CPAN::Meta 2.150010
Cwd 3.74
ExtUtils::CBuilder 0.280230
ExtUtils::Command 7.34
ExtUtils::Install 2.14
ExtUtils::MakeMaker 7.34
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.35
File::Spec 3.74
JSON 2.97001
JSON::PP 2.97001
Module::Build 0.4224
Module::Signature 0.81
Parse::CPAN::Meta 2.150010
Test::Harness 3.42
Test::More 1.302133
YAML 1.24
YAML::Syck 1.30
version 0.9918
--
Summary of my perl5 (revision 5 version 24 subversion 4) configuration:
Platform:
osname=linux, osvers=4.4.0-116-generic, archname=x86_64-linux
uname='linux ubuntu16 4.4.0-116-generic #140-ubuntu smp mon feb 12 21:23:04 utc 2018 x86_64 x86_64 x86_64 gnulinux '
config_args='-ds -e -Dprefix=/opt/perl-5.24.4-RC1 -Dcf_email=srezic@cpan.org'
hint=recommended, useposix=true, d_sigaction=define
useithreads=undef, usemultiplicity=undef
use64bitint=define, use64bitall=define, uselongdouble=undef
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',
cppflags='-fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
ccversion='', gccversion='5.4.0 20160609', 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='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=8, 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/5/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 -lgdbm -ldb -ldl -lm -lcrypt -lutil -lc -lgdbm_compat
perllibs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
libc=libc-2.23.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.23'
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-strong'
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES PERLIO_LAYERS PERL_COPY_ON_WRITE
PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD PERL_MALLOC_WRAP
PERL_PRESERVE_IVUV 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_PERLIO USE_PERL_ATOF
Locally applied patches:
RC1
Built under linux
Compiled at Mar 24 2018 19:56:23
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="9762"
PERL5_CPAN_IS_RUNNING="9762"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="15283,9762"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2018032603/cpanreporter_001_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_PARALLEL_SMOKER="yes"
@INC:
/opt/perl-5.24.4-RC1/lib/site_perl/5.24.4/x86_64-linux
/opt/perl-5.24.4-RC1/lib/site_perl/5.24.4
/opt/perl-5.24.4-RC1/lib/5.24.4/x86_64-linux
/opt/perl-5.24.4-RC1/lib/5.24.4
.