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From: metabase:user:314402c4-2aae-11df-837a-5e0a49663a4f
Subject: FAIL Bio_AssemblyImprovement-1.160490 v5.25.6 GNU/Linux
Date: 2016-10-28T21:33:46Z
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 5.25.6, 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:
none provided
------------------------------
PROGRAM OUTPUT
------------------------------
Output from '/usr/bin/make test':
PERL_DL_NONLAZY=1 "/bbbike/perl-5.25.6/bin/perl5.25.6" "-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 "/tmpfs/.cpan-build-cpansand/2016102809/Bio_AssemblyImprovement-1.160490-0/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: /tmpfs/.cpan-build-cpansand/2016102809/Bio_AssemblyImprovement-1.160490-0/t/dummy_iva_qc_script_raise_error.py -f /tmpfs/.cpan-build-cpansand/2016102809/Bio_AssemblyImprovement-1.160490-0/t/data/forward.fastq -r /tmpfs/.cpan-build-cpansand/2016102809/Bio_AssemblyImprovement-1.160490-0/t/data/reverse.fastq --ref_db /tmpfs/.cpan-build-cpansand/2016102809/Bio_AssemblyImprovement-1.160490-0/t/data/database /tmpfs/.cpan-build-cpansand/2016102809/Bio_AssemblyImprovement-1.160490-0/t/data/contigs.fa test_iva_qc
t/IvaQC/Main.t .......................... ok
t/Overall/CheckAllModulesCompile.t ...... ok
t/PrepareForSubmission/RenameContigs.t .. ok
# Failed test 'Results file exists in expected location'
# at t/PrimerRemoval/Main.t line 39.
# Failed test 'Results file exists in expected location'
# at t/PrimerRemoval/Main.t line 39.
# Looks like you failed 2 tests of 6.
t/PrimerRemoval/Main.t ..................
Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/6 subtests
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
/tmpfs/.cpan-build-cpansand/2016102809/Bio_AssemblyImprovement-1.160490-0/t/does_not_exist.pl does not exist. Using default: /tmpfs/.cpan-build-cpansand/2016102809/Bio_AssemblyImprovement-1.160490-0/t/dummy_gap_filler_script.pl at lib/Bio/AssemblyImprovement/Validate/Executable.pm line 29.
t/Validate/Executable.t ................. ok
Test Summary Report
-------------------
t/PrimerRemoval/Main.t (Wstat: 512 Tests: 6 Failed: 2)
Failed tests: 5-6
Non-zero exit status: 2
Files=24, Tests=246, 7 wallclock secs ( 0.09 usr 0.06 sys + 5.16 cusr 1.19 csys = 6.50 CPU)
Result: FAIL
Failed 1/24 test programs. 2/246 subtests failed.
Makefile:1129: recipe for target 'test_dynamic' failed
make: *** [test_dynamic] Error 255
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------- ---- --------
Bio::SeqIO 0 1.007000
Cwd 0 3.62
File::Basename 0 2.85
File::Copy 0 2.32
File::Path 2.07 2.12_01
File::Spec 0 3.62
File::Temp 0 0.2304
File::Which 0 1.21
Getopt::Long 0 2.49
Getopt::Std 0 1.11
IO::Compress::Gzip 0 2.069_01
IO::Uncompress::Gunzip 0 2.069_01
lib 0 0.63
Moose 0 2.1806
Moose::Role 0 2.1806
POSIX 0 1.73
Statistics::Lite 0 3.62
strict 0 1.11
Switch 0 2.17
warnings 0 1.37
build_requires:
Module Need Have
---------------------- ---- --------
Env::Path 0 0.19
ExtUtils::MakeMaker 0 7.24
File::Slurp 0 9999.19
Test::File::Contents 0 0.23
Test::Most 0 0.35
configure_requires:
Module Need Have
---------------------- ---- --------
ExtUtils::MakeMaker 0 7.24
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
LANG = C
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 = 32170
PERL5_CPAN_IS_RUNNING = 32170
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 21381,32170
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /run/user/1023/cpansmoker/2016102806/cpanreporter_001_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_PARALLEL_SMOKER = yes
PERL_USE_UNSAFE_INC = 1
SHELL = /bin/zsh
TERM = screen
TMPDIR = /run/user/1023/cpansmoker/2016102806
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /bbbike/perl-5.25.6/bin/perl5.25.6
$UID/$EUID = 1023 / 1023
$GID = 1023 1023
$EGID = 1023 1023
Perl module toolchain versions installed:
Module Have
------------------- ----------
CPAN 2.14
CPAN::Meta 2.150010
Cwd 3.62
ExtUtils::CBuilder 0.280225
ExtUtils::Command 7.24
ExtUtils::Install 2.04
ExtUtils::MakeMaker 7.24
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.33
File::Spec 3.62
JSON 2.90
JSON::PP 2.27400_01
Module::Build 0.4220
Module::Signature 0.81
Parse::CPAN::Meta 2.150010
Test::Harness 3.36
Test::More 1.302062
YAML 1.18
YAML::Syck 1.29
version 0.9917
--
Summary of my perl5 (revision 5 version 25 subversion 6) configuration:
Platform:
osname=linux
osvers=3.16.0-4-amd64
archname=x86_64-linux
uname='linux eserte 3.16.0-4-amd64 #1 smp debian 3.16.36-1+deb8u2 (2016-10-19) x86_64 gnulinux '
config_args='-ds -e -Dprefix=/opt/perl-5.25.6 -Dusedevel -Dusemallocwrap=no -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 -D_FORTIFY_SOURCE=2'
optimize='-O2'
cppflags='-fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
ccversion=''
gccversion='4.9.2'
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/4.9/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-2.19.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-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_OP_PARENT
PERL_PRESERVE_IVUV
PERL_USE_DEVEL
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
Built under linux
Compiled at Oct 25 2016 21:54:53
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="32170"
PERL5_CPAN_IS_RUNNING="32170"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="21381,32170"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/run/user/1023/cpansmoker/2016102806/cpanreporter_001_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_PARALLEL_SMOKER="yes"
PERL_USE_UNSAFE_INC="1"
@INC:
/opt/perl-5.25.6/lib/site_perl/5.25.6/x86_64-linux
/opt/perl-5.25.6/lib/site_perl/5.25.6
/opt/perl-5.25.6/lib/5.25.6/x86_64-linux
/opt/perl-5.25.6/lib/5.25.6
.