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From: metabase:user:314402c4-2aae-11df-837a-5e0a49663a4f
Subject: FAIL Bio_AssemblyImprovement-1.160490 v5.22.3 RC5 GNU/Linux
Date: 2017-01-07T16:54:02Z
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 5.22.3, 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:
none provided
------------------------------
PROGRAM OUTPUT
------------------------------
Output from '/usr/bin/make test':
PERL_DL_NONLAZY=1 "/bbbike/perl-5.22.3-RC5/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 "/tmpfs/.cpan-build-cpansand/2017010712/Bio_AssemblyImprovement-1.160490-THHn1T/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/2017010712/Bio_AssemblyImprovement-1.160490-THHn1T/t/dummy_iva_qc_script_raise_error.py -f /tmpfs/.cpan-build-cpansand/2017010712/Bio_AssemblyImprovement-1.160490-THHn1T/t/data/forward.fastq -r /tmpfs/.cpan-build-cpansand/2017010712/Bio_AssemblyImprovement-1.160490-THHn1T/t/data/reverse.fastq --ref_db /tmpfs/.cpan-build-cpansand/2017010712/Bio_AssemblyImprovement-1.160490-THHn1T/t/data/database /tmpfs/.cpan-build-cpansand/2017010712/Bio_AssemblyImprovement-1.160490-THHn1T/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/2017010712/Bio_AssemblyImprovement-1.160490-THHn1T/t/does_not_exist.pl does not exist. Using default: /tmpfs/.cpan-build-cpansand/2017010712/Bio_AssemblyImprovement-1.160490-THHn1T/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, 44 wallclock secs ( 0.09 usr 0.06 sys + 5.62 cusr 1.46 csys = 7.23 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 1.007001
Cwd 0 3.56_02
File::Basename 0 2.85
File::Copy 0 2.30
File::Path 2.07 2.12
File::Spec 0 3.56_02
File::Temp 0 0.2304
File::Which 0 1.21
Getopt::Long 0 2.45
Getopt::Std 0 1.11
IO::Compress::Gzip 0 2.070
IO::Uncompress::Gunzip 0 2.070
lib 0 0.63
Moose 0 2.1807
Moose::Role 0 2.1807
POSIX 0 1.53_01
Statistics::Lite 0 3.62
strict 0 1.09
Switch 0 2.17
warnings 0 1.34
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 = 13034
PERL5_CPAN_IS_RUNNING = 13034
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 6025,13034
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2017010706/cpanreporter_002_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_PARALLEL_SMOKER = yes
PERL_USE_UNSAFE_INC = 1
SHELL = /bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1023/2017010706
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /bbbike/perl-5.22.3-RC5/bin/perl
$UID/$EUID = 1023 / 1023
$GID = 1023 1023
$EGID = 1023 1023
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.11_01
CPAN::Meta 2.150010
Cwd 3.56_02
ExtUtils::CBuilder 0.280221
ExtUtils::Command 7.24
ExtUtils::Install 2.04
ExtUtils::MakeMaker 7.24
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.28
File::Spec 3.56_02
JSON 2.90
JSON::PP 2.27400
Module::Build 0.4220
Module::Signature 0.81
Parse::CPAN::Meta 2.150010
Test::Harness 3.35_01
Test::More 1.302073
YAML 1.21
YAML::Syck 1.29
version 0.9917
--
Summary of my perl5 (revision 5 version 22 subversion 3) 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-5.22.3-RC5 -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_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD PERL_MALLOC_WRAP
PERL_NEW_COPY_ON_WRITE 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:
RC5
Built under linux
Compiled at Jan 5 2017 19:28:05
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="13034"
PERL5_CPAN_IS_RUNNING="13034"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="6025,13034"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2017010706/cpanreporter_002_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_PARALLEL_SMOKER="yes"
PERL_USE_UNSAFE_INC="1"
@INC:
/opt/perl-5.22.3-RC5/lib/site_perl/5.22.3/x86_64-linux
/opt/perl-5.22.3-RC5/lib/site_perl/5.22.3
/opt/perl-5.22.3-RC5/lib/5.22.3/x86_64-linux
/opt/perl-5.22.3-RC5/lib/5.22.3
.