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From: metabase:user:314402c4-2aae-11df-837a-5e0a49663a4f
Subject: FAIL Bio_AssemblyImprovement-1.160490 v5.18.4 GNU/Linux
Date: 2016-02-18T18:08:30Z
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-1.2011.
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-5.18.4t/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
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
Error running Trimmomatic with:
java -Xmx1000m -jar t/DummyTrimmomatic.jar PE -threads 1 t/data/trimmo_reads_1.fastq t/data/trimmo_reads_2.fastq trimmed.paired_1.fastq trimmed.unpaired_1.fastq trimmed.paired_2.fastq trimmed.unpaired_2.fastq ILLUMINACLIP:/tmpfs/.cpan-build-cpansand/2016021815/Bio_AssemblyImprovement-1.160490-oqzmuw/t/data/trimmo_adapters.fasta:2:10:7:1 MINLEN:50 at lib/Bio/AssemblyImprovement/AdapterRemoval/Trimmomatic/Main.pm line 45.
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 1 just after 2.
t/AdapterRemoval/Trimmomatic/Main.t .....
Dubious, test returned 1 (wstat 256, 0x100)
All 2 subtests passed
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/2016021815/Bio_AssemblyImprovement-1.160490-oqzmuw/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/2016021815/Bio_AssemblyImprovement-1.160490-oqzmuw/t/dummy_iva_qc_script_raise_error.py -f /tmpfs/.cpan-build-cpansand/2016021815/Bio_AssemblyImprovement-1.160490-oqzmuw/t/data/forward.fastq -r /tmpfs/.cpan-build-cpansand/2016021815/Bio_AssemblyImprovement-1.160490-oqzmuw/t/data/reverse.fastq --ref_db /tmpfs/.cpan-build-cpansand/2016021815/Bio_AssemblyImprovement-1.160490-oqzmuw/t/data/database /tmpfs/.cpan-build-cpansand/2016021815/Bio_AssemblyImprovement-1.160490-oqzmuw/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/2016021815/Bio_AssemblyImprovement-1.160490-oqzmuw/t/does_not_exist.pl does not exist. Using default: /tmpfs/.cpan-build-cpansand/2016021815/Bio_AssemblyImprovement-1.160490-oqzmuw/t/dummy_gap_filler_script.pl at lib/Bio/AssemblyImprovement/Validate/Executable.pm line 29.
t/Validate/Executable.t ................. ok
Test Summary Report
-------------------
t/AdapterRemoval/Trimmomatic/Main.t (Wstat: 256 Tests: 2 Failed: 0)
Non-zero exit status: 1
Parse errors: No plan found in TAP output
t/PrimerRemoval/Main.t (Wstat: 512 Tests: 6 Failed: 2)
Failed tests: 5-6
Non-zero exit status: 2
Files=24, Tests=242, 9 wallclock secs ( 0.09 usr 0.11 sys + 6.22 cusr 2.11 csys = 8.53 CPU)
Result: FAIL
Failed 2/24 test programs. 2/242 subtests failed.
make: *** [test_dynamic] Fehler 255
------------------------------
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 2.09
File::Spec 0 3.47
File::Temp 0 0.2304
File::Which 0 1.09
Getopt::Long 0 2.39
Getopt::Std 0 1.07
IO::Compress::Gzip 0 2.066
IO::Uncompress::Gunzip 0 2.066
lib 0 0.63
Moose 0 2.1402
Moose::Role 0 2.1402
POSIX 0 1.32
Statistics::Lite 0 3.2
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 7.02
File::Slurp 0 9999.19
Test::File::Contents 0 0.21
Test::Most 0 0.34
configure_requires:
Module Need Have
---------------------- ---- -------
ExtUtils::MakeMaker 0 7.02
------------------------------
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 = /home/cpansand/.cpan/build/2016021815/Env-Path-0.19-vyv4KT/blib/arch:/home/cpansand/.cpan/build/2016021815/Env-Path-0.19-vyv4KT/blib/lib:/home/cpansand/.cpan/build/2016021815/Dist-Zilla-Plugin-PkgAuthority-0.05-uZHHLn/blib/arch:/home/cpansand/.cpan/build/2016021815/Dist-Zilla-Plugin-PkgAuthority-0.05-uZHHLn/blib/lib:/home/cpansand/.cpan/build/2016021815/Tapper-TAP-Harness-5.0.5-EpS6Xr/blib/arch:/home/cpansand/.cpan/build/2016021815/Tapper-TAP-Harness-5.0.5-EpS6Xr/blib/lib:/home/cpansand/.cpan/build/2016021815/Business-Fixflo-0.17-1_rRGq/blib/arch:/home/cpansand/.cpan/build/2016021815/Business-Fixflo-0.17-1_rRGq/blib/lib:/home/cpansand/.cpan/build/2016021815/Raisin-0.63-Y3XPc6/blib/arch:/home/cpansand/.cpan/build/2016021815/Raisin-0.63-Y3XPc6/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 22805
PERL5_CPAN_IS_RUNNING = 22805
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 19955,22805
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2016021815/cpanreporter_001_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_PARALLEL_SMOKER = yes
SHELL = /bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1023/2016021815
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /bbbike/perl-5.18.4t/bin/perl
$UID/$EUID = 1023 / 1023
$GID = 1023 1023
$EGID = 1023 1023
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.00
CPAN::Meta 2.142690
Cwd 3.47
ExtUtils::CBuilder 0.280210
ExtUtils::Command 1.17
ExtUtils::Install 1.59
ExtUtils::MakeMaker 7.02
ExtUtils::Manifest 1.68
ExtUtils::ParseXS 3.24
File::Spec 3.47
JSON 2.90
JSON::PP 2.27203
Module::Build 0.4210
Module::Signature 0.73
Parse::CPAN::Meta 1.4414
Test::Harness 3.34
Test::More 1.001014
YAML 1.13
YAML::Syck 1.27
version 0.9909
--
Summary of my perl5 (revision 5 version 18 subversion 4) configuration:
Platform:
osname=linux, osvers=3.2.0-4-amd64, archname=x86_64-linux-thread-multi
uname='linux eserte 3.2.0-4-amd64 #1 smp debian 3.2.63-2+deb7u1 x86_64 gnulinux '
config_args='-ds -e -Dprefix=/opt/perl-5.18.4t -Dusethreads'
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='4.7.2', 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 -ldb -ldl -lm -lcrypt -lutil -lpthread -lc
perllibs=-lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
libc=, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.13'
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 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 15 2014 13:31:56
%ENV:
PERL5LIB="/home/cpansand/.cpan/build/2016021815/Env-Path-0.19-vyv4KT/blib/arch:/home/cpansand/.cpan/build/2016021815/Env-Path-0.19-vyv4KT/blib/lib:/home/cpansand/.cpan/build/2016021815/Dist-Zilla-Plugin-PkgAuthority-0.05-uZHHLn/blib/arch:/home/cpansand/.cpan/build/2016021815/Dist-Zilla-Plugin-PkgAuthority-0.05-uZHHLn/blib/lib:/home/cpansand/.cpan/build/2016021815/Tapper-TAP-Harness-5.0.5-EpS6Xr/blib/arch:/home/cpansand/.cpan/build/2016021815/Tapper-TAP-Harness-5.0.5-EpS6Xr/blib/lib:/home/cpansand/.cpan/build/2016021815/Business-Fixflo-0.17-1_rRGq/blib/arch:/home/cpansand/.cpan/build/2016021815/Business-Fixflo-0.17-1_rRGq/blib/lib:/home/cpansand/.cpan/build/2016021815/Raisin-0.63-Y3XPc6/blib/arch:/home/cpansand/.cpan/build/2016021815/Raisin-0.63-Y3XPc6/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="22805"
PERL5_CPAN_IS_RUNNING="22805"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="19955,22805"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2016021815/cpanreporter_001_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_PARALLEL_SMOKER="yes"
@INC:
/home/cpansand/.cpan/build/2016021815/Env-Path-0.19-vyv4KT/blib/arch
/home/cpansand/.cpan/build/2016021815/Env-Path-0.19-vyv4KT/blib/lib
/home/cpansand/.cpan/build/2016021815/Dist-Zilla-Plugin-PkgAuthority-0.05-uZHHLn/blib/arch
/home/cpansand/.cpan/build/2016021815/Dist-Zilla-Plugin-PkgAuthority-0.05-uZHHLn/blib/lib
/home/cpansand/.cpan/build/2016021815/Tapper-TAP-Harness-5.0.5-EpS6Xr/blib/arch
/home/cpansand/.cpan/build/2016021815/Tapper-TAP-Harness-5.0.5-EpS6Xr/blib/lib
/home/cpansand/.cpan/build/2016021815/Business-Fixflo-0.17-1_rRGq/blib/arch
/home/cpansand/.cpan/build/2016021815/Business-Fixflo-0.17-1_rRGq/blib/lib
/home/cpansand/.cpan/build/2016021815/Raisin-0.63-Y3XPc6/blib/arch
/home/cpansand/.cpan/build/2016021815/Raisin-0.63-Y3XPc6/blib/lib
/opt/perl-5.18.4t/lib/site_perl/5.18.4/x86_64-linux-thread-multi
/opt/perl-5.18.4t/lib/site_perl/5.18.4
/opt/perl-5.18.4t/lib/5.18.4/x86_64-linux-thread-multi
/opt/perl-5.18.4t/lib/5.18.4
.