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From: metabase:user:31d414ea-2aae-11df-837a-5e0a49663a4f
Subject: FAIL Bio_AssemblyImprovement-1.160490 v5.22.1 GNU/Linux
Date: 2016-02-22T17:38:33Z
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 5.22.1, created by CPAN-Reporter-1.2015.
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:
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/david/cpantesting/perl-5.22.1/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
Can't exec "java": No such file or directory at lib/Bio/AssemblyImprovement/AdapterRemoval/Trimmomatic/Main.pm line 44.
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:/home/david/cpantesting/perl-5.22.1/.cpan/build/Bio_AssemblyImprovement-1.160490-HpWh5f/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 2 just after 2.
t/AdapterRemoval/Trimmomatic/Main.t .....
Dubious, test returned 2 (wstat 512, 0x200)
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 "/home/david/cpantesting/perl-5.22.1/.cpan/build/Bio_AssemblyImprovement-1.160490-HpWh5f/t/dummy_iva_qc_script_raise_error.py", line 7, in ?
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/david/cpantesting/perl-5.22.1/.cpan/build/Bio_AssemblyImprovement-1.160490-HpWh5f/t/dummy_iva_qc_script_raise_error.py -f /home/david/cpantesting/perl-5.22.1/.cpan/build/Bio_AssemblyImprovement-1.160490-HpWh5f/t/data/forward.fastq -r /home/david/cpantesting/perl-5.22.1/.cpan/build/Bio_AssemblyImprovement-1.160490-HpWh5f/t/data/reverse.fastq --ref_db /home/david/cpantesting/perl-5.22.1/.cpan/build/Bio_AssemblyImprovement-1.160490-HpWh5f/t/data/database /home/david/cpantesting/perl-5.22.1/.cpan/build/Bio_AssemblyImprovement-1.160490-HpWh5f/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
# Failed test 'java in PATH'
# at t/requires_external.t line 8.
# Looks like you failed 1 test of 1.
t/requires_external.t ...................
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/1 subtests
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/david/cpantesting/perl-5.22.1/.cpan/build/Bio_AssemblyImprovement-1.160490-HpWh5f/t/does_not_exist.pl does not exist. Using default: /home/david/cpantesting/perl-5.22.1/.cpan/build/Bio_AssemblyImprovement-1.160490-HpWh5f/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: 512 Tests: 2 Failed: 0)
Non-zero exit status: 2
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
t/requires_external.t (Wstat: 256 Tests: 1 Failed: 1)
Failed test: 1
Non-zero exit status: 1
Files=24, Tests=242, 19 wallclock secs ( 0.07 usr 0.08 sys + 5.49 cusr 1.15 csys = 6.79 CPU)
Result: FAIL
Failed 3/24 test programs. 3/242 subtests failed.
make: *** [test_dynamic] Error 255
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------- ---- -------
Bio::SeqIO 0 0
Cwd 0 3.56
File::Basename 0 2.85
File::Copy 0 2.30
File::Path 2.07 2.09
File::Spec 0 3.56
File::Temp 0 0.2304
File::Which 0 1.19
Getopt::Long 0 2.45
Getopt::Std 0 1.11
IO::Compress::Gzip 0 2.068
IO::Uncompress::Gunzip 0 2.068
lib 0 0.63
Moose 0 2.1605
Moose::Role 0 2.1605
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 7.04_01
File::Slurp 0 9999.19
Test::File::Contents 0 0.21
Test::Most 0 0.34
configure_requires:
Module Need Have
---------------------- ---- -------
ExtUtils::MakeMaker 0 7.04_01
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
NONINTERACTIVE_TESTING = 1
PATH = /usr/local/bin:/usr/bin:/bin:/usr/games
PERL = 5.22.1
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 326
PERL5_CPAN_IS_RUNNING = 326
PERLVER = 5.22.1
PERL_INLINE_DIRECTORY = /home/david/.Inline-5.22.1
PERL_MM_USE_DEFAULT = 1
SHELL = /bin/bash
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/david/cpantesting/perl-5.22.1/bin/perl
$UID/$EUID = 1000 / 1000
$GID = 1000 1000
$EGID = 1000 1000
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.11
CPAN::Meta 2.150001
Cwd 3.56
ExtUtils::CBuilder 0.280221
ExtUtils::Command 1.20
ExtUtils::Install 2.04
ExtUtils::MakeMaker 7.04_01
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.28
File::Spec 3.56
JSON 2.90
JSON::PP 2.27300
Module::Build 0.4214
Module::Signature n/a
Parse::CPAN::Meta 1.4414
Test::Harness 3.35
Test::More 1.001014
YAML n/a
YAML::Syck n/a
version 0.9909
--
Summary of my perl5 (revision 5 version 22 subversion 1) configuration:
Platform:
osname=linux, osvers=3.16.0-4-amd64, archname=x86_64-linux-thread-multi
uname='linux pigsty.barnyard.co.uk 3.16.0-4-amd64 #1 smp debian 3.16.7-ckt2-1 (2014-12-08) x86_64 gnulinux '
config_args='-de -Dprefix=/home/david/cpantesting/perl-5.22.1 -Dusethreads -Duse64bitall'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
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 -D_FORTIFY_SOURCE=2',
optimize='-O2',
cppflags='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='4.1.2 20061115 (prerelease) (Debian 4.1.1-21)', 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 -L/usr/local/lib'
libpth=/usr/local/lib /usr/lib /lib /lib64 /usr/lib64
libs=-lpthread -lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lc -lgdbm_compat
perllibs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
libc=libc-2.3.6.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.3.6'
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_NEW_COPY_ON_WRITE PERL_PRESERVE_IVUV
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_LOCALE_TIME
USE_PERLIO USE_PERL_ATOF USE_REENTRANT_API
Built under linux
Compiled at Jan 7 2016 17:43:18
%ENV:
PERL="5.22.1"
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="326"
PERL5_CPAN_IS_RUNNING="326"
PERLVER="5.22.1"
PERL_INLINE_DIRECTORY="/home/david/.Inline-5.22.1"
PERL_MM_USE_DEFAULT="1"
@INC:
/home/david/cpantesting/perl-5.22.1/lib/site_perl/5.22.1/x86_64-linux-thread-multi
/home/david/cpantesting/perl-5.22.1/lib/site_perl/5.22.1
/home/david/cpantesting/perl-5.22.1/lib/5.22.1/x86_64-linux-thread-multi
/home/david/cpantesting/perl-5.22.1/lib/5.22.1
.