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From: metabase:user:30f4dfbe-2aae-11df-837a-5e0a49663a4f
Subject: FAIL Bio_AssemblyImprovement-1.160490 v5.14.3 GNU/Linux
Date: 2016-02-19T04:06:58Z
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 5.14.3, 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/njh/perl5/perlbrew/perls/perl-5.14.3/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:/home/njh/.cpan/build/Bio_AssemblyImprovement-1.160490-hVSik4/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.
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 "/home/njh/.cpan/build/Bio_AssemblyImprovement-1.160490-hVSik4/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/njh/.cpan/build/Bio_AssemblyImprovement-1.160490-hVSik4/t/dummy_iva_qc_script_raise_error.py -f /home/njh/.cpan/build/Bio_AssemblyImprovement-1.160490-hVSik4/t/data/forward.fastq -r /home/njh/.cpan/build/Bio_AssemblyImprovement-1.160490-hVSik4/t/data/reverse.fastq --ref_db /home/njh/.cpan/build/Bio_AssemblyImprovement-1.160490-hVSik4/t/data/database /home/njh/.cpan/build/Bio_AssemblyImprovement-1.160490-hVSik4/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
/home/njh/.cpan/build/Bio_AssemblyImprovement-1.160490-hVSik4/t/does_not_exist.pl does not exist. Using default: /home/njh/.cpan/build/Bio_AssemblyImprovement-1.160490-hVSik4/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, 7 wallclock secs ( 0.05 usr 0.03 sys + 5.24 cusr 0.42 csys = 5.74 CPU)
Result: FAIL
Failed 2/24 test programs. 2/242 subtests failed.
Makefile:1178: recipe for target 'test_dynamic' failed
make: *** [test_dynamic] Error 255
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------- ---- -------
Bio::SeqIO 0 0
Cwd 0 3.40
File::Basename 0 2.82
File::Copy 0 2.21
File::Path 2.07 2.09
File::Spec 0 3.40
File::Temp 0 0.2301
File::Which 0 1.09
Getopt::Long 0 2.41
Getopt::Std 0 1.06
IO::Compress::Gzip 0 2.061
IO::Uncompress::Gunzip 0 2.061
lib 0 0.63
Moose 0 2.0802
Moose::Role 0 2.0802
POSIX 0 1.24
Statistics::Lite 0 3.62
strict 0 1.04
Switch 0 2.17
warnings 0 1.12
build_requires:
Module Need Have
---------------------- ---- -------
Env::Path 0 0.19
ExtUtils::MakeMaker 0 7.10
File::Slurp 0 9999.19
Test::File::Contents 0 0.21
Test::Most 0 0.31
configure_requires:
Module Need Have
---------------------- ---- -------
ExtUtils::MakeMaker 0 7.10
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_GB.UTF-8
LANGUAGE = en_GB:en
LD_LIBRARY_PATH = /usr/local/lib::
PATH = /home/njh/perl5/perlbrew/bin:/home/njh/perl5/perlbrew/perls/perl-5.14.3/bin:/home/njh/perl5/perlbrew/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/home/njh/bin:/sbin
PERL5LIB = /home/njh/.cpan/build/Test-File-Contents-0.21-Hp8KgP/blib/arch:/home/njh/.cpan/build/Test-File-Contents-0.21-Hp8KgP/blib/lib:/home/njh/.cpan/build/BioPerl-1.6.924-pN8ZDn/blib/arch:/home/njh/.cpan/build/BioPerl-1.6.924-pN8ZDn/blib/lib:/home/njh/.cpan/build/Data-Stag-0.14-bvo2kI/blib/arch:/home/njh/.cpan/build/Data-Stag-0.14-bvo2kI/blib/lib:/home/njh/.cpan/build/Env-Path-0.19-I_PDwp/blib/arch:/home/njh/.cpan/build/Env-Path-0.19-I_PDwp/blib/lib:/home/njh/.cpan/build/Switch-2.17-kNaGTZ/blib/arch:/home/njh/.cpan/build/Switch-2.17-kNaGTZ/blib/lib:/home/njh/.cpan/build/Statistics-Lite-3.62-G2nOeH/blib/arch:/home/njh/.cpan/build/Statistics-Lite-3.62-G2nOeH/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 725
PERL5_CPAN_IS_RUNNING = 725
PERL5_MINISMOKEBOX = 0.58
PERLBREW_BASHRC_VERSION = 0.73
PERLBREW_HOME = /home/njh/.perlbrew
PERLBREW_LIB =
PERLBREW_MANPATH = /home/njh/perl5/perlbrew/perls/perl-5.14.3/man
PERLBREW_PATH = /home/njh/perl5/perlbrew/bin:/home/njh/perl5/perlbrew/perls/perl-5.14.3/bin
PERLBREW_PERL = perl-5.14.3
PERLBREW_ROOT = /home/njh/perl5/perlbrew
PERLBREW_VERSION = 0.73
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_LOCAL_LIB_ROOT =
PERL_MM_USE_DEFAULT = 1
SHELL = /bin/bash
TMPDIR = /home/njh/tmp
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/njh/perl5/perlbrew/perls/perl-5.14.3/bin/perl
$UID/$EUID = 1000 / 1000
$GID = 1000 4 24 25 29 30 44 46 108 112 1000
$EGID = 1000 4 24 25 29 30 44 46 108 112 1000
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.10
CPAN::Meta 2.143240
Cwd 3.40
ExtUtils::CBuilder 0.280216
ExtUtils::Command 7.10
ExtUtils::Install 1.56
ExtUtils::MakeMaker 7.10
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.18
File::Spec 3.40
JSON 2.59
JSON::PP 2.27203
Module::Build 0.4206
Module::Signature 0.73
Parse::CPAN::Meta 1.4414
Test::Harness 3.30
Test::More 0.98
YAML 1.15
YAML::Syck 1.29
version 0.9902
--
Summary of my perl5 (revision 5 version 14 subversion 3) configuration:
Platform:
osname=linux, osvers=3.2.0-4-amd64, archname=x86_64-linux-thread-multi
uname='linux nigelhorne.force9.co.uk 3.2.0-4-amd64 #1 smp debian 3.2.32-1 x86_64 gnulinux '
config_args='-de -Dprefix=/home/njh/perl5/perlbrew/perls/perl-5.14.3 -Duseithreads -Dusemultiplicity -Accflags=-O2 -W -Wformat=2 -Wswitch -Wshadow -Wwrite-strings -Wuninitialized -Wall -pipe -mtune=native -march=native -fomit-frame-pointer -mfpmath=sse -pedantic -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wstrict-prototypes -fstack-protector -Wstack-protector -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wdisabled-optimization -Wendif-labels -Wfloat-equal -Wformat-nonliteral -Winline -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wundef -Wformat-security -Aeval:scriptdir=/home/njh/perl5/perlbrew/perls/perl-5.14.3/bin'
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 -O2 -W -Wformat=2 -Wswitch -Wshadow -Wwrite-strings -Wuninitialized -Wall -pipe -mtune=native -march=native -fomit-frame-pointer -mfpmath=sse -pedantic -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wstrict-prototypes -fstack-protector -Wstack-protector -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wdisabled-optimization -Wendif-labels -Wfloat-equal -Wformat-nonliteral -Winline -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wundef -Wformat-security -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2',
cppflags='-D_REENTRANT -D_GNU_SOURCE -O2 -W -Wformat=2 -Wswitch -Wshadow -Wwrite-strings -Wuninitialized -Wall -pipe -mtune=native -march=native -fomit-frame-pointer -mfpmath=sse -pedantic -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wstrict-prototypes -fstack-protector -Wstack-protector -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wdisabled-optimization -Wendif-labels -Wfloat-equal -Wformat-nonliteral -Winline -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wundef -Wformat-security -fno-strict-aliasing -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 -lgdbm -ldb -ldl -lm -lcrypt -lutil -lpthread -lc -lgdbm_compat
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: MULTIPLICITY PERL_DONT_CREATE_GVSV
PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
PERL_PRESERVE_IVUV USE_64_BIT_ALL USE_64_BIT_INT
USE_ITHREADS USE_LARGE_FILES USE_PERLIO USE_PERL_ATOF
USE_REENTRANT_API
Built under linux
Compiled at Mar 5 2013 02:01:19
%ENV:
PERL5LIB="/home/njh/.cpan/build/Test-File-Contents-0.21-Hp8KgP/blib/arch:/home/njh/.cpan/build/Test-File-Contents-0.21-Hp8KgP/blib/lib:/home/njh/.cpan/build/BioPerl-1.6.924-pN8ZDn/blib/arch:/home/njh/.cpan/build/BioPerl-1.6.924-pN8ZDn/blib/lib:/home/njh/.cpan/build/Data-Stag-0.14-bvo2kI/blib/arch:/home/njh/.cpan/build/Data-Stag-0.14-bvo2kI/blib/lib:/home/njh/.cpan/build/Env-Path-0.19-I_PDwp/blib/arch:/home/njh/.cpan/build/Env-Path-0.19-I_PDwp/blib/lib:/home/njh/.cpan/build/Switch-2.17-kNaGTZ/blib/arch:/home/njh/.cpan/build/Switch-2.17-kNaGTZ/blib/lib:/home/njh/.cpan/build/Statistics-Lite-3.62-G2nOeH/blib/arch:/home/njh/.cpan/build/Statistics-Lite-3.62-G2nOeH/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="725"
PERL5_CPAN_IS_RUNNING="725"
PERL5_MINISMOKEBOX="0.58"
PERLBREW_BASHRC_VERSION="0.73"
PERLBREW_HOME="/home/njh/.perlbrew"
PERLBREW_LIB=""
PERLBREW_MANPATH="/home/njh/perl5/perlbrew/perls/perl-5.14.3/man"
PERLBREW_PATH="/home/njh/perl5/perlbrew/bin:/home/njh/perl5/perlbrew/perls/perl-5.14.3/bin"
PERLBREW_PERL="perl-5.14.3"
PERLBREW_ROOT="/home/njh/perl5/perlbrew"
PERLBREW_VERSION="0.73"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_LOCAL_LIB_ROOT=""
PERL_MM_USE_DEFAULT="1"
@INC:
/home/njh/.cpan/build/Test-File-Contents-0.21-Hp8KgP/blib/arch
/home/njh/.cpan/build/Test-File-Contents-0.21-Hp8KgP/blib/lib
/home/njh/.cpan/build/BioPerl-1.6.924-pN8ZDn/blib/arch
/home/njh/.cpan/build/BioPerl-1.6.924-pN8ZDn/blib/lib
/home/njh/.cpan/build/Data-Stag-0.14-bvo2kI/blib/arch
/home/njh/.cpan/build/Data-Stag-0.14-bvo2kI/blib/lib
/home/njh/.cpan/build/Env-Path-0.19-I_PDwp/blib/arch
/home/njh/.cpan/build/Env-Path-0.19-I_PDwp/blib/lib
/home/njh/.cpan/build/Switch-2.17-kNaGTZ/blib/arch
/home/njh/.cpan/build/Switch-2.17-kNaGTZ/blib/lib
/home/njh/.cpan/build/Statistics-Lite-3.62-G2nOeH/blib/arch
/home/njh/.cpan/build/Statistics-Lite-3.62-G2nOeH/blib/lib
/home/njh/perl5/perlbrew/perls/perl-5.14.3/lib/site_perl/5.14.3/x86_64-linux-thread-multi
/home/njh/perl5/perlbrew/perls/perl-5.14.3/lib/site_perl/5.14.3
/home/njh/perl5/perlbrew/perls/perl-5.14.3/lib/5.14.3/x86_64-linux-thread-multi
/home/njh/perl5/perlbrew/perls/perl-5.14.3/lib/5.14.3
.