Bio_AssemblyImprovement v1.160490 Perl 5 v5.18.4 x86_64-linux
- Status
- Fail
- From
- Serguei Trouchelle (STRO)
- Dist
-
Bio_AssemblyImprovement v1.160490
- Platform
- Perl 5 v5.18.4 x86_64-linux
- Date
- 2016-02-22 18:56:37
- ID
- 00153d56-d996-11e5-a344-37d3c06ce8b2
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-1.2015.
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/stro/perl/5.18.4/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/stro/cpan/build/5.18.4/build/Bio_AssemblyImprovement-1.160490-0/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/stro/cpan/build/5.18.4/build/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: /home/stro/cpan/build/5.18.4/build/Bio_AssemblyImprovement-1.160490-0/t/dummy_iva_qc_script_raise_error.py -f /home/stro/cpan/build/5.18.4/build/Bio_AssemblyImprovement-1.160490-0/t/data/forward.fastq -r /home/stro/cpan/build/5.18.4/build/Bio_AssemblyImprovement-1.160490-0/t/data/reverse.fastq --ref_db /home/stro/cpan/build/5.18.4/build/Bio_AssemblyImprovement-1.160490-0/t/data/database /home/stro/cpan/build/5.18.4/build/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
# 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/stro/cpan/build/5.18.4/build/Bio_AssemblyImprovement-1.160490-0/t/does_not_exist.pl does not exist. Using default: /home/stro/cpan/build/5.18.4/build/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/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, 6 wallclock secs ( 0.07 usr 0.01 sys + 5.17 cusr 0.33 csys = 5.58 CPU)
Result: FAIL
Failed 3/24 test programs. 3/242 subtests failed.
Makefile:1054: 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 3.62
File::Basename 0 2.84
File::Copy 0 2.26
File::Path 2.07 2.12
File::Spec 0 3.62
File::Temp 0 0.2304
File::Which 0 1.19
Getopt::Long 0 2.48
Getopt::Std 0 1.07
IO::Compress::Gzip 0 2.069
IO::Uncompress::Gunzip 0 2.069
lib 0 0.63
Moose 0 2.1605
Moose::Role 0 2.1605
POSIX 0 1.32
Statistics::Lite 0 3.62
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 7.10
File::Slurp 0 9999.19
Test::File::Contents 0 0.21
Test::Most 0 0.34
configure_requires:
Module Need Have
---------------------- ---- -------
ExtUtils::MakeMaker 0 7.10
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_US.UTF-8
PATH = /usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 23663
PERL5_CPAN_IS_RUNNING = 23663
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 23116,23663
PERL_CR_SMOKER_CURRENT = Bio_AssemblyImprovement-1.160490
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_MM_USE_DEFAULT = 1
SHELL = /bin/bash
TERM = xterm
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/stro/perl/5.18.4/bin/perl
$UID/$EUID = 1000 / 1000
$GID = 1000 24 25 29 30 44 46 108 114 1000
$EGID = 1000 24 25 29 30 44 46 108 114 1000
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.12
CPAN::Meta 2.150005
Cwd 3.62
ExtUtils::CBuilder 0.280224
ExtUtils::Command 7.10
ExtUtils::Install 1.59
ExtUtils::MakeMaker 7.10
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.30
File::Spec 3.62
JSON 2.90
JSON::PP 2.27300
Module::Build 0.4216
Module::Signature n/a
Parse::CPAN::Meta 1.4417
Test::Harness 3.35
Test::More 1.001014
YAML 1.15
YAML::Syck 1.29
version 0.9913
--
Summary of my perl5 (revision 5 version 18 subversion 4) configuration:
Platform:
osname=linux, osvers=3.16.0-4-amd64, archname=x86_64-linux
uname='linux vm-debian-001 3.16.0-4-amd64 #1 smp debian 3.16.7-ckt11-1 (2015-05-24) x86_64 gnulinux '
config_args=''
hint=recommended, useposix=true, d_sigaction=define
useithreads=undef, usemultiplicity=undef
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2',
cppflags='-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='4.9.2', 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 -ldl -lm -lcrypt -lutil -lc
perllibs=-lnsl -ldl -lm -lcrypt -lutil -lc
libc=, 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'
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_PRESERVE_IVUV PERL_SAWAMPERSAND USE_64_BIT_ALL
USE_64_BIT_INT USE_LARGE_FILES USE_LOCALE
USE_LOCALE_COLLATE USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC USE_PERLIO USE_PERL_ATOF
Built under linux
Compiled at Jul 10 2015 18:48:34
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="23663"
PERL5_CPAN_IS_RUNNING="23663"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="23116,23663"
PERL_CR_SMOKER_CURRENT="Bio_AssemblyImprovement-1.160490"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_MM_USE_DEFAULT="1"
@INC:
/home/stro/perl/5.18.4/lib/site_perl/5.18.4/x86_64-linux
/home/stro/perl/5.18.4/lib/site_perl/5.18.4
/home/stro/perl/5.18.4/lib/5.18.4/x86_64-linux
/home/stro/perl/5.18.4/lib/5.18.4
.