Bio_AssemblyImprovement v1.160490 Perl 5 v5.30.0 RC1 x86_64-linux-thread-multi
- Status
- Fail
- From
- Slaven Rezić (SREZIC)
- Dist
-
Bio_AssemblyImprovement v1.160490
- Platform
- Perl 5 v5.30.0 RC1 x86_64-linux-thread-multi
- Date
- 2019-05-15 21:33:47
- ID
- 1fa6c98c-7759-11e9-bce5-ce4b1f24ea8f
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 5.30.0, 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 "/opt/perl-5.30.0-RC1t/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
Useless use of concatenation (.) or string in void context at lib/Bio/AssemblyImprovement/Abacas/Main.pm line 33.
t/Abacas/Iterative.t .................... ok
Useless use of concatenation (.) or string in void context at lib/Bio/AssemblyImprovement/Abacas/Main.pm line 33.
t/Abacas/Main.t ......................... ok
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/cpansand/.cpan/build/2019051520/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 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 "/home/cpansand/.cpan/build/2019051520/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/cpansand/.cpan/build/2019051520/Bio_AssemblyImprovement-1.160490-0/t/dummy_iva_qc_script_raise_error.py -f /home/cpansand/.cpan/build/2019051520/Bio_AssemblyImprovement-1.160490-0/t/data/forward.fastq -r /home/cpansand/.cpan/build/2019051520/Bio_AssemblyImprovement-1.160490-0/t/data/reverse.fastq --ref_db /home/cpansand/.cpan/build/2019051520/Bio_AssemblyImprovement-1.160490-0/t/data/database /home/cpansand/.cpan/build/2019051520/Bio_AssemblyImprovement-1.160490-0/t/data/contigs.fa test_iva_qc
t/IvaQC/Main.t .......................... ok
Useless use of concatenation (.) or string in void context at lib/Bio/AssemblyImprovement/Abacas/Main.pm line 33, <$modules> line 10.
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/cpansand/.cpan/build/2019051520/Bio_AssemblyImprovement-1.160490-0/t/does_not_exist.pl does not exist. Using default: /home/cpansand/.cpan/build/2019051520/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: 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, 8 wallclock secs ( 0.09 usr 0.07 sys + 5.56 cusr 2.09 csys = 7.81 CPU)
Result: FAIL
Failed 2/24 test programs. 2/242 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 1.7.5
Cwd 0 3.78
File::Basename 0 2.85
File::Copy 0 2.34
File::Path 2.07 2.16
File::Spec 0 3.78
File::Temp 0 0.2309
File::Which 0 1.23
Getopt::Long 0 2.5
Getopt::Std 0 1.12
IO::Compress::Gzip 0 2.086
IO::Uncompress::Gunzip 0 2.086
lib 0 0.65
Moose 0 2.2011
Moose::Role 0 2.2011
POSIX 0 1.88
Statistics::Lite 0 3.62
strict 0 1.11
Switch 0 2.17
warnings 0 1.44
build_requires:
Module Need Have
---------------------- ---- -------
Env::Path 0 0.19
ExtUtils::MakeMaker 0 7.34
File::Slurp 0 9999.27
Test::File::Contents 0 0.23
Test::Most 0 0.35
configure_requires:
Module Need Have
---------------------- ---- -------
ExtUtils::MakeMaker 0 7.34
------------------------------
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/2019051520/Switch-2.17-0/blib/arch:/home/cpansand/.cpan/build/2019051520/Switch-2.17-0/blib/lib:/home/cpansand/.cpan/build/2019051520/Statistics-Lite-3.62-0/blib/arch:/home/cpansand/.cpan/build/2019051520/Statistics-Lite-3.62-0/blib/lib:/home/cpansand/.cpan/build/2019051520/Env-Path-0.19-0/blib/arch:/home/cpansand/.cpan/build/2019051520/Env-Path-0.19-0/blib/lib:/home/cpansand/.cpan/build/2019051520/BioPerl-1.7.5-0/blib/arch:/home/cpansand/.cpan/build/2019051520/BioPerl-1.7.5-0/blib/lib:/home/cpansand/.cpan/build/2019051520/XML-DOM-XPath-0.14-0/blib/arch:/home/cpansand/.cpan/build/2019051520/XML-DOM-XPath-0.14-0/blib/lib:/home/cpansand/.cpan/build/2019051520/XML-XPathEngine-0.14-0/blib/arch:/home/cpansand/.cpan/build/2019051520/XML-XPathEngine-0.14-0/blib/lib:/home/cpansand/.cpan/build/2019051520/XML-DOM-1.46-0/blib/arch:/home/cpansand/.cpan/build/2019051520/XML-DOM-1.46-0/blib/lib:/home/cpansand/.cpan/build/2019051520/XML-RegExp-0.04-0/blib/arch:/home/cpansand/.cpan/build/2019051520/XML-RegExp-0.04-0/blib/lib:/home/cpansand/.cpan/build/2019051520/libxml-perl-0.08-0/blib/arch:/home/cpansand/.cpan/build/2019051520/libxml-perl-0.08-0/blib/lib:/home/cpansand/.cpan/build/2019051520/Test-Weaken-3.022000-0/blib/arch:/home/cpansand/.cpan/build/2019051520/Test-Weaken-3.022000-0/blib/lib:/home/cpansand/.cpan/build/2019051520/Data-Stag-0.14-0/blib/arch:/home/cpansand/.cpan/build/2019051520/Data-Stag-0.14-0/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 28438
PERL5_CPAN_IS_RUNNING = 28438
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 28407,28438
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2019051520/cpanreporter_000_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_USE_UNSAFE_INC = 1
SHELL = /usr/bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1023/2019051520
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /opt/perl-5.30.0-RC1t/bin/perl
$UID/$EUID = 1023 / 1023
$GID = 1023 1023
$EGID = 1023 1023
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.22
CPAN::Meta 2.150010
Cwd 3.78
ExtUtils::CBuilder 0.280231
ExtUtils::Command 7.34
ExtUtils::Install 2.14
ExtUtils::MakeMaker 7.34
ExtUtils::Manifest 1.72
ExtUtils::ParseXS 3.40
File::Spec 3.78
JSON 4.02
JSON::PP 4.02
Module::Build 0.4229
Module::Signature n/a
Parse::CPAN::Meta 2.150010
Test::Harness 3.42
Test::More 1.302162
YAML 1.29
YAML::Syck 1.31
version 0.9924
--
Summary of my perl5 (revision 5 version 30 subversion 0) configuration:
Platform:
osname=linux
osvers=3.16.0-8-amd64
archname=x86_64-linux-thread-multi
uname='linux debian8 3.16.0-8-amd64 #1 smp debian 3.16.64-2 (2019-04-01) x86_64 gnulinux '
config_args='-ds -e -Dprefix=/opt/perl-5.30.0-RC1t -Dusethreads -Dcf_email=srezic@cpan.org'
hint=recommended
useposix=true
d_sigaction=define
useithreads=define
usemultiplicity=define
use64bitint=define
use64bitall=define
uselongdouble=undef
usemymalloc=n
default_inc_excludes_dot=define
bincompat5005=undef
Compiler:
cc='cc'
ccflags ='-D_REENTRANT -D_GNU_SOURCE -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='-D_REENTRANT -D_GNU_SOURCE -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
MULTIPLICITY
PERLIO_LAYERS
PERL_COPY_ON_WRITE
PERL_DONT_CREATE_GVSV
PERL_IMPLICIT_CONTEXT
PERL_MALLOC_WRAP
PERL_OP_PARENT
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
USE_THREAD_SAFE_LOCALE
Locally applied patches:
RC1
Built under linux
Compiled at May 12 2019 17:29:50
%ENV:
PERL5LIB="/home/cpansand/.cpan/build/2019051520/Switch-2.17-0/blib/arch:/home/cpansand/.cpan/build/2019051520/Switch-2.17-0/blib/lib:/home/cpansand/.cpan/build/2019051520/Statistics-Lite-3.62-0/blib/arch:/home/cpansand/.cpan/build/2019051520/Statistics-Lite-3.62-0/blib/lib:/home/cpansand/.cpan/build/2019051520/Env-Path-0.19-0/blib/arch:/home/cpansand/.cpan/build/2019051520/Env-Path-0.19-0/blib/lib:/home/cpansand/.cpan/build/2019051520/BioPerl-1.7.5-0/blib/arch:/home/cpansand/.cpan/build/2019051520/BioPerl-1.7.5-0/blib/lib:/home/cpansand/.cpan/build/2019051520/XML-DOM-XPath-0.14-0/blib/arch:/home/cpansand/.cpan/build/2019051520/XML-DOM-XPath-0.14-0/blib/lib:/home/cpansand/.cpan/build/2019051520/XML-XPathEngine-0.14-0/blib/arch:/home/cpansand/.cpan/build/2019051520/XML-XPathEngine-0.14-0/blib/lib:/home/cpansand/.cpan/build/2019051520/XML-DOM-1.46-0/blib/arch:/home/cpansand/.cpan/build/2019051520/XML-DOM-1.46-0/blib/lib:/home/cpansand/.cpan/build/2019051520/XML-RegExp-0.04-0/blib/arch:/home/cpansand/.cpan/build/2019051520/XML-RegExp-0.04-0/blib/lib:/home/cpansand/.cpan/build/2019051520/libxml-perl-0.08-0/blib/arch:/home/cpansand/.cpan/build/2019051520/libxml-perl-0.08-0/blib/lib:/home/cpansand/.cpan/build/2019051520/Test-Weaken-3.022000-0/blib/arch:/home/cpansand/.cpan/build/2019051520/Test-Weaken-3.022000-0/blib/lib:/home/cpansand/.cpan/build/2019051520/Data-Stag-0.14-0/blib/arch:/home/cpansand/.cpan/build/2019051520/Data-Stag-0.14-0/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="28438"
PERL5_CPAN_IS_RUNNING="28438"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="28407,28438"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2019051520/cpanreporter_000_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_USE_UNSAFE_INC="1"
@INC:
/home/cpansand/.cpan/build/2019051520/Switch-2.17-0/blib/arch
/home/cpansand/.cpan/build/2019051520/Switch-2.17-0/blib/lib
/home/cpansand/.cpan/build/2019051520/Statistics-Lite-3.62-0/blib/arch
/home/cpansand/.cpan/build/2019051520/Statistics-Lite-3.62-0/blib/lib
/home/cpansand/.cpan/build/2019051520/Env-Path-0.19-0/blib/arch
/home/cpansand/.cpan/build/2019051520/Env-Path-0.19-0/blib/lib
/home/cpansand/.cpan/build/2019051520/BioPerl-1.7.5-0/blib/arch
/home/cpansand/.cpan/build/2019051520/BioPerl-1.7.5-0/blib/lib
/home/cpansand/.cpan/build/2019051520/XML-DOM-XPath-0.14-0/blib/arch
/home/cpansand/.cpan/build/2019051520/XML-DOM-XPath-0.14-0/blib/lib
/home/cpansand/.cpan/build/2019051520/XML-XPathEngine-0.14-0/blib/arch
/home/cpansand/.cpan/build/2019051520/XML-XPathEngine-0.14-0/blib/lib
/home/cpansand/.cpan/build/2019051520/XML-DOM-1.46-0/blib/arch
/home/cpansand/.cpan/build/2019051520/XML-DOM-1.46-0/blib/lib
/home/cpansand/.cpan/build/2019051520/XML-RegExp-0.04-0/blib/arch
/home/cpansand/.cpan/build/2019051520/XML-RegExp-0.04-0/blib/lib
/home/cpansand/.cpan/build/2019051520/libxml-perl-0.08-0/blib/arch
/home/cpansand/.cpan/build/2019051520/libxml-perl-0.08-0/blib/lib
/home/cpansand/.cpan/build/2019051520/Test-Weaken-3.022000-0/blib/arch
/home/cpansand/.cpan/build/2019051520/Test-Weaken-3.022000-0/blib/lib
/home/cpansand/.cpan/build/2019051520/Data-Stag-0.14-0/blib/arch
/home/cpansand/.cpan/build/2019051520/Data-Stag-0.14-0/blib/lib
/opt/perl-5.30.0-RC1t/lib/site_perl/5.30.0/x86_64-linux-thread-multi
/opt/perl-5.30.0-RC1t/lib/site_perl/5.30.0
/opt/perl-5.30.0-RC1t/lib/5.30.0/x86_64-linux-thread-multi
/opt/perl-5.30.0-RC1t/lib/5.30.0
.