Bio-VertRes-Config v1.133090 Perl 5 v5.27.5 x86_64-linux
- Status
- Fail
- From
- Slaven Rezić (SREZIC)
- Dist
-
Bio-VertRes-Config v1.133090
- Platform
- Perl 5 v5.27.5 x86_64-linux
- Date
- 2017-10-29 00:09:04
- ID
- 5feccd1c-bc3d-11e7-b686-8892b1ea9a90
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-VertRes-Config-1.133090
on perl 5.27.5, 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-5.27.5/bin/perl5.27.5" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/Bio/VertRes/Config/*.t t/Bio/VertRes/Config/CommandLine/*.t t/Bio/VertRes/Config/Pipelines/*.t t/Bio/VertRes/Config/Recipes/*.t t/bin/*.t
t/bin/bacteria_assembly_and_annotation.t ........................... ok
t/bin/bacteria_assembly_single_cell.t .............................. ok
t/bin/bacteria_mapping.t ........................................... ok
t/bin/bacteria_register_and_qc_study.t ............................. ok
t/bin/bacteria_rna_seq_expression.t ................................ ok
t/bin/bacteria_snp_calling.t ....................................... ok
t/bin/eukaryote_assembly.t ......................................... ok
t/bin/eukaryote_mapping.t .......................................... ok
t/bin/eukaryote_register_and_qc_study.t ............................ ok
t/bin/eukaryote_rna_seq_expression.t ............................... ok
t/bin/eukaryote_snp_calling.t ...................................... ok
t/bin/helminth_mapping.t ........................................... ok
t/bin/helminth_register_and_qc_study.t ............................. ok
t/bin/helminth_rna_seq_expression.t ................................ ok
t/bin/helminth_snp_calling.t ....................................... ok
# Failed test 'log file has been created for eukaryote_snp_calling'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for setup_global_configs'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for bacteria_assembly_single_cell'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for eukaryote_mapping'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for virus_register_and_qc_study'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for helminth_rna_seq_expression'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for helminth_mapping'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for eukaryote_assembly'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for virus_mapping'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for bacteria_register_and_qc_study'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for helminth_register_and_qc_study'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for eukaryote_register_and_qc_study'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for bacteria_assembly_and_annotation'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for virus_assembly_and_annotation'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for virus_snp_calling'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for bacteria_snp_calling'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for virus_rna_seq_expression'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for bacteria_rna_seq_expression'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for eukaryote_rna_seq_expression'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for helminth_snp_calling'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Failed test 'log file has been created for bacteria_mapping'
# at t/bin/log_parameters.t line 23.
readline() on closed filehandle $fh at t/bin/log_parameters.t line 25.
Use of uninitialized value in pattern match (m//) at t/bin/log_parameters.t line 25.
# Failed test 'correct format of log file'
# at t/bin/log_parameters.t line 25.
# Looks like you failed 42 tests of 42.
t/bin/log_parameters.t .............................................
Dubious, test returned 42 (wstat 10752, 0x2a00)
Failed 42/42 subtests
# Failed test 'files created as expected for ./bin/setup_global_configs -d pathogen_euk_track -c /var/tmp/cpansmoker-1023/2017102812/muRrM5dvII -l t/data/refs.index'
# at t/lib/TestHelper.pm line 25.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Failed test 'files created as expected for ./bin/setup_global_configs -d some_other_db_name -c /var/tmp/cpansmoker-1023/2017102812/j5Q3UoWrWx -l t/data/refs.index'
# at t/lib/TestHelper.pm line 25.
# Structures begin differing at:
# $got->[0] = Does not exist
# $expected->[0] = 'command_line.log'
# Looks like you failed 2 tests of 2.
t/bin/setup_global_configs.t .......................................
Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/2 subtests
t/bin/virus_assembly_and_annotation.t .............................. ok
t/bin/virus_mapping.t .............................................. ok
t/bin/virus_register_and_qc_study.t ................................ ok
t/bin/virus_rna_seq_expression.t ................................... ok
t/bin/virus_snp_calling.t .......................................... ok
t/Bio/VertRes/Config/CommandLine/Common.t .......................... ok
t/Bio/VertRes/Config/CommandLine/ConstructLimits.t ................. ok
t/Bio/VertRes/Config/CommandLine/LogParameters.t ................... ok
t/Bio/VertRes/Config/CommandLine/StudyNameSearch.t ................. ok
t/Bio/VertRes/Config/MultipleTopLevelFiles.t ....................... ok
t/Bio/VertRes/Config/Pipelines/AnnotateAssembly.t .................. ok
t/Bio/VertRes/Config/Pipelines/Assembly.t .......................... ok
t/Bio/VertRes/Config/Pipelines/BamImprovement.t .................... ok
t/Bio/VertRes/Config/Pipelines/Bowtie2Mapping.t .................... ok
t/Bio/VertRes/Config/Pipelines/BwaMapping.t ........................ ok
t/Bio/VertRes/Config/Pipelines/Common.t ............................ ok
t/Bio/VertRes/Config/Pipelines/Import.t ............................ ok
t/Bio/VertRes/Config/Pipelines/Mapping.t ........................... ok
t/Bio/VertRes/Config/Pipelines/QC.t ................................ ok
t/Bio/VertRes/Config/Pipelines/RnaSeqExpression.t .................. ok
t/Bio/VertRes/Config/Pipelines/SmaltMapping.t ...................... ok
t/Bio/VertRes/Config/Pipelines/SnpCalling.t ........................ ok
t/Bio/VertRes/Config/Pipelines/SpadesAssembly.t .................... ok
t/Bio/VertRes/Config/Pipelines/Ssaha2Mapping.t ..................... ok
t/Bio/VertRes/Config/Pipelines/StampyMapping.t ..................... ok
t/Bio/VertRes/Config/Pipelines/Store.t ............................. ok
t/Bio/VertRes/Config/Pipelines/Tradis.t ............................ ok
t/Bio/VertRes/Config/Pipelines/VelvetAssembly.t .................... ok
t/Bio/VertRes/Config/Recipes/BacteriaAssemblyAndAnnotation.t ....... ok
t/Bio/VertRes/Config/Recipes/BacteriaAssemblySingleCell.t .......... ok
t/Bio/VertRes/Config/Recipes/BacteriaRegisterAndQCStudy.t .......... ok
t/Bio/VertRes/Config/Recipes/BacteriaRnaSeqExpressionUsingBwa.t .... ok
t/Bio/VertRes/Config/Recipes/BacteriaRnaSeqExpressionUsingSmalt.t .. ok
t/Bio/VertRes/Config/Recipes/BacteriaSnpCallingUsingBwa.t .......... ok
t/Bio/VertRes/Config/Recipes/BacteriaSnpCallingUsingSmalt.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesAssembly.t .................. ok
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingBwa.t ........... ok
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingSmalt.t ......... ok
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingSsaha2.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingStampy.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesRegisterAndQCStudy.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesRnaSeqExpression.t .......... ok
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingBwa.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingSmalt.t ...... ok
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingSsaha2.t ..... ok
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingStampy.t ..... ok
t/Bio/VertRes/Config/Recipes/Global.t .............................. ok
t/Bio/VertRes/Config/Recipes/HelminthRegisterAndQCStudy.t .......... ok
t/Bio/VertRes/Config/Recipes/VirusAssemblyAndAnnotation.t .......... ok
t/Bio/VertRes/Config/Recipes/VirusRegisterAndQCStudy.t ............. ok
t/Bio/VertRes/Config/References.t .................................. ok
t/Bio/VertRes/Config/RegisterStudy.t ............................... ok
t/Bio/VertRes/Config/TopLevel.t .................................... ok
Test Summary Report
-------------------
t/bin/log_parameters.t (Wstat: 10752 Tests: 42 Failed: 42)
Failed tests: 1-42
Non-zero exit status: 42
t/bin/setup_global_configs.t (Wstat: 512 Tests: 2 Failed: 2)
Failed tests: 1-2
Non-zero exit status: 2
Files=70, Tests=802, 25 wallclock secs ( 0.17 usr 0.30 sys + 22.57 cusr 2.58 csys = 25.62 CPU)
Result: FAIL
Failed 2/70 test programs. 44/802 subtests failed.
Makefile:1602: die Regel für Ziel âÂÂtest_dynamicâ scheiterte
make: *** [test_dynamic] Fehler 255
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------------- ---- -------
Data::Dumper 0 2.161
DBI 0 1.637
Exception::Class 0 1.43
File::Basename 0 2.85
File::Path 0 2.15
File::Slurp 0 9999.19
Getopt::Long 0 2.5
Moose 0 2.2006
Moose::Role 0 2.2006
Moose::Util::TypeConstraints 0 2.2006
build_requires:
Module Need Have
---------------------------- ---- -------
File::Find 0 1.34
File::Temp 0 0.2304
strict 0 1.11
Test::Most 0 0.35
warnings 0 1.37
configure_requires:
Module Need Have
---------------------------- ---- -------
ExtUtils::MakeMaker 6.30 7.30
------------------------------
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 =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 22204
PERL5_CPAN_IS_RUNNING = 22204
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 28080,22204
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2017102812/cpanreporter_001_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_PARALLEL_SMOKER = yes
PERL_USE_UNSAFE_INC = 1
SHELL = /usr/bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1023/2017102812
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /opt/perl-5.27.5/bin/perl5.27.5
$UID/$EUID = 1023 / 1023
$GID = 1023 1023
$EGID = 1023 1023
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.16
CPAN::Meta 2.150010
Cwd 3.62
ExtUtils::CBuilder 0.280226
ExtUtils::Command 7.30
ExtUtils::Install 2.14
ExtUtils::MakeMaker 7.30
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.35
File::Spec 3.62
JSON 2.94
JSON::PP 2.94
Module::Build 0.4224
Module::Signature 0.81
Parse::CPAN::Meta 2.150010
Test::Harness 3.39
Test::More 1.302106
YAML 1.23
YAML::Syck 1.30
version 0.9918
--
Summary of my perl5 (revision 5 version 27 subversion 5) configuration:
Platform:
osname=linux
osvers=4.9.0-3-amd64
archname=x86_64-linux
uname='linux debian9 4.9.0-3-amd64 #1 smp debian 4.9.30-2+deb9u5 (2017-09-19) x86_64 gnulinux '
config_args='-ds -e -Dprefix=/opt/perl-5.27.5 -Dusedevel -Dusemallocwrap=no -Dcf_email=srezic@cpan.org'
hint=recommended
useposix=true
d_sigaction=define
useithreads=undef
usemultiplicity=undef
use64bitint=define
use64bitall=define
uselongdouble=undef
usemymalloc=n
default_inc_excludes_dot=define
bincompat5005=undef
Compiler:
cc='cc'
ccflags ='-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='-fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
ccversion=''
gccversion='6.3.0 20170516'
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/6/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-2.24.so
so=so
useshrplib=false
libperl=libperl.a
gnulibc_version='2.24'
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
PERLIO_LAYERS
PERL_COPY_ON_WRITE
PERL_DONT_CREATE_GVSV
PERL_OP_PARENT
PERL_PRESERVE_IVUV
PERL_USE_DEVEL
USE_64_BIT_ALL
USE_64_BIT_INT
USE_LARGE_FILES
USE_LOCALE
USE_LOCALE_COLLATE
USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC
USE_LOCALE_TIME
USE_PERLIO
USE_PERL_ATOF
Built under linux
Compiled at Oct 25 2017 16:03:52
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="22204"
PERL5_CPAN_IS_RUNNING="22204"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="28080,22204"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2017102812/cpanreporter_001_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_PARALLEL_SMOKER="yes"
PERL_USE_UNSAFE_INC="1"
@INC:
/opt/perl-5.27.5/lib/site_perl/5.27.5/x86_64-linux
/opt/perl-5.27.5/lib/site_perl/5.27.5
/opt/perl-5.27.5/lib/5.27.5/x86_64-linux
/opt/perl-5.27.5/lib/5.27.5
.