Bio-VertRes-Config v1.133090 Perl 5 v5.22.2 x86_64-linux-thread-multi
- Status
- Fail
- From
- Andreas J. König (ANDK)
- Dist
-
Bio-VertRes-Config v1.133090
- Platform
- Perl 5 v5.22.2 x86_64-linux-thread-multi
- Date
- 2017-12-02 22:57:28
- ID
- 2ba41a64-d7b4-11e7-9cb1-bfb8c4fe1824
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 5.22.2, 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:
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/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.22.2/f11c/bin/perl" "-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 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 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 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 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 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 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 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 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_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_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_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 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 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 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 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 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 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 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 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.
# 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 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.
# 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 /tmp/T7UqrcTqpq -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 /tmp/mLy3z2zppd -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, 64 wallclock secs ( 0.21 usr 0.35 sys + 30.97 cusr 3.91 csys = 35.44 CPU)
Result: FAIL
Failed 2/70 test programs. 44/802 subtests failed.
Makefile:1601: recipe for target 'test_dynamic' failed
make: *** [test_dynamic] Error 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 1.29
File::Temp 0 0.2304
strict 0 1.09
Test::Most 0 0.35
warnings 0 1.34
configure_requires:
Module Need Have
---------------------------- ---- -------
ExtUtils::MakeMaker 6.30 7.30
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_US.UTF-8
PATH = /home/sand/bin:/usr/local/bin:/usr/bin:/bin:/usr/games:/usr/local/perl/bin:/usr/X11/bin:/sbin:/usr/sbin
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 15872
PERL5_CPAN_IS_RUNNING = 15872
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 1821,15872
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_MM_USE_DEFAULT = 1
PERL_USE_UNSAFE_INC = 1
SHELL = /usr/bin/zsh
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.22.2/f11c/bin/perl
$UID/$EUID = 1005 / 1005
$GID = 1005 1005
$EGID = 1005 1005
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.18
CPAN::Meta 2.150010
Cwd 3.62
ExtUtils::CBuilder 0.280226
ExtUtils::Command 7.30
ExtUtils::Install 2.06
ExtUtils::MakeMaker 7.30
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.35
File::Spec 3.62
JSON 2.96
JSON::PP 2.94
Module::Build 0.4224
Module::Signature 0.81
Parse::CPAN::Meta 2.150010
Test::Harness 3.39
Test::More 1.302119
YAML 1.24
YAML::Syck 1.30
version 0.9918
--
Summary of my perl5 (revision 5 version 22 subversion 2) configuration:
Derived from: 9cbffb38735712e3a34e6f537892b6ef06fb815f
Platform:
osname=linux, osvers=4.12.0-2-amd64, archname=x86_64-linux-thread-multi
uname='linux k93msid 4.12.0-2-amd64 #1 smp debian 4.12.13-1 (2017-09-19) x86_64 gnulinux '
config_args='-Dprefix=/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.22.2/f11c -Dmyhostname=k93msid -Dinstallusrbinperl=n -Uversiononly -Dusedevel -des -Ui_db -Dlibswanted=cl pthread socket inet nsl gdbm dbm malloc dl ld sun m crypt sec util c cposix posix ucb BSD gdbm_compat -Duseithreads -Uuselongdouble -DDEBUGGING=-g'
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 -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2 -g',
cppflags='-D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
ccversion='', gccversion='7.2.0', 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/7/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 -ldl -lm -lcrypt -lutil -lc
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 -g -L/usr/local/lib -fstack-protector-strong'
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
PERL_USE_DEVEL 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
Locally applied patches:
uncommitted-changes
Built under linux
Compiled at Oct 4 2017 00:59:36
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="15872"
PERL5_CPAN_IS_RUNNING="15872"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="1821,15872"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_MM_USE_DEFAULT="1"
PERL_USE_UNSAFE_INC="1"
@INC:
/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.22.2/f11c/lib/site_perl/5.22.2/x86_64-linux-thread-multi
/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.22.2/f11c/lib/site_perl/5.22.2
/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.22.2/f11c/lib/5.22.2/x86_64-linux-thread-multi
/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.22.2/f11c/lib/5.22.2
.