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From: metabase:user:a0e144f2-373b-11e6-8edd-c6848980b093
Subject: FAIL Bio-VertRes-Config-1.133090 v5.25.6 GNU/Linux
Date: 2016-10-18T10:45:20Z
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 5.25.6, 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/cpan2/install/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_register_and_qc_study.t ............................. ok
t/bin/bacteria_rna_seq_expression.t ................................ ok
t/bin/bacteria_mapping.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
# 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 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 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 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 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_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 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 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_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_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_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_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 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 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_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_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/GmAKaJFa4j -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/OmFxn7DBvI -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/helminth_rna_seq_expression.t ................................ ok
t/bin/helminth_snp_calling.t ....................................... ok
t/bin/virus_assembly_and_annotation.t .............................. ok
t/bin/virus_mapping.t .............................................. ok
t/bin/virus_register_and_qc_study.t ................................ ok
t/Bio/VertRes/Config/CommandLine/Common.t .......................... ok
t/bin/virus_rna_seq_expression.t ................................... ok
t/Bio/VertRes/Config/CommandLine/ConstructLimits.t ................. ok
t/Bio/VertRes/Config/CommandLine/LogParameters.t ................... ok
t/bin/virus_snp_calling.t .......................................... ok
t/Bio/VertRes/Config/CommandLine/StudyNameSearch.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/MultipleTopLevelFiles.t ....................... ok
t/Bio/VertRes/Config/Pipelines/Bowtie2Mapping.t .................... ok
t/Bio/VertRes/Config/Pipelines/Common.t ............................ ok
t/Bio/VertRes/Config/Pipelines/BwaMapping.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/Store.t ............................. ok
t/Bio/VertRes/Config/Pipelines/StampyMapping.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/BacteriaRnaSeqExpressionUsingSmalt.t .. ok
t/Bio/VertRes/Config/Recipes/BacteriaSnpCallingUsingBwa.t .......... ok
t/Bio/VertRes/Config/Recipes/BacteriaRnaSeqExpressionUsingBwa.t .... ok
t/Bio/VertRes/Config/Recipes/EukaryotesAssembly.t .................. ok
t/Bio/VertRes/Config/Recipes/BacteriaSnpCallingUsingSmalt.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingSmalt.t ......... ok
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingBwa.t ........... ok
t/Bio/VertRes/Config/Recipes/EukaryotesRegisterAndQCStudy.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingSsaha2.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesMappingUsingStampy.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesRnaSeqExpression.t .......... ok
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingSsaha2.t ..... ok
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingSmalt.t ...... ok
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingBwa.t ........ ok
t/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingStampy.t ..... ok
t/Bio/VertRes/Config/Recipes/Global.t .............................. ok
t/Bio/VertRes/Config/References.t .................................. ok
t/Bio/VertRes/Config/Recipes/VirusAssemblyAndAnnotation.t .......... ok
t/Bio/VertRes/Config/Recipes/HelminthRegisterAndQCStudy.t .......... ok
t/Bio/VertRes/Config/Recipes/VirusRegisterAndQCStudy.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, 16 wallclock secs ( 0.37 usr 0.10 sys + 71.74 cusr 2.37 csys = 74.58 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 1.634
Exception::Class 0 1.40
File::Basename 0 2.85
File::Path 0 2.12
File::Slurp 0 9999.19
Getopt::Long 0 2.49
Moose 0 2.1900
Moose::Role 0 2.1900
Moose::Util::TypeConstraints 0 2.1900
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 7.24
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
HARNESS_OPTIONS = j5
LANG = en_US.UTF-8
PATH = /usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 10775
PERL5_CPAN_IS_RUNNING = 10775
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 4454,10775
PERLBREW_BASHRC_VERSION = 0.76
PERLBREW_HOME = /home/dcollins/.perlbrew
PERLBREW_ROOT = /home/dcollins/toolchain/perl5
PERL_CR_SMOKER_CURRENT = Bio-VertRes-Config-1.133090
PERL_CR_SMOKER_RUNONCE = 1
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_MM_USE_DEFAULT = 1
SHELL = /bin/bash
TERM = putty
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/cpan2/install/bin/perl
$UID/$EUID = 1003 / 1003
$GID = 1003 1003
$EGID = 1003 1003
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.14
CPAN::Meta 2.150010
Cwd 3.62
ExtUtils::CBuilder 0.280224
ExtUtils::Command 7.24
ExtUtils::Install 2.04
ExtUtils::MakeMaker 7.24
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.30
File::Spec 3.62
JSON 2.90
JSON::PP 2.27400
Module::Build 0.4220
Module::Signature 0.81
Parse::CPAN::Meta 2.150010
Test::Harness 3.36
Test::More 1.302061
YAML 1.18
YAML::Syck 1.29
version 0.9917
--
Summary of my perl5 (revision 5 version 25 subversion 6) configuration:
Commit id: 11a12be6c2df2fcd9601f9fde8c7df8c7538c956
Platform:
osname=linux
osvers=3.16.0-4-amd64
archname=x86_64-linux-thread-multi
uname='linux digitalis 3.16.0-4-amd64 #1 smp debian 3.16.36-1+deb8u1 (2016-09-03) x86_64 gnulinux '
config_args='-Dusedevel -DDEBUGGING -Dusethreads -Dprefix=/home/cpan2/install -Uversiononly -des'
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 -DDEBUGGING -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 -g'
cppflags='-D_REENTRANT -D_GNU_SOURCE -fwrapv -DDEBUGGING -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 -ldl -lm -lcrypt -lutil -lc
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 -g -L/usr/local/lib -fstack-protector-strong'
Characteristics of this binary (from libperl):
Compile-time options:
DEBUGGING
HAS_TIMES
MULTIPLICITY
PERLIO_LAYERS
PERL_COPY_ON_WRITE
PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
PERL_IMPLICIT_CONTEXT
PERL_MALLOC_WRAP
PERL_OP_PARENT
PERL_PRESERVE_IVUV
PERL_TRACK_MEMPOOL
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
Built under linux
Compiled at Oct 11 2016 16:20:18
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="10775"
PERL5_CPAN_IS_RUNNING="10775"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="4454,10775"
PERLBREW_BASHRC_VERSION="0.76"
PERLBREW_HOME="/home/dcollins/.perlbrew"
PERLBREW_ROOT="/home/dcollins/toolchain/perl5"
PERL_CR_SMOKER_CURRENT="Bio-VertRes-Config-1.133090"
PERL_CR_SMOKER_RUNONCE="1"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_MM_USE_DEFAULT="1"
@INC:
/home/cpan2/install/lib/perl5/site_perl/5.25.6/x86_64-linux-thread-multi
/home/cpan2/install/lib/perl5/site_perl/5.25.6
/home/cpan2/install/lib/perl5/5.25.6/x86_64-linux-thread-multi
/home/cpan2/install/lib/perl5/5.25.6
.