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From: metabase:user:9c36dc84-a30f-11e0-a9fc-0a18abbd4f2f
Subject: FAIL Bio-RetrieveAssemblies-1.1.5 v5.20.2 OpenBSD
Date: 2016-11-16T18:50:43Z
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-RetrieveAssemblies-1.1.5
on perl 5.20.2, 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 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/Bio/*.t t/Bio/RetrieveAssemblies/*.t
t/00_requires_external.t .................. ok
# Failed test 'Expected file for command -q Mycobacterium -a -f gff PRJEB8877 exists: downloaded_files/CVMX01.1.gbff.gz.gff'
# at t/lib/TestHelper.pm line 31.
# Failed test 'Expected file for command -q Mycobacterium -f fasta PRJEB8877 exists: downloaded_files/CVMX01.1.fsa_nt.gz'
# at t/lib/TestHelper.pm line 31.
# Failed test 'Expected file for command -q Mycobacterium -f gff PRJEB8877 exists: downloaded_files/CVMX01.1.gbff.gz.gff'
# at t/lib/TestHelper.pm line 31.
# Failed test 'Expected file for command -q Mycobacterium -o my_dir PRJEB8877 exists: my_dir/CVMX01.1.gbff.gz'
# at t/lib/TestHelper.pm line 31.
# Failed test 'Expected file for command -q Mycobacterium PRJEB8877 exists: downloaded_files/CVMX01.1.gbff.gz'
# at t/lib/TestHelper.pm line 31.
# Looks like you failed 5 tests of 6.
t/Bio/RetrieveAssemblies.t ................
Dubious, test returned 5 (wstat 1280, 0x500)
Failed 5/6 subtests
All arguments to easy_init should be either an integer log level or a hash reference. at lib/Bio/RetrieveAssemblies/LoggingRole.pm line 15.
Possible precedence issue with control flow operator at /home/foo/perl5/bin/bp_genbank2gff3.pl line 690.
t/Bio/RetrieveAssemblies/AccessionFile.t .. ok
All arguments to easy_init should be either an integer log level or a hash reference. at lib/Bio/RetrieveAssemblies/LoggingRole.pm line 15.
t/Bio/RetrieveAssemblies/RefWeak.t ........ ok
All arguments to easy_init should be either an integer log level or a hash reference. at lib/Bio/RetrieveAssemblies/LoggingRole.pm line 15.
All arguments to easy_init should be either an integer log level or a hash reference. at lib/Bio/RetrieveAssemblies/LoggingRole.pm line 15.
t/Bio/RetrieveAssemblies/WGS.t ............ ok
Test Summary Report
-------------------
t/Bio/RetrieveAssemblies.t (Wstat: 1280 Tests: 6 Failed: 5)
Failed tests: 2-6
Non-zero exit status: 5
Files=5, Tests=34, 10 wallclock secs ( 0.06 usr 0.04 sys + 2.41 cusr 1.56 csys = 4.07 CPU)
Result: FAIL
Failed 1/5 test programs. 5/34 subtests failed.
*** Error 255 in /cpan_build/foo/Bio-RetrieveAssemblies-1.1.5-0 (Makefile:930 'test_dynamic')
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------------- ---- --------
Bio::Perl 0 1.006924
Bio::SeqIO 0 0
Data::Validate::URI 0 0.07
Exception::Class 0 1.40
File::Basename 0 2.85
File::Copy 0 2.30
File::Path 0 2.12_001
File::Slurp::Tiny 0 0.004
Getopt::Long 0 2.49
Log::Log4perl 0 1.47
Moose 0 2.1902
Moose::Role 0 2.1902
Moose::Util::TypeConstraints 0 2.1902
Text::CSV 0 1.33
build_requires:
Module Need Have
---------------------------- ---- --------
Cwd 0 3.62
Data::Dumper 0 2.161
Env::Path 0 0.19
ExtUtils::MakeMaker 0 7.24
FindBin 0 1.51
strict 0 1.08
Test::Most 0 0.35
warnings 0 1.23
configure_requires:
Module Need Have
---------------------------- ---- --------
ExtUtils::MakeMaker 0 7.24
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
PATH = /home/foo/bin:/home/foo/perl5/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/X11R6/bin:/usr/local/bin:/usr/local/sbin
PERL5LIB = /home/foo/perl5/lib/perl5
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 5368
PERL5_CPAN_IS_RUNNING = 5368
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 4022,5368
PERL_CR_SMOKER_CURRENT = Bio-RetrieveAssemblies-1.1.5
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_LOCAL_LIB_ROOT = /home/foo/perl5
PERL_MB_OPT = --install_base "/home/foo/perl5"
PERL_MM_OPT = INSTALL_BASE=/home/foo/perl5
PERL_MM_USE_DEFAULT = 1
SHELL = /usr/local/bin/bash
TERM = vt220
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /usr/bin/perl
$UID/$EUID = 1001 / 1001
$GID = 1001 1001
$EGID = 1001 1001
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 1.67
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 n/a
Parse::CPAN::Meta 2.150010
Test::Harness 3.36
Test::More 1.302062
YAML 1.18
YAML::Syck 1.29
version 0.9917
--
Summary of my perl5 (revision 5 version 20 subversion 2) configuration:
Platform:
osname=openbsd, osvers=5.9, archname=amd64-openbsd
uname='openbsd'
config_args='-dsE -Dopenbsd_distribution=defined -Dccflags=-DNO_LOCALE_NUMERIC -DNO_LOCALE_COLLATE -Dmksymlinks'
hint=recommended, useposix=true, d_sigaction=define
useithreads=undef, usemultiplicity=undef
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-DNO_LOCALE_NUMERIC -DNO_LOCALE_COLLATE -fno-strict-aliasing -fno-delete-null-pointer-checks -pipe -fstack-protector -I/usr/local/include',
optimize='-O2',
cppflags='-DNO_LOCALE_NUMERIC -DNO_LOCALE_COLLATE -fno-strict-aliasing -fno-delete-null-pointer-checks -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='4.2.1 20070719 ', gccosandvers='openbsd5.9'
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 ='-Wl,-E -fstack-protector -L/usr/local/lib'
libpth=/usr/lib /usr/local/lib
libs=-lm -lutil -lc
perllibs=-lm -lutil -lc
libc=/usr/lib/libc.a, so=so, useshrplib=true, libperl=libperl.so.17.1
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-R/usr/libdata/perl5/amd64-openbsd/5.20.2/CORE'
cccdlflags='-DPIC -fPIC ', lddlflags='-shared -fPIC -fstack-protector -L/usr/local/lib'
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_NEW_COPY_ON_WRITE PERL_PRESERVE_IVUV
USE_64_BIT_ALL USE_64_BIT_INT USE_LARGE_FILES
USE_LOCALE USE_LOCALE_CTYPE USE_PERLIO USE_PERL_ATOF
Built under openbsd
Compiled at Feb 26 2016 01:02:08
%ENV:
PERL5LIB="/home/foo/perl5/lib/perl5"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="5368"
PERL5_CPAN_IS_RUNNING="5368"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="4022,5368"
PERL_CR_SMOKER_CURRENT="Bio-RetrieveAssemblies-1.1.5"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_LOCAL_LIB_ROOT="/home/foo/perl5"
PERL_MB_OPT="--install_base "/home/foo/perl5""
PERL_MM_OPT="INSTALL_BASE=/home/foo/perl5"
PERL_MM_USE_DEFAULT="1"
@INC:
/home/foo/perl5/lib/perl5/5.20.2/amd64-openbsd
/home/foo/perl5/lib/perl5/5.20.2
/home/foo/perl5/lib/perl5/amd64-openbsd
/home/foo/perl5/lib/perl5
/usr/local/libdata/perl5/site_perl/amd64-openbsd
/usr/libdata/perl5/site_perl/amd64-openbsd
/usr/local/libdata/perl5/site_perl
/usr/libdata/perl5/site_perl
/usr/libdata/perl5/amd64-openbsd/5.20.2
/usr/local/libdata/perl5/amd64-openbsd/5.20.2
/usr/libdata/perl5
/usr/local/libdata/perl5
.