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From: metabase:user:314402c4-2aae-11df-837a-5e0a49663a4f
Subject: FAIL Bio-RetrieveAssemblies-1.1.5 v5.22.3 GNU/Linux
Date: 2017-07-02T17:01:12Z
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 5.22.3, 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 'make test':
PERL_DL_NONLAZY=1 "/opt/perl-5.22.3/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
# Failed test 'bp_genbank2gff3.pl in PATH'
# at t/00_requires_external.t line 19.
# Looks like you failed 1 test of 2.
t/00_requires_external.t ..................
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/2 subtests
# 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.
Can't exec "bp_genbank2gff3.pl": No such file or directory at lib/Bio/RetrieveAssemblies/AccessionFile.pm line 92.
Couldnt convert CVCD01 GenBank file to GFF3# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 2 just after 14.
t/Bio/RetrieveAssemblies/AccessionFile.t ..
Dubious, test returned 2 (wstat 512, 0x200)
All 14 subtests passed
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/00_requires_external.t (Wstat: 256 Tests: 2 Failed: 1)
Failed test: 2
Non-zero exit status: 1
t/Bio/RetrieveAssemblies.t (Wstat: 1280 Tests: 6 Failed: 5)
Failed tests: 2-6
Non-zero exit status: 5
t/Bio/RetrieveAssemblies/AccessionFile.t (Wstat: 512 Tests: 14 Failed: 0)
Non-zero exit status: 2
Parse errors: No plan found in TAP output
Files=5, Tests=31, 4 wallclock secs ( 0.02 usr 0.03 sys + 1.10 cusr 0.24 csys = 1.39 CPU)
Result: FAIL
Failed 3/5 test programs. 6/31 subtests failed.
make: *** [test_dynamic] Error 255
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------------- ---- --------
Bio::Perl 0 1.007001
Bio::SeqIO 0 1.007001
Data::Validate::URI 0 0.07
Exception::Class 0 1.42
File::Basename 0 2.85
File::Copy 0 2.30
File::Path 0 2.14
File::Slurp::Tiny 0 0.004
Getopt::Long 0 2.5
Log::Log4perl 0 1.49
Moose 0 2.2005
Moose::Role 0 2.2005
Moose::Util::TypeConstraints 0 2.2005
Text::CSV 0 1.95
build_requires:
Module Need Have
---------------------------- ---- --------
Cwd 0 3.56_02
Data::Dumper 0 2.158
Env::Path 0 0.19
ExtUtils::MakeMaker 0 7.30
FindBin 0 1.51
strict 0 1.09
Test::Most 0 0.35
warnings 0 1.34
configure_requires:
Module Need Have
---------------------------- ---- --------
ExtUtils::MakeMaker 0 7.30
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
LANG = en_US.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 = 32009
PERL5_CPAN_IS_RUNNING = 32009
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 6678,32009
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2017070215/cpanreporter_003_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
SHELL = /bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1023/2017070215
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /opt/perl-5.22.3/bin/perl
$UID/$EUID = 1023 / 1023
$GID = 1023 1023
$EGID = 1023 1023
Perl module toolchain versions installed:
Module Have
------------------- ----------
CPAN 2.11_01
CPAN::Meta 2.150001
Cwd 3.56_02
ExtUtils::CBuilder 0.280221
ExtUtils::Command 7.30
ExtUtils::Install 2.06
ExtUtils::MakeMaker 7.30
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.28
File::Spec 3.56_02
JSON 2.94
JSON::PP 2.94
Module::Build 0.4224
Module::Signature n/a
Parse::CPAN::Meta 1.4414_001
Test::Harness 3.35_01
Test::More 1.302086
YAML 1.23
YAML::Syck 1.30
version 0.9909
--
Summary of my perl5 (revision 5 version 22 subversion 3) configuration:
Platform:
osname=linux, osvers=2.6.32-696.3.1.el6.x86_64, archname=x86_64-linux
uname='linux centos6 2.6.32-696.3.1.el6.x86_64 #1 smp tue may 30 19:52:55 utc 2017 x86_64 x86_64 x86_64 gnulinux '
config_args='-ds -e -Dprefix=/opt/perl-5.22.3 -Dcf_email=srezic@cpan.org'
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 ='-fwrapv -fno-strict-aliasing -pipe -fstack-protector -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 -I/usr/local/include'
ccversion='', gccversion='4.4.7 20120313 (Red Hat 4.4.7-18)', 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 -L/usr/local/lib'
libpth=/usr/local/lib /usr/lib /lib/../lib64 /usr/lib/../lib64 /lib /lib64 /usr/lib64 /usr/local/lib64
libs=-lpthread -lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lc
perllibs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
libc=libc-2.12.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.12'
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'
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_COLLATE USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC USE_LOCALE_TIME USE_PERLIO
USE_PERL_ATOF
Built under linux
Compiled at Jun 21 2017 19:22:49
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="32009"
PERL5_CPAN_IS_RUNNING="32009"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="6678,32009"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2017070215/cpanreporter_003_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
@INC:
/opt/perl-5.22.3/lib/site_perl/5.22.3/x86_64-linux
/opt/perl-5.22.3/lib/site_perl/5.22.3
/opt/perl-5.22.3/lib/5.22.3/x86_64-linux
/opt/perl-5.22.3/lib/5.22.3
.