Back
From: metabase:user:320bfe00-2aae-11df-837a-5e0a49663a4f
Subject: FAIL Bio-RetrieveAssemblies-1.1.5 v5.14.4 GNU/Linux
Date: 2017-08-07T09:08:37Z
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 5.14.4, 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/v5.14.4/d2d1/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
Redirecting output to âwget-logâ.
# 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.
Redirecting output to âwget-log.1â.
# 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.
Redirecting output to âwget-log.2â.
# 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.
Redirecting output to âwget-log.3â.
# 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.
Redirecting output to âwget-log.4â.
# 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, 10 wallclock secs ( 0.03 usr 0.03 sys + 1.61 cusr 0.31 csys = 1.98 CPU)
Result: FAIL
Failed 3/5 test programs. 6/31 subtests failed.
Makefile:931: recipe for target 'test_dynamic' 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 2.82
File::Copy 0 2.21
File::Path 0 2.14
File::Slurp::Tiny 0 0.004
Getopt::Long 0 2.5
Log::Log4perl 0 1.49
Moose 0 2.2006
Moose::Role 0 2.2006
Moose::Util::TypeConstraints 0 2.2006
Text::CSV 0 1.95
build_requires:
Module Need Have
---------------------------- ---- --------
Cwd 0 3.62
Data::Dumper 0 2.161
Env::Path 0 0.19
ExtUtils::MakeMaker 0 7.31_03
FindBin 0 1.50
strict 0 1.04
Test::Most 0 0.35
warnings 0 1.12
configure_requires:
Module Need Have
---------------------------- ---- --------
ExtUtils::MakeMaker 0 7.31_03
------------------------------
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 = 7541
PERL5_CPAN_IS_RUNNING = 7541
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/v5.14.4/d2d1/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 7.31_03
ExtUtils::Install 2.06
ExtUtils::MakeMaker 7.31_03
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 3.40_01
Test::More 1.302090
YAML 1.23
YAML::Syck 1.30
version 0.9918
--
Summary of my perl5 (revision 5 version 14 subversion 4) configuration:
Derived from: 26c5c13a4ece9084f310610bb17fb2f24c72a73e
Platform:
osname=linux, osvers=4.9.0-2-amd64, archname=x86_64-linux
uname='linux k93msid 4.9.0-2-amd64 #1 smp debian 4.9.18-1 (2017-03-30) x86_64 gnulinux '
config_args='-Dprefix=/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.14.4/d2d1 -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 -Uuseithreads -Uuselongdouble -DDEBUGGING=both'
hint=recommended, useposix=true, d_sigaction=define
useithreads=undef, usemultiplicity=undef
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-DDEBUGGING -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2 -g',
cppflags='-DDEBUGGING -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='6.3.0 20170406', gccosandvers=''
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 =' -fstack-protector -L/usr/local/lib'
libpth=/usr/local/lib /lib/x86_64-linux-gnu /lib/../lib /usr/lib/x86_64-linux-gnu /usr/lib/../lib /lib /usr/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'
Characteristics of this binary (from libperl):
Compile-time options: DEBUGGING PERL_DONT_CREATE_GVSV PERL_MALLOC_WRAP
PERL_PRESERVE_IVUV PERL_USE_DEVEL USE_64_BIT_ALL
USE_64_BIT_INT USE_LARGE_FILES USE_PERLIO
USE_PERL_ATOF
Locally applied patches:
uncommitted-changes
Built under linux
Compiled at Jun 21 2017 00:23:21
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="7541"
PERL5_CPAN_IS_RUNNING="7541"
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/v5.14.4/d2d1/lib/site_perl/5.14.4/x86_64-linux
/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.14.4/d2d1/lib/site_perl/5.14.4
/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.14.4/d2d1/lib/5.14.4/x86_64-linux
/home/sand/src/perl/repoperls/installed-perls/host/k93msid/v5.14.4/d2d1/lib/5.14.4
.