Bio-RetrieveAssemblies v1.1.5 Perl 5 v5.27.9 x86_64-linux
- Status
- Fail
- From
- Slaven Rezić (SREZIC)
- Dist
-
Bio-RetrieveAssemblies v1.1.5
- Platform
- Perl 5 v5.27.9 x86_64-linux
- Date
- 2018-02-26 23:29:26
- ID
- e281f1c6-1b4c-11e8-af39-cf9655f6bba7
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 5.27.9, 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 '/usr/bin/make test':
PERL_DL_NONLAZY=1 "/opt/perl-5.27.9/bin/perl5.27.9" "-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": Datei oder Verzeichnis nicht gefunden 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 ( 0.03 usr 0.01 sys + 0.99 cusr 0.28 csys = 1.31 CPU)
Result: FAIL
Failed 3/5 test programs. 6/31 subtests failed.
Makefile:931: die Regel für Ziel âÂÂtest_dynamicâ scheiterte
make: *** [test_dynamic] Fehler 255
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------------- ---- --------
Bio::Perl 0 1.007002
Bio::SeqIO 0 1.007002
Data::Validate::URI 0 0.07
Exception::Class 0 1.44
File::Basename 0 2.85
File::Copy 0 2.33
File::Path 0 2.15
File::Slurp::Tiny 0 0.004
Getopt::Long 0 2.5
Log::Log4perl 0 1.49
Moose 0 2.2010
Moose::Role 0 2.2010
Moose::Util::TypeConstraints 0 2.2010
Text::CSV 0 1.95
build_requires:
Module Need Have
---------------------------- ---- --------
Cwd 0 3.74
Data::Dumper 0 2.161
Env::Path 0 0.19
ExtUtils::MakeMaker 0 7.32
FindBin 0 1.51
strict 0 1.11
Test::Most 0 0.35
warnings 0 1.41
configure_requires:
Module Need Have
---------------------------- ---- --------
ExtUtils::MakeMaker 0 7.32
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
LANG = C
LC_ALL = de_DE.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 = 11259
PERL5_CPAN_IS_RUNNING = 11259
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 17452,11259
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2018022418/cpanreporter_000_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_PARALLEL_SMOKER = yes
PERL_USE_UNSAFE_INC = 1
SHELL = /usr/bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1023/2018022418
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /opt/perl-5.27.9/bin/perl5.27.9
$UID/$EUID = 1023 / 1023
$GID = 1023 1023
$EGID = 1023 1023
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.16
CPAN::Meta 2.150010
Cwd 3.74
ExtUtils::CBuilder 0.280230
ExtUtils::Command 7.32
ExtUtils::Install 2.14
ExtUtils::MakeMaker 7.32
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.35
File::Spec 3.74
JSON 2.97001
JSON::PP 2.97001
Module::Build 0.4224
Module::Signature 0.81
Parse::CPAN::Meta 2.150010
Test::Harness 3.39
Test::More 1.302125
YAML 1.24
YAML::Syck 1.30
version 0.9918
--
Summary of my perl5 (revision 5 version 27 subversion 9) configuration:
Platform:
osname=linux
osvers=4.9.0-3-amd64
archname=x86_64-linux
uname='linux debian9 4.9.0-3-amd64 #1 smp debian 4.9.30-2+deb9u5 (2017-09-19) x86_64 gnulinux '
config_args='-ds -e -Dprefix=/opt/perl-5.27.9 -Dusedevel -Dusemallocwrap=no -Dcf_email=srezic@cpan.org'
hint=recommended
useposix=true
d_sigaction=define
useithreads=undef
usemultiplicity=undef
use64bitint=define
use64bitall=define
uselongdouble=undef
usemymalloc=n
default_inc_excludes_dot=define
bincompat5005=undef
Compiler:
cc='cc'
ccflags ='-fwrapv -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'
cppflags='-fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
ccversion=''
gccversion='6.3.0 20170516'
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/6/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 -lgdbm -ldb -ldl -lm -lcrypt -lutil -lc -lgdbm_compat
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 -L/usr/local/lib -fstack-protector-strong'
Characteristics of this binary (from libperl):
Compile-time options:
HAS_TIMES
PERLIO_LAYERS
PERL_COPY_ON_WRITE
PERL_DONT_CREATE_GVSV
PERL_OP_PARENT
PERL_PRESERVE_IVUV
PERL_USE_DEVEL
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 Feb 20 2018 21:05:34
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="11259"
PERL5_CPAN_IS_RUNNING="11259"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="17452,11259"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2018022418/cpanreporter_000_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_PARALLEL_SMOKER="yes"
PERL_USE_UNSAFE_INC="1"
@INC:
/opt/perl-5.27.9/lib/site_perl/5.27.9/x86_64-linux
/opt/perl-5.27.9/lib/site_perl/5.27.9
/opt/perl-5.27.9/lib/5.27.9/x86_64-linux
/opt/perl-5.27.9/lib/5.27.9
.