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From: metabase:user:320bfe00-2aae-11df-837a-5e0a49663a4f
Subject: FAIL Bio-ToolBox-1.36 v5.22.2 RC1 GNU/Linux
Date: 2016-04-29T04:13:56Z
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 Timothy Parnell,
This is a computer-generated report for Bio-ToolBox-1.36
on perl 5.22.2, created by CPAN-Reporter-1.2017.
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 './Build test':
t/01.Data.t ....... ok
Possible precedence issue with control flow operator at /home/sand/src/perl/repoperls/installed-perls/perl/v5.22.2-RC1/de40/lib/site_perl/5.22.2/Bio/DB/IndexedBase.pm line 791.
# Failed test 'mean score across second bed feature with alt chromo'
# at t/02.DB.t line 265.
# got: '0.50'
# expected: '0.49'
# Looks like you failed 1 test of 60.
t/02.DB.t .........
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/60 subtests
t/03.Bam.t ........ skipped: Optional module Bio::DB::Sam not available
t/04.BigBed.t ..... skipped: Optional module Bio::DB::BigBed not available
t/05.BigWig.t ..... skipped: Optional module Bio::DB::BigWig not available
t/06.BigWigSet.t .. skipped: Optional module Bio::DB::BigWigSet not available
t/07.USeq.t ....... ok
t/08.Wiggle.t ..... skipped: Optional module Bio::Graphics not available
t/09.parser.t ..... ok
Test Summary Report
-------------------
t/02.DB.t (Wstat: 256 Tests: 60 Failed: 1)
Failed test: 60
Non-zero exit status: 1
Files=9, Tests=314, 3 wallclock secs ( 0.07 usr 0.07 sys + 1.31 cusr 0.24 csys = 1.69 CPU)
Result: FAIL
Failed 1/9 test programs. 1/314 subtests failed.
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
----------------------- --------- --------
Bio::DB::USeq 0.2 0.23
Bio::Root::Version 1.0069022 1.006924
Config::Simple 4.58 4.58
Module::Load 0 0.32
Statistics::Descriptive 3 3.0612
Statistics::Lite 3.2 3.62
configure_requires:
Module Need Have
----------------------- --------- --------
Module::Build 0 0.4216
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_US.UTF-8
LANGUAGE = en_US:en
PATH = /usr/lib/ccache:/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 = 30023
PERL5_CPAN_IS_RUNNING = 30023
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_MM_USE_DEFAULT = 1
SHELL = /usr/bin/zsh
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/sand/src/perl/repoperls/installed-perls/perl/v5.22.2-RC1/de40/bin/perl
$UID/$EUID = 1005 / 1005
$GID = 1005 1005
$EGID = 1005 1005
Perl module toolchain versions installed:
Module Have
------------------- ------------
CPAN 2.11
CPAN::Meta 2.150005
Cwd 3.62
ExtUtils::CBuilder 0.280224
ExtUtils::Command 7.15_02
ExtUtils::Install 2.04
ExtUtils::MakeMaker 7.15_02
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.30
File::Spec 3.62
JSON 2.90
JSON::PP 2.27300
Module::Build 0.4216
Module::Signature 0.79
Parse::CPAN::Meta 1.4418
Test::Harness 3.36
Test::More 1.302014_009
YAML 1.15
YAML::Syck 1.29
version 0.9916
--
Summary of my perl5 (revision 5 version 22 subversion 2) configuration:
Commit id: 1b027307a936ccbc52a7291729dae1c16f10576a
Platform:
osname=linux, osvers=4.3.0-1-amd64, archname=x86_64-linux-thread-multi-ld
uname='linux k83 4.3.0-1-amd64 #1 smp debian 4.3.3-7 (2016-01-19) x86_64 gnulinux '
config_args='-Dprefix=/home/sand/src/perl/repoperls/installed-perls/perl/v5.22.2-RC1/de40 -Dmyhostname=k83 -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 -Duseithreads -Duselongdouble'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
use64bitint=define, use64bitall=define, uselongdouble=define
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -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='-D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
ccversion='', gccversion='5.3.1 20160121', 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='long double', nvsize=16, Off_t='off_t', lseeksize=8
alignbytes=16, 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/5/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 -ldl -lm -lcrypt -lutil -lc -lgdbm_compat
perllibs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
libc=libc-2.21.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.21'
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 MULTIPLICITY PERLIO_LAYERS
PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
PERL_NEW_COPY_ON_WRITE PERL_PRESERVE_IVUV
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_LONG_DOUBLE
USE_PERLIO USE_PERL_ATOF USE_REENTRANT_API
Locally applied patches:
RC1
Built under linux
Compiled at Apr 11 2016 00:32:28
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="30023"
PERL5_CPAN_IS_RUNNING="30023"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_MM_USE_DEFAULT="1"
@INC:
/home/sand/src/perl/repoperls/installed-perls/perl/v5.22.2-RC1/de40/lib/site_perl/5.22.2/x86_64-linux-thread-multi-ld
/home/sand/src/perl/repoperls/installed-perls/perl/v5.22.2-RC1/de40/lib/site_perl/5.22.2
/home/sand/src/perl/repoperls/installed-perls/perl/v5.22.2-RC1/de40/lib/5.22.2/x86_64-linux-thread-multi-ld
/home/sand/src/perl/repoperls/installed-perls/perl/v5.22.2-RC1/de40/lib/5.22.2
.