Bio-ToolBox v1.68 Perl 5 v5.12.5 x86_64-linux-thread-multi
- Status
- Fail
- From
- David Cantrell (DCANTRELL)
- Dist
-
Bio-ToolBox v1.68
- Platform
- Perl 5 v5.12.5 x86_64-linux-thread-multi
- Date
- 2021-01-25 23:43:23
- ID
- 1ce93336-5f67-11eb-a6de-a85d6d6b008a
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-1.68
on perl 5.12.5, 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 './Build test':
No Strand column to update! at t/01.Data.t line 285.
No Type column to update! at t/01.Data.t line 290.
t/01.Data.t ............ ok
Unable to update Start coordinate for parsed SeqFeature objects at t/02.parser.t line 682.
Unable to update Start coordinate for parsed SeqFeature objects at t/02.parser.t line 762.
Unable to update Start coordinate for parsed SeqFeature objects at t/02.parser.t line 825.
Unable to update Start coordinate for parsed SeqFeature objects at t/02.parser.t line 876.
# Looks like you planned 380 tests but ran 408.
t/02.parser.t ..........
Dubious, test returned 255 (wstat 65280, 0xff00)
All 380 subtests passed
t/03.GeneTools.t ....... ok
t/04.DB.t .............. skipped: Bio::DB::SeqFeature::Store not available
t/05.Bam-HTS.t ......... skipped: Optional module Bio::DB::HTS not available
t/05.Bam-Samtools.t .... skipped: Optional module Bio::DB::Sam not available
t/06.BigBed-UCSC.t ..... skipped: Optional module Bio::DB::BigBed not available
t/06.BigBed-big.t ...... skipped: Optional module Bio::DB::Big not available
t/07.BigWig-UCSC.t ..... skipped: Optional module Bio::DB::BigWig not available
t/07.BigWig-big.t ...... skipped: Optional module Bio::DB::Big not available
t/08.BigWigSet-UCSC.t .. skipped: Optional module Bio::DB::BigWigSet not available
t/08.BigWigSet-big.t ... skipped: Optional module Bio::DB::Big not available
t/09.USeq.t ............ skipped: Optional module Bio::DB::USeq not available
t/10.Wiggle.t .......... skipped: Optional module Bio::Graphics not available
Test Summary Report
-------------------
t/02.parser.t (Wstat: 65280 Tests: 408 Failed: 28)
Failed tests: 381-408
Non-zero exit status: 255
Parse errors: Bad plan. You planned 380 tests but ran 408.
Files=14, Tests=689, 11 wallclock secs ( 0.28 usr 0.06 sys + 3.10 cusr 0.37 csys = 3.81 CPU)
Result: FAIL
Failed 1/14 test programs. 28/689 subtests failed.
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
----------------------- ---- --------
Config::Simple 4.58 4.58
File::Which 0 1.23
Getopt::Long 2.24 2.52
List::MoreUtils 0 0.430
List::Util 0 1.55
Module::Load 0 0.34
Statistics::Descriptive 3 3.0800
Statistics::Lite 3.2 3.62
build_requires:
Module Need Have
----------------------- ---- --------
Test::More 0 1.302183
configure_requires:
Module Need Have
----------------------- ---- --------
Module::Build 0 0.4231
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_GB.UTF-8
LANGUAGE = en_GB:en
LC_TERMINAL = iTerm2
LC_TERMINAL_VERSION = 3.4.3
NONINTERACTIVE_TESTING = 1
PATH = /home/david/perl5/perlbrew/bin:/home/david/perl5/perlbrew/perls/perl-5.30.2/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
PERL = 5.12.5
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 32022
PERL5_CPAN_IS_RUNNING = 32022
PERLBREW_HOME = /home/david/.perlbrew
PERLBREW_MANPATH = /home/david/perl5/perlbrew/perls/perl-5.30.2/man
PERLBREW_PATH = /home/david/perl5/perlbrew/bin:/home/david/perl5/perlbrew/perls/perl-5.30.2/bin
PERLBREW_PERL = perl-5.30.2
PERLBREW_ROOT = /home/david/perl5/perlbrew
PERLBREW_SHELLRC_VERSION = 0.89
PERLBREW_VERSION = 0.89
PERLVER = 5.12.5
PERL_INLINE_DIRECTORY = /home/david/.Inline-5.12.5
PERL_MM_USE_DEFAULT = 1
PERL_USE_UNSAFE_INC = 0
SHELL = /bin/bash
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/david/cpantesting/perl-5.12.5/bin/perl
$UID/$EUID = 1000 / 1000
$GID = 1000 24 25 27 29 30 44 46 109 1000
$EGID = 1000 24 25 27 29 30 44 46 109 1000
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 1.94_56
CPAN::Meta 2.143240
Cwd 3.31
ExtUtils::CBuilder 0.280235
ExtUtils::Command 7.34
ExtUtils::Install 2.06
ExtUtils::MakeMaker 7.34
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.35
File::Spec 3.31_01
JSON 4.03
JSON::PP 4.02
Module::Build 0.4231
Module::Signature n/a
Parse::CPAN::Meta 1.4414
Test::Harness 3.42
Test::More 1.302183
YAML 1.30
YAML::Syck n/a
version 0.9924
--
Summary of my perl5 (revision 5 version 12 subversion 5) configuration:
Platform:
osname=linux, osvers=4.9.0-8-amd64, archname=x86_64-linux-thread-multi
uname='linux pigsty 4.9.0-8-amd64 #1 smp debian 4.9.144-3 (2019-02-02) x86_64 gnulinux '
config_args='-de -Duse64bitall -Dusethreads -Dprefix=/home/david/cpantesting/perl-5.12.5 -A ccflags=-fwrapv'
hint=previous, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fwrapv',
optimize='-O2',
cppflags='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fwrapv'
ccversion='', gccversion='6.3.0 20170516', 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=-lnsl -ldb -ldl -lm -lcrypt -lutil -lpthread -lc
perllibs=-lnsl -ldl -lm -lcrypt -lutil -lpthread -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'
Characteristics of this binary (from libperl):
Compile-time options: MULTIPLICITY PERL_DONT_CREATE_GVSV
PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP USE_64_BIT_ALL
USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
USE_PERLIO USE_PERL_ATOF USE_REENTRANT_API
Locally applied patches:
Devel::PatchPerl 1.56
Built under linux
Compiled at Apr 25 2019 17:06:45
%ENV:
PERL="5.12.5"
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="32022"
PERL5_CPAN_IS_RUNNING="32022"
PERLBREW_HOME="/home/david/.perlbrew"
PERLBREW_MANPATH="/home/david/perl5/perlbrew/perls/perl-5.30.2/man"
PERLBREW_PATH="/home/david/perl5/perlbrew/bin:/home/david/perl5/perlbrew/perls/perl-5.30.2/bin"
PERLBREW_PERL="perl-5.30.2"
PERLBREW_ROOT="/home/david/perl5/perlbrew"
PERLBREW_SHELLRC_VERSION="0.89"
PERLBREW_VERSION="0.89"
PERLVER="5.12.5"
PERL_INLINE_DIRECTORY="/home/david/.Inline-5.12.5"
PERL_MM_USE_DEFAULT="1"
PERL_USE_UNSAFE_INC="0"
@INC:
/home/david/cpantesting/perl-5.12.5/lib/site_perl/5.12.5/x86_64-linux-thread-multi
/home/david/cpantesting/perl-5.12.5/lib/site_perl/5.12.5
/home/david/cpantesting/perl-5.12.5/lib/5.12.5/x86_64-linux-thread-multi
/home/david/cpantesting/perl-5.12.5/lib/5.12.5
.