Bio-ToolBox v1.69 Perl 5 v5.8.9 x86_64-linux
- Status
- Fail
- From
- David Cantrell (DCANTRELL)
- Dist
-
Bio-ToolBox v1.69
- Platform
- Perl 5 v5.8.9 x86_64-linux
- Date
- 2022-09-25 07:21:23
- ID
- a8b32bbe-3ca2-11ed-b5ce-e70ed065599d
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-1.69
on perl 5.8.9, 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:
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/00.utility.t ......... ok
Use of implicit split to @_ is deprecated at /home/david/cpantesting/perl-5.8.9/.cpan/build/Bio-ToolBox-1.69-0/blib/lib/Bio/ToolBox/Data/file.pm line 370.
Use of implicit split to @_ is deprecated at /home/david/cpantesting/perl-5.8.9/.cpan/build/Bio-ToolBox-1.69-0/blib/lib/Bio/ToolBox/Data/file.pm line 376.
Use of implicit split to @_ is deprecated at /home/david/cpantesting/perl-5.8.9/.cpan/build/Bio-ToolBox-1.69-0/blib/lib/Bio/ToolBox/Data/file.pm line 382.
Use of uninitialized value in length at /home/david/cpantesting/perl-5.8.9/.cpan/build/Bio-ToolBox-1.69-0/blib/lib/Bio/ToolBox/Data/Feature.pm line 1076.
No Strand column to update! at t/01.Data.t line 313.
No Type column to update! at t/01.Data.t line 318.
t/01.Data.t ............ ok
Use of implicit split to @_ is deprecated at /home/david/cpantesting/perl-5.8.9/.cpan/build/Bio-ToolBox-1.69-0/blib/lib/Bio/ToolBox/Data/file.pm line 370.
Use of implicit split to @_ is deprecated at /home/david/cpantesting/perl-5.8.9/.cpan/build/Bio-ToolBox-1.69-0/blib/lib/Bio/ToolBox/Data/file.pm line 376.
Use of implicit split to @_ is deprecated at /home/david/cpantesting/perl-5.8.9/.cpan/build/Bio-ToolBox-1.69-0/blib/lib/Bio/ToolBox/Data/file.pm line 382.
Unable to update Start coordinate for parsed SeqFeature objects at t/02.parser.t line 683.
Unable to update Start coordinate for parsed SeqFeature objects at t/02.parser.t line 764.
Unable to update Start coordinate for parsed SeqFeature objects at t/02.parser.t line 827.
Unable to update Start coordinate for parsed SeqFeature objects at t/02.parser.t line 878.
# Looks like you planned 384 tests but ran 414.
t/02.parser.t ..........
Dubious, test returned 255 (wstat 65280, 0xff00)
All 384 subtests passed
Use of implicit split to @_ is deprecated at /home/david/cpantesting/perl-5.8.9/.cpan/build/Bio-ToolBox-1.69-0/blib/lib/Bio/ToolBox/Data/file.pm line 370.
Use of implicit split to @_ is deprecated at /home/david/cpantesting/perl-5.8.9/.cpan/build/Bio-ToolBox-1.69-0/blib/lib/Bio/ToolBox/Data/file.pm line 376.
Use of implicit split to @_ is deprecated at /home/david/cpantesting/perl-5.8.9/.cpan/build/Bio-ToolBox-1.69-0/blib/lib/Bio/ToolBox/Data/file.pm line 382.
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: 414 Failed: 30)
Failed tests: 385-414
Non-zero exit status: 255
Parse errors: Bad plan. You planned 384 tests but ran 414.
Files=15, Tests=738, 5 wallclock secs ( 0.11 usr 0.03 sys + 0.96 cusr 0.15 csys = 1.25 CPU)
Result: FAIL
Failed 1/15 test programs. 30/738 subtests failed.
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
----------------------- ---- --------
Config::Simple 4.58 4.58
File::Which 0 1.27
Getopt::Long 2.24 2.52
List::MoreUtils 0 0.430
List::Util 0 1.63
Module::Load 0 0.36
Statistics::Descriptive 3 3.0800
Statistics::Lite 3.2 3.62
build_requires:
Module Need Have
----------------------- ---- --------
Test::More 0 1.302188
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 = 3.4.16
NONINTERACTIVE_TESTING = 1
PATH = /home/david/perl5/perlbrew/bin:/home/david/perl5/perlbrew/perls/perl-5.30.2/bin:/home/david/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
PERL = 5.8.9
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 1650515
PERL5_CPAN_IS_RUNNING = 1650515
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 = 5.8.9
PERL_INLINE_DIRECTORY = /home/david/.Inline-5.8.9
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-5.8.9/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 2.29
CPAN::Meta 2.143240
Cwd 3.75
ExtUtils::CBuilder 0.280236
ExtUtils::Command 7.64
ExtUtils::Install 2.06
ExtUtils::MakeMaker 7.64
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.44
File::Spec 3.75
JSON 4.09
JSON::PP 4.07
Module::Build 0.4231
Module::Signature n/a
Parse::CPAN::Meta 1.4414
Test::Harness 3.42
Test::More 1.302188
YAML 1.30
YAML::Syck n/a
version 0.9929
--
Summary of my perl5 (revision 5 version 8 subversion 9) configuration:
Platform:
osname=linux, osvers=5.10.0-11-amd64, archname=x86_64-linux
uname='linux cpantesting-linux-utm 5.10.0-11-amd64 #1 smp debian 5.10.92-1 (2022-01-18) x86_64 gnulinux '
config_args='-de -Dprefix=/home/david/cpantesting/perl-5.8.9 -A ccflags=-fwrapv'
hint=recommended, useposix=true, d_sigaction=define
usethreads=undef use5005threads=undef 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 ='-fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2',
cppflags='-fwrapv -fno-strict-aliasing -pipe -I/usr/local/include'
ccversion='', gccversion='10.2.1 20210110', 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 =' -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 /lib64 /usr/lib64
libs=-lnsl -ldl -lm -lcrypt -lutil -lc
perllibs=-lnsl -ldl -lm -lcrypt -lutil -lc
libc=libc-2.31.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.31'
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
cccdlflags='-fPIC', lddlflags='-shared -O2 -L/usr/local/lib'
Characteristics of this binary (from libperl):
Compile-time options: PERL_MALLOC_WRAP USE_64_BIT_ALL USE_64_BIT_INT
USE_FAST_STDIO USE_LARGE_FILES USE_PERLIO
Locally applied patches:
Devel::PatchPerl 2.08
Built under linux
Compiled at Feb 5 2022 22:16:28
%ENV:
PERL="5.8.9"
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="1650515"
PERL5_CPAN_IS_RUNNING="1650515"
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="5.8.9"
PERL_INLINE_DIRECTORY="/home/david/.Inline-5.8.9"
PERL_MM_USE_DEFAULT="1"
PERL_USE_UNSAFE_INC="0"
@INC:
/home/david/cpantesting/perl-5.8.9/lib/5.8.9/x86_64-linux
/home/david/cpantesting/perl-5.8.9/lib/5.8.9
/home/david/cpantesting/perl-5.8.9/lib/site_perl/5.8.9/x86_64-linux
/home/david/cpantesting/perl-5.8.9/lib/site_perl/5.8.9
.