Bio-ToolBox v1.68 Perl 5 v5.16.2 armv7l-linux
- Status
- Fail
- From
- Nigel Horne
- Dist
-
Bio-ToolBox v1.68
- Platform
- Perl 5 v5.16.2 armv7l-linux
- Date
- 2021-01-24 20:52:52
- ID
- 2027dd86-5e86-11eb-b9db-b6c7a8faccfa
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 5.16.2, 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/04.DB.t .............. skipped: Bio::DB::SeqFeature::Store not available
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
t/03.GeneTools.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.
t/05.Bam-Samtools.t .... skipped: Optional module Bio::DB::Sam not available
t/05.Bam-HTS.t ......... skipped: Optional module Bio::DB::HTS not available
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.
t/06.BigBed-UCSC.t ..... skipped: Optional module Bio::DB::BigBed not available
# 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/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/08.BigWigSet-UCSC.t .. skipped: Optional module Bio::DB::BigWigSet not available
t/07.BigWig-big.t ...... skipped: Optional module Bio::DB::Big not available
t/08.BigWigSet-big.t ... skipped: Optional module Bio::DB::Big not available
t/10.Wiggle.t .......... skipped: Optional module Bio::Graphics not available
t/09.USeq.t ............ skipped: Optional module Bio::DB::USeq 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, 1 wallclock secs ( 0.23 usr 0.09 sys + 3.29 cusr 1.47 csys = 5.08 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 2.51
List::MoreUtils 0 0.428
List::Util 0 1.54
Module::Load 0 0.22
Statistics::Descriptive 3 3.0702
Statistics::Lite 3.2 3.62
configure_requires:
Module Need Have
----------------------- ---- -------
Module::Build 0 0.39_01
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
HARNESS_OPTIONS = j4
NONINTERACTIVE_TESTING = 1
PATH = /home/smoker/perl5/perlbrew/bin:/home/smoker/perl5/perlbrew/perls/perl-5.16.2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
PERL5LIB = /tmp/build/Statistics-Lite-3.62-0/blib/arch:/tmp/build/Statistics-Lite-3.62-0/blib/lib:/tmp/build/Statistics-Descriptive-3.0702-0/blib/arch:/tmp/build/Statistics-Descriptive-3.0702-0/blib/lib:/tmp/build/List-MoreUtils-0.428-0/blib/arch:/tmp/build/List-MoreUtils-0.428-0/blib/lib:/tmp/build/Test-LeakTrace-0.16-0/blib/arch:/tmp/build/Test-LeakTrace-0.16-0/blib/lib:/tmp/build/List-MoreUtils-XS-0.428-0/blib/arch:/tmp/build/List-MoreUtils-XS-0.428-0/blib/lib:/tmp/build/XSLoader-0.24-0/blib/arch:/tmp/build/XSLoader-0.24-0/blib/lib:/tmp/build/Exporter-Tiny-1.002001-0/blib/arch:/tmp/build/Exporter-Tiny-1.002001-0/blib/lib:/tmp/build/Config-Simple-4.58-0/blib/arch:/tmp/build/Config-Simple-4.58-0/blib/lib:/tmp/build/Time-OlsonTZ-Data-0.202101-0/blib/arch:/tmp/build/Time-OlsonTZ-Data-0.202101-0/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 3891
PERL5_CPAN_IS_RUNNING = 3891
PERLBREW_HOME = /home/smoker/.perlbrew
PERLBREW_MANPATH = /home/smoker/perl5/perlbrew/perls/perl-5.16.2/man
PERLBREW_PATH = /home/smoker/perl5/perlbrew/bin:/home/smoker/perl5/perlbrew/perls/perl-5.16.2/bin
PERLBREW_PERL = perl-5.16.2
PERLBREW_ROOT = /home/smoker/perl5/perlbrew
PERLBREW_SHELLRC_VERSION = 0.88
PERLBREW_VERSION = 0.88
PERL_MM_USE_DEFAULT = 1
PERL_USE_UNSAFE_INC = 1
SHELL = /bin/bash
TERM = xterm
TMPDIR = /tmp/testwrapper.3880
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/smoker/perl5/perlbrew/perls/perl-5.16.2/bin/perl5.16.2
$UID/$EUID = 1000 / 1000
$GID = 1000
$EGID = 1000
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.27
CPAN::Meta 2.143240
Cwd 3.75
ExtUtils::CBuilder 0.280206
ExtUtils::Command 7.44
ExtUtils::Install 2.06
ExtUtils::MakeMaker 7.44
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.16
File::Spec 3.75
JSON 4.02
JSON::PP 2.27203
Module::Build 0.39_01
Module::Signature n/a
Parse::CPAN::Meta 1.4414
Test::Harness 3.42
Test::More 1.302171
YAML 1.30
YAML::Syck 1.32
version 0.99
--
Summary of my perl5 (revision 5 version 16 subversion 2) configuration:
Platform:
osname=linux, osvers=4.19.75-v7l+, archname=armv7l-linux
uname='linux 5912da58b734 4.19.75-v7l+ #1270 smp tue sep 24 18:51:41 bst 2019 armv7l gnulinux '
config_args='-de -Dprefix=/home/smoker/perl5/perlbrew/perls/perl-5.16.2 -Dusedevel -Accflags=-O2 -pipe -Wall -Wextra -mtune=native -march=native -Aeval:scriptdir=/home/smoker/perl5/perlbrew/perls/perl-5.16.2/bin'
hint=recommended, useposix=true, d_sigaction=define
useithreads=undef, usemultiplicity=undef
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=undef, use64bitall=undef, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-O2 -pipe -Wall -Wextra -mtune=native -march=native -fwrapv -fno-strict-aliasing -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2',
cppflags='-O2 -pipe -Wall -Wextra -mtune=native -march=native -fwrapv -fno-strict-aliasing -fstack-protector -I/usr/local/include'
ccversion='', gccversion='8.3.0', gccosandvers=''
intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=8
ivtype='long', ivsize=4, 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/arm-linux-gnueabihf /lib /usr/lib/arm-linux-gnueabihf /usr/lib
libs=-lnsl -ldl -lm -lcrypt -lutil -lc
perllibs=-lnsl -ldl -lm -lcrypt -lutil -lc
libc=libc-2.28.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.28'
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: HAS_TIMES PERLIO_LAYERS PERL_DONT_CREATE_GVSV
PERL_MALLOC_WRAP PERL_PRESERVE_IVUV PERL_USE_DEVEL
USE_LARGE_FILES USE_LOCALE USE_LOCALE_COLLATE
USE_LOCALE_CTYPE USE_LOCALE_NUMERIC USE_PERLIO
USE_PERL_ATOF
Locally applied patches:
Devel::PatchPerl 1.84
Built under linux
Compiled at Feb 2 2020 20:30:33
%ENV:
PERL5LIB="/tmp/build/Statistics-Lite-3.62-0/blib/arch:/tmp/build/Statistics-Lite-3.62-0/blib/lib:/tmp/build/Statistics-Descriptive-3.0702-0/blib/arch:/tmp/build/Statistics-Descriptive-3.0702-0/blib/lib:/tmp/build/List-MoreUtils-0.428-0/blib/arch:/tmp/build/List-MoreUtils-0.428-0/blib/lib:/tmp/build/Test-LeakTrace-0.16-0/blib/arch:/tmp/build/Test-LeakTrace-0.16-0/blib/lib:/tmp/build/List-MoreUtils-XS-0.428-0/blib/arch:/tmp/build/List-MoreUtils-XS-0.428-0/blib/lib:/tmp/build/XSLoader-0.24-0/blib/arch:/tmp/build/XSLoader-0.24-0/blib/lib:/tmp/build/Exporter-Tiny-1.002001-0/blib/arch:/tmp/build/Exporter-Tiny-1.002001-0/blib/lib:/tmp/build/Config-Simple-4.58-0/blib/arch:/tmp/build/Config-Simple-4.58-0/blib/lib:/tmp/build/Time-OlsonTZ-Data-0.202101-0/blib/arch:/tmp/build/Time-OlsonTZ-Data-0.202101-0/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="3891"
PERL5_CPAN_IS_RUNNING="3891"
PERLBREW_HOME="/home/smoker/.perlbrew"
PERLBREW_MANPATH="/home/smoker/perl5/perlbrew/perls/perl-5.16.2/man"
PERLBREW_PATH="/home/smoker/perl5/perlbrew/bin:/home/smoker/perl5/perlbrew/perls/perl-5.16.2/bin"
PERLBREW_PERL="perl-5.16.2"
PERLBREW_ROOT="/home/smoker/perl5/perlbrew"
PERLBREW_SHELLRC_VERSION="0.88"
PERLBREW_VERSION="0.88"
PERL_MM_USE_DEFAULT="1"
PERL_USE_UNSAFE_INC="1"
@INC:
/tmp/build/Statistics-Lite-3.62-0/blib/arch
/tmp/build/Statistics-Lite-3.62-0/blib/lib
/tmp/build/Statistics-Descriptive-3.0702-0/blib/arch
/tmp/build/Statistics-Descriptive-3.0702-0/blib/lib
/tmp/build/List-MoreUtils-0.428-0/blib/arch
/tmp/build/List-MoreUtils-0.428-0/blib/lib
/tmp/build/Test-LeakTrace-0.16-0/blib/arch
/tmp/build/Test-LeakTrace-0.16-0/blib/lib
/tmp/build/List-MoreUtils-XS-0.428-0/blib/arch
/tmp/build/List-MoreUtils-XS-0.428-0/blib/lib
/tmp/build/XSLoader-0.24-0/blib/arch
/tmp/build/XSLoader-0.24-0/blib/lib
/tmp/build/Exporter-Tiny-1.002001-0/blib/arch
/tmp/build/Exporter-Tiny-1.002001-0/blib/lib
/tmp/build/Config-Simple-4.58-0/blib/arch
/tmp/build/Config-Simple-4.58-0/blib/lib
/tmp/build/Time-OlsonTZ-Data-0.202101-0/blib/arch
/tmp/build/Time-OlsonTZ-Data-0.202101-0/blib/lib
/home/smoker/perl5/perlbrew/perls/perl-5.16.2/lib/site_perl/5.16.2/armv7l-linux
/home/smoker/perl5/perlbrew/perls/perl-5.16.2/lib/site_perl/5.16.2
/home/smoker/perl5/perlbrew/perls/perl-5.16.2/lib/5.16.2/armv7l-linux
/home/smoker/perl5/perlbrew/perls/perl-5.16.2/lib/5.16.2
.