Bio-ToolBox v1.62 Perl 5 v5.26.2 x86_64-linux-thread-multi
- Status
- Pass
- From
- Slaven Rezić (SREZIC)
- Dist
-
Bio-ToolBox v1.62
- Platform
- Perl 5 v5.26.2 x86_64-linux-thread-multi
- Date
- 2018-09-05 08:52:42
- ID
- 0c9e8eb0-b0e9-11e8-b6d1-d0efd0e04852
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-1.62
on perl 5.26.2, created by CPAN-Reporter-1.2018.
Thank you for uploading your work to CPAN. Congratulations!
All tests were successful.
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 './Build test':
t/01.Data.t ............ ok
t/02.parser.t .......... ok
t/03.GeneTools.t ....... ok
Possible precedence issue with control flow operator at /opt/perl-5.26.2t/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 845.
False [] range "\w-" in regex; marked by <-- HERE in m/^([\w- <-- HERE \.]+):([\w-\.]*)$/ at /opt/perl-5.26.2t/lib/site_perl/5.26.2/Bio/DB/GFF/Typename.pm line 55.
False [] range "\w-" in regex; marked by <-- HERE in m/^([\w-\.]+):([\w- <-- HERE \.]*)$/ at /opt/perl-5.26.2t/lib/site_perl/5.26.2/Bio/DB/GFF/Typename.pm line 55.
Subroutine Bio::DB::IndexedBase::_strip_crnl redefined at /opt/perl-5.26.2t/lib/5.26.2/x86_64-linux-thread-multi/DynaLoader.pm line 210.
t/04.DB.t .............. ok
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
All tests successful.
Files=14, Tests=849, 2 wallclock secs ( 0.06 usr 0.09 sys + 1.34 cusr 0.29 csys = 1.78 CPU)
Result: PASS
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
----------------------- --------- --------
Bio::Root::Version 1.0069023 1.007002
Config::Simple 4.58 4.58
File::Which 0 1.22
Getopt::Long 2.24 2.5
List::Util 0 1.50
Module::Load 0 0.32
Statistics::Descriptive 3 3.0700
Statistics::Lite 3.2 3.62
build_requires:
Module Need Have
----------------------- --------- --------
Test::More 0 1.302136
configure_requires:
Module Need Have
----------------------- --------- --------
Module::Build 0 0.4224
opt_requires:
Module Need Have
----------------------- --------- --------
! Bio::DB::Big 1 n/a
! Bio::DB::HTS 2.1 n/a
! Bio::DB::USeq 0.23 n/a
DBD::SQLite 0 1.58
Net::FTP 0 3.11
Parallel::ForkManager 1.02 1.19
Set::IntervalTree 0.1 0.11
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
LANG = C
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 = 26799
PERL5_CPAN_IS_RUNNING = 26799
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 26719,26799
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2018090508/cpanreporter_000_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_USE_UNSAFE_INC = 1
SHELL = /usr/bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1023/2018090508
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /opt/perl-5.26.2t/bin/perl
$UID/$EUID = 1023 / 1023
$GID = 1023 1023
$EGID = 1023 1023
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.18
CPAN::Meta 2.150010
Cwd 3.74
ExtUtils::CBuilder 0.280230
ExtUtils::Command 7.34
ExtUtils::Install 2.06
ExtUtils::MakeMaker 7.34
ExtUtils::Manifest 1.71
ExtUtils::ParseXS 3.34
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 3.42
Test::More 1.302136
YAML 1.26
YAML::Syck 1.30
version 0.9923
--
Summary of my perl5 (revision 5 version 26 subversion 2) configuration:
Platform:
osname=linux
osvers=3.16.0-5-amd64
archname=x86_64-linux-thread-multi
uname='linux debian8 3.16.0-5-amd64 #1 smp debian 3.16.51-3+deb8u1 (2018-01-08) x86_64 gnulinux '
config_args='-ds -e -Dprefix=/opt/perl-5.26.2t -Dusethreads -Dcf_email=srezic@cpan.org'
hint=recommended
useposix=true
d_sigaction=define
useithreads=define
usemultiplicity=define
use64bitint=define
use64bitall=define
uselongdouble=undef
usemymalloc=n
default_inc_excludes_dot=define
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='4.9.2'
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/4.9/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-2.19.so
so=so
useshrplib=false
libperl=libperl.a
gnulibc_version='2.19'
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_COPY_ON_WRITE
PERL_DONT_CREATE_GVSV
PERL_IMPLICIT_CONTEXT
PERL_MALLOC_WRAP
PERL_OP_PARENT
PERL_PRESERVE_IVUV
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_PERLIO
USE_PERL_ATOF
USE_REENTRANT_API
Built under linux
Compiled at Apr 17 2018 05:14:42
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="26799"
PERL5_CPAN_IS_RUNNING="26799"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="26719,26799"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2018090508/cpanreporter_000_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_USE_UNSAFE_INC="1"
@INC:
/opt/perl-5.26.2t/lib/site_perl/5.26.2/x86_64-linux-thread-multi
/opt/perl-5.26.2t/lib/site_perl/5.26.2
/opt/perl-5.26.2t/lib/5.26.2/x86_64-linux-thread-multi
/opt/perl-5.26.2t/lib/5.26.2
.