Bio-ToolBox v1.69 Perl 5 v5.14.4 amd64-freebsd
- Status
- Pass
- From
- Slaven Rezić
- Dist
-
Bio-ToolBox v1.69
- Platform
- Perl 5 v5.14.4 amd64-freebsd
- Date
- 2022-09-24 02:37:41
- ID
- dcaf44e4-3bb1-11ed-8969-f9f26d8775ea
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 5.14.4, 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/00.utility.t ......... ok
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
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.
t/02.parser.t .......... ok
t/03.GeneTools.t ....... ok
False [] range "\w-" in regex; marked by <-- HERE in m/^([\w- <-- HERE \.]+):([\w-\.]*)$/ at /usr/perl5.14.4/lib/site_perl/5.14.4/Bio/DB/GFF/Typename.pm line 55.
False [] range "\w-" in regex; marked by <-- HERE in m/^([\w-\.]+):([\w- <-- HERE \.]*)$/ at /usr/perl5.14.4/lib/site_perl/5.14.4/Bio/DB/GFF/Typename.pm line 55.
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 ............ ok
False [] range "\w-" in regex; marked by <-- HERE in m/^([\w- <-- HERE \.]+):([\w-\.]*)$/ at /usr/perl5.14.4/lib/site_perl/5.14.4/Bio/DB/GFF/Typename.pm line 55.
False [] range "\w-" in regex; marked by <-- HERE in m/^([\w-\.]+):([\w- <-- HERE \.]*)$/ at /usr/perl5.14.4/lib/site_perl/5.14.4/Bio/DB/GFF/Typename.pm line 55.
t/10.Wiggle.t .......... ok
All tests successful.
Files=15, Tests=1091, 4 wallclock secs ( 0.10 usr 0.04 sys + 1.38 cusr 0.13 csys = 1.66 CPU)
Result: PASS
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
----------------------- ---- --------
Bio::Root::Root 0 1.7.7
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 1.302191
configure_requires:
Module Need Have
----------------------- ---- --------
Module::Build 0 0.4231
opt_requires:
Module Need Have
----------------------- ---- --------
! Bio::DB::Big 1 n/a
! Bio::DB::HTS 2.1 n/a
Bio::DB::USeq 0.23 0.23
Net::FTP 0 3.13
Parallel::ForkManager 1.02 2.02
! Set::IntervalTree 0.1 n/a
Set::IntSpan::Fast::XS 0 0.05
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
LC_ALL = de_DE.ISO8859-1
PATH = /usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/cpansand/bin/freebsd9.3:/home/cpansand/bin/sh:/home/cpansand/bin:/usr/games:/home/cpansand/devel:/usr/home/eserte/src/srezic-misc/scripts
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 58159
PERL5_CPAN_IS_RUNNING = 58159
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 56071,58159
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2022092404/cpanreporter_000_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_USE_UNSAFE_INC = 1
SHELL = /usr/local/bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1023/2022092404
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /usr/perl5.14.4/bin/perl
$UID/$EUID = 1023 / 1023
$GID = 1023 1023
$EGID = 1023 1023
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.34
CPAN::Meta 2.150010
Cwd 3.75
ExtUtils::CBuilder 0.280236
ExtUtils::Command 7.64
ExtUtils::Install 2.20
ExtUtils::MakeMaker 7.64
ExtUtils::Manifest 1.73
ExtUtils::ParseXS 3.35
File::Spec 3.75
JSON 4.09
JSON::PP 4.11
Module::Build 0.4231
Module::Signature 0.88
Parse::CPAN::Meta 2.150010
Test::Harness 3.44
Test::More 1.302191
YAML 1.30
YAML::Syck 1.34
version 0.9929
--
Summary of my perl5 (revision 5 version 14 subversion 4) configuration:
Platform:
osname=freebsd, osvers=9.2-release-p4, archname=amd64-freebsd
uname='freebsd cvrsnica-freebsd-92 9.2-release-p4 freebsd 9.2-release-p4 #0: tue apr 8 18:08:22 utc 2014 root@amd64-builder.daemonology.net:usrobjusrsrcsysgeneric amd64 '
config_args='-ds -e -Dprefix=/usr/perl5.14.4'
hint=recommended, useposix=true, d_sigaction=define
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 ='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include',
optimize='-O',
cppflags='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='4.2.1 20070831 patched [FreeBSD]', 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 ='-Wl,-E -fstack-protector -L/usr/local/lib'
libpth=/usr/lib /usr/local/lib
libs=-lgdbm -lm -lcrypt -lutil -lc
perllibs=-lm -lcrypt -lutil -lc
libc=, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags=' '
cccdlflags='-DPIC -fPIC', lddlflags='-shared -L/usr/local/lib -fstack-protector'
Characteristics of this binary (from libperl):
Compile-time options: PERL_DONT_CREATE_GVSV PERL_MALLOC_WRAP
PERL_PRESERVE_IVUV USE_64_BIT_ALL USE_64_BIT_INT
USE_LARGE_FILES USE_PERLIO USE_PERL_ATOF
Built under freebsd
Compiled at May 16 2014 00:20:44
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="58159"
PERL5_CPAN_IS_RUNNING="58159"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="56071,58159"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2022092404/cpanreporter_000_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_USE_UNSAFE_INC="1"
@INC:
/usr/perl5.14.4/lib/site_perl/5.14.4/amd64-freebsd
/usr/perl5.14.4/lib/site_perl/5.14.4
/usr/perl5.14.4/lib/5.14.4/amd64-freebsd
/usr/perl5.14.4/lib/5.14.4
.