Bio-ToolBox v2.00 Perl 5 v5.26.0 amd64-freebsd
- Status
- Fail
- From
- Slaven Rezić
- Dist
-
Bio-ToolBox v2.00
- Platform
- Perl 5 v5.26.0 amd64-freebsd
- Date
- 2024-07-21 14:23:53
- ID
- db3a9c26-476c-11ef-a5c1-ce326e8775ea
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-2.00
on perl 5.26.0, created by CPAN-Reporter-1.2019.
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:
none provided
------------------------------
PROGRAM OUTPUT
------------------------------
Output from './Build test':
t/00.utility.t ......... ok
t/01.Data.t ............ ok
t/02.parser.t .......... ok
t/03.GeneTools.t ....... ok
False [] range "\w-" in regex; marked by <-- HERE in m/^([\w- <-- HERE \.]+):([\w-\.]*)$/ at /usr/perl5.26.0p/lib/site_perl/5.26.0/Bio/DB/GFF/Typename.pm line 55.
False [] range "\w-" in regex; marked by <-- HERE in m/^([\w-\.]+):([\w- <-- HERE \.]*)$/ at /usr/perl5.26.0p/lib/site_perl/5.26.0/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
Number found where operator expected at t/10.Wiggle.t line 35, near "chromosome 1"
(Do you need to predeclare chromosome?)
Number found where operator expected at t/10.Wiggle.t line 35, near "1 230218"
(Missing operator before 230218?)
Number found where operator expected at t/10.Wiggle.t line 36, near "1 230218"
(Missing operator before 230218?)
Semicolon seems to be missing at t/10.Wiggle.t line 36.
syntax error at t/10.Wiggle.t line 35, near "chromosome 1"
syntax error at t/10.Wiggle.t line 35, near "NCBI:"
syntax error at t/10.Wiggle.t line 36, near "1 230218"
syntax error at t/10.Wiggle.t line 38, near "$wigfile
GFF
"
Bareword "GFF" not allowed while "strict subs" in use at t/10.Wiggle.t line 33.
Execution of t/10.Wiggle.t aborted due to compilation errors.
# Looks like your test exited with 255 before it could output anything.
t/10.Wiggle.t ..........
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 17/17 subtests
Test Summary Report
-------------------
t/10.Wiggle.t (Wstat: 65280 (exited 255) Tests: 0 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 17 tests but ran 0.
Files=15, Tests=1082, 3 wallclock secs ( 0.14 usr 0.02 sys + 0.96 cusr 0.83 csys = 1.95 CPU)
Result: FAIL
Failed 1/15 test programs. 0/1082 subtests failed.
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
----------------------- -------- --------
Bio::Root::Version 1.006924 1.7.8
Config::Simple 4.58 4.58
File::Which 1.17 1.27
Getopt::Long 2.24 2.55
IO::Prompt::Tiny 0.003 0.003
List::MoreUtils 0.4 0.430
List::Util 1.45 1.63
Module::Load 0.32 0.36
Scalar::Util 1.45 1.63
Statistics::Descriptive 3 3.0702
Statistics::Lite 3.2 3.62
build_requires:
Module Need Have
----------------------- -------- --------
Test::More 1.302 1.302198
Test::Warn 0.36 0.37
configure_requires:
Module Need Have
----------------------- -------- --------
Module::Build 0.42 0.4234
------------------------------
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/freebsd10.3:/home/cpansand/bin/sh:/home/cpansand/bin:/usr/games:/home/cpansand/devel:/home/eserte/src/srezic-misc/scripts
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 14608
PERL5_CPAN_IS_RUNNING = 14608
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 9820,14608
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2024072100/cpanreporter_000_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_USE_UNSAFE_INC = 1
SHELL = /usr/local/bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1023/2024072100
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /usr/perl5.26.0p/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 7.70
ExtUtils::Install 2.22
ExtUtils::MakeMaker 7.70
ExtUtils::Manifest 1.75
ExtUtils::ParseXS 3.51
File::Spec 3.75
JSON 4.10
JSON::PP 4.16
Module::Build 0.4234
Module::Signature 0.87
Parse::CPAN::Meta 2.150010
Test2 1.302198
Test::Harness 3.47
Test::More 1.302198
YAML 1.30
YAML::Syck 1.34
version 0.9930
--
Summary of my perl5 (revision 5 version 26 subversion 0) configuration:
Platform:
osname=freebsd
osvers=10.3-release-p11
archname=amd64-freebsd
uname='freebsd cvrsnica-freebsd-101.herceg.de 10.3-release-p11 freebsd 10.3-release-p11 #0: mon oct 24 18:49:24 utc 2016 root@amd64-builder.daemonology.net:usrobjusrsrcsysgeneric amd64 '
config_args='-ds -e -Dprefix=/usr/perl5.26.0p -Dcf_email=srezic@cpan.org -Doptimize=-O2 -pipe'
hint=recommended
useposix=true
d_sigaction=define
useithreads=undef
usemultiplicity=undef
use64bitint=define
use64bitall=define
uselongdouble=undef
usemymalloc=n
default_inc_excludes_dot=define
bincompat5005=undef
Compiler:
cc='cc'
ccflags ='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_FORTIFY_SOURCE=2'
optimize='-O2 -pipe'
cppflags='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion=''
gccversion='4.2.1 Compatible FreeBSD Clang 3.4.1 (tags/RELEASE_34/dot1-final 208032)'
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 ='-pthread -Wl,-E -fstack-protector -L/usr/local/lib'
libpth=/usr/lib /usr/local/lib /usr/include/clang/3.4.1 /usr/lib
libs=-lpthread -lgdbm -lm -lcrypt -lutil -lc -lelf
perllibs=-lpthread -lm -lcrypt -lutil -lc -lelf
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:
HAS_TIMES
PERLIO_LAYERS
PERL_COPY_ON_WRITE
PERL_DONT_CREATE_GVSV
PERL_MALLOC_WRAP
PERL_OP_PARENT
PERL_PRESERVE_IVUV
USE_64_BIT_ALL
USE_64_BIT_INT
USE_LARGE_FILES
USE_LOCALE
USE_LOCALE_COLLATE
USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC
USE_LOCALE_TIME
USE_PERLIO
USE_PERL_ATOF
Built under freebsd
Compiled at Jun 3 2017 22:58:33
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="14608"
PERL5_CPAN_IS_RUNNING="14608"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="9820,14608"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2024072100/cpanreporter_000_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_USE_UNSAFE_INC="1"
@INC:
/usr/perl5.26.0p/lib/site_perl/5.26.0/amd64-freebsd
/usr/perl5.26.0p/lib/site_perl/5.26.0
/usr/perl5.26.0p/lib/5.26.0/amd64-freebsd
/usr/perl5.26.0p/lib/5.26.0
.