Bio-Variation v1.7.5 Perl 5 v5.32.1 x86_64-linux
- Status
- Pass
- From
- Slaven Rezić
- Dist
-
Bio-Variation v1.7.5
- Platform
- Perl 5 v5.32.1 x86_64-linux
- Date
- 2023-12-27 23:57:42
- ID
- b95e3d0c-a513-11ee-9007-1f366e8775ea
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 Christopher Fields,
This is a computer-generated report for Bio-Variation-1.7.5
on perl 5.32.1, created by CPAN-Reporter-1.2019.
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 '/usr/bin/make test':
PERL_DL_NONLAZY=1 "/opt/perl-5.32.1/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/00-compile.t ........... ok
t/AAChange.t ............. ok
t/AAReverseMutate.t ...... ok
t/Allele.t ............... ok
t/author-mojibake.t ...... skipped: these tests are for testing by the author
t/author-pod-coverage.t .. skipped: these tests are for testing by the author
t/author-pod-syntax.t .... skipped: these tests are for testing by the author
t/DNAMutation.t .......... ok
t/RNAChange.t ............ ok
t/SeqDiff.t .............. ok
t/SNP.t .................. ok
t/Variation_IO.t ......... ok
All tests successful.
Files=12, Tests=221, 2 wallclock secs ( 0.06 usr 0.02 sys + 1.87 cusr 0.55 csys = 2.50 CPU)
Result: PASS
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------------ ----- ---------
base 0 2.27
Bio::DBLinkContainerI 0 1.7.8
Bio::PrimarySeq 0 1.7.8
Bio::Root::IO 0 1.7.8
Bio::Root::Root 0 1.7.8
Bio::SeqFeature::Generic 0 1.7.8
Bio::SeqIO 0 1.7.8
Bio::Tools::CodonTable 0 1.7.8
constant 0 1.33
Getopt::Long 0 2.51
IO::String 0 1.08
perl 5.006 5.032001
strict 0 1.11
Text::Wrap 0 2013.0523
utf8 0 1.22
vars 0 1.05
warnings 0 1.47
XML::Twig 0 3.52
XML::Writer 0.4 0.900
build_requires:
Module Need Have
------------------------ ----- ---------
Bio::Root::Test 0 1.7.8
ExtUtils::MakeMaker 0 7.44
File::Spec 0 3.78
IO::Handle 0 1.42
IPC::Open3 0 1.21
lib 0 0.65
Test::More 0 1.302198
configure_requires:
Module Need Have
------------------------ ----- ---------
ExtUtils::MakeMaker 0 7.44
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
LANG = en_CA.UTF-8
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 = /home/cpansand/.cpan/build/2023122722/BioPerl-1.7.8-0/blib/arch:/home/cpansand/.cpan/build/2023122722/BioPerl-1.7.8-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-Writer-0.900-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-Writer-0.900-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-Twig-3.52-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-Twig-3.52-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-SAX-Writer-0.57-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-SAX-Writer-0.57-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-Filter-BufferText-1.01-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-Filter-BufferText-1.01-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-LibXML-2.0209-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-LibXML-2.0209-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-SAX-1.02-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-SAX-1.02-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-SAX-Base-1.09-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-SAX-Base-1.09-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-NamespaceSupport-1.12-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-NamespaceSupport-1.12-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Alien-Libxml2-0.19-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Alien-Libxml2-0.19-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Alien-Build-Plugin-Download-GitLab-0.01-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Alien-Build-Plugin-Download-GitLab-0.01-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Alien-Build-2.80-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Alien-Build-2.80-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Path-Tiny-0.144-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Path-Tiny-0.144-0/blib/lib:/home/cpansand/.cpan/build/2023122722/File-chdir-0.1011-0/blib/arch:/home/cpansand/.cpan/build/2023122722/File-chdir-0.1011-0/blib/lib:/home/cpansand/.cpan/build/2023122722/FFI-CheckLib-0.31-0/blib/arch:/home/cpansand/.cpan/build/2023122722/FFI-CheckLib-0.31-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Test2-Suite-0.000159-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Test2-Suite-0.000159-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Test-Simple-1.302198-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Test-Simple-1.302198-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Term-Table-0.018-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Term-Table-0.018-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-DOM-1.46-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-DOM-1.46-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-RegExp-0.04-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-RegExp-0.04-0/blib/lib:/home/cpansand/.cpan/build/2023122722/libxml-perl-0.08-0/blib/arch:/home/cpansand/.cpan/build/2023122722/libxml-perl-0.08-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-Parser-2.46-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-Parser-2.46-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Test-Weaken-3.022000-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Test-Weaken-3.022000-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Test-Most-0.38-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Test-Most-0.38-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Test-Warn-0.37-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Test-Warn-0.37-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Test-Exception-0.43-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Test-Exception-0.43-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Sub-Uplevel-0.2800-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Sub-Uplevel-0.2800-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Test-Differences-0.71-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Test-Differences-0.71-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Exception-Class-1.45-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Exception-Class-1.45-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Devel-StackTrace-2.04-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Devel-StackTrace-2.04-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Class-Data-Inheritable-0.09-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Class-Data-Inheritable-0.09-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Test-Memory-Cycle-1.06-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Test-Memory-Cycle-1.06-0/blib/lib:/home/cpansand/.cpan/build/2023122722/PadWalker-2.5-0/blib/arch:/home/cpansand/.cpan/build/2023122722/PadWalker-2.5-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Devel-Cycle-1.12-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Devel-Cycle-1.12-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Set-Scalar-1.29-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Set-Scalar-1.29-0/blib/lib:/home/cpansand/.cpan/build/2023122722/List-MoreUtils-0.430-0/blib/arch:/home/cpansand/.cpan/build/2023122722/List-MoreUtils-0.430-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Test-LeakTrace-0.1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arch:/home/cpansand/.cpan/build/2023122722/Error-0.17029-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Module-Build-0.4234-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Module-Build-0.4234-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Data-Stag-0.14-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Data-Stag-0.14-0/blib/lib:/home/cpansand/.cpan/build/2023122722/IO-String-1.08-0/blib/arch:/home/cpansand/.cpan/build/2023122722/IO-String-1.08-0/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 7344
PERL5_CPAN_IS_RUNNING = 7344
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 7328,7344
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2023122722/cpanreporter_000_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_USE_UNSAFE_INC = 1
SHELL = /usr/bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1023/2023122722
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /opt/perl-5.32.1/bin/perl
$UID/$EUID = 1023 / 1023
$GID = 1023 1023
$EGID = 1023 1023
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.27
CPAN::Meta 2.150010
Cwd 3.78
ExtUtils::CBuilder 0.280234
ExtUtils::Command 7.44
ExtUtils::Install 2.14
ExtUtils::MakeMaker 7.44
ExtUtils::Manifest 1.72
ExtUtils::ParseXS 3.40
File::Spec 3.78
JSON n/a
JSON::PP 4.04
Module::Build 0.4234
Module::Signature n/a
Parse::CPAN::Meta 2.150010
Test2 1.302198
Test::Harness 3.42
Test::More 1.302198
YAML 1.30
YAML::Syck 1.34
version 0.9924
--
Summary of my perl5 (revision 5 version 32 subversion 1) configuration:
Platform:
osname=linux
osvers=4.19.0-25-amd64
archname=x86_64-linux
uname='linux cloud12.bbbike.org 4.19.0-25-amd64 #1 smp debian 4.19.289-2 (2023-08-08) x86_64 gnulinux '
config_args='-ds -e -Dprefix=/opt/perl-5.32.1 -Dcf_email=srezic@cpan.org'
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 ='-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='-fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
ccversion=''
gccversion='8.3.0'
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/8/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 /lib64 /usr/lib64
libs=-lpthread -lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lc
perllibs=-lpthread -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-strong'
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 linux
Compiled at Dec 27 2023 08:34:55
%ENV:
PERL5LIB="/home/cpansand/.cpan/build/2023122722/BioPerl-1.7.8-0/blib/arch:/home/cpansand/.cpan/build/2023122722/BioPerl-1.7.8-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-Writer-0.900-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-Writer-0.900-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-Twig-3.52-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-Twig-3.52-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-SAX-Writer-0.57-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-SAX-Writer-0.57-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-Filter-BufferText-1.01-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-Filter-BufferText-1.01-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-LibXML-2.0209-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-LibXML-2.0209-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-SAX-1.02-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-SAX-1.02-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-SAX-Base-1.09-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-SAX-Base-1.09-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-NamespaceSupport-1.12-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-NamespaceSupport-1.12-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Alien-Libxml2-0.19-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Alien-Libxml2-0.19-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Alien-Build-Plugin-Download-GitLab-0.01-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Alien-Build-Plugin-Download-GitLab-0.01-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Alien-Build-2.80-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Alien-Build-2.80-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Path-Tiny-0.144-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Path-Tiny-0.144-0/blib/lib:/home/cpansand/.cpan/build/2023122722/File-chdir-0.1011-0/blib/arch:/home/cpansand/.cpan/build/2023122722/File-chdir-0.1011-0/blib/lib:/home/cpansand/.cpan/build/2023122722/FFI-CheckLib-0.31-0/blib/arch:/home/cpansand/.cpan/build/2023122722/FFI-CheckLib-0.31-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Test2-Suite-0.000159-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Test2-Suite-0.000159-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Test-Simple-1.302198-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Test-Simple-1.302198-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Term-Table-0.018-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Term-Table-0.018-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-DOM-1.46-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-DOM-1.46-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-RegExp-0.04-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-RegExp-0.04-0/blib/lib:/home/cpansand/.cpan/build/2023122722/libxml-perl-0.08-0/blib/arch:/home/cpansand/.cpan/build/2023122722/libxml-perl-0.08-0/blib/lib:/home/cpansand/.cpan/build/2023122722/XML-Parser-2.46-0/blib/arch:/home/cpansand/.cpan/build/2023122722/XML-Parser-2.46-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Test-Weaken-3.022000-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Test-Weaken-3.022000-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Test-Most-0.38-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Test-Most-0.38-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Test-Warn-0.37-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Test-Warn-0.37-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Test-Exception-0.43-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Test-Exception-0.43-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Sub-Uplevel-0.2800-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Sub-Uplevel-0.2800-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Test-Differences-0.71-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Test-Differences-0.71-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Exception-Class-1.45-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Exception-Class-1.45-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Devel-StackTrace-2.04-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Devel-StackTrace-2.04-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Class-Data-Inheritable-0.09-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Class-Data-Inheritable-0.09-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Test-Memory-Cycle-1.06-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Test-Memory-Cycle-1.06-0/blib/lib:/home/cpansand/.cpan/build/2023122722/PadWalker-2.5-0/blib/arch:/home/cpansand/.cpan/build/2023122722/PadWalker-2.5-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Devel-Cycle-1.12-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Devel-Cycle-1.12-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Set-Scalar-1.29-0/blib/arch:/home/cpansand/.cpan/build/2023122722/Set-Scalar-1.29-0/blib/lib:/home/cpansand/.cpan/build/2023122722/List-MoreUtils-0.430-0/blib/arch:/home/cpansand/.cpan/build/2023122722/List-MoreUtils-0.430-0/blib/lib:/home/cpansand/.cpan/build/2023122722/Test-Lea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PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="7344"
PERL5_CPAN_IS_RUNNING="7344"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="7328,7344"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2023122722/cpanreporter_000_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_USE_UNSAFE_INC="1"
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