Bio_AssemblyImprovement v1.160490 Perl 5 v5.34.0 x86_64-linux
- Status
- Pass
- From
- Slaven Rezić
- Dist
-
Bio_AssemblyImprovement v1.160490
- Platform
- Perl 5 v5.34.0 x86_64-linux
- Date
- 2022-02-22 07:13:24
- ID
- ec5968e4-93ae-11ec-9af9-0c441f24ea8f
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 Andrew Page,
This is a computer-generated report for Bio_AssemblyImprovement-1.160490
on perl 5.34.0, 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 '/usr/bin/make test':
PERL_DL_NONLAZY=1 "/opt/perl-5.34.0/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/Abacas/*.t t/AdapterRemoval/Trimmomatic/*.t t/Assemble/SGA/*.t t/Circlator/*.t t/DigitalNormalisation/Khmer/*.t t/FillGaps/*.t t/IvaQC/*.t t/Overall/*.t t/PrepareForSubmission/*.t t/PrimerRemoval/*.t t/Quiver/*.t t/Scaffold/*.t t/Util/*.t t/Validate/*.t
Useless use of concatenation (.) or string in void context at lib/Bio/AssemblyImprovement/Abacas/Main.pm line 33.
t/Abacas/Iterative.t .................... ok
Useless use of concatenation (.) or string in void context at lib/Bio/AssemblyImprovement/Abacas/Main.pm line 33.
t/Abacas/Main.t ......................... ok
t/AdapterRemoval/Trimmomatic/Main.t ..... ok
t/Assemble/SGA/IndexAndCorrectReads.t ... ok
t/Assemble/SGA/Main.t ................... ok
t/Assemble/SGA/PreprocessReads.t ........ ok
t/Circlator/Main.t ...................... ok
t/DigitalNormalisation/Khmer/Main.t ..... ok
t/FillGaps/GapFillerConfig.t ............ ok
t/FillGaps/Iterative.t .................. ok
Traceback (most recent call last):
File "/home/cpansand/.cpan/build/2022022206/Bio_AssemblyImprovement-1.160490-5/t/dummy_iva_qc_script_raise_error.py", line 7, in <module>
raise Error ('Could not run iva_qc check - ignore error message')
__main__.Error: Could not run iva_qc check - ignore error message
Error running iva_qc with: /home/cpansand/.cpan/build/2022022206/Bio_AssemblyImprovement-1.160490-5/t/dummy_iva_qc_script_raise_error.py -f /home/cpansand/.cpan/build/2022022206/Bio_AssemblyImprovement-1.160490-5/t/data/forward.fastq -r /home/cpansand/.cpan/build/2022022206/Bio_AssemblyImprovement-1.160490-5/t/data/reverse.fastq --ref_db /home/cpansand/.cpan/build/2022022206/Bio_AssemblyImprovement-1.160490-5/t/data/database /home/cpansand/.cpan/build/2022022206/Bio_AssemblyImprovement-1.160490-5/t/data/contigs.fa test_iva_qc
t/IvaQC/Main.t .......................... ok
Useless use of concatenation (.) or string in void context at lib/Bio/AssemblyImprovement/Abacas/Main.pm line 33, <$modules> line 1.
t/Overall/CheckAllModulesCompile.t ...... ok
t/PrepareForSubmission/RenameContigs.t .. ok
t/PrimerRemoval/Main.t .................. ok
t/Quiver/Main.t ......................... ok
t/requires_external.t ................... ok
t/Scaffold/Descaffold.t ................. ok
t/Scaffold/Iterative.t .................. ok
t/Scaffold/PreprocessInputFiles.t ....... ok
t/Scaffold/SSpaceConfig.t ............... ok
t/Util/FastaTools.t ..................... ok
t/Util/FastqTools.t ..................... ok
t/Util/OrderContigsByLength.t ........... ok
/home/cpansand/.cpan/build/2022022206/Bio_AssemblyImprovement-1.160490-5/t/does_not_exist.pl does not exist. Using default: /home/cpansand/.cpan/build/2022022206/Bio_AssemblyImprovement-1.160490-5/t/dummy_gap_filler_script.pl at lib/Bio/AssemblyImprovement/Validate/Executable.pm line 29.
t/Validate/Executable.t ................. ok
All tests successful.
Files=24, Tests=246, 6 wallclock secs ( 0.07 usr 0.02 sys + 4.86 cusr 0.97 csys = 5.92 CPU)
Result: PASS
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------- ---- -------
Bio::SeqIO 0 1.7.8
Cwd 0 3.80
File::Basename 0 2.85
File::Copy 0 2.35
File::Path 2.07 2.18
File::Spec 0 3.80
File::Temp 0 0.2311
File::Which 0 1.27
Getopt::Long 0 2.52
Getopt::Std 0 1.13
IO::Compress::Gzip 0 2.102
IO::Uncompress::Gunzip 0 2.102
lib 0 0.65
Moose 0 2.2015
Moose::Role 0 2.2015
POSIX 0 1.97
Statistics::Lite 0 3.62
strict 0 1.12
Switch 0 2.17
warnings 0 1.51
build_requires:
Module Need Have
---------------------- ---- -------
Env::Path 0 0.19
ExtUtils::MakeMaker 0 7.62
File::Slurp 0 9999.32
Test::File::Contents 0 0.23
Test::Most 0 0.37
configure_requires:
Module Need Have
---------------------- ---- -------
ExtUtils::MakeMaker 0 7.62
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
LANG = en_US.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/.local/share/.cpan/build/2022022206/Switch-2.17-0/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/Switch-2.17-0/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/Statistics-Lite-3.62-0/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/Statistics-Lite-3.62-0/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/Env-Path-0.19-0/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/Env-Path-0.19-0/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/BioPerl-1.7.8-2/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/BioPerl-1.7.8-2/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/XML-Twig-3.52-2/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/XML-Twig-3.52-2/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/XML-SAX-Writer-0.57-2/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/XML-SAX-Writer-0.57-2/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/XML-Filter-BufferText-1.01-2/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/XML-Filter-BufferText-1.01-2/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/XML-DOM-1.46-2/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/XML-DOM-1.46-2/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/XML-RegExp-0.04-2/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/XML-RegExp-0.04-2/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/libxml-perl-0.08-2/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/libxml-perl-0.08-2/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/Test-Weaken-3.022000-2/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/Test-Weaken-3.022000-2/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/Data-Stag-0.14-2/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/Data-Stag-0.14-2/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 2160580
PERL5_CPAN_IS_RUNNING = 2160580
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 2156239,2160580
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2022022206/cpanreporter_001_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_USE_UNSAFE_INC = 1
SHELL = /usr/bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1023/2022022206
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /opt/perl-5.34.0/bin/perl
$UID/$EUID = 1023 / 1023
$GID = 1023 1023
$EGID = 1023 1023
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.28
CPAN::Meta 2.150010
Cwd 3.80
ExtUtils::CBuilder 0.280236
ExtUtils::Command 7.62
ExtUtils::Install 2.20
ExtUtils::MakeMaker 7.62
ExtUtils::Manifest 1.73
ExtUtils::ParseXS 3.44
File::Spec 3.80
JSON 4.05
JSON::PP 4.06
Module::Build 0.4231
Module::Signature n/a
Parse::CPAN::Meta 2.150010
Test::Harness 3.43
Test::More 1.302187
YAML 1.30
YAML::Syck 1.34
version 0.9928
--
Summary of my perl5 (revision 5 version 34 subversion 0) configuration:
Platform:
osname=linux
osvers=5.4.0-73-generic
archname=x86_64-linux
uname='linux cloud8.bbbike.org 5.4.0-73-generic #82-ubuntu smp wed apr 14 17:39:42 utc 2021 x86_64 x86_64 x86_64 gnulinux '
config_args='-ds -e -Dprefix=/opt/perl-5.34.0 -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
Compiler:
cc='cc'
ccflags ='-fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'
optimize='-O2'
cppflags='-fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
ccversion=''
gccversion='9.3.0'
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/x86_64-linux-gnu /usr/lib /lib/x86_64-linux-gnu /lib
libs=-lpthread -lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lc
perllibs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
libc=libc-2.31.so
so=so
useshrplib=false
libperl=libperl.a
gnulibc_version='2.31'
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 May 25 2021 20:16:54
%ENV:
PERL5LIB="/home/cpansand/.local/share/.cpan/build/2022022206/Switch-2.17-0/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/Switch-2.17-0/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/Statistics-Lite-3.62-0/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/Statistics-Lite-3.62-0/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/Env-Path-0.19-0/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/Env-Path-0.19-0/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/BioPerl-1.7.8-2/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/BioPerl-1.7.8-2/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/XML-Twig-3.52-2/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/XML-Twig-3.52-2/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/XML-SAX-Writer-0.57-2/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/XML-SAX-Writer-0.57-2/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/XML-Filter-BufferText-1.01-2/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/XML-Filter-BufferText-1.01-2/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/XML-DOM-1.46-2/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/XML-DOM-1.46-2/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/XML-RegExp-0.04-2/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/XML-RegExp-0.04-2/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/libxml-perl-0.08-2/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/libxml-perl-0.08-2/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/Test-Weaken-3.022000-2/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/Test-Weaken-3.022000-2/blib/lib:/home/cpansand/.local/share/.cpan/build/2022022206/Data-Stag-0.14-2/blib/arch:/home/cpansand/.local/share/.cpan/build/2022022206/Data-Stag-0.14-2/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="2160580"
PERL5_CPAN_IS_RUNNING="2160580"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="2156239,2160580"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2022022206/cpanreporter_001_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_USE_UNSAFE_INC="1"
@INC:
/home/cpansand/.local/share/.cpan/build/2022022206/Switch-2.17-0/blib/arch
/home/cpansand/.local/share/.cpan/build/2022022206/Switch-2.17-0/blib/lib
/home/cpansand/.local/share/.cpan/build/2022022206/Statistics-Lite-3.62-0/blib/arch
/home/cpansand/.local/share/.cpan/build/2022022206/Statistics-Lite-3.62-0/blib/lib
/home/cpansand/.local/share/.cpan/build/2022022206/Env-Path-0.19-0/blib/arch
/home/cpansand/.local/share/.cpan/build/2022022206/Env-Path-0.19-0/blib/lib
/home/cpansand/.local/share/.cpan/build/2022022206/BioPerl-1.7.8-2/blib/arch
/home/cpansand/.local/share/.cpan/build/2022022206/BioPerl-1.7.8-2/blib/lib
/home/cpansand/.local/share/.cpan/build/2022022206/XML-Twig-3.52-2/blib/arch
/home/cpansand/.local/share/.cpan/build/2022022206/XML-Twig-3.52-2/blib/lib
/home/cpansand/.local/share/.cpan/build/2022022206/XML-SAX-Writer-0.57-2/blib/arch
/home/cpansand/.local/share/.cpan/build/2022022206/XML-SAX-Writer-0.57-2/blib/lib
/home/cpansand/.local/share/.cpan/build/2022022206/XML-Filter-BufferText-1.01-2/blib/arch
/home/cpansand/.local/share/.cpan/build/2022022206/XML-Filter-BufferText-1.01-2/blib/lib
/home/cpansand/.local/share/.cpan/build/2022022206/XML-DOM-1.46-2/blib/arch
/home/cpansand/.local/share/.cpan/build/2022022206/XML-DOM-1.46-2/blib/lib
/home/cpansand/.local/share/.cpan/build/2022022206/XML-RegExp-0.04-2/blib/arch
/home/cpansand/.local/share/.cpan/build/2022022206/XML-RegExp-0.04-2/blib/lib
/home/cpansand/.local/share/.cpan/build/2022022206/libxml-perl-0.08-2/blib/arch
/home/cpansand/.local/share/.cpan/build/2022022206/libxml-perl-0.08-2/blib/lib
/home/cpansand/.local/share/.cpan/build/2022022206/Test-Weaken-3.022000-2/blib/arch
/home/cpansand/.local/share/.cpan/build/2022022206/Test-Weaken-3.022000-2/blib/lib
/home/cpansand/.local/share/.cpan/build/2022022206/Data-Stag-0.14-2/blib/arch
/home/cpansand/.local/share/.cpan/build/2022022206/Data-Stag-0.14-2/blib/lib
/opt/perl-5.34.0/lib/site_perl/5.34.0/x86_64-linux
/opt/perl-5.34.0/lib/site_perl/5.34.0
/opt/perl-5.34.0/lib/5.34.0/x86_64-linux
/opt/perl-5.34.0/lib/5.34.0
.