Bio_AssemblyImprovement v1.160490 Perl 5 v5.18.4 x86_64-linux
- Status
- Fail
- From
- Slaven Rezić
- Dist
-
Bio_AssemblyImprovement v1.160490
- Platform
- Perl 5 v5.18.4 x86_64-linux
- Date
- 2022-02-22 20:03:38
- ID
- 8668f1d2-941a-11ec-8b13-5c331f24ea8f
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 5.18.4, created by CPAN-Reporter-1.2018.
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 '/usr/bin/make test':
PERL_DL_NONLAZY=1 "/opt/perl-5.18.4/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
t/Abacas/Iterative.t .................... ok
t/Abacas/Main.t ......................... ok
Can't exec "java": No such file or directory at lib/Bio/AssemblyImprovement/AdapterRemoval/Trimmomatic/Main.pm line 44.
Error running Trimmomatic with:
java -Xmx1000m -jar t/DummyTrimmomatic.jar PE -threads 1 t/data/trimmo_reads_1.fastq t/data/trimmo_reads_2.fastq trimmed.paired_1.fastq trimmed.unpaired_1.fastq trimmed.paired_2.fastq trimmed.unpaired_2.fastq ILLUMINACLIP:/home/cpansand/.cpan/build/2021112322/2022022207/Bio_AssemblyImprovement-1.160490-6/t/data/trimmo_adapters.fasta:2:10:7:1 MINLEN:50 at lib/Bio/AssemblyImprovement/AdapterRemoval/Trimmomatic/Main.pm line 45.
# Tests were run but no plan was declared and done_testing() was not seen.
# Looks like your test exited with 2 just after 2.
t/AdapterRemoval/Trimmomatic/Main.t .....
Dubious, test returned 2 (wstat 512, 0x200)
All 2 subtests passed
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/2021112322/2022022207/Bio_AssemblyImprovement-1.160490-6/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/2021112322/2022022207/Bio_AssemblyImprovement-1.160490-6/t/dummy_iva_qc_script_raise_error.py -f /home/cpansand/.cpan/build/2021112322/2022022207/Bio_AssemblyImprovement-1.160490-6/t/data/forward.fastq -r /home/cpansand/.cpan/build/2021112322/2022022207/Bio_AssemblyImprovement-1.160490-6/t/data/reverse.fastq --ref_db /home/cpansand/.cpan/build/2021112322/2022022207/Bio_AssemblyImprovement-1.160490-6/t/data/database /home/cpansand/.cpan/build/2021112322/2022022207/Bio_AssemblyImprovement-1.160490-6/t/data/contigs.fa test_iva_qc
t/IvaQC/Main.t .......................... ok
t/Overall/CheckAllModulesCompile.t ...... ok
t/PrepareForSubmission/RenameContigs.t .. ok
# Failed test 'Results file exists in expected location'
# at t/PrimerRemoval/Main.t line 39.
# Failed test 'Results file exists in expected location'
# at t/PrimerRemoval/Main.t line 39.
# Looks like you failed 2 tests of 6.
t/PrimerRemoval/Main.t ..................
Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/6 subtests
t/Quiver/Main.t ......................... ok
# Failed test 'java in PATH'
# at t/requires_external.t line 8.
# Looks like you failed 1 test of 1.
t/requires_external.t ...................
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/1 subtests
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/2021112322/2022022207/Bio_AssemblyImprovement-1.160490-6/t/does_not_exist.pl does not exist. Using default: /home/cpansand/.cpan/build/2021112322/2022022207/Bio_AssemblyImprovement-1.160490-6/t/dummy_gap_filler_script.pl at lib/Bio/AssemblyImprovement/Validate/Executable.pm line 29.
t/Validate/Executable.t ................. ok
Test Summary Report
-------------------
t/AdapterRemoval/Trimmomatic/Main.t (Wstat: 512 Tests: 2 Failed: 0)
Non-zero exit status: 2
Parse errors: No plan found in TAP output
t/PrimerRemoval/Main.t (Wstat: 512 Tests: 6 Failed: 2)
Failed tests: 5-6
Non-zero exit status: 2
t/requires_external.t (Wstat: 256 Tests: 1 Failed: 1)
Failed test: 1
Non-zero exit status: 1
Files=24, Tests=242, 6 wallclock secs ( 0.12 usr 0.01 sys + 5.05 cusr 0.73 csys = 5.91 CPU)
Result: FAIL
Failed 3/24 test programs. 3/242 subtests failed.
make: *** [Makefile:1130: test_dynamic] Error 255
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------- ---- -------
Bio::SeqIO 0 1.7.8
Cwd 0 3.75
File::Basename 0 2.84
File::Copy 0 2.26
File::Path 2.07 2.18
File::Spec 0 3.75
File::Temp 0 0.2311
File::Which 0 1.27
Getopt::Long 0 2.52
Getopt::Std 0 1.07
IO::Compress::Gzip 0 2.102
IO::Uncompress::Gunzip 0 2.102
lib 0 0.63
Moose 0 2.2201
Moose::Role 0 2.2201
POSIX 0 1.32
Statistics::Lite 0 3.62
strict 0 1.07
Switch 0 2.17
warnings 0 1.18
build_requires:
Module Need Have
---------------------- ---- -------
Env::Path 0 0.19
ExtUtils::MakeMaker 0 7.64
File::Slurp 0 9999.32
Test::File::Contents 0 0.23
Test::Most 0 0.37
configure_requires:
Module Need Have
---------------------- ---- -------
ExtUtils::MakeMaker 0 7.64
------------------------------
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/.cpan/build/2021112322/2022022207/Statistics-Lite-3.62-6/blib/arch:/home/cpansand/.cpan/build/2021112322/2022022207/Statistics-Lite-3.62-6/blib/lib:/home/cpansand/.cpan/build/2021112322/2022022207/BioPerl-1.7.8-6/blib/arch:/home/cpansand/.cpan/build/2021112322/2022022207/BioPerl-1.7.8-6/blib/lib:/home/cpansand/.cpan/build/2021112322/2022022207/Test-Weaken-3.022000-6/blib/arch:/home/cpansand/.cpan/build/2021112322/2022022207/Test-Weaken-3.022000-6/blib/lib:/home/cpansand/.cpan/build/2021112322/2022022207/Data-Stag-0.14-6/blib/arch:/home/cpansand/.cpan/build/2021112322/2022022207/Data-Stag-0.14-6/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 1670
PERL5_CPAN_IS_RUNNING = 1670
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 19435,1670
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2022022207/cpanreporter_000_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_USE_UNSAFE_INC = 1
SHELL = /usr/bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1023/2022022207
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /opt/perl-5.18.4/bin/perl
$UID/$EUID = 1023 / 1023
$GID = 1023 1023
$EGID = 1023 1023
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.29
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 1.70
ExtUtils::ParseXS 3.44
File::Spec 3.75
JSON 4.05
JSON::PP 4.07
Module::Build 0.4231
Module::Signature 0.88
Parse::CPAN::Meta 2.150010
Test::Harness 3.42
Test::More 1.302188
YAML 1.30
YAML::Syck 1.34
version 0.9929
--
Summary of my perl5 (revision 5 version 18 subversion 4) configuration:
Platform:
osname=linux, osvers=4.19.0-17-amd64, archname=x86_64-linux
uname='linux cloud12.bbbike.org 4.19.0-17-amd64 #1 smp debian 4.19.194-3 (2021-07-18) x86_64 gnulinux '
config_args='-ds -e -Dprefix=/opt/perl-5.18.4 -Dcf_email=srezic@cpan.org'
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 ='-fwrapv -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2',
cppflags='-fwrapv -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='8.3.0', 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 =' -fstack-protector -L/usr/local/lib'
libpth=/usr/local/lib /lib/x86_64-linux-gnu /lib/../lib /usr/lib/x86_64-linux-gnu /usr/lib/../lib /lib /usr/lib /lib64 /usr/lib64
libs=-lnsl -ldb -ldl -lm -lcrypt -lutil -lc
perllibs=-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'
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES PERLIO_LAYERS PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD PERL_MALLOC_WRAP
PERL_PRESERVE_IVUV PERL_SAWAMPERSAND USE_64_BIT_ALL
USE_64_BIT_INT USE_LARGE_FILES USE_LOCALE
USE_LOCALE_COLLATE USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC USE_PERLIO USE_PERL_ATOF
Locally applied patches:
Devel::PatchPerl 2.08
Built under linux
Compiled at Sep 5 2021 11:20:44
%ENV:
PERL5LIB="/home/cpansand/.cpan/build/2021112322/2022022207/Statistics-Lite-3.62-6/blib/arch:/home/cpansand/.cpan/build/2021112322/2022022207/Statistics-Lite-3.62-6/blib/lib:/home/cpansand/.cpan/build/2021112322/2022022207/BioPerl-1.7.8-6/blib/arch:/home/cpansand/.cpan/build/2021112322/2022022207/BioPerl-1.7.8-6/blib/lib:/home/cpansand/.cpan/build/2021112322/2022022207/Test-Weaken-3.022000-6/blib/arch:/home/cpansand/.cpan/build/2021112322/2022022207/Test-Weaken-3.022000-6/blib/lib:/home/cpansand/.cpan/build/2021112322/2022022207/Data-Stag-0.14-6/blib/arch:/home/cpansand/.cpan/build/2021112322/2022022207/Data-Stag-0.14-6/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="1670"
PERL5_CPAN_IS_RUNNING="1670"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="19435,1670"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2022022207/cpanreporter_000_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_USE_UNSAFE_INC="1"
@INC:
/home/cpansand/.cpan/build/2021112322/2022022207/Statistics-Lite-3.62-6/blib/arch
/home/cpansand/.cpan/build/2021112322/2022022207/Statistics-Lite-3.62-6/blib/lib
/home/cpansand/.cpan/build/2021112322/2022022207/BioPerl-1.7.8-6/blib/arch
/home/cpansand/.cpan/build/2021112322/2022022207/BioPerl-1.7.8-6/blib/lib
/home/cpansand/.cpan/build/2021112322/2022022207/Test-Weaken-3.022000-6/blib/arch
/home/cpansand/.cpan/build/2021112322/2022022207/Test-Weaken-3.022000-6/blib/lib
/home/cpansand/.cpan/build/2021112322/2022022207/Data-Stag-0.14-6/blib/arch
/home/cpansand/.cpan/build/2021112322/2022022207/Data-Stag-0.14-6/blib/lib
/opt/perl-5.18.4/lib/site_perl/5.18.4/x86_64-linux
/opt/perl-5.18.4/lib/site_perl/5.18.4
/opt/perl-5.18.4/lib/5.18.4/x86_64-linux
/opt/perl-5.18.4/lib/5.18.4
.