Bio_AssemblyImprovement v1.160490 Perl 5 v5.26.1 OpenBSD.amd64-openbsd
- Status
- Fail
- From
- Alceu Rodrigues de Freitas Junior
- Dist
-
Bio_AssemblyImprovement v1.160490
- Platform
- Perl 5 v5.26.1 OpenBSD.amd64-openbsd
- Date
- 2017-11-24 08:30:03
- ID
- ab00864a-d0f1-11e7-b5a5-14b65215edbd
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 5.26.1, 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:
this report is from an automated smoke testing program
and was not reviewed by a human for accuracy
------------------------------
PROGRAM OUTPUT
------------------------------
Output from '/usr/bin/make test':
PERL_DL_NONLAZY=1 "/home/foo/perl5/perlbrew/perls/perl-5.26.1/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:/mnt/cpan_build_dir/foo/Bio_AssemblyImprovement-1.160490-0/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
gzip failed: input file '/mnt/cpan_build_dir/foo/Bio_AssemblyImprovement-1.160490-0/variable_length.fastq.keep' does not exist
# 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/DigitalNormalisation/Khmer/Main.t .....
Dubious, test returned 2 (wstat 512, 0x200)
All 2 subtests passed
t/FillGaps/GapFillerConfig.t ............ ok
t/FillGaps/Iterative.t .................. ok
Can't exec "/mnt/cpan_build_dir/foo/Bio_AssemblyImprovement-1.160490-0/t/dummy_iva_qc_script_raise_error.py": No such file or directory at lib/Bio/AssemblyImprovement/IvaQC/Main.pm line 48.
Error running iva_qc with: /mnt/cpan_build_dir/foo/Bio_AssemblyImprovement-1.160490-0/t/dummy_iva_qc_script_raise_error.py -f /mnt/cpan_build_dir/foo/Bio_AssemblyImprovement-1.160490-0/t/data/forward.fastq -r /mnt/cpan_build_dir/foo/Bio_AssemblyImprovement-1.160490-0/t/data/reverse.fastq --ref_db /mnt/cpan_build_dir/foo/Bio_AssemblyImprovement-1.160490-0/t/data/database /mnt/cpan_build_dir/foo/Bio_AssemblyImprovement-1.160490-0/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
/mnt/cpan_build_dir/foo/Bio_AssemblyImprovement-1.160490-0/t/does_not_exist.pl does not exist. Using default: /mnt/cpan_build_dir/foo/Bio_AssemblyImprovement-1.160490-0/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/DigitalNormalisation/Khmer/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=239, 18 wallclock secs ( 0.10 usr 0.19 sys + 10.96 cusr 4.40 csys = 15.65 CPU)
Result: FAIL
Failed 4/24 test programs. 3/239 subtests failed.
*** Error 255 in /mnt/cpan_build_dir/foo/Bio_AssemblyImprovement-1.160490-0 (Makefile:1003 'test_dynamic')
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
---------------------- ---- --------
Bio::SeqIO 0 1.007002
Cwd 0 3.67
File::Basename 0 2.85
File::Copy 0 2.32
File::Path 2.07 2.15
File::Spec 0 3.67
File::Temp 0 0.2304
File::Which 0 1.22
Getopt::Long 0 2.5
Getopt::Std 0 1.12
IO::Compress::Gzip 0 2.074
IO::Uncompress::Gunzip 0 2.074
lib 0 0.64
Moose 0 2.2008
Moose::Role 0 2.2008
POSIX 0 1.76
Statistics::Lite 0 3.62
strict 0 1.11
Switch 0 2.17
warnings 0 1.37
build_requires:
Module Need Have
---------------------- ---- --------
Env::Path 0 0.19
ExtUtils::MakeMaker 0 7.31_04
File::Slurp 0 9999.19
Test::File::Contents 0 0.23
Test::Most 0 0.35
configure_requires:
Module Need Have
---------------------- ---- --------
ExtUtils::MakeMaker 0 7.31_04
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
PATH = /home/foo/perl5/perlbrew/bin:/home/foo/perl5/perlbrew/perls/perl-5.26.1/bin:/home/foo/bin:/sbin:/usr/sbin:/bin:/usr/bin:/usr/X11R6/bin:/usr/local/sbin:/usr/local/bin
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 43415
PERL5_CPAN_IS_RUNNING = 43415
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 76900,43415
PERLBREW_BASHRC_VERSION = 0.80
PERLBREW_HOME = /home/foo/.perlbrew
PERLBREW_MANPATH = /home/foo/perl5/perlbrew/perls/perl-5.26.1/man
PERLBREW_PATH = /home/foo/perl5/perlbrew/bin:/home/foo/perl5/perlbrew/perls/perl-5.26.1/bin
PERLBREW_PERL = perl-5.26.1
PERLBREW_ROOT = /home/foo/perl5/perlbrew
PERLBREW_VERSION = 0.80
PERL_CR_SMOKER_CURRENT = Bio_AssemblyImprovement-1.160490
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_MM_USE_DEFAULT = 1
SHELL = /usr/local/bin/bash
TERM = xterm
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/foo/perl5/perlbrew/perls/perl-5.26.1/bin/perl
$UID/$EUID = 1001 / 1001
$GID = 999 999 1001
$EGID = 999 999 1001
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.16
CPAN::Meta 2.150010
Cwd 3.67
ExtUtils::CBuilder 0.280230
ExtUtils::Command 7.31_04
ExtUtils::Install 2.14
ExtUtils::MakeMaker 7.31_04
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.35
File::Spec 3.67
JSON 2.97000
JSON::PP 2.97000
Module::Build 0.4224
Module::Signature 0.81
Parse::CPAN::Meta 2.150010
Test::Harness 3.39
Test::More 1.302115
YAML 1.24
YAML::Syck 1.30
version 0.9918
--
Summary of my perl5 (revision 5 version 26 subversion 1) configuration:
Platform:
osname=openbsd
osvers=6.1
archname=OpenBSD.amd64-openbsd
uname='openbsd cpansmoker.my.domain 6.1 generic.mp#20 amd64 '
config_args='-de -Dprefix=/home/foo/perl5/perlbrew/perls/perl-5.26.1 -Aeval:scriptdir=/home/foo/perl5/perlbrew/perls/perl-5.26.1/bin'
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 ='-fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_FORTIFY_SOURCE=2'
optimize='-O2'
cppflags='-fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
ccversion=''
gccversion='4.2.1 20070719 '
gccosandvers='openbsd6.1'
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 ='-Wl,-E -fstack-protector-strong -L/usr/local/lib'
libpth=/usr/lib /usr/local/lib
libs=-lpthread -lm -lutil -lc
perllibs=-lpthread -lm -lutil -lc
libc=/usr/lib/libc.so.89.3
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 -fPIC -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
Locally applied patches:
Devel::PatchPerl 1.48
Built under openbsd
Compiled at Nov 10 2017 20:02:38
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="43415"
PERL5_CPAN_IS_RUNNING="43415"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="76900,43415"
PERLBREW_BASHRC_VERSION="0.80"
PERLBREW_HOME="/home/foo/.perlbrew"
PERLBREW_MANPATH="/home/foo/perl5/perlbrew/perls/perl-5.26.1/man"
PERLBREW_PATH="/home/foo/perl5/perlbrew/bin:/home/foo/perl5/perlbrew/perls/perl-5.26.1/bin"
PERLBREW_PERL="perl-5.26.1"
PERLBREW_ROOT="/home/foo/perl5/perlbrew"
PERLBREW_VERSION="0.80"
PERL_CR_SMOKER_CURRENT="Bio_AssemblyImprovement-1.160490"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_MM_USE_DEFAULT="1"
@INC:
/home/foo/perl5/perlbrew/perls/perl-5.26.1/lib/site_perl/5.26.1/OpenBSD.amd64-openbsd
/home/foo/perl5/perlbrew/perls/perl-5.26.1/lib/site_perl/5.26.1
/home/foo/perl5/perlbrew/perls/perl-5.26.1/lib/5.26.1/OpenBSD.amd64-openbsd
/home/foo/perl5/perlbrew/perls/perl-5.26.1/lib/5.26.1