Bio-AutomatedAnnotation v1.133090 Perl 5 v5.29.2 OpenBSD.amd64-openbsd
- Status
- Fail
- From
- Alceu Rodrigues de Freitas Junior
- Dist
-
Bio-AutomatedAnnotation v1.133090
- Platform
- Perl 5 v5.29.2 OpenBSD.amd64-openbsd
- Date
- 2018-09-06 05:14:46
- ID
- c55d4806-b193-11e8-844f-ee57a6f199d0
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-AutomatedAnnotation-1.133090
on perl 5.29.2, 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/vegeta/perl5/perlbrew/perls/perl-blead/bin/perl5.29.2" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/Bio/*.t t/Bio/AutomatedAnnotation/*.t t/Bio/AutomatedAnnotation/CommandLine/*.t t/Bio/AutomatedAnnotation/External/*.t
t/Bio/AutomatedAnnotation.t ................................. ok
# Failed test 'Actual and expected output match for '-o different_output_filename t/data/example_annotation.gff''
# at t/lib/TestHelper.pm line 29.
# got: '"File","argF","hly","speH","yfnB","arcC1"
# "t/data/example_annotation.gff","1","1","1","1","1"
# "% Total","1","1","1","1","1"
# '
# expected: '"File","speH","hly","arcC1","yfnB","argF"
# "t/data/example_annotation.gff","1","1","1","1","1"
# "% Total","1","1","1","1","1"
# '
# Failed test 'Actual and expected output match for 't/data/example_annotation.gff''
# at t/lib/TestHelper.pm line 29.
# got: '"File","hly","speH","arcC1","yfnB","argF"
# "t/data/example_annotation.gff","1","1","1","1","1"
# "% Total","1","1","1","1","1"
# '
# expected: '"File","speH","hly","arcC1","yfnB","argF"
# "t/data/example_annotation.gff","1","1","1","1","1"
# "% Total","1","1","1","1","1"
# '
# Failed test 'Actual and expected output match for 't/data/example_annotation.gff t/data/copy_of_example_annotation.gff t/data/empty_annotation.gff t/data/different_to_example_annotation.gff''
# at t/lib/TestHelper.pm line 29.
# got: '"File","argF","speH","hly","yfnB","arcC1","another_argF","another_arcC1","another_speH","another_yfnB","another_hly"
# "t/data/empty_annotation.gff","0","0","0","0","0","0","0","0","0","0"
# "t/data/example_annotation.gff","1","1","1","1","1","0","0","0","0","0"
# "t/data/different_to_example_annotation.gff","0","0","0","0","0","1","1","1","1","1"
# "t/data/copy_of_example_annotation.gff","1","1","1","1","1","0","0","0","0","0"
# "% Total","0.5","0.5","0.5","0.5","0.5","0.25","0.25","0.25","0.25","0.25"
# '
# expected: '"File","speH","hly","arcC1","yfnB","argF","another_argF","another_hly","another_yfnB","another_arcC1","another_speH"
# "t/data/example_annotation.gff","1","1","1","1","1","0","0","0","0","0"
# "t/data/empty_annotation.gff","0","0","0","0","0","0","0","0","0","0"
# "t/data/copy_of_example_annotation.gff","1","1","1","1","1","0","0","0","0","0"
# "t/data/different_to_example_annotation.gff","0","0","0","0","0","1","1","1","1","1"
# "% Total","0.5","0.5","0.5","0.5","0.5","0.25","0.25","0.25","0.25","0.25"
# '
# Failed test 'Actual and expected output match for 't/data/example_annotation.gff t/data/empty_annotation.gff''
# at t/lib/TestHelper.pm line 29.
# got: '"File","argF","speH","hly","arcC1","yfnB"
# "t/data/example_annotation.gff","1","1","1","1","1"
# "t/data/empty_annotation.gff","0","0","0","0","0"
# "% Total","0.5","0.5","0.5","0.5","0.5"
# '
# expected: '"File","speH","hly","arcC1","yfnB","argF"
# "t/data/example_annotation.gff","1","1","1","1","1"
# "t/data/empty_annotation.gff","0","0","0","0","0"
# "% Total","0.5","0.5","0.5","0.5","0.5"
# '
# Looks like you failed 4 tests of 9.
t/Bio/AutomatedAnnotation/CommandLine/GeneNameOccurances.t ..
Dubious, test returned 4 (wstat 1024, 0x400)
Failed 4/9 subtests
t/Bio/AutomatedAnnotation/CommandLine/ParseGenesFromGFFs.t .. ok
t/Bio/AutomatedAnnotation/External/Cmscan.t ................. ok
# Failed test 'gene names sorted by value desc'
# at t/Bio/AutomatedAnnotation/GeneNameOccurances.t line 150.
# Structures begin differing at:
# $got->[0] = 'argF'
# $expected->[0] = 'speH'
# Looks like you failed 1 test of 14.
t/Bio/AutomatedAnnotation/GeneNameOccurances.t ..............
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/14 subtests
t/Bio/AutomatedAnnotation/GeneNamesFromGFF.t ................ ok
t/Bio/AutomatedAnnotation/ParseGenesFromGFF.t ............... ok
--------------------- WARNING ---------------------
MSG: Got a sequence without letters. Could not guess alphabet
---------------------------------------------------
t/Bio/AutomatedAnnotation/ParseGenesFromGFFs.t .............. ok
t/Bio/AutomatedAnnotation/Prokka.t .......................... ok
# Failed test 'Spredsheet data as expected'
# at t/Bio/AutomatedAnnotation/SpreadsheetOfGeneOccurances.t line 30.
# got: '"File","speH","argF","yfnB","arcC1","hly","another_hly","another_speH","another_yfnB","another_arcC1","another_argF"
# "t/data/copy_of_example_annotation.gff","1","1","1","1","1","0","0","0","0","0"
# "t/data/empty_annotation.gff","0","0","0","0","0","0","0","0","0","0"
# "t/data/different_to_example_annotation.gff","0","0","0","0","0","1","1","1","1","1"
# "t/data/example_annotation.gff","1","1","1","1","1","0","0","0","0","0"
# "% Total","0.5","0.5","0.5","0.5","0.5","0.25","0.25","0.25","0.25","0.25"
# '
# expected: '"File","speH","hly","arcC1","yfnB","argF","another_argF","another_hly","another_yfnB","another_arcC1","another_speH"
# "t/data/example_annotation.gff","1","1","1","1","1","0","0","0","0","0"
# "t/data/empty_annotation.gff","0","0","0","0","0","0","0","0","0","0"
# "t/data/copy_of_example_annotation.gff","1","1","1","1","1","0","0","0","0","0"
# "t/data/different_to_example_annotation.gff","0","0","0","0","0","1","1","1","1","1"
# "% Total","0.5","0.5","0.5","0.5","0.5","0.25","0.25","0.25","0.25","0.25"
# '
# Looks like you failed 1 test of 5.
t/Bio/AutomatedAnnotation/SpreadsheetOfGeneOccurances.t .....
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/5 subtests
# Failed test 'makeblastdb in PATH'
# at t/requires_external.t line 8.
# Failed test 'blastp in PATH'
# at t/requires_external.t line 8.
# Failed test 'prodigal in PATH'
# at t/requires_external.t line 8.
# Failed test 'hmmscan in PATH'
# at t/requires_external.t line 8.
# Looks like you failed 4 tests of 11.
t/requires_external.t .......................................
Dubious, test returned 4 (wstat 1024, 0x400)
Failed 4/11 subtests
Test Summary Report
-------------------
t/Bio/AutomatedAnnotation/CommandLine/GeneNameOccurances.t (Wstat: 1024 Tests: 9 Failed: 4)
Failed tests: 3, 5, 7, 9
Non-zero exit status: 4
t/Bio/AutomatedAnnotation/GeneNameOccurances.t (Wstat: 256 Tests: 14 Failed: 1)
Failed test: 14
Non-zero exit status: 1
t/Bio/AutomatedAnnotation/SpreadsheetOfGeneOccurances.t (Wstat: 256 Tests: 5 Failed: 1)
Failed test: 5
Non-zero exit status: 1
t/requires_external.t (Wstat: 1024 Tests: 11 Failed: 4)
Failed tests: 7-9, 11
Non-zero exit status: 4
Files=11, Tests=118, 9 wallclock secs ( 0.00 usr 0.14 sys + 5.42 cusr 3.15 csys = 8.71 CPU)
Result: FAIL
Failed 4/11 test programs. 10/118 subtests failed.
*** Error 4 in /mnt/cpan_build_dir/vegeta/Bio-AutomatedAnnotation-1.133090-0 (Makefile:939 'test_dynamic')
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------------ ---- --------
Bio::Perl 0 1.007002
Bio::PrimarySeq 0 1.007002
Bio::SearchIO 0 0
Bio::Seq 0 0
Bio::SeqFeature::Generic 0 0
Bio::SeqIO 0 0
Bio::Tools::GFF 0 0
Cwd 0 3.74
Exception::Class 0 1.44
File::Basename 0 2.85
File::Copy 0 2.33
File::Temp 0 0.2306
FindBin 0 1.51
Getopt::Long 0 2.5
List::Util 0 1.50
Moose 0 2.2011
POSIX 0 1.84
Scalar::Util 0 1.50
Text::CSV 0 1.97
Time::Piece 0 1.33
Time::Seconds 0 1.33
warnings 0 1.43
XML::Simple 0 2.25
build_requires:
Module Need Have
------------------------ ---- --------
Data::Dumper 0 2.161
Env::Path 0 0.19
File::Find 0 1.34
File::Slurp 0 9999.19
Moose::Role 0 2.2011
strict 0 1.11
Test::Most 0 0.35
configure_requires:
Module Need Have
------------------------ ---- --------
ExtUtils::MakeMaker 6.30 7.34
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
DBD_MYSQL_TESTDB = test
DBD_MYSQL_TESTHOST = localhost
DBD_MYSQL_TESTPASSWORD =
DBD_MYSQL_TESTPORT = 3306
DBD_MYSQL_TESTUSER = vegeta
EXTENDED_TESTING = 1
PATH = /home/vegeta/perl5/perlbrew/bin:/home/vegeta/perl5/perlbrew/perls/perl-blead/bin:/home/vegeta/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/X11R6/bin:/usr/local/bin:/usr/local/sbin
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 31039
PERL5_CPAN_IS_RUNNING = 31039
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 6785,31039
PERLBREW_HOME = /home/vegeta/.perlbrew
PERLBREW_MANPATH = /home/vegeta/perl5/perlbrew/perls/perl-blead/man
PERLBREW_PATH = /home/vegeta/perl5/perlbrew/bin:/home/vegeta/perl5/perlbrew/perls/perl-blead/bin
PERLBREW_PERL = perl-blead
PERLBREW_ROOT = /home/vegeta/perl5/perlbrew
PERLBREW_SHELLRC_VERSION = 0.84
PERLBREW_VERSION = 0.84
PERL_CR_SMOKER_CURRENT = Bio-AutomatedAnnotation-1.133090
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_MM_USE_DEFAULT = 1
SHELL = /usr/local/bin/bash
TERM = vt220
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/vegeta/perl5/perlbrew/perls/perl-blead/bin/perl5.29.2
$UID/$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 3.74
ExtUtils::CBuilder 0.280230
ExtUtils::Command 7.34
ExtUtils::Install 2.14
ExtUtils::MakeMaker 7.34
ExtUtils::Manifest 1.71
ExtUtils::ParseXS 3.35
File::Spec 3.74
JSON 2.97001
JSON::PP 2.97001
Module::Build 0.4224
Module::Signature 0.81
Parse::CPAN::Meta 2.150010
Test::Harness 3.42
Test::More 1.302140
YAML 1.26
YAML::Syck n/a
version 0.9924
--
Summary of my perl5 (revision 5 version 29 subversion 2) configuration:
Snapshot of: cef721997e14497f2fbc4be17ab736ad7ddfda29
Platform:
osname=openbsd
osvers=6.3
archname=OpenBSD.amd64-openbsd
uname='openbsd cpan-smoker-openbsd 6.3 generic.mp#107 amd64 '
config_args='-de -Dprefix=/home/vegeta/perl5/perlbrew/perls/perl-blead -Dman1dir=none -Dman3dir=none -Dusedevel -Aeval:scriptdir=/home/vegeta/perl5/perlbrew/perls/perl-blead/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 Compatible OpenBSD Clang 5.0.1 (tags/RELEASE_501/final)'
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 ='-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.92.3
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
PERL_USE_DEVEL
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 1.52
Built under openbsd
Compiled at Aug 2 2018 18:57:44
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="31039"
PERL5_CPAN_IS_RUNNING="31039"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="6785,31039"
PERLBREW_HOME="/home/vegeta/.perlbrew"
PERLBREW_MANPATH="/home/vegeta/perl5/perlbrew/perls/perl-blead/man"
PERLBREW_PATH="/home/vegeta/perl5/perlbrew/bin:/home/vegeta/perl5/perlbrew/perls/perl-blead/bin"
PERLBREW_PERL="perl-blead"
PERLBREW_ROOT="/home/vegeta/perl5/perlbrew"
PERLBREW_SHELLRC_VERSION="0.84"
PERLBREW_VERSION="0.84"
PERL_CR_SMOKER_CURRENT="Bio-AutomatedAnnotation-1.133090"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_MM_USE_DEFAULT="1"
@INC:
/home/vegeta/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.29.2/OpenBSD.amd64-openbsd
/home/vegeta/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.29.2
/home/vegeta/perl5/perlbrew/perls/perl-blead/lib/5.29.2/OpenBSD.amd64-openbsd
/home/vegeta/perl5/perlbrew/perls/perl-blead/lib/5.29.2