Bio-AutomatedAnnotation v1.182770 Perl 5 v5.14.4 x86_64-linux-multi
- Status
- Fail
- From
- Serguei Trouchelle (STRO)
- Dist
-
Bio-AutomatedAnnotation v1.182770
- Platform
- Perl 5 v5.14.4 x86_64-linux-multi
- Date
- 2018-10-15 16:40:39
- ID
- 0cbd948e-d099-11e8-8d3d-8dc390d61c74
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 Victoria Offord,
This is a computer-generated report for Bio-AutomatedAnnotation-1.182770
on perl 5.14.4, 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:
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/stro/perl/5.14.4m/bin/perl" "-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
t/Bio/AutomatedAnnotation/CommandLine/GeneNameOccurances.t .. ok
t/Bio/AutomatedAnnotation/CommandLine/ParseGenesFromGFFs.t .. ok
t/Bio/AutomatedAnnotation/External/Cmscan.t ................. ok
t/Bio/AutomatedAnnotation/GeneNameOccurances.t .............. ok
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
t/Bio/AutomatedAnnotation/SpreadsheetOfGeneOccurances.t ..... ok
t/Bio/SearchIOhmm.t ......................................... ok
# 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 'parallel 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 5 tests of 11.
t/requires_external.t .......................................
Dubious, test returned 5 (wstat 1280, 0x500)
Failed 5/11 subtests
Test Summary Report
-------------------
t/requires_external.t (Wstat: 1280 Tests: 11 Failed: 5)
Failed tests: 7-11
Non-zero exit status: 5
Files=12, Tests=123, 8 wallclock secs ( 0.05 usr 0.00 sys + 2.82 cusr 0.18 csys = 3.05 CPU)
Result: FAIL
Failed 1/12 test programs. 5/123 subtests failed.
Makefile:945: recipe for target 'test_dynamic' failed
make: *** [test_dynamic] Error 5
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------------ ---- --------
Bio::Perl 0 1.007002
Bio::PrimarySeq 0 0
Bio::SearchIO 0 0
Bio::Seq 0 1.007002
Bio::SeqFeature::Generic 0 0
Bio::SeqIO 0 0
Bio::Tools::GFF 0 0
Cwd 0 3.75
Exception::Class 0 1.44
File::Basename 0 2.82
File::Copy 0 2.21
File::Temp 0 0.2308
FindBin 0 1.50
Getopt::Long 0 2.5
List::Util 0 1.50
Moose 0 2.2011
POSIX 0 1.24
Scalar::Util 0 1.50
Text::CSV 0 1.95
Time::Piece 0 1.3204
Time::Seconds 0 1.3204
warnings 0 1.12
XML::Simple 0 2.25
build_requires:
Module Need Have
------------------------ ---- --------
Data::Dumper 0 2.172
Env::Path 0.18 0.19
ExtUtils::MakeMaker 0 7.34
File::Find 0 1.19
File::Slurper 0 0.012
Moose::Role 0 2.2011
strict 0 1.04
Test::Most 0 0.35
configure_requires:
Module Need Have
------------------------ ---- --------
ExtUtils::MakeMaker 0 7.34
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_US.UTF-8
PATH = /usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 13530
PERL5_CPAN_IS_RUNNING = 13530
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 9807,13530
PERL_CR_SMOKER_CURRENT = Bio-AutomatedAnnotation-1.182770
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_MM_USE_DEFAULT = 1
SHELL = /bin/bash
TERM = xterm
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/stro/perl/5.14.4m/bin/perl
$UID/$EUID = 1000 / 1000
$GID = 1000 24 25 29 30 44 46 108 114 1000
$EGID = 1000 24 25 29 30 44 46 108 114 1000
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.16
CPAN::Meta 2.150010
Cwd 3.75
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 3.75
JSON 2.97001
JSON::PP 2.97001
Module::Build 0.4224
Module::Signature 0.83
Parse::CPAN::Meta 2.150010
Test::Harness 3.42
Test::More 1.302140
YAML 1.26
YAML::Syck 1.30
version 0.9924
--
Summary of my perl5 (revision 5 version 14 subversion 4) configuration:
Platform:
osname=linux, osvers=3.16.0-4-amd64, archname=x86_64-linux-multi
uname='linux vm-debian-001 3.16.0-4-amd64 #1 smp debian 3.16.7-ckt11-1 (2015-05-24) x86_64 gnulinux '
config_args=''
hint=recommended, useposix=true, d_sigaction=define
useithreads=undef, usemultiplicity=define
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2',
cppflags='-fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='4.9.2', 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
libs=-lnsl -ldl -lm -lcrypt -lutil -lc
perllibs=-lnsl -ldl -lm -lcrypt -lutil -lc
libc=, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.19'
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: MULTIPLICITY PERL_DONT_CREATE_GVSV
PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
PERL_PRESERVE_IVUV USE_64_BIT_ALL USE_64_BIT_INT
USE_LARGE_FILES USE_PERLIO USE_PERL_ATOF
Built under linux
Compiled at Sep 30 2017 20:50:10
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="13530"
PERL5_CPAN_IS_RUNNING="13530"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="9807,13530"
PERL_CR_SMOKER_CURRENT="Bio-AutomatedAnnotation-1.182770"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_MM_USE_DEFAULT="1"
@INC:
/home/stro/perl/5.14.4m/lib/site_perl/5.14.4/x86_64-linux-multi
/home/stro/perl/5.14.4m/lib/site_perl/5.14.4
/home/stro/perl/5.14.4m/lib/5.14.4/x86_64-linux-multi
/home/stro/perl/5.14.4m/lib/5.14.4
.