Bio-AutomatedAnnotation v1.182770 Perl 5 v5.24.3 x86_64-linux-thread-multi
- Status
- Fail
- From
- David Cantrell (DCANTRELL)
- Dist
-
Bio-AutomatedAnnotation v1.182770
- Platform
- Perl 5 v5.24.3 x86_64-linux-thread-multi
- Date
- 2018-10-06 07:15:06
- ID
- 8d1ffb6c-c937-11e8-8dcb-1e3a7347484a
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 5.24.3, 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/david/cpantesting/perl-5.24.3/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, 7 wallclock secs ( 0.05 usr 0.02 sys + 2.85 cusr 0.93 csys = 3.85 CPU)
Result: FAIL
Failed 1/12 test programs. 5/123 subtests failed.
Makefile:1004: 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 0
Bio::SeqFeature::Generic 0 1.007002
Bio::SeqIO 0 0
Bio::Tools::GFF 0 0
Cwd 0 3.63_01
Exception::Class 0 1.44
File::Basename 0 2.85
File::Copy 0 2.31
File::Temp 0 0.2304
FindBin 0 1.51
Getopt::Long 0 2.48
List::Util 0 1.50
Moose 0 2.2011
POSIX 0 1.65_01
Scalar::Util 0 1.50
Text::CSV 0 1.97
Time::Piece 0 1.31
Time::Seconds 0 1.31
warnings 0 1.36
XML::Simple 0 2.25
build_requires:
Module Need Have
------------------------ ---- --------
Data::Dumper 0 2.160
Env::Path 0.18 0.19
ExtUtils::MakeMaker 0 7.10_02
File::Find 0 1.34
File::Slurper 0 0.012
Moose::Role 0 2.2011
strict 0 1.11
Test::Most 0 0.35
configure_requires:
Module Need Have
------------------------ ---- --------
ExtUtils::MakeMaker 0 7.10_02
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
NONINTERACTIVE_TESTING = 1
PATH = /usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
PERL = 5.24.3
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 31825
PERL5_CPAN_IS_RUNNING = 31825
PERLVER = 5.24.3
PERL_INLINE_DIRECTORY = /home/david/.Inline-5.24.3
PERL_MM_USE_DEFAULT = 1
PERL_USE_UNSAFE_INC = 0
SHELL = /bin/bash
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/david/cpantesting/perl-5.24.3/bin/perl
$UID/$EUID = 1000 / 1000
$GID = 1000 1000
$EGID = 1000 1000
Perl module toolchain versions installed:
Module Have
------------------- ----------
CPAN 2.11_01
CPAN::Meta 2.150005
Cwd 3.63_01
ExtUtils::CBuilder 0.280225
ExtUtils::Command 7.10_02
ExtUtils::Install 2.04
ExtUtils::MakeMaker 7.10_02
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.31
File::Spec 3.63_01
JSON 2.97001
JSON::PP 2.27300_01
Module::Build 0.4224
Module::Signature n/a
Parse::CPAN::Meta 1.4417_001
Test::Harness 3.36_01
Test::More 1.302140
YAML 1.26
YAML::Syck n/a
version 0.9916
--
Summary of my perl5 (revision 5 version 24 subversion 3) configuration:
Platform:
osname=linux, osvers=3.16.0-4-amd64, archname=x86_64-linux-thread-multi
uname='linux pigsty.barnyard.co.uk 3.16.0-4-amd64 #1 smp debian 3.16.36-1+deb8u1 (2016-09-03) x86_64 gnulinux '
config_args='-de -Duse64bitall -Dusethreads -Dprefix=/home/david/cpantesting/perl-5.24.3'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2',
optimize='-O2',
cppflags='-D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
ccversion='', gccversion='4.9.2', 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/gcc/x86_64-linux-gnu/4.9/include-fixed /usr/include/x86_64-linux-gnu /usr/lib /lib/x86_64-linux-gnu /lib/../lib /usr/lib/x86_64-linux-gnu /usr/lib/../lib /lib
libs=-lpthread -lnsl -ldb -ldl -lm -lcrypt -lutil -lc
perllibs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
libc=libc-2.19.so, 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-strong'
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS
PERL_COPY_ON_WRITE PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
PERL_PRESERVE_IVUV USE_64_BIT_ALL USE_64_BIT_INT
USE_ITHREADS USE_LARGE_FILES USE_LOCALE
USE_LOCALE_COLLATE USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC USE_LOCALE_TIME USE_PERLIO
USE_PERL_ATOF USE_REENTRANT_API
Built under linux
Compiled at Sep 26 2017 16:23:50
%ENV:
PERL="5.24.3"
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="31825"
PERL5_CPAN_IS_RUNNING="31825"
PERLVER="5.24.3"
PERL_INLINE_DIRECTORY="/home/david/.Inline-5.24.3"
PERL_MM_USE_DEFAULT="1"
PERL_USE_UNSAFE_INC="0"
@INC:
/home/david/cpantesting/perl-5.24.3/lib/site_perl/5.24.3/x86_64-linux-thread-multi
/home/david/cpantesting/perl-5.24.3/lib/site_perl/5.24.3
/home/david/cpantesting/perl-5.24.3/lib/5.24.3/x86_64-linux-thread-multi
/home/david/cpantesting/perl-5.24.3/lib/5.24.3
.