Bio-AutomatedAnnotation v1.182770 Perl 5 v5.8.9 x86_64-gnukfreebsd-thread-multi
- Status
- Fail
- From
- Chris Williams (BINGOS)
- Dist
-
Bio-AutomatedAnnotation v1.182770
- Platform
- Perl 5 v5.8.9 x86_64-gnukfreebsd-thread-multi
- Date
- 2018-10-11 15:23:17
- ID
- 943c3c0e-cd69-11e8-98d5-bb14e5798fec
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 VOFFFORD,
This is a computer-generated error report created automatically by
CPANPLUS, version 0.9176. Testers personal comments may appear
at the end of this report.
Thank you for uploading your work to CPAN. However, it appears that
there were some problems testing your distribution.
TEST RESULTS:
Below is the error stack from stage 'make test':
PERL_DL_NONLAZY=1 "/home/cpan/pit/thr/perl-5.8.9/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, 11 wallclock secs ( 0.07 usr 0.07 sys + 3.75 cusr 6.43 csys = 10.32 CPU)
Result: FAIL
Failed 1/12 test programs. 5/123 subtests failed.
Makefile:989: recipe for target 'test_dynamic' failed
make: *** [test_dynamic] Error 5
PREREQUISITES:
Here is a list of prerequisites you specified and versions we
managed to load:
Module Name Have Want
Bio::Perl 0 0
Bio::PrimarySeq 0 0
Bio::SearchIO 0 0
Bio::Seq 0 0
Bio::SeqFeature::Generic 0 0
Bio::SeqIO 0 0
Bio::Tools::GFF 0 0
Cwd 3.74 0
Data::Dumper 2.172 0
Env::Path 0.19 0.18
Exception::Class 1.44 0
ExtUtils::MakeMaker 7.34 0
File::Basename 2.77 0
File::Copy 2.13 0
File::Find 1.13 0
File::Slurper 0.012 0
File::Temp 0.2306 0
FindBin 1.49 0
Getopt::Long 2.37 0
List::Util 1.50 0
Moose 2.2011 0
Moose::Role 2.2011 0
POSIX 1.15 0
Scalar::Util 1.50 0
Test::Most 0.35 0
Text::CSV 1.97 0
Time::Piece 1.33 0
Time::Seconds 1.33 0
XML::Simple 2.25 0
strict 1.03 0
warnings 1.05_01 0
Perl module toolchain versions installed:
Module Name Have
CPANPLUS 0.9176
CPANPLUS::Dist::Build 0.90
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
Module::Build 0.4224
Pod::Parser 1.35
Pod::Simple 3.32
Test2 1.302136
Test::Harness 3.42
Test::More 1.302136
version 0.9924
******************************** NOTE ********************************
The comments above are created mechanically, possibly without manual
checking by the sender. As there are many people performing automatic
tests on each upload to CPAN, it is likely that you will receive
identical messages about the same problem.
If you believe that the message is mistaken, please reply to the first
one with correction and/or additional informations, and do not take
it personally. We appreciate your patience. :)
**********************************************************************
Additional comments:
This report was machine-generated by CPANPLUS::Dist::YACSmoke 1.02.
Powered by minismokebox version 0.68
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_GB.UTF-8
LANGUAGE = en_GB:en
NONINTERACTIVE_TESTING = 1
PATH = /home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/zi8b5GO6Yx/Bio-AutomatedAnnotation-1.182770/blib/script:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/v4yWncCLtT/libwww-perl-6.36/blib/script:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/6zPYEE9pio/Moose-2.2011/blib/script:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/yccC0pGnRz/Package-Stash-0.37/blib/script:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/hurNK8IW5Z/Env-Path-0.19/blib/script:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/6bPONEvmmi/BioPerl-1.007002/blib/script:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/uzDwYW5Vis/Data-Stag-0.14/blib/script:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
PERL5LIB = 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/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/pys5DGpNCN/Sub-Exporter-0.987/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/ES1aDkISNK/File-pushd-1.016/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/ES1aDkISNK/File-pushd-1.016/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/H7GICBR64f/Variable-Magic-0.62/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/H7GICBR64f/Variable-Magic-0.62/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/LfFPFHMTgC/B-Hooks-EndOfScope-0.24/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/LfFPFHMTgC/B-Hooks-EndOfScope-0.24/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/zzJPOGd3Lr/namespace-clean-0.27/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/zzJPOGd3Lr/namespace-clean-0.27/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/t641yrn1eQ/Test-CleanNamespaces-0.23/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/t641yrn1eQ/Test-CleanNamespaces-0.23/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/6zPYEE9pio/Moose-2.2011/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/6zPYEE9pio/Moose-2.2011/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/uqgoWk9_0t/Text-CSV-1.97/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/uqgoWk9_0t/Text-CSV-1.97/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/nICv5rdovX/Time-Piece-1.33/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/nICv5rdovX/Time-Piece-1.33/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/9_snd1ZhbB/XML-NamespaceSupport-1.12/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/9_snd1ZhbB/XML-NamespaceSupport-1.12/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/CYIw0bCUGp/XML-SAX-Base-1.09/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/CYIw0bCUGp/XML-SAX-Base-1.09/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/YmHqoFfAVQ/XML-SAX-1.00/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/YmHqoFfAVQ/XML-SAX-1.00/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/o2bTszIoJV/Encode-Locale-1.05/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/o2bTszIoJV/Encode-Locale-1.05/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/a21NPzsQkl/HTTP-Date-6.02/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/a21NPzsQkl/HTTP-Date-6.02/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/FGFJtB2MBm/File-Listing-6.04/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/FGFJtB2MBm/File-Listing-6.04/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/2kYrHtjpEY/HTML-Tagset-3.20/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/2kYrHtjpEY/HTML-Tagset-3.20/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/OzXJTE0yh6/HTML-Parser-3.72/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/OzXJTE0yh6/HTML-Parser-3.72/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/TWNvBPIubU/IO-HTML-1.001/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/TWNvBPIubU/IO-HTML-1.001/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/B_APuTulmU/LWP-MediaTypes-6.02/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/B_APuTulmU/LWP-MediaTypes-6.02/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/qm9vkf6E2E/HTTP-Message-6.18/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/qm9vkf6E2E/HTTP-Message-6.18/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/UDOiOqG0pa/HTTP-Cookies-6.04/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/UDOiOqG0pa/HTTP-Cookies-6.04/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/FlZs03VdUK/HTTP-Daemon-6.01/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/FlZs03VdUK/HTTP-Daemon-6.01/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/KnEqTTCFDC/HTTP-Negotiate-6.01/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/KnEqTTCFDC/HTTP-Negotiate-6.01/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/lYLDWIMup7/Net-HTTP-6.18/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/lYLDWIMup7/Net-HTTP-6.18/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/jdQZOdZX1c/Test-RequiresInternet-0.05/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/jdQZOdZX1c/Test-RequiresInternet-0.05/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/wZ94x1Vmv2/WWW-RobotRules-6.02/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/wZ94x1Vmv2/WWW-RobotRules-6.02/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/v4yWncCLtT/libwww-perl-6.36/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/v4yWncCLtT/libwww-perl-6.36/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/RTqi26iFb4/XML-Parser-2.44/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/RTqi26iFb4/XML-Parser-2.44/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/eXq3U8ffYc/XML-SAX-Expat-0.51/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/eXq3U8ffYc/XML-SAX-Expat-0.51/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/AprdI9eexC/XML-Simple-2.25/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/AprdI9eexC/XML-Simple-2.25/blib/arch:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/zi8b5GO6Yx/Bio-AutomatedAnnotation-1.182770/blib/lib:/home/cpan/pit/thr/conf/perl-5.8.9/.cpanplus/5.8.9/build/zi8b5GO6Yx/Bio-AutomatedAnnotation-1.182770/blib/arch
PERL5_CPANPLUS_IS_RUNNING = 26801
PERL5_CPANPLUS_IS_VERSION = 0.9176
PERL5_MINISMOKEBOX = 0.68
PERL5_YACSMOKE_BASE = /home/cpan/pit/thr/conf/perl-5.8.9
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_MM_USE_DEFAULT = 1
SHELL = /bin/bash
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
Perl: $^X = /home/cpan/pit/thr/perl-5.8.9/bin/perl
UID: $< = 1001
EUID: $> = 1001
GID: $( = 1001 1001
EGID: $) = 1001 1001
-------------------------------
--
Summary of my perl5 (revision 5 version 8 subversion 9) configuration:
Platform:
osname=gnukfreebsd, osvers=10.1-0-amd64, archname=x86_64-gnukfreebsd-thread-multi
uname='gnukfreebsd kondor 10.1-0-amd64 #0 wed, 16 mar 2016 23:16:33 +0000 x86_64 amd64 qemu virtual cpu version 2.0.0 gnukfreebsd '
config_args='-des -Dprefix=/home/cpan/pit/thr/perl-5.8.9 -Dusethreads'
hint=recommended, useposix=true, d_sigaction=define
usethreads=define use5005threads=undef useithreads=define 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 ='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2',
cppflags='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -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 =' -L/usr/local/lib'
libpth=/usr/local/lib /lib/x86_64-kfreebsd-gnu /lib/../lib /usr/lib/x86_64-kfreebsd-gnu /usr/lib/../lib /lib /usr/lib
libs=-lnsl -lgdbm -ldl -lm -lcrypt -lutil -lpthread -lc -lgdbm_compat
perllibs=-lnsl -ldl -lm -lcrypt -lutil -lpthread -lc -lgdbm_compat
libc=/usr/lib/x86_64-kfreebsd-gnu/libc.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'
Characteristics of this binary (from libperl):
Compile-time options: MULTIPLICITY PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
USE_64_BIT_ALL USE_64_BIT_INT USE_FAST_STDIO
USE_ITHREADS USE_LARGE_FILES USE_PERLIO
USE_REENTRANT_API
Locally applied patches:
Devel::PatchPerl 1.42
Built under gnukfreebsd
Compiled at May 7 2016 02:21:13
%ENV:
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PERL5_CPANPLUS_IS_RUNNING="26801"
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PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_MM_USE_DEFAULT="1"
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