Bio-AutomatedAnnotation v1.182685 Perl 5 v5.18.3 amd64-freebsd
- Status
- Fail
- From
- Chris Williams (BINGOS)
- Dist
-
Bio-AutomatedAnnotation v1.182685
- Platform
- Perl 5 v5.18.3 amd64-freebsd
- Date
- 2018-09-29 07:33:24
- ID
- f2cecf0c-c3b9-11e8-98d5-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 "/usr/home/cpan/pit/bare/perl-5.18.3/bin/perl5.18.3" "-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, 29 wallclock secs ( 0.12 usr 0.23 sys + 7.97 cusr 20.12 csys = 28.45 CPU)
Result: FAIL
Failed 1/12 test programs. 5/123 subtests failed.
*** Error code 5
Stop.
make: stopped in /usr/home/cpan/pit/bare/conf/perl-5.18.3/.cpanplus/5.18.3/build/zUlqxsLo_3/Bio-AutomatedAnnotation-1.182685
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 2.145 0
Env::Path 0.19 0.18
Exception::Class 1.44 0
ExtUtils::MakeMaker 7.34 0
File::Basename 2.84 0
File::Copy 2.26 0
File::Find 1.23 0
File::Slurper 0.012 0
File::Temp 0.2308 0
FindBin 1.51 0
Getopt::Long 2.39 0
List::Util 1.50 0
Moose 2.2011 0
Moose::Role 2.2011 0
POSIX 1.32 0
Scalar::Util 1.50 0
Test::Most 0.35 0
Text::CSV 1.97 0
Time::Piece 1.20_01 0
Time::Seconds 0 0
XML::Simple 2.25 0
strict 1.07 0
warnings 1.18 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 1.60
Pod::Simple 3.28
Test2 1.302138
Test::Harness 3.42
Test::More 1.302138
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
NONINTERACTIVE_TESTING = 1
PATH = /usr/home/cpan/pit/bare/conf/perl-5.18.3/.cpanplus/5.18.3/build/zUlqxsLo_3/Bio-AutomatedAnnotation-1.182685/blib/script:/usr/home/cpan/pit/bare/conf/perl-5.18.3/.cpanplus/5.18.3/build/hxa5UiarOK/libwww-perl-6.35/blib/script:/usr/home/cpan/pit/bare/conf/perl-5.18.3/.cpanplus/5.18.3/build/_uj6g2l5sW/Moose-2.2011/blib/script:/usr/home/cpan/pit/bare/conf/perl-5.18.3/.cpanplus/5.18.3/build/81q9M8mLyg/Package-Stash-0.37/blib/script:/usr/home/cpan/pit/bare/conf/perl-5.18.3/.cpanplus/5.18.3/build/kjHzfuG9QD/Env-Path-0.19/blib/script:/usr/home/cpan/pit/bare/conf/perl-5.18.3/.cpanplus/5.18.3/build/XsrKxMvVxk/BioPerl-1.007002/blib/script:/usr/home/cpan/pit/bare/conf/perl-5.18.3/.cpanplus/5.18.3/build/VwUlWrnBCd/Data-Stag-0.14/blib/script:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/home/cpan/bin
PERL5LIB = 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/conf/perl-5.18.3/.cpanplus/5.18.3/build/hxa5UiarOK/libwww-perl-6.35/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.18.3/.cpanplus/5.18.3/build/hxa5UiarOK/libwww-perl-6.35/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.18.3/.cpanplus/5.18.3/build/WvhBBudH0a/XML-Parser-2.44/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.18.3/.cpanplus/5.18.3/build/WvhBBudH0a/XML-Parser-2.44/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.18.3/.cpanplus/5.18.3/build/8PyhaJMILU/XML-SAX-Expat-0.51/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.18.3/.cpanplus/5.18.3/build/8PyhaJMILU/XML-SAX-Expat-0.51/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.18.3/.cpanplus/5.18.3/build/B5pHxG3Cgp/XML-Simple-2.25/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.18.3/.cpanplus/5.18.3/build/B5pHxG3Cgp/XML-Simple-2.25/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.18.3/.cpanplus/5.18.3/build/zUlqxsLo_3/Bio-AutomatedAnnotation-1.182685/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.18.3/.cpanplus/5.18.3/build/zUlqxsLo_3/Bio-AutomatedAnnotation-1.182685/blib/arch
PERL5_CPANPLUS_IS_RUNNING = 32480
PERL5_CPANPLUS_IS_VERSION = 0.9176
PERL5_MINISMOKEBOX = 0.68
PERL5_YACSMOKE_BASE = /usr/home/cpan/pit/bare/conf/perl-5.18.3
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_MM_USE_DEFAULT = 1
SHELL = /usr/local/bin/bash
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
Perl: $^X = /usr/home/cpan/pit/bare/perl-5.18.3/bin/perl5.18.3
UID: $< = 1002
EUID: $> = 1002
GID: $( = 1002 1002
EGID: $) = 1002 1002
-------------------------------
--
Summary of my perl5 (revision 5 version 18 subversion 3) configuration:
Platform:
osname=freebsd, osvers=11.1-release, archname=amd64-freebsd
uname='freebsd fforc 11.1-release freebsd 11.1-release #0 r321309: fri jul 21 02:08:28 utc 2017 root@releng2.nyi.freebsd.org:usrobjusrsrcsysgeneric amd64 '
config_args='-des -Dprefix=/usr/home/cpan/pit/bare/perl-5.18.3'
hint=recommended, useposix=true, d_sigaction=define
useithreads=undef, usemultiplicity=undef
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include',
optimize='-O',
cppflags='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='4.2.1 Compatible FreeBSD Clang 4.0.0 (tags/RELEASE_400/final 297347)', 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 ='-Wl,-E -fstack-protector -L/usr/local/lib'
libpth=/usr/lib /usr/local/lib
libs=-lgdbm -lm -lcrypt -lutil -lc
perllibs=-lm -lcrypt -lutil -lc
libc=, 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 -L/usr/local/lib -fstack-protector'
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES PERLIO_LAYERS PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD PERL_MALLOC_WRAP
PERL_PRESERVE_IVUV PERL_SAWAMPERSAND USE_64_BIT_ALL
USE_64_BIT_INT USE_LARGE_FILES USE_LOCALE
USE_LOCALE_COLLATE USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC USE_PERLIO USE_PERL_ATOF
Locally applied patches:
Devel::PatchPerl 1.48
Built under freebsd
Compiled at Jul 26 2017 22:43:01
%ENV:
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PERL5_CPANPLUS_IS_RUNNING="32480"
PERL5_CPANPLUS_IS_VERSION="0.9176"
PERL5_MINISMOKEBOX="0.68"
PERL5_YACSMOKE_BASE="/usr/home/cpan/pit/bare/conf/perl-5.18.3"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_MM_USE_DEFAULT="1"
@INC:
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