Bio-AutomatedAnnotation v1.182685 Perl 5 v5.26.1 amd64-freebsd
- Status
- Fail
- From
- Slaven Rezić (SREZIC)
- Dist
-
Bio-AutomatedAnnotation v1.182685
- Platform
- Perl 5 v5.26.1 amd64-freebsd
- Date
- 2018-09-25 17:46:59
- ID
- 00e3f9f4-c0eb-11e8-b0ce-bba9fdb88e26
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-1.182685
on perl 5.26.1, 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:
none provided
------------------------------
PROGRAM OUTPUT
------------------------------
Output from '/usr/bin/make test':
PERL_DL_NONLAZY=1 "/usr/perl5.26.1p/bin/perl5.26.1" "-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, 5 wallclock secs ( 0.05 usr 0.04 sys + 3.72 cusr 1.25 csys = 5.06 CPU)
Result: FAIL
Failed 1/12 test programs. 5/123 subtests failed.
*** Error code 5
Stop.
make: stopped in /home/cpansand/.cpan/build/2018092601/Bio-AutomatedAnnotation-1.182685-0
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------------ ---- --------
Bio::Perl 0 1.007002
Bio::PrimarySeq 0 0
Bio::SearchIO 0 1.007002
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 1.43
File::Basename 0 2.85
File::Copy 0 2.32
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 1.76
Scalar::Util 0 1.50
Text::CSV 0 1.95
Time::Piece 0 1.31
Time::Seconds 0 1.31
warnings 0 1.37
XML::Simple 0 2.24
build_requires:
Module Need Have
------------------------ ---- --------
Data::Dumper 0 2.167
Env::Path 0.18 0.19
ExtUtils::MakeMaker 0 7.34
File::Find 0 1.34
File::Slurper 0 0.010
Moose::Role 0 2.2011
strict 0 1.11
Test::Most 0 0.35
configure_requires:
Module Need Have
------------------------ ---- --------
ExtUtils::MakeMaker 0 7.34
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
PATH = /usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/cpansand/bin/sh:/home/cpansand/bin:/usr/games:/home/cpansand/devel:/home/eserte/src/srezic-misc/scripts
PERL5LIB = /home/cpansand/.cpan/build/2018092601/BioPerl-1.007002-0/blib/arch:/home/cpansand/.cpan/build/2018092601/BioPerl-1.007002-0/blib/lib:/home/cpansand/.cpan/build/2018092601/Data-Stag-0.14-0/blib/arch:/home/cpansand/.cpan/build/2018092601/Data-Stag-0.14-0/blib/lib:/home/cpansand/.cpan/build/2018092601/LinkEmbedder-1.00-0/blib/arch:/home/cpansand/.cpan/build/2018092601/LinkEmbedder-1.00-0/blib/lib:/home/cpansand/.cpan/build/2018092601/Mojolicious-8.01-2/blib/arch:/home/cpansand/.cpan/build/2018092601/Mojolicious-8.01-2/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 46427
PERL5_CPAN_IS_RUNNING = 46427
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 46357,46427
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2018092601/cpanreporter_000_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_USE_UNSAFE_INC = 1
SHELL = /bin/sh
TMPDIR = /var/tmp/cpansmoker-1023/2018092601
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /usr/perl5.26.1p/bin/perl5.26.1
$UID/$EUID = 1023 / 1023
$GID = 1023 1023
$EGID = 1023 1023
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.18
CPAN::Meta 2.150010
Cwd 3.74
ExtUtils::CBuilder 0.280230
ExtUtils::Command 7.34
ExtUtils::Install 2.06
ExtUtils::MakeMaker 7.34
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.34
File::Spec 3.74
JSON 2.97001
JSON::PP 2.94
Module::Build 0.4224
Module::Signature 0.81
Parse::CPAN::Meta 2.150010
Test::Harness 3.42
Test::More 1.302136
YAML 1.26
YAML::Syck 1.30
version 0.9917
--
Summary of my perl5 (revision 5 version 26 subversion 1) configuration:
Platform:
osname=freebsd
osvers=11.1-release-p2
archname=amd64-freebsd
uname='freebsd ali2.bbbike.org 11.1-release-p2 freebsd 11.1-release-p2 #0 r313908+e96f1f21705(releng11.1)-dirty: thu oct 19 12:14:33 utc 2017 root@ali2.bbbike.org:usrobjhomeprojectsfreebsdsysgeneric amd64 '
config_args='-ds -e -Dprefix=/usr/perl5.26.1p -Dcf_email=srezic@cpan.org -Doptimize=-O2 -pipe'
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 ='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_FORTIFY_SOURCE=2'
optimize='-O2 -pipe'
cppflags='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -fstack-protector-strong -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
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 ='-pthread -Wl,-E -fstack-protector-strong -L/usr/local/lib'
libpth=/usr/lib /usr/local/lib /usr/bin/../lib/clang/4.0.0/lib /usr/lib
libs=-lpthread -lgdbm -lm -lcrypt -lutil -lc
perllibs=-lpthread -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-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
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
Built under freebsd
Compiled at Oct 28 2017 07:46:07
%ENV:
PERL5LIB="/home/cpansand/.cpan/build/2018092601/BioPerl-1.007002-0/blib/arch:/home/cpansand/.cpan/build/2018092601/BioPerl-1.007002-0/blib/lib:/home/cpansand/.cpan/build/2018092601/Data-Stag-0.14-0/blib/arch:/home/cpansand/.cpan/build/2018092601/Data-Stag-0.14-0/blib/lib:/home/cpansand/.cpan/build/2018092601/LinkEmbedder-1.00-0/blib/arch:/home/cpansand/.cpan/build/2018092601/LinkEmbedder-1.00-0/blib/lib:/home/cpansand/.cpan/build/2018092601/Mojolicious-8.01-2/blib/arch:/home/cpansand/.cpan/build/2018092601/Mojolicious-8.01-2/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="46427"
PERL5_CPAN_IS_RUNNING="46427"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="46357,46427"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2018092601/cpanreporter_000_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_USE_UNSAFE_INC="1"
@INC:
/home/cpansand/.cpan/build/2018092601/BioPerl-1.007002-0/blib/arch
/home/cpansand/.cpan/build/2018092601/BioPerl-1.007002-0/blib/lib
/home/cpansand/.cpan/build/2018092601/Data-Stag-0.14-0/blib/arch
/home/cpansand/.cpan/build/2018092601/Data-Stag-0.14-0/blib/lib
/home/cpansand/.cpan/build/2018092601/LinkEmbedder-1.00-0/blib/arch
/home/cpansand/.cpan/build/2018092601/LinkEmbedder-1.00-0/blib/lib
/home/cpansand/.cpan/build/2018092601/Mojolicious-8.01-2/blib/arch
/home/cpansand/.cpan/build/2018092601/Mojolicious-8.01-2/blib/lib
/usr/perl5.26.1p/lib/site_perl/5.26.1/amd64-freebsd
/usr/perl5.26.1p/lib/site_perl/5.26.1
/usr/perl5.26.1p/lib/5.26.1/amd64-freebsd
/usr/perl5.26.1p/lib/5.26.1
.