Bio-AutomatedAnnotation v1.182680 Perl 5 v5.24.0 x86_64-linux
- Status
- Fail
- From
- Slaven Rezić (SREZIC)
- Dist
-
Bio-AutomatedAnnotation v1.182680
- Platform
- Perl 5 v5.24.0 x86_64-linux
- Date
- 2018-09-25 17:49:00
- ID
- 487fb2ee-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-1.182680
on perl 5.24.0, 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 "/opt/perl-5.24.0/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, 3 wallclock secs ( 0.04 usr 0.04 sys + 2.31 cusr 0.82 csys = 3.21 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
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------------ ---- --------
Bio::Perl 0 1.007001
Bio::PrimarySeq 0 0
Bio::SearchIO 0 0
Bio::Seq 0 0
Bio::SeqFeature::Generic 0 0
Bio::SeqIO 0 1.007001
Bio::Tools::GFF 0 0
Cwd 0 3.75
Exception::Class 0 1.44
File::Basename 0 2.85
File::Copy 0 2.31
File::Temp 0 0.2308
FindBin 0 1.51
Getopt::Long 0 2.5
List::Util 0 1.50
Moose 0 2.2011
POSIX 0 1.65
Scalar::Util 0 1.50
Text::CSV 0 1.97
Time::Piece 0 1.33
Time::Seconds 0 1.33
warnings 0 1.36
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 1.34
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 7.34
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
LANG = C
PATH = /usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/cpansand/bin/linux-gnu:/home/cpansand/bin/sh:/home/cpansand/bin:/usr/games:/home/cpansand/devel:/home/eserte/src/srezic-misc/scripts
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 362
PERL5_CPAN_IS_RUNNING = 362
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 31614,362
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2018092513/cpanreporter_000_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_USE_UNSAFE_INC = 1
SHELL = /usr/bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1023/2018092513
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /opt/perl-5.24.0/bin/perl
$UID/$EUID = 1023 / 1023
$GID = 1023 1023
$EGID = 1023 1023
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 2.06
ExtUtils::MakeMaker 7.34
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.31
File::Spec 3.75
JSON 2.97001
JSON::PP 2.95
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 0.9923
--
Summary of my perl5 (revision 5 version 24 subversion 0) configuration:
Platform:
osname=linux, osvers=4.9.0-3-amd64, archname=x86_64-linux
uname='linux debian9 4.9.0-3-amd64 #1 smp debian 4.9.30-2+deb9u1 (2017-06-18) x86_64 gnulinux '
config_args='-ds -e -Dprefix=/opt/perl-5.24.0 -Dcf_email=srezic@cpan.org'
hint=recommended, useposix=true, d_sigaction=define
useithreads=undef, usemultiplicity=undef
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2',
cppflags='-fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
ccversion='', gccversion='6.3.0 20170516', 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/6/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 -lgdbm -ldb -ldl -lm -lcrypt -lutil -lc -lgdbm_compat
perllibs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
libc=libc-2.24.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.24'
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 PERLIO_LAYERS PERL_COPY_ON_WRITE
PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD PERL_MALLOC_WRAP
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 linux
Compiled at Jun 20 2017 18:06:36
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="362"
PERL5_CPAN_IS_RUNNING="362"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="31614,362"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2018092513/cpanreporter_000_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_USE_UNSAFE_INC="1"
@INC:
/opt/perl-5.24.0/lib/site_perl/5.24.0/x86_64-linux
/opt/perl-5.24.0/lib/site_perl/5.24.0
/opt/perl-5.24.0/lib/5.24.0/x86_64-linux
/opt/perl-5.24.0/lib/5.24.0
.