Bio-AutomatedAnnotation v1.182770 Perl 5 v5.18.2 amd64-freebsd
- Status
- Fail
- From
- Slaven Rezić (SREZIC)
- Dist
-
Bio-AutomatedAnnotation v1.182770
- Platform
- Perl 5 v5.18.2 amd64-freebsd
- Date
- 2018-10-04 16:57:46
- ID
- 9df9ff42-c7f6-11e8-a3bb-a4faee9c4200
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 5.18.2, 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/perl5.18.2/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, 5 wallclock secs ( 0.04 usr 0.05 sys + 2.65 cusr 0.58 csys = 3.32 CPU)
Result: FAIL
Failed 1/12 test programs. 5/123 subtests failed.
*** [test_dynamic] Error code 5
Stop in /usr/home/eserte/.cpan/build/2018100415/Bio-AutomatedAnnotation-1.182770-1.
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------------ ---- --------
Bio::Perl 0 1.007001
Bio::PrimarySeq 0 0
Bio::SearchIO 0 0
Bio::Seq 0 1.007001
Bio::SeqFeature::Generic 0 0
Bio::SeqIO 0 0
Bio::Tools::GFF 0 0
Cwd 0 3.74
Exception::Class 0 1.44
File::Basename 0 2.84
File::Copy 0 2.26
File::Temp 0 0.2308
FindBin 0 1.51
Getopt::Long 0 2.5
List::Util 0 1.50
Moose 0 2.2010
POSIX 0 1.32
Scalar::Util 0 1.50
Text::CSV 0 1.97
Time::Piece 0 1.33
Time::Seconds 0 1.33
warnings 0 1.18
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 1.23
File::Slurper 0 0.012
Moose::Role 0 2.2010
strict 0 1.07
Test::Most 0 0.35
configure_requires:
Module Need Have
------------------------ ---- --------
ExtUtils::MakeMaker 0 7.34
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
LC_ALL = de_DE.ISO8859-1
PATH = /usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/cpansand/bin/freebsd9.3:/home/cpansand/bin/sh:/home/cpansand/bin:/usr/games:/home/cpansand/devel:/usr/home/eserte/src/srezic-misc/scripts
PERL5LIB =
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 75851
PERL5_CPAN_IS_RUNNING = 75851
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 75805,75851
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2018100415/cpanreporter_000_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
SHELL = /usr/local/bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1023/2018100415
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /usr/perl5.18.2/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 3.74
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
JSON 2.97001
JSON::PP 2.97001
Module::Build 0.4224
Module::Signature 0.81
Parse::CPAN::Meta 2.150010
Test::Harness 3.41
Test::More 1.302140
YAML 1.24
YAML::Syck 1.30
version 0.9924
--
Summary of my perl5 (revision 5 version 18 subversion 2) configuration:
Platform:
osname=freebsd, osvers=9.2-release-p4, archname=amd64-freebsd
uname='freebsd cvrsnica-freebsd-92 9.2-release-p4 freebsd 9.2-release-p4 #0: tue apr 8 18:08:22 utc 2014 root@amd64-builder.daemonology.net:usrobjusrsrcsysgeneric amd64 '
config_args='-ds -e -Dprefix=/usr/perl5.18.2'
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 20070831 patched [FreeBSD]', 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
Built under freebsd
Compiled at May 16 2014 01:27:28
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="75851"
PERL5_CPAN_IS_RUNNING="75851"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="75805,75851"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2018100415/cpanreporter_000_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
@INC:
/usr/perl5.18.2/lib/site_perl/5.18.2/amd64-freebsd
/usr/perl5.18.2/lib/site_perl/5.18.2
/usr/perl5.18.2/lib/5.18.2/amd64-freebsd
/usr/perl5.18.2/lib/5.18.2
.