Bio-Gonzales v0.073 Perl 5 v5.26.0 x86_64-linux
- Status
- Pass
- From
- raytestinger
- Dist
-
Bio-Gonzales v0.073
- Platform
- Perl 5 v5.26.0 x86_64-linux
- Date
- 2018-02-04 20:16:07
- ID
- 3BDEB0EA-09E8-11E8-9BFA-059DA6ADE2D7
From: "raytestinger" <testinger@yahoo.com>
X-Test-Reporter-Distfile: JWB/Bio-Gonzales-0.073.tar.gz
X-Test-Reporter-Perl: v5.26.0
Subject: PASS Bio-Gonzales-0.073 x86_64-linux 4.10.0-30-generic
Report: 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 JWB,
This is a computer-generated report for Bio-Gonzales-0.073
on perl 5.26.0, created by App::cpanminus::reporter 0.17 (1.7043).
Thank you for uploading your work to CPAN. Congratulations!
All tests were successful.
Sections of this report:
* Tester comments
* Program output
* Prerequisites
* Environment and other context
------------------------------
TESTER COMMENTS
------------------------------
Additional comments from tester:
this report is from an automated smoke testing program
and was not reviewed by a human for accuracy
------------------------------
PROGRAM OUTPUT
------------------------------
Output from '':
Building and testing Bio-Gonzales-0.073
Building Bio-Gonzales
# Testing Bio::Gonzales 0.073, Perl 5.026000, /home/ray/perl5/perlbrew/perls/perl-5.26.0/bin/perl
t/00-load.t ................................ ok
t/Bio-Gonzales-Align-IO.t .................. ok
Track length: 130
Track length: 130
t/Bio-Gonzales-Align-Jalview.t ............. ok
t/Bio-Gonzales-Domain-Group.t .............. ok
feature has no id, made artificial one: __noid_exon_0 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_exon_1 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_exon_2 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_CDS_3 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_CDS_4 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_CDS_5 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_match1_match_6 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_match2_match_7 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_match3_match_8 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_exon_9 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_exon_10 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_exon_11 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_match4_assembly_component_12 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_match5_assembly_component_13 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_match6_assembly_component_14 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_match7_assembly_component_15 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_UTR_16 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_CDS_17 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_CDS_18 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_CDS_19 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_UTR_20 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_five_prime_UTR_21 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_CDS_22 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_CDS_23 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_three_prime_UTR_24 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_three_prime_UTR_25 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_five_prime_UTR_26 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_CDS_27 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_shared_exon_CDS_28 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
feature has no id, made artificial one: __noid_CDS_29 at t/Bio-Gonzales-Feat-IO-BED.t line 23.
t/Bio-Gonzales-Feat-IO-BED.t ............... ok
t/Bio-Gonzales-Feat-IO-GFF3.t .............. skipped: FIXME
t/Bio-Gonzales-Feat-IO-SWISS.t ............. ok
multiple ID entries, taking the first at t/Bio-Gonzales-Feat.t line 43.
t/Bio-Gonzales-Feat.t ...................... ok
t/Bio-Gonzales-Matrix-IO-mcl.t ............. skipped: deprecated, develop new with my mio pkg
t/Bio-Gonzales-Matrix-IO.t ................. ok
t/Bio-Gonzales-Matrix-Util.t ............... ok
t/Bio-Gonzales-Project-Functions.t ......... ok
t/Bio-Gonzales-Project.t ................... ok
t/Bio-Gonzales-Range-Cluster.t ............. ok
t/Bio-Gonzales-Range-Overlap.t ............. ok
empty ranges at t/Bio-Gonzales-Range-Util.t line 96.
empty ranges at t/Bio-Gonzales-Range-Util.t line 99.
t/Bio-Gonzales-Range-Util.t ................ ok
t/Bio-Gonzales-Role-BioPerl-Constructor.t .. ok
t/Bio-Gonzales-Search-IO-HMMER3.t .......... ok
t/Bio-Gonzales-Seq-Filter.t ................ ok
Name "main::phred_fp2chr_raw" used only once: possible typo at t/Bio-Gonzales-Seq-IO-fastq.t line 67.
t/Bio-Gonzales-Seq-IO-fastq.t .............. ok
t/Bio-Gonzales-Seq-Util.t .................. ok
t/Bio-Gonzales-Seq-Validate-fasta.t ........ ok
t/Bio-Gonzales-Seq.t ....................... ok
t/Bio-Gonzales-SummarizedExperiment.t ...... ok
t/Bio-Gonzales-Tools-SeqMask.t ............. ok
t/Bio-Gonzales-Util-Cerial.t ............... ok
# /bin/gzip
t/Bio-Gonzales-Util-File.t ................. ok
t/Bio-Gonzales-Util-Log.t .................. ok
t/Bio-Gonzales-Util-Log_threads.t .......... skipped: Perl not compiled with 'useithreads'
t/Bio-Gonzales-Util-Math.t ................. ok
t/Bio-Gonzales-Util-Text.t ................. ok
t/Bio-Gonzales-Util.t ...................... ok
# $VAR1 = [
# '0/0:10',
# '1/1:11',
# '2/2:22:33:44'
# ];
# $VAR1 = [
# '0/0:10',
# '3/3:11',
# '4/4:22:33:44'
# ];
# $VAR1 = [
# '0/0:10',
# '3/3:11',
# '4/4:22:33:44'
# ];
t/Bio-Gonzales-Var-Util.t .................. ok
t/IDMapIO.t ................................ skipped: needs revision
Training idx: $VAR1 = [
1,
3
];
(1, 0) => 1
(3, 0) => 2
0 -> $VAR1 = [
1
];
(1, 2) => 10
(3, 2) => 2
2 -> $VAR1 = [
3
];
t/Math-kNN-via-Distances.t ................. ok
t/boilerplate.t ............................ ok
t/gonz_unmap.t ............................. ok
t/manifest.t ............................... skipped: Author tests not required for installation
All tests successful.
Files=38, Tests=239, 10 wallclock secs ( 0.11 usr 0.05 sys + 6.33 cusr 0.38 csys = 6.87 CPU)
Result: PASS
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
No requirements found
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
LANG = en_US.UTF-8
LANGUAGE = en_US
NONINTERACTIVE_TESTING = 1
PATH = /home/ray/perl5/perlbrew/bin:/home/ray/perl5/perlbrew/perls/perl-5.26.0/bin:/home/ray/bin:/home/ray/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
PERL5_CPANPLUS_IS_RUNNING = 30364
PERL5_CPAN_IS_RUNNING = 30364
PERLBREW_BASHRC_VERSION = 0.74
PERLBREW_HOME = /home/ray/.perlbrew
PERLBREW_MANPATH = /home/ray/perl5/perlbrew/perls/perl-5.26.0/man
PERLBREW_PATH = /home/ray/perl5/perlbrew/bin:/home/ray/perl5/perlbrew/perls/perl-5.26.0/bin
PERLBREW_PERL = perl-5.26.0
PERLBREW_ROOT = /home/ray/perl5/perlbrew
PERLBREW_VERSION = 0.80
PERL_CPANM_HOME = /tmp/7xuWRehZ0P
PERL_CPAN_REPORTER_CONFIG = /tmp/7xuWRehZ0P/config.ini
SHELL = /bin/bash
TERM = xterm
Perl special variables (and OS-specific diagnostics, for MSWin32):
EGID = 1000 4 24 27 30 46 113 130 1000
EUID = 1000
EXECUTABLE_NAME = /home/ray/perl5/perlbrew/perls/perl-5.26.0/bin/perl
GID = 1000 4 24 27 30 46 113 130 1000
UID = 1000
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.18
CPAN::Meta 2.150010
Cwd 3.67
ExtUtils::CBuilder 0.280230
ExtUtils::Command 7.30
ExtUtils::Install 2.06
ExtUtils::MakeMaker 7.30
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.34
File::Spec 3.67
JSON 2.94
JSON::PP 2.97000
Module::Build 0.4224
Module::Signature 0.81
Parse::CPAN::Meta 2.150010
Test::Harness 3.39
Test::More 1.302120
YAML 1.24
YAML::Syck 1.30
version 0.9917
--
Summary of my perl5 (revision 5 version 26 subversion 0) configuration:
Platform:
osname=linux
osvers=4.10.0-30-generic
archname=x86_64-linux
uname='linux ray-hp-250-g5-notebook-pc 4.10.0-30-generic #34~16.04.1-ubuntu smp wed aug 2 02:13:56 utc 2017 x86_64 x86_64 x86_64 gnulinux '
config_args='-de -Dprefix=/home/ray/perl5/perlbrew/perls/perl-5.26.0 -Aeval:scriptdir=/home/ray/perl5/perlbrew/perls/perl-5.26.0/bin'
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 ='-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='5.4.0 20160609'
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/5/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 -ldl -lm -lcrypt -lutil -lc
perllibs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
libc=libc-2.23.so
so=so
useshrplib=false
libperl=libperl.a
gnulibc_version='2.23'
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_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
Locally applied patches:
Devel::PatchPerl 1.48
Built under linux
Compiled at Aug 5 2017 21:05:23
%ENV:
PERL5_CPANPLUS_IS_RUNNING="30364"
PERL5_CPAN_IS_RUNNING="30364"
PERLBREW_BASHRC_VERSION="0.74"
PERLBREW_HOME="/home/ray/.perlbrew"
PERLBREW_MANPATH="/home/ray/perl5/perlbrew/perls/perl-5.26.0/man"
PERLBREW_PATH="/home/ray/perl5/perlbrew/bin:/home/ray/perl5/perlbrew/perls/perl-5.26.0/bin"
PERLBREW_PERL="perl-5.26.0"
PERLBREW_ROOT="/home/ray/perl5/perlbrew"
PERLBREW_VERSION="0.80"
PERL_CPANM_HOME="/tmp/7xuWRehZ0P"
PERL_CPAN_REPORTER_CONFIG="/tmp/7xuWRehZ0P/config.ini"
@INC:
/home/ray/perl5/perlbrew/perls/perl-5.26.0/lib/site_perl/5.26.0/x86_64-linux
/home/ray/perl5/perlbrew/perls/perl-5.26.0/lib/site_perl/5.26.0
/home/ray/perl5/perlbrew/perls/perl-5.26.0/lib/5.26.0/x86_64-linux
/home/ray/perl5/perlbrew/perls/perl-5.26.0/lib/5.26.0