Bio-Grid-Run-SGE v0.065 Perl 5 v5.28.0 x86_64-linux
- Status
- Pass
- From
- Slaven Rezić (SREZIC)
- Dist
-
Bio-Grid-Run-SGE v0.065
- Platform
- Perl 5 v5.28.0 x86_64-linux
- Date
- 2018-07-04 21:43:01
- ID
- 39c7f08a-7fd3-11e8-a4f2-c5ec01375e5c
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 Joachim Bargsten,
This is a computer-generated report for Bio-Grid-Run-SGE-0.065
on perl 5.28.0, created by CPAN-Reporter-1.2018.
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:
none provided
------------------------------
PROGRAM OUTPUT
------------------------------
Output from './Build test':
# USAGE
# STANDARD USAGE INFO OF Bio::Grid::Run::SGE
# cl_env.pl [-hr] [long options...] [<config_file>] [<arg1> <arg2> ... <argn>]
# cl_env.pl [-hr] [long options...] _ [<arg1> <arg2> ... <argn>]
# -h --help print help message and exit
# --stage STR run post task with job id of previous task
# -r STR --range STR run predefined range
# --job_id STR run under this job_id
# --task_id STR run under this task id
# --no_prompt ask no confirmation stuff for running a job
#
#
# CLUSTER SCRIPT USAGE INFO
# The script takes an list like index, prints element(s) to <result_prefix>.item.json.
# Additionally, the current environment will be stored in <result_prefix>.env.json.
#
# EXAMPLE CONFIG:
# ---
# input:
# - elements:
# - a
# - b
# - c
# - d
# - e
# - f
# format: List
# job_name: <job_name>
# mode: Consecutive
# 1st test
[04 Jul 21:40:22] [INFO]: INDEXING ....
[04 Jul 21:40:22] [INFO]: CONFIGURATION:
(/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB/test_env.tmp/test_env.job.conf.json)
{
args => [],
idx_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB/idx",
input => [
{
elements => ["a" .. "f"],
format => "List",
idx_file => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB/idx/test_env.0.idx",
},
],
job_name => "test_env",
log_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB/test_env.tmp/log",
mode => "Consecutive",
no_prompt => 1,
num_parts => 6,
prefix_output_dirs => 1,
result_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB/r",
stderr_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB/test_env.tmp/err",
stdout_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB/test_env.tmp/out",
submit_bin => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB/qfake.pl",
submit_params => [],
tmp_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB/test_env.tmp",
working_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB",
}
[04 Jul 21:40:22] [INFO]: Running: /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB/qfake.pl -t 1-6 -S /opt/perl-5.28.0/bin/perl -N test_env -e /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB/test_env.tmp/err -o /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB/test_env.tmp/out /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB/test_env.tmp/env.test_env.pl /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/scripts/cl_env.pl --stage worker /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB/test_env.tmp/test_env.job.conf.json
[04 Jul 21:40:29] [INFO]: >>job_id:1530740422
[04 Jul 21:40:29] [INFO]: post processing: /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB/qfake.pl -S /opt/perl-5.28.0/bin/perl -N p1530740422_test_env -e /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB/test_env.tmp/err -o /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB/test_env.tmp/out -hold_jid 1530740422 /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB/test_env.tmp/env.test_env.pl /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/scripts/cl_env.pl --stage post_task --job_id 1530740422 /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/nVFerxQ4VB/test_env.tmp/test_env.job.conf.json
# THIS TEST MIGHT TAKE UP TO 30 MINUTES
# next poll in 2 seconds
t/00-basic_qfake.t ................................ ok
# STANDARD USAGE INFO OF Bio::Grid::Run::SGE
# cl_fail_on_purpose.pl [-hr] [long options...] [<config_file>] [<arg1> <arg2> ... <argn>]
# cl_fail_on_purpose.pl [-hr] [long options...] _ [<arg1> <arg2> ... <argn>]
# -h --help print help message and exit
# --stage STR run post task with job id of previous task
# -r STR --range STR run predefined range
# --job_id STR run under this job_id
# --task_id STR run under this task id
# --no_prompt ask no confirmation stuff for running a job
#
#
# CLUSTER SCRIPT USAGE INFO
# The script takes an list like index, prints element(s) to <result_prefix>.item.json.
# Additionally, the current environment will be stored in <result_prefix>.env.json.
#
# EXAMPLE CONFIG:
# ---
# input:
# - elements:
# - a
# - b
# - c
# - d
# - e
# - f
# format: List
# job_name: <job_name>
# mode: Consecutive
[04 Jul 21:40:32] [INFO]: INDEXING ....
[04 Jul 21:40:32] [INFO]: CONFIGURATION:
(/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp/test_all_fail.tmp/test_all_fail.job.conf.json)
{
args => [],
idx_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp/idx",
input => [
{
elements => ["a" .. "f"],
format => "List",
idx_file => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp/idx/test_all_fail.0.idx",
},
],
job_name => "test_all_fail",
log_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp/test_all_fail.tmp/log",
mode => "Consecutive",
no_prompt => 1,
num_parts => 6,
prefix_output_dirs => 1,
result_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp/r",
stderr_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp/test_all_fail.tmp/err",
stdout_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp/test_all_fail.tmp/out",
submit_bin => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp/qfake.pl",
submit_params => [],
tmp_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp/test_all_fail.tmp",
working_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp",
}
[04 Jul 21:40:32] [INFO]: Running: /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp/qfake.pl -t 1-6 -S /opt/perl-5.28.0/bin/perl -N test_all_fail -e /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp/test_all_fail.tmp/err -o /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp/test_all_fail.tmp/out /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp/test_all_fail.tmp/env.test_all_fail.pl /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/scripts/cl_fail_on_purpose.pl --stage worker /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp/test_all_fail.tmp/test_all_fail.job.conf.json
[04 Jul 21:40:40] [INFO]: >>job_id:1530740432
[04 Jul 21:40:40] [INFO]: post processing: /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp/qfake.pl -S /opt/perl-5.28.0/bin/perl -N p1530740432_test_all_fail -e /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp/test_all_fail.tmp/err -o /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp/test_all_fail.tmp/out -hold_jid 1530740432 /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp/test_all_fail.tmp/env.test_all_fail.pl /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/scripts/cl_fail_on_purpose.pl --stage post_task --job_id 1530740432 /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/bPkKQoeCsp/test_all_fail.tmp/test_all_fail.job.conf.json
# THIS TEST MIGHT TAKE UP TO 30 MINUTES
# next poll in 1 seconds
t/00-basic_qfake_err.t ............................ ok
# STANDARD USAGE INFO OF Bio::Grid::Run::SGE
# cl_syntax_error.pl [-hr] [long options...] [<config_file>] [<arg1> <arg2> ... <argn>]
# cl_syntax_error.pl [-hr] [long options...] _ [<arg1> <arg2> ... <argn>]
# -h --help print help message and exit
# --stage STR run post task with job id of previous task
# -r STR --range STR run predefined range
# --job_id STR run under this job_id
# --task_id STR run under this task id
# --no_prompt ask no confirmation stuff for running a job
#
#
# CLUSTER SCRIPT USAGE INFO
# The script takes an list like index, prints element(s) to <result_prefix>.item.json.
# Additionally, the current environment will be stored in <result_prefix>.env.json.
#
# EXAMPLE CONFIG:
# ---
# input:
# - elements:
# - a
# - b
# - c
# - d
# - e
# - f
# format: List
# job_name: <job_name>
# mode: Consecutive
[04 Jul 21:40:42] [INFO]: INDEXING ....
[04 Jul 21:40:42] [INFO]: CONFIGURATION:
(/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT/test_all_fail.tmp/test_all_fail.job.conf.json)
{
args => [],
idx_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT/idx",
input => [
{
elements => ["a" .. "f"],
format => "List",
idx_file => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT/idx/test_all_fail.0.idx",
},
],
job_name => "test_all_fail",
log_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT/test_all_fail.tmp/log",
mode => "Consecutive",
no_prompt => 1,
num_parts => 6,
prefix_output_dirs => 1,
result_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT/r",
stderr_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT/test_all_fail.tmp/err",
stdout_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT/test_all_fail.tmp/out",
submit_bin => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT/qfake.pl",
submit_params => [],
tmp_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT/test_all_fail.tmp",
working_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT",
}
[04 Jul 21:40:42] [INFO]: Running: /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT/qfake.pl -t 1-6 -S /opt/perl-5.28.0/bin/perl -N test_all_fail -e /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT/test_all_fail.tmp/err -o /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT/test_all_fail.tmp/out /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT/test_all_fail.tmp/env.test_all_fail.pl /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/scripts/cl_syntax_error.pl --stage worker /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT/test_all_fail.tmp/test_all_fail.job.conf.json
[04 Jul 21:40:50] [INFO]: >>job_id:1530740442
[04 Jul 21:40:50] [INFO]: post processing: /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT/qfake.pl -S /opt/perl-5.28.0/bin/perl -N p1530740442_test_all_fail -e /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT/test_all_fail.tmp/err -o /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT/test_all_fail.tmp/out -hold_jid 1530740442 /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT/test_all_fail.tmp/env.test_all_fail.pl /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/scripts/cl_syntax_error.pl --stage post_task --job_id 1530740442 /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/EuiW_9SOeT/test_all_fail.tmp/test_all_fail.job.conf.json
# THIS TEST MIGHT TAKE UP TO 30 MINUTES
# next poll in 2 seconds
t/00-basic_qfake_syntax_error.t ................... ok
# STANDARD USAGE INFO OF Bio::Grid::Run::SGE
# cl_env.pl [-hr] [long options...] [<config_file>] [<arg1> <arg2> ... <argn>]
# cl_env.pl [-hr] [long options...] _ [<arg1> <arg2> ... <argn>]
# -h --help print help message and exit
# --stage STR run post task with job id of previous task
# -r STR --range STR run predefined range
# --job_id STR run under this job_id
# --task_id STR run under this task id
# --no_prompt ask no confirmation stuff for running a job
#
#
# CLUSTER SCRIPT USAGE INFO
# The script takes an list like index, prints element(s) to <result_prefix>.item.json.
# Additionally, the current environment will be stored in <result_prefix>.env.json.
#
# EXAMPLE CONFIG:
# ---
# input:
# - elements:
# - a
# - b
# - c
# - d
# - e
# - f
# format: List
# job_name: <job_name>
# mode: Consecutive
[04 Jul 21:40:53] [INFO]: INDEXING ....
[04 Jul 21:40:53] [INFO]: CONFIGURATION:
(/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50/test_env.tmp/test_env.job.conf.json)
{
args => [],
idx_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50/idx",
input => [
{
elements => ["a" .. "e", "...", "v" .. "z"],
format => "List",
idx_file => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50/idx/test_env.0.idx",
},
],
job_name => "test_env",
log_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50/test_env.tmp/log",
mode => "Consecutive",
no_prompt => 1,
num_parts => 26,
prefix_output_dirs => 1,
result_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50/r",
stderr_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50/test_env.tmp/err",
stdout_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50/test_env.tmp/out",
submit_bin => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50/qfork.pl",
submit_params => [],
tmp_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50/test_env.tmp",
working_dir => "/home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50",
}
[04 Jul 21:40:53] [INFO]: Running: /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50/qfork.pl -t 1-26 -S /opt/perl-5.28.0/bin/perl -N test_env -e /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50/test_env.tmp/err -o /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50/test_env.tmp/out /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50/test_env.tmp/env.test_env.pl /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/scripts/cl_env.pl --stage worker /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50/test_env.tmp/test_env.job.conf.json
[04 Jul 21:41:07] [INFO]: >>job_id:1530740453
[04 Jul 21:41:07] [INFO]: post processing: /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50/qfork.pl -S /opt/perl-5.28.0/bin/perl -N p1530740453_test_env -e /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50/test_env.tmp/err -o /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50/test_env.tmp/out -hold_jid 1530740453 /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50/test_env.tmp/env.test_env.pl /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/scripts/cl_env.pl --stage post_task --job_id 1530740453 /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7/tmp_test/PhGva4iI50/test_env.tmp/test_env.job.conf.json
# THIS TEST MIGHT TAKE UP TO 30 MINUTES
# next poll in 2 seconds
t/00-basic_qfork.t ................................ ok
# Testing Bio::Grid::Run::SGE 0.065, Perl 5.028000, /opt/perl-5.28.0/bin/perl
t/00-load.t ....................................... ok
t/Bio-Grid-Run-SGE-Index-Dummy.t .................. ok
[04 Jul 21:41:10] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Index-FileList.t ............... ok
[04 Jul 21:41:10] [INFO]: INDEXING ....
# 4303
# $VAR1 = {
# 'file' => 't/data/S_lycopersicum_chromosomes.2.40.fa.bg.gz.fai',
# 'key' => 'eins',
# 'data' => [
# 'SL2.40ch00 21805821 12 80 81',
# 'SL2.40ch01 90304244 22078418 80 81',
# 'SL2.40ch02 49918294 113511478 80 81',
# 'SL2.40ch03 64840714 164053763 80 81',
# 'SL2.40ch04 64064312 229704998 80 81',
# 'SL2.40ch05 65021438 294570126 80 81',
# 'SL2.40ch06 46041636 360404344 80 81'
# ]
# };
# $VAR1 = {
# 'key' => 'eins',
# 'file' => 't/data/S_lycopersicum_chromosomes.2.40.fa.bg.gz.fai',
# 'data' => [
# 'SL2.40ch07 65268621 407021513 80 81',
# 'SL2.40ch08 63032657 473106004 80 81',
# 'SL2.40ch09 67662091 536926582 80 81',
# 'SL2.40ch10 64834305 605434462 80 81',
# 'SL2.40ch11 53386025 671079208 80 81',
# 'SL2.40ch12 65486253 725132571 80 81'
# ]
# };
# $VAR1 = {
# 'file' => 't/data/S_lycopersicum_contigs.2.40.fa.bg.gz.fai',
# 'key' => 'zwei',
# 'data' => [
# 'SL2.40ct00001 1652 15 80 81',
# 'SL2.40ct00002 2066 1703 80 81',
# 'SL2.40ct00003 4871 3810 80 81',
# 'SL2.40ct00004 2086 8757 80 81',
# 'SL2.40ct00005 1622 10885 80 81',
# 'SL2.40ct00006 1679 12543 80 81',
# 'SL2.40ct00007 1166 14258 80 81'
# ]
# };
t/Bio-Grid-Run-SGE-Index-FileRecordsFromNDJSON.t .. ok
[04 Jul 21:41:10] [INFO]: INDEXING ....
[04 Jul 21:41:10] [INFO]: INDEXING ....
[04 Jul 21:41:10] [INFO]: INDEXING ....
[04 Jul 21:41:10] [INFO]: INDEXING ....
[04 Jul 21:41:10] [INFO]: INDEXING ....
[04 Jul 21:41:10] [INFO]: INDEXING ....
[04 Jul 21:41:10] [INFO]: INDEXING ....
[04 Jul 21:41:10] [INFO]: SKIPPING INDEXING STEP, THE INDEX IS UP TO DATE
t/Bio-Grid-Run-SGE-Index-General.t ................ ok
[04 Jul 21:41:11] [INFO]: INDEXING ....
[04 Jul 21:41:11] [WARN]: chunk_size differs between old index and new index, REINDEXING NECESSARY
[04 Jul 21:41:11] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Index-List.t ................... ok
[04 Jul 21:41:11] [INFO]: INDEXING ....
[04 Jul 21:41:11] [WARN]: chunk_size differs between old index and new index, REINDEXING NECESSARY
[04 Jul 21:41:11] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Index-ListFromFile.t ........... ok
[04 Jul 21:41:11] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Index-NDJSON.t ................. ok
[04 Jul 21:41:11] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Index-Range.t .................. ok
t/Bio-Grid-Run-SGE-Index.t ........................ ok
t/Bio-Grid-Run-SGE-Iterator-AllvsAllNoRep.t ....... ok
[04 Jul 21:41:11] [INFO]: INDEXING ....
[04 Jul 21:41:11] [INFO]: INDEXING ....
[04 Jul 21:41:12] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Iterator-AvsB.t ................ ok
[04 Jul 21:41:12] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Iterator-Consecutive.t ......... ok
t/Bio-Grid-Run-SGE-Log-Analysis.t ................. ok
# [
# "env",
# "config",
# "log",
# "iterator"
# ]
[04 Jul 21:41:12] [INFO]: INDEXING ....
[04 Jul 21:41:12] [INFO]: Running: /var/tmp/cpansmoker-1023/2018070421/Tn_dQFl5wn/Bio-Grid-Run-SGE-Master.qsub.pl -t 1-45 -S /opt/perl-5.28.0/bin/perl -N cluster_job -e /var/tmp/cpansmoker-1023/2018070421/Tn_dQFl5wn/cluster_job.tmp/err -o /var/tmp/cpansmoker-1023/2018070421/Tn_dQFl5wn/cluster_job.tmp/out /var/tmp/cpansmoker-1023/2018070421/Tn_dQFl5wn/cluster_job.tmp/env.cluster_job.pl t/Bio-Grid-Run-SGE-Master.script.pl --stage worker /var/tmp/cpansmoker-1023/2018070421/Tn_dQFl5wn/cluster_job.tmp/cluster_job.job.conf.json
[SUBMIT_WARNING] could not parse job id, using -1 as job id.
STDOUT:
STDERR:
t/Bio-Grid-Run-SGE-Master.t ....................... ok
t/Bio-Grid-Run-SGE-Role-Iterable.t ................ ok
t/Bio-Grid-Run-SGE-Util-Blast.t ................... ok
# /home/cpansand/.cpan/build/2018070421/Bio-Grid-Run-SGE-0.065-7
t/Bio-Grid-Run-SGE-Util.t ......................... ok
t/Bio-Grid-Run-SGE-Worker.t ....................... skipped: 1
t/Bio-Grid-Run-SGE.t .............................. ok
t/boilerplate.t ................................... ok
t/manifest.t ...................................... skipped: Author tests not required for installation
t/pod-coverage.t .................................. skipped: no pod coverage checks
t/pod.t ........................................... ok
t/zz-00-basic_qsub_live.t ......................... skipped: This test requires qsub
All tests successful.
Files=29, Tests=2701, 52 wallclock secs ( 0.07 usr 0.15 sys + 17.95 cusr 3.48 csys = 21.65 CPU)
Result: PASS
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------------- ----- --------
AnyEvent 0 7.14
AnyEvent::XMPP 0 0.55
Bio::Gonzales 0.068 0.082
Capture::Tiny 0 0.48
Clone 0 0.39
Config::Auto 0 0.44
Config::IniFiles 0 2.98
Data::Dump 0 1.23
Email::Sender::Simple 0 1.300031
Email::Simple 0 2.216
Email::Simple::Creator 0 2.216
Error 0 0.17026
File::Copy 0 2.33
File::HomeDir 0 1.004
File::Next 0 1.16
File::Spec 0 3.74
File::Which 0 1.22
Getopt::Long::Descriptive 0 0.102
HTTP::Date 0 6.02
IO::Prompt::Tiny 0 0.003
JSON::XS 0 3.04
List::MoreUtils 0 0.428
List::Util 0 1.50
Mouse 0 v2.5.4
Parallel::ForkManager 0 1.19
Params::Util 0 1.07
parent 0 0.236
Path::Tiny 0 0.104
perl 5.010 5.028000
Proc::Daemon 0 0.23
Storable 0 3.08
String::ShellQuote 0 1.04
Try::Tiny 0 0.30
URI 0 1.74
XML::LibXML 0 2.0132
build_requires:
Module Need Have
------------------------- ----- --------
Module::Build 0.28 0.4224
Test2::V0 0 0.000114
Test::More 0 1.302136
configure_requires:
Module Need Have
------------------------- ----- --------
Module::Build 0.28 0.4224
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
LANG = en_US.UTF-8
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 = 16509
PERL5_CPAN_IS_RUNNING = 16509
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 12243,16509
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2018070421/cpanreporter_000_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_USE_UNSAFE_INC = 1
SHELL = /bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1023/2018070421
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /opt/perl-5.28.0/bin/perl
$UID/$EUID = 1023 / 1023
$GID = 1023 1023
$EGID = 1023 1023
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.20
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 1.70
ExtUtils::ParseXS 3.39
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 3.42
Test::More 1.302136
YAML 1.26
YAML::Syck 1.30
version 0.9923
--
Summary of my perl5 (revision 5 version 28 subversion 0) configuration:
Platform:
osname=linux
osvers=2.6.32-696.3.1.el6.x86_64
archname=x86_64-linux
uname='linux centos6 2.6.32-696.3.1.el6.x86_64 #1 smp tue may 30 19:52:55 utc 2017 x86_64 x86_64 x86_64 gnulinux '
config_args='-ds -e -Dprefix=/opt/perl-5.28.0 -Dcf_email=srezic@cpan.org'
hint=recommended
useposix=true
d_sigaction=define
useithreads=undef
usemultiplicity=undef
use64bitint=define
use64bitall=define
uselongdouble=undef
usemymalloc=n
default_inc_excludes_dot=define
bincompat5005=undef
Compiler:
cc='cc'
ccflags ='-fwrapv -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2'
optimize='-O2'
cppflags='-fwrapv -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion=''
gccversion='4.4.7 20120313 (Red Hat 4.4.7-18)'
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 -L/usr/local/lib'
libpth=/usr/local/lib /usr/lib /lib/../lib64 /usr/lib/../lib64 /lib /lib64 /usr/lib64 /usr/local/lib64
libs=-lpthread -lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lc
perllibs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
libc=libc-2.12.so
so=so
useshrplib=false
libperl=libperl.a
gnulibc_version='2.12'
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'
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 linux
Compiled at Jun 23 2018 06:41:58
%ENV:
PERL5LIB=""
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="16509"
PERL5_CPAN_IS_RUNNING="16509"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="12243,16509"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2018070421/cpanreporter_000_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_USE_UNSAFE_INC="1"
@INC:
/opt/perl-5.28.0/lib/site_perl/5.28.0/x86_64-linux
/opt/perl-5.28.0/lib/site_perl/5.28.0
/opt/perl-5.28.0/lib/5.28.0/x86_64-linux
/opt/perl-5.28.0/lib/5.28.0
.