Report for Bio-Grid-Run-SGE-0.065

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From: Slaven Rezić (SREZIC) 
Subject: PASS Bio-Grid-Run-SGE-0.065 5.26.0 FreeBSD
Date: 2018-07-04T21:29:07Z

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 5.26.0, 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
[05 Jul 06:24:00] [INFO]: INDEXING ....
[05 Jul 06:24:00] [INFO]: CONFIGURATION:
                          (/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2/test_env.tmp/test_env.job.conf.json)
                          {
                            args               => [],
                            idx_dir            => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2/idx",
                            input              => [
                                                    {
                                                      elements => ["a" .. "f"],
                                                      format   => "List",
                                                      idx_file => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2/idx/test_env.0.idx",
                                                    },
                                                  ],
                            job_name           => "test_env",
                            log_dir            => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2/test_env.tmp/log",
                            mode               => "Consecutive",
                            no_prompt          => 1,
                            num_parts          => 6,
                            prefix_output_dirs => 1,
                            result_dir         => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2/r",
                            stderr_dir         => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2/test_env.tmp/err",
                            stdout_dir         => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2/test_env.tmp/out",
                            submit_bin         => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2/qfake.pl",
                            submit_params      => [],
                            tmp_dir            => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2/test_env.tmp",
                            working_dir        => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2",
                          }
[05 Jul 06:24:00] [INFO]: Running: /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2/qfake.pl -t 1-6 -S /usr/perl5.26.0p/bin/perl5.26.0 -N test_env -e /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2/test_env.tmp/err -o /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2/test_env.tmp/out /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2/test_env.tmp/env.test_env.pl /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/scripts/cl_env.pl --stage worker /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2/test_env.tmp/test_env.job.conf.json 
[05 Jul 06:24:24] [INFO]: >>job_id:1530797040
[05 Jul 06:24:24] [INFO]: post processing: /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2/qfake.pl -S /usr/perl5.26.0p/bin/perl5.26.0 -N p1530797040_test_env -e /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2/test_env.tmp/err -o /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2/test_env.tmp/out -hold_jid 1530797040 /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2/test_env.tmp/env.test_env.pl /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/scripts/cl_env.pl --stage post_task --job_id 1530797040 /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/3vukwGvwR2/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
[05 Jul 06:24:35] [INFO]: INDEXING ....
[05 Jul 06:24:35] [INFO]: CONFIGURATION:
                          (/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr/test_all_fail.tmp/test_all_fail.job.conf.json)
                          {
                            args               => [],
                            idx_dir            => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr/idx",
                            input              => [
                                                    {
                                                      elements => ["a" .. "f"],
                                                      format   => "List",
                                                      idx_file => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr/idx/test_all_fail.0.idx",
                                                    },
                                                  ],
                            job_name           => "test_all_fail",
                            log_dir            => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr/test_all_fail.tmp/log",
                            mode               => "Consecutive",
                            no_prompt          => 1,
                            num_parts          => 6,
                            prefix_output_dirs => 1,
                            result_dir         => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr/r",
                            stderr_dir         => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr/test_all_fail.tmp/err",
                            stdout_dir         => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr/test_all_fail.tmp/out",
                            submit_bin         => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr/qfake.pl",
                            submit_params      => [],
                            tmp_dir            => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr/test_all_fail.tmp",
                            working_dir        => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr",
                          }
[05 Jul 06:24:35] [INFO]: Running: /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr/qfake.pl -t 1-6 -S /usr/perl5.26.0p/bin/perl5.26.0 -N test_all_fail -e /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr/test_all_fail.tmp/err -o /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr/test_all_fail.tmp/out /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr/test_all_fail.tmp/env.test_all_fail.pl /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/scripts/cl_fail_on_purpose.pl --stage worker /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr/test_all_fail.tmp/test_all_fail.job.conf.json 
[05 Jul 06:24:55] [INFO]: >>job_id:1530797076
[05 Jul 06:24:55] [INFO]: post processing: /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr/qfake.pl -S /usr/perl5.26.0p/bin/perl5.26.0 -N p1530797076_test_all_fail -e /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr/test_all_fail.tmp/err -o /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr/test_all_fail.tmp/out -hold_jid 1530797076 /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr/test_all_fail.tmp/env.test_all_fail.pl /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/scripts/cl_fail_on_purpose.pl --stage post_task --job_id 1530797076 /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/yOE0HwLfWr/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
[05 Jul 06:25:05] [INFO]: INDEXING ....
[05 Jul 06:25:05] [INFO]: CONFIGURATION:
                          (/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb/test_all_fail.tmp/test_all_fail.job.conf.json)
                          {
                            args               => [],
                            idx_dir            => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb/idx",
                            input              => [
                                                    {
                                                      elements => ["a" .. "f"],
                                                      format   => "List",
                                                      idx_file => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb/idx/test_all_fail.0.idx",
                                                    },
                                                  ],
                            job_name           => "test_all_fail",
                            log_dir            => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb/test_all_fail.tmp/log",
                            mode               => "Consecutive",
                            no_prompt          => 1,
                            num_parts          => 6,
                            prefix_output_dirs => 1,
                            result_dir         => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb/r",
                            stderr_dir         => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb/test_all_fail.tmp/err",
                            stdout_dir         => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb/test_all_fail.tmp/out",
                            submit_bin         => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb/qfake.pl",
                            submit_params      => [],
                            tmp_dir            => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb/test_all_fail.tmp",
                            working_dir        => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb",
                          }
[05 Jul 06:25:05] [INFO]: Running: /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb/qfake.pl -t 1-6 -S /usr/perl5.26.0p/bin/perl5.26.0 -N test_all_fail -e /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb/test_all_fail.tmp/err -o /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb/test_all_fail.tmp/out /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb/test_all_fail.tmp/env.test_all_fail.pl /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/scripts/cl_syntax_error.pl --stage worker /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb/test_all_fail.tmp/test_all_fail.job.conf.json 
[05 Jul 06:25:26] [INFO]: >>job_id:1530797106
[05 Jul 06:25:26] [INFO]: post processing: /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb/qfake.pl -S /usr/perl5.26.0p/bin/perl5.26.0 -N p1530797106_test_all_fail -e /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb/test_all_fail.tmp/err -o /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb/test_all_fail.tmp/out -hold_jid 1530797106 /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb/test_all_fail.tmp/env.test_all_fail.pl /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/scripts/cl_syntax_error.pl --stage post_task --job_id 1530797106 /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/tMxPT3vZnb/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
[05 Jul 06:25:43] [INFO]: INDEXING ....
[05 Jul 06:25:43] [INFO]: CONFIGURATION:
                          (/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b/test_env.tmp/test_env.job.conf.json)
                          {
                            args               => [],
                            idx_dir            => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b/idx",
                            input              => [
                                                    {
                                                      elements => ["a" .. "e", "...", "v" .. "z"],
                                                      format   => "List",
                                                      idx_file => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b/idx/test_env.0.idx",
                                                    },
                                                  ],
                            job_name           => "test_env",
                            log_dir            => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b/test_env.tmp/log",
                            mode               => "Consecutive",
                            no_prompt          => 1,
                            num_parts          => 26,
                            prefix_output_dirs => 1,
                            result_dir         => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b/r",
                            stderr_dir         => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b/test_env.tmp/err",
                            stdout_dir         => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b/test_env.tmp/out",
                            submit_bin         => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b/qfork.pl",
                            submit_params      => [],
                            tmp_dir            => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b/test_env.tmp",
                            working_dir        => "/home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b",
                          }
[05 Jul 06:25:43] [INFO]: Running: /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b/qfork.pl -t 1-26 -S /usr/perl5.26.0p/bin/perl5.26.0 -N test_env -e /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b/test_env.tmp/err -o /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b/test_env.tmp/out /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b/test_env.tmp/env.test_env.pl /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/scripts/cl_env.pl --stage worker /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b/test_env.tmp/test_env.job.conf.json 
[05 Jul 06:26:23] [INFO]: >>job_id:1530797144
[05 Jul 06:26:23] [INFO]: post processing: /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b/qfork.pl -S /usr/perl5.26.0p/bin/perl5.26.0 -N p1530797144_test_env -e /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b/test_env.tmp/err -o /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b/test_env.tmp/out -hold_jid 1530797144 /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b/test_env.tmp/env.test_env.pl /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/scripts/cl_env.pl --stage post_task --job_id 1530797144 /home/cpansand/.cpan/build/2018070506/Bio-Grid-Run-SGE-0.065-0/tmp_test/SHxoOLRD4b/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 5.026000, /usr/perl5.26.0p/bin/perl5.26.0
t/00-load.t ....................................... ok
t/Bio-Grid-Run-SGE-Index-Dummy.t .................. ok
[05 Jul 06:26:33] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Index-FileList.t ............... ok
[05 Jul 06:26:34] [INFO]: INDEXING ....
# 4303
# $VAR1 = {
#           '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'
#                     ],
#           'file' => 't/data/S_lycopersicum_chromosomes.2.40.fa.bg.gz.fai',
#           'key' => 'eins'
#         };
# $VAR1 = {
#           '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'
#                     ],
#           'file' => 't/data/S_lycopersicum_chromosomes.2.40.fa.bg.gz.fai',
#           'key' => 'eins'
#         };
# $VAR1 = {
#           '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'
#                     ],
#           'key' => 'zwei',
#           'file' => 't/data/S_lycopersicum_contigs.2.40.fa.bg.gz.fai'
#         };
t/Bio-Grid-Run-SGE-Index-FileRecordsFromNDJSON.t .. ok
[05 Jul 06:26:35] [INFO]: INDEXING ....
[05 Jul 06:26:36] [INFO]: INDEXING ....
[05 Jul 06:26:36] [INFO]: INDEXING ....
[05 Jul 06:26:37] [INFO]: INDEXING ....
[05 Jul 06:26:37] [INFO]: INDEXING ....
[05 Jul 06:26:38] [INFO]: INDEXING ....
[05 Jul 06:26:38] [INFO]: INDEXING ....
[05 Jul 06:26:38] [INFO]: SKIPPING INDEXING STEP, THE INDEX IS UP TO DATE
t/Bio-Grid-Run-SGE-Index-General.t ................ ok
[05 Jul 06:26:39] [INFO]: INDEXING ....
[05 Jul 06:26:40] [WARN]: chunk_size differs between old index and new index, REINDEXING NECESSARY
[05 Jul 06:26:41] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Index-List.t ................... ok
[05 Jul 06:26:42] [INFO]: INDEXING ....
[05 Jul 06:26:42] [WARN]: chunk_size differs between old index and new index, REINDEXING NECESSARY
[05 Jul 06:26:43] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Index-ListFromFile.t ........... ok
[05 Jul 06:26:46] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Index-NDJSON.t ................. ok
[05 Jul 06:26:46] [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
[05 Jul 06:26:48] [INFO]: INDEXING ....
[05 Jul 06:26:49] [INFO]: INDEXING ....
[05 Jul 06:28:00] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Iterator-AvsB.t ................ ok
[05 Jul 06:28:10] [INFO]: INDEXING ....
t/Bio-Grid-Run-SGE-Iterator-Consecutive.t ......... ok
t/Bio-Grid-Run-SGE-Log-Analysis.t ................. ok
# [
#    "env",
#    "config",
#    "log",
#    "iterator"
# ]
[05 Jul 06:28:13] [INFO]: INDEXING ....
[05 Jul 06:28:13] [INFO]: Running: /var/tmp/cpansmoker-1023/2018070506/Bp3Z1n_9AF/Bio-Grid-Run-SGE-Master.qsub.pl -t 1-45 -S /usr/perl5.26.0p/bin/perl5.26.0 -N cluster_job -e /var/tmp/cpansmoker-1023/2018070506/Bp3Z1n_9AF/cluster_job.tmp/err -o /var/tmp/cpansmoker-1023/2018070506/Bp3Z1n_9AF/cluster_job.tmp/out /var/tmp/cpansmoker-1023/2018070506/Bp3Z1n_9AF/cluster_job.tmp/env.cluster_job.pl t/Bio-Grid-Run-SGE-Master.script.pl --stage worker /var/tmp/cpansmoker-1023/2018070506/Bp3Z1n_9AF/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/2018070506/Bio-Grid-Run-SGE-0.065-0
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, 275 wallclock secs ( 0.63 usr  0.16 sys + 33.15 cusr  6.34 csys = 40.28 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     0.46    
    Clone                     0     0.39    
    Config::Auto              0     0.44    
    Config::IniFiles          0     2.94    
    Data::Dump                0     1.23    
    Email::Sender::Simple     0     1.300031
    Email::Simple             0     2.214   
    Email::Simple::Creator    0     2.214   
    Error                     0     0.17025 
    File::Copy                0     2.32    
    File::HomeDir             0     1.004   
    File::Next                0     1.16    
    File::Spec                0     3.74    
    File::Which               0     1.22    
    Getopt::Long::Descriptive 0     0.100   
    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 5.026000
    Proc::Daemon              0     0.23    
    Storable                  0     2.62    
    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:

    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/2018070506/Config-Auto-0.44-0/blib/arch:/home/cpansand/.cpan/build/2018070506/Config-Auto-0.44-0/blib/lib
    PERL5OPT = 
    PERL5_CPANPLUS_IS_RUNNING = 4405
    PERL5_CPAN_IS_RUNNING = 4405
    PERL5_CPAN_IS_RUNNING_IN_RECURSION = 4355,4405
    PERL_BATCH = yes
    PERL_CANARY_STABILITY_NOPROMPT = 1
    PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2018070506/cpanreporter_000_config.ini
    PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
    PERL_USE_UNSAFE_INC = 1
    SHELL = /bin/sh
    TMPDIR = /var/tmp/cpansmoker-1023/2018070506

Perl special variables (and OS-specific diagnostics, for MSWin32):

    $^X = /usr/perl5.26.0p/bin/perl5.26.0
    $UID/$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             0.9922  


--

Summary of my perl5 (revision 5 version 26 subversion 0) configuration:
   
  Platform:
    osname=freebsd
    osvers=11.1-prerelease
    archname=amd64-freebsd
    uname='freebsd ali3.bbbike.org 11.1-prerelease freebsd 11.1-prerelease #0 r313908+426f153a020(stable11): fri sep 1 20:49:08 cst 2017 root@ali3.bbbike.org:usrobjhomeprojectsfreebsdsysgeneric amd64 '
    config_args='-ds -e -Dprefix=/usr/perl5.26.0p -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 Sep  1 2017 22:07:18
  %ENV:
    PERL5LIB="/home/cpansand/.cpan/build/2018070506/Config-Auto-0.44-0/blib/arch:/home/cpansand/.cpan/build/2018070506/Config-Auto-0.44-0/blib/lib"
    PERL5OPT=""
    PERL5_CPANPLUS_IS_RUNNING="4405"
    PERL5_CPAN_IS_RUNNING="4405"
    PERL5_CPAN_IS_RUNNING_IN_RECURSION="4355,4405"
    PERL_BATCH="yes"
    PERL_CANARY_STABILITY_NOPROMPT="1"
    PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2018070506/cpanreporter_000_config.ini"
    PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
    PERL_USE_UNSAFE_INC="1"
  @INC:
    /home/cpansand/.cpan/build/2018070506/Config-Auto-0.44-0/blib/arch
    /home/cpansand/.cpan/build/2018070506/Config-Auto-0.44-0/blib/lib
    /usr/perl5.26.0p/lib/site_perl/5.26.0/amd64-freebsd
    /usr/perl5.26.0p/lib/site_perl/5.26.0
    /usr/perl5.26.0p/lib/5.26.0/amd64-freebsd
    /usr/perl5.26.0p/lib/5.26.0
    .