Back
From: metabase:user:314402c4-2aae-11df-837a-5e0a49663a4f
Subject: FAIL BioX-Workflow-0.18 v5.18.2 GNU/Linux
Date: 2015-12-09T19:50:24Z
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 Jillian Rowe,
This is a computer-generated report for BioX-Workflow-0.18
on perl 5.18.2, created by CPAN-Reporter-1.2015.
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 './Build test':
t/author-pod-syntax.t .. skipped: these tests are for testing by the author
t/basic.t .............. ok
# Failed test 'Got expected output!'
# at t/lib/TestsFor/BioX/Workflow/Test001.pm line 133.
# got: '
# Samples: sample1, sample2, sample3, sample4, sample5
#
#
# Starting Workflow
#
#
# Global Variables:
# indir: t/example/data/raw/test001
# outdir: t/example/data/processed/test001
# file_rule: (.csv)$
#
#
#
#
#
# Starting backup
#
#
#
#
#
# Variables
# Indir: t/example/data/raw/test001
# Outdir: t/example/data/processed/test001/backup
#
#
# cp t/example/data/raw/test001/sample1.csv t/example/data/processed/test001/backup/sample1.csv
#
# cp t/example/data/raw/test001/sample2.csv t/example/data/processed/test001/backup/sample2.csv
#
# cp t/example/data/raw/test001/sample3.csv t/example/data/processed/test001/backup/sample3.csv
#
# cp t/example/data/raw/test001/sample4.csv t/example/data/processed/test001/backup/sample4.csv
#
# cp t/example/data/raw/test001/sample5.csv t/example/data/processed/test001/backup/sample5.csv
#
#
# wait
#
#
# Ending backup
#
#
#
#
#
#
# Starting grep_VARA
#
#
#
#
#
# Variables
# Indir: t/example/data/processed/test001/backup
# Outdir: t/example/data/processed/test001/grep_VARA
#
#
# echo "Working on t/example/data/processed/test001/backup/sample1.csv"
# grep -i "VARA" t/example/data/processed/test001/backup/sample1.csv >> t/example/data/processed/test001/grep_VARA/sample1.grep_VARA.csv
#
#
# echo "Working on t/example/data/processed/test001/backup/sample2.csv"
# grep -i "VARA" t/example/data/processed/test001/backup/sample2.csv >> t/example/data/processed/test001/grep_VARA/sample2.grep_VARA.csv
#
#
# echo "Working on t/example/data/processed/test001/backup/sample3.csv"
# grep -i "VARA" t/example/data/processed/test001/backup/sample3.csv >> t/example/data/processed/test001/grep_VARA/sample3.grep_VARA.csv
#
#
# echo "Working on t/example/data/processed/test001/backup/sample4.csv"
# grep -i "VARA" t/example/data/processed/test001/backup/sample4.csv >> t/example/data/processed/test001/grep_VARA/sample4.grep_VARA.csv
#
#
# echo "Working on t/example/data/processed/test001/backup/sample5.csv"
# grep -i "VARA" t/example/data/processed/test001/backup/sample5.csv >> t/example/data/processed/test001/grep_VARA/sample5.grep_VARA.csv
#
#
#
# wait
#
#
# Ending grep_VARA
#
#
#
#
#
#
# Starting grep_VARB
#
#
#
#
#
# Variables
# Indir: t/example/data/processed/test001/grep_VARA
# Outdir: t/example/data/processed/test001/grep_VARB
#
#
# grep -i "VARB" t/example/data/processed/test001/grep_VARA/sample1.grep_VARA.csv >> t/example/data/processed/test001/grep_VARB/sample1.grep_VARA.grep_VARB.csv
#
#
# grep -i "VARB" t/example/data/processed/test001/grep_VARA/sample2.grep_VARA.csv >> t/example/data/processed/test001/grep_VARB/sample2.grep_VARA.grep_VARB.csv
#
#
# grep -i "VARB" t/example/data/processed/test001/grep_VARA/sample3.grep_VARA.csv >> t/example/data/processed/test001/grep_VARB/sample3.grep_VARA.grep_VARB.csv
#
#
# grep -i "VARB" t/example/data/processed/test001/grep_VARA/sample4.grep_VARA.csv >> t/example/data/processed/test001/grep_VARB/sample4.grep_VARA.grep_VARB.csv
#
#
# grep -i "VARB" t/example/data/processed/test001/grep_VARA/sample5.grep_VARA.csv >> t/example/data/processed/test001/grep_VARB/sample5.grep_VARA.grep_VARB.csv
#
#
#
# wait
#
#
# Ending grep_VARB
#
#
#
# Ending Workflow
#
# '
# expected: '#
# # Samples: sample1, sample2, sample3, sample4, sample5
# #
# #
# # Starting Workflow
# #
# #
# # Global Variables:
# # indir: t/example/data/raw/test001
# # outdir: t/example/data/processed/test001
# # file_rule: (.csv)$
# #
#
# #
# #
#
# # Starting backup
# #
#
#
#
# #
# # Variables
# # Indir: t/example/data/raw/test001
# # Outdir: t/example/data/processed/test001/backup
# #
#
# cp t/example/data/raw/test001/sample1.csv t/example/data/processed/test001/backup/sample1.csv
#
# cp t/example/data/raw/test001/sample2.csv t/example/data/processed/test001/backup/sample2.csv
#
# cp t/example/data/raw/test001/sample3.csv t/example/data/processed/test001/backup/sample3.csv
#
# cp t/example/data/raw/test001/sample4.csv t/example/data/processed/test001/backup/sample4.csv
#
# cp t/example/data/raw/test001/sample5.csv t/example/data/processed/test001/backup/sample5.csv
#
#
# wait
#
# #
# # Ending backup
# #
#
#
# #
# #
#
# # Starting grep_VARA
# #
#
#
#
# #
# # Variables
# # Indir: t/example/data/processed/test001/backup
# # Outdir: t/example/data/processed/test001/grep_VARA
# #
#
# echo "Working on t/example/data/processed/test001/backup/sample1.csv"
# grep -i "VARA" t/example/data/processed/test001/backup/sample1.csv >> t/example/data/processed/test001/grep_VARA/sample1.grep_VARA.csv
#
#
# echo "Working on t/example/data/processed/test001/backup/sample2.csv"
# grep -i "VARA" t/example/data/processed/test001/backup/sample2.csv >> t/example/data/processed/test001/grep_VARA/sample2.grep_VARA.csv
#
#
# echo "Working on t/example/data/processed/test001/backup/sample3.csv"
# grep -i "VARA" t/example/data/processed/test001/backup/sample3.csv >> t/example/data/processed/test001/grep_VARA/sample3.grep_VARA.csv
#
#
# echo "Working on t/example/data/processed/test001/backup/sample4.csv"
# grep -i "VARA" t/example/data/processed/test001/backup/sample4.csv >> t/example/data/processed/test001/grep_VARA/sample4.grep_VARA.csv
#
#
# echo "Working on t/example/data/processed/test001/backup/sample5.csv"
# grep -i "VARA" t/example/data/processed/test001/backup/sample5.csv >> t/example/data/processed/test001/grep_VARA/sample5.grep_VARA.csv
#
#
#
# wait
#
# #
# # Ending grep_VARA
# #
#
#
# #
# #
#
# # Starting grep_VARB
# #
#
#
#
# #
# # Variables
# # Indir: t/example/data/processed/test001/grep_VARA
# # Outdir: t/example/data/processed/test001/grep_VARB
# #
#
# grep -i "VARB" t/example/data/processed/test001/grep_VARA/sample1.grep_VARA.csv >> t/example/data/processed/test001/grep_VARB/sample1.grep_VARA.grep_VARB.csv
#
#
# grep -i "VARB" t/example/data/processed/test001/grep_VARA/sample2.grep_VARA.csv >> t/example/data/processed/test001/grep_VARB/sample2.grep_VARA.grep_VARB.csv
#
#
# grep -i "VARB" t/example/data/processed/test001/grep_VARA/sample3.grep_VARA.csv >> t/example/data/processed/test001/grep_VARB/sample3.grep_VARA.grep_VARB.csv
#
#
# grep -i "VARB" t/example/data/processed/test001/grep_VARA/sample4.grep_VARA.csv >> t/example/data/processed/test001/grep_VARB/sample4.grep_VARA.grep_VARB.csv
#
#
# grep -i "VARB" t/example/data/processed/test001/grep_VARA/sample5.grep_VARA.csv >> t/example/data/processed/test001/grep_VARB/sample5.grep_VARA.grep_VARB.csv
#
#
#
# wait
#
# #
# # Ending grep_VARB
# #
#
# #
# # Ending Workflow
# #
# '
# Looks like you failed 1 test of 6.
# Failed test 'test_006'
# at /opt/perl-5.18.2t/lib/site_perl/5.18.2/Test/Class/Moose/Role/Executor.pm line 103.
# Looks like you failed 1 test of 6.
# Failed test 'TestsFor::BioX::Workflow::Test001'
# at /opt/perl-5.18.2t/lib/site_perl/5.18.2/x86_64-linux-thread-multi/Moose/Meta/Method/Delegation.pm line 110.
# Failed test 'Got expected output!'
# at t/lib/TestsFor/BioX/Workflow/Test002.pm line 38.
# got: '
# Samples: sample1, sample2, sample3, sample4, sample5
#
#
# Starting Workflow
#
#
# Global Variables:
# indir: t/example/data/raw/test002
# outdir: t/example/data/processed/test002
# file_rule: (sample.*)$
# by_sample_outdir: 1
# find_by_dir: 1
#
#
#
#
#
# Starting backup
#
#
#
#
#
# Variables
# Indir: t/example/data/raw/test002
# Outdir: t/example/data/processed/test002/backup
#
#
# cp t/example/data/raw/test002/sample1/sample1.csv t/example/data/processed/test002/sample1/backup/sample1.csv
#
# cp t/example/data/raw/test002/sample2/sample2.csv t/example/data/processed/test002/sample2/backup/sample2.csv
#
# cp t/example/data/raw/test002/sample3/sample3.csv t/example/data/processed/test002/sample3/backup/sample3.csv
#
# cp t/example/data/raw/test002/sample4/sample4.csv t/example/data/processed/test002/sample4/backup/sample4.csv
#
# cp t/example/data/raw/test002/sample5/sample5.csv t/example/data/processed/test002/sample5/backup/sample5.csv
#
#
# wait
#
#
# Ending backup
#
#
#
#
#
#
# Starting grep_VARA
#
#
#
#
#
# Variables
# Indir: t/example/data/processed/test002/backup
# Outdir: t/example/data/processed/test002/grep_VARA
#
#
# echo "Working on t/example/data/processed/test002/sample1/backup/sample1.csv"
# grep -i "VARA" t/example/data/processed/test002/sample1/backup/sample1.csv >> t/example/data/processed/test002/sample1/grep_VARA/sample1.grep_VARA.csv
#
#
# echo "Working on t/example/data/processed/test002/sample2/backup/sample2.csv"
# grep -i "VARA" t/example/data/processed/test002/sample2/backup/sample2.csv >> t/example/data/processed/test002/sample2/grep_VARA/sample2.grep_VARA.csv
#
#
# echo "Working on t/example/data/processed/test002/sample3/backup/sample3.csv"
# grep -i "VARA" t/example/data/processed/test002/sample3/backup/sample3.csv >> t/example/data/processed/test002/sample3/grep_VARA/sample3.grep_VARA.csv
#
#
# echo "Working on t/example/data/processed/test002/sample4/backup/sample4.csv"
# grep -i "VARA" t/example/data/processed/test002/sample4/backup/sample4.csv >> t/example/data/processed/test002/sample4/grep_VARA/sample4.grep_VARA.csv
#
#
# echo "Working on t/example/data/processed/test002/sample5/backup/sample5.csv"
# grep -i "VARA" t/example/data/processed/test002/sample5/backup/sample5.csv >> t/example/data/processed/test002/sample5/grep_VARA/sample5.grep_VARA.csv
#
#
#
# wait
#
#
# Ending grep_VARA
#
#
#
#
#
#
# Starting grep_VARB
#
#
#
#
#
# Variables
# Indir: t/example/data/processed/test002/grep_VARA
# Outdir: t/example/data/processed/test002/grep_VARB
#
#
# grep -i "VARB" t/example/data/processed/test002/sample1/grep_VARA/sample1.grep_VARA.csv >> t/example/data/processed/test002/sample1/grep_VARB/sample1.grep_VARA.grep_VARB.csv
#
#
# grep -i "VARB" t/example/data/processed/test002/sample2/grep_VARA/sample2.grep_VARA.csv >> t/example/data/processed/test002/sample2/grep_VARB/sample2.grep_VARA.grep_VARB.csv
#
#
# grep -i "VARB" t/example/data/processed/test002/sample3/grep_VARA/sample3.grep_VARA.csv >> t/example/data/processed/test002/sample3/grep_VARB/sample3.grep_VARA.grep_VARB.csv
#
#
# grep -i "VARB" t/example/data/processed/test002/sample4/grep_VARA/sample4.grep_VARA.csv >> t/example/data/processed/test002/sample4/grep_VARB/sample4.grep_VARA.grep_VARB.csv
#
#
# grep -i "VARB" t/example/data/processed/test002/sample5/grep_VARA/sample5.grep_VARA.csv >> t/example/data/processed/test002/sample5/grep_VARB/sample5.grep_VARA.grep_VARB.csv
#
#
#
# wait
#
#
# Ending grep_VARB
#
#
#
# Ending Workflow
#
# '
# expected: '#
# # Samples: sample1, sample2, sample3, sample4, sample5
# #
# #
# # Starting Workflow
# #
# #
# # Global Variables:
# # indir: t/example/data/raw/test002
# # outdir: t/example/data/processed/test002
# # file_rule: (sample.*)$
# # by_sample_outdir: 1
# # find_by_dir: 1
# #
#
# #
# #
#
# # Starting backup
# #
#
#
#
# #
# # Variables
# # Indir: t/example/data/raw/test002
# # Outdir: t/example/data/processed/test002/backup
# #
#
# cp t/example/data/raw/test002/sample1/sample1.csv t/example/data/processed/test002/sample1/backup/sample1.csv
#
# cp t/example/data/raw/test002/sample2/sample2.csv t/example/data/processed/test002/sample2/backup/sample2.csv
#
# cp t/example/data/raw/test002/sample3/sample3.csv t/example/data/processed/test002/sample3/backup/sample3.csv
#
# cp t/example/data/raw/test002/sample4/sample4.csv t/example/data/processed/test002/sample4/backup/sample4.csv
#
# cp t/example/data/raw/test002/sample5/sample5.csv t/example/data/processed/test002/sample5/backup/sample5.csv
#
#
# wait
#
# #
# # Ending backup
# #
#
#
# #
# #
#
# # Starting grep_VARA
# #
#
#
#
# #
# # Variables
# # Indir: t/example/data/processed/test002/backup
# # Outdir: t/example/data/processed/test002/grep_VARA
# #
#
# echo "Working on t/example/data/processed/test002/sample1/backup/sample1.csv"
# grep -i "VARA" t/example/data/processed/test002/sample1/backup/sample1.csv >> t/example/data/processed/test002/sample1/grep_VARA/sample1.grep_VARA.csv
#
#
# echo "Working on t/example/data/processed/test002/sample2/backup/sample2.csv"
# grep -i "VARA" t/example/data/processed/test002/sample2/backup/sample2.csv >> t/example/data/processed/test002/sample2/grep_VARA/sample2.grep_VARA.csv
#
#
# echo "Working on t/example/data/processed/test002/sample3/backup/sample3.csv"
# grep -i "VARA" t/example/data/processed/test002/sample3/backup/sample3.csv >> t/example/data/processed/test002/sample3/grep_VARA/sample3.grep_VARA.csv
#
#
# echo "Working on t/example/data/processed/test002/sample4/backup/sample4.csv"
# grep -i "VARA" t/example/data/processed/test002/sample4/backup/sample4.csv >> t/example/data/processed/test002/sample4/grep_VARA/sample4.grep_VARA.csv
#
#
# echo "Working on t/example/data/processed/test002/sample5/backup/sample5.csv"
# grep -i "VARA" t/example/data/processed/test002/sample5/backup/sample5.csv >> t/example/data/processed/test002/sample5/grep_VARA/sample5.grep_VARA.csv
#
#
#
# wait
#
# #
# # Ending grep_VARA
# #
#
#
# #
# #
#
# # Starting grep_VARB
# #
#
#
#
# #
# # Variables
# # Indir: t/example/data/processed/test002/grep_VARA
# # Outdir: t/example/data/processed/test002/grep_VARB
# #
#
# grep -i "VARB" t/example/data/processed/test002/sample1/grep_VARA/sample1.grep_VARA.csv >> t/example/data/processed/test002/sample1/grep_VARB/sample1.grep_VARA.grep_VARB.csv
#
#
# grep -i "VARB" t/example/data/processed/test002/sample2/grep_VARA/sample2.grep_VARA.csv >> t/example/data/processed/test002/sample2/grep_VARB/sample2.grep_VARA.grep_VARB.csv
#
#
# grep -i "VARB" t/example/data/processed/test002/sample3/grep_VARA/sample3.grep_VARA.csv >> t/example/data/processed/test002/sample3/grep_VARB/sample3.grep_VARA.grep_VARB.csv
#
#
# grep -i "VARB" t/example/data/processed/test002/sample4/grep_VARA/sample4.grep_VARA.csv >> t/example/data/processed/test002/sample4/grep_VARB/sample4.grep_VARA.grep_VARB.csv
#
#
# grep -i "VARB" t/example/data/processed/test002/sample5/grep_VARA/sample5.grep_VARA.csv >> t/example/data/processed/test002/sample5/grep_VARB/sample5.grep_VARA.grep_VARB.csv
#
#
#
# wait
#
# #
# # Ending grep_VARB
# #
#
# #
# # Ending Workflow
# #
# '
# Looks like you failed 1 test of 18.
# Failed test 'test_006'
# at /opt/perl-5.18.2t/lib/site_perl/5.18.2/Test/Class/Moose/Role/Executor.pm line 103.
# Looks like you failed 1 test of 2.
# Failed test 'TestsFor::BioX::Workflow::Test002'
# at /opt/perl-5.18.2t/lib/site_perl/5.18.2/x86_64-linux-thread-multi/Moose/Meta/Method/Delegation.pm line 110.
# Failed test 'Got expected output!'
# at t/lib/TestsFor/BioX/Workflow/Test003.pm line 38.
# got: '
# Samples: sample1, sample2, sample3, sample4, sample5
#
#
# Starting Workflow
#
#
# Global Variables:
# indir: t/example/data/raw/test003
# outdir: t/example/data/processed/test003
# ROOT: t/example/data/processed/test003
# file_rule: (sample.*)$
# by_sample_outdir: 1
# find_by_dir: 1
# LOCAL_VAR: This should be overwritten
#
#
#
#
#
# Starting backup
#
#
#
#
#
# Variables
# Indir: t/example/data/raw/test003
# Outdir: t/example/data/processed/test003/backup
# Local Variables:
# LOCAL_VAR: my_local_var
# analysis_dir: {$self->ROOT}/analysis
# outdir: t/example/data/processed/test003/backup
# indir: t/example/data/raw/test003
#
#
# echo "my_local_var" && \
# echo t/example/data/processed/test003/analysis && \
# cp t/example/data/raw/test003/sample1/sample1.csv t/example/data/processed/test003/sample1/backup/sample1.csv
#
#
# echo "my_local_var" && \
# echo t/example/data/processed/test003/analysis && \
# cp t/example/data/raw/test003/sample2/sample2.csv t/example/data/processed/test003/sample2/backup/sample2.csv
#
#
# echo "my_local_var" && \
# echo t/example/data/processed/test003/analysis && \
# cp t/example/data/raw/test003/sample3/sample3.csv t/example/data/processed/test003/sample3/backup/sample3.csv
#
#
# echo "my_local_var" && \
# echo t/example/data/processed/test003/analysis && \
# cp t/example/data/raw/test003/sample4/sample4.csv t/example/data/processed/test003/sample4/backup/sample4.csv
#
#
# echo "my_local_var" && \
# echo t/example/data/processed/test003/analysis && \
# cp t/example/data/raw/test003/sample5/sample5.csv t/example/data/processed/test003/sample5/backup/sample5.csv
#
#
#
# wait
#
#
# Ending backup
#
#
#
#
#
#
# Starting grep_VARA
#
#
#
#
#
# Variables
# Indir: t/example/data/processed/test003/backup
# Outdir: t/example/data/processed/test003/grep_VARA
# Local Variables:
# LOCAL_VAR: my_local_new_var
# outdir: t/example/data/processed/test003/grep_VARA
# indir: t/example/data/processed/test003/backup
#
#
# echo "my_local_new_var" && \
# echo "Working on t/example/data/processed/test003/sample1/backup/sample1.csv"
# grep -i "VARA" t/example/data/processed/test003/sample1/backup/sample1.csv >> t/example/data/processed/test003/sample1/grep_VARA/sample1.grep_VARA.csv
#
#
# echo "my_local_new_var" && \
# echo "Working on t/example/data/processed/test003/sample2/backup/sample2.csv"
# grep -i "VARA" t/example/data/processed/test003/sample2/backup/sample2.csv >> t/example/data/processed/test003/sample2/grep_VARA/sample2.grep_VARA.csv
#
#
# echo "my_local_new_var" && \
# echo "Working on t/example/data/processed/test003/sample3/backup/sample3.csv"
# grep -i "VARA" t/example/data/processed/test003/sample3/backup/sample3.csv >> t/example/data/processed/test003/sample3/grep_VARA/sample3.grep_VARA.csv
#
#
# echo "my_local_new_var" && \
# echo "Working on t/example/data/processed/test003/sample4/backup/sample4.csv"
# grep -i "VARA" t/example/data/processed/test003/sample4/backup/sample4.csv >> t/example/data/processed/test003/sample4/grep_VARA/sample4.grep_VARA.csv
#
#
# echo "my_local_new_var" && \
# echo "Working on t/example/data/processed/test003/sample5/backup/sample5.csv"
# grep -i "VARA" t/example/data/processed/test003/sample5/backup/sample5.csv >> t/example/data/processed/test003/sample5/grep_VARA/sample5.grep_VARA.csv
#
#
#
# wait
#
#
# Ending grep_VARA
#
#
#
#
#
#
# Starting grep_VARB
#
#
#
#
#
# Variables
# Indir: t/example/data/processed/test003/grep_VARA
# Outdir: t/example/data/processed/test003/grep_VARB
#
#
# echo "This should be overwritten" && \
# grep -i "VARB" t/example/data/processed/test003/sample1/grep_VARA/sample1.grep_VARA.csv >> t/example/data/processed/test003/sample1/grep_VARB/sample1.grep_VARA.grep_VARB.csv
#
#
# echo "This should be overwritten" && \
# grep -i "VARB" t/example/data/processed/test003/sample2/grep_VARA/sample2.grep_VARA.csv >> t/example/data/processed/test003/sample2/grep_VARB/sample2.grep_VARA.grep_VARB.csv
#
#
# echo "This should be overwritten" && \
# grep -i "VARB" t/example/data/processed/test003/sample3/grep_VARA/sample3.grep_VARA.csv >> t/example/data/processed/test003/sample3/grep_VARB/sample3.grep_VARA.grep_VARB.csv
#
#
# echo "This should be overwritten" && \
# grep -i "VARB" t/example/data/processed/test003/sample4/grep_VARA/sample4.grep_VARA.csv >> t/example/data/processed/test003/sample4/grep_VARB/sample4.grep_VARA.grep_VARB.csv
#
#
# echo "This should be overwritten" && \
# grep -i "VARB" t/example/data/processed/test003/sample5/grep_VARA/sample5.grep_VARA.csv >> t/example/data/processed/test003/sample5/grep_VARB/sample5.grep_VARA.grep_VARB.csv
#
#
#
# wait
#
#
# Ending grep_VARB
#
#
#
# Ending Workflow
#
# '
# expected: '#
# # Samples: sample1, sample2, sample3, sample4, sample5
# #
# #
# # Starting Workflow
# #
# #
# # Global Variables:
# # indir: t/example/data/raw/test003
# # outdir: t/example/data/processed/test003
# # ROOT: t/example/data/processed/test003
# # file_rule: (sample.*)$
# # by_sample_outdir: 1
# # find_by_dir: 1
# # LOCAL_VAR: This should be overwritten
# #
#
# #
# #
#
# # Starting backup
# #
#
#
#
# #
# # Variables
# # Indir: t/example/data/raw/test003
# # Outdir: t/example/data/processed/test003/backup
# # Local Variables:
# # LOCAL_VAR: my_local_var
# # analysis_dir: {$self->ROOT}/analysis
# # outdir: t/example/data/processed/test003/backup
# # indir: t/example/data/raw/test003
# #
#
# echo "my_local_var" && \
# echo t/example/data/processed/test003/analysis && \
# cp t/example/data/raw/test003/sample1/sample1.csv t/example/data/processed/test003/sample1/backup/sample1.csv
#
#
# echo "my_local_var" && \
# echo t/example/data/processed/test003/analysis && \
# cp t/example/data/raw/test003/sample2/sample2.csv t/example/data/processed/test003/sample2/backup/sample2.csv
#
#
# echo "my_local_var" && \
# echo t/example/data/processed/test003/analysis && \
# cp t/example/data/raw/test003/sample3/sample3.csv t/example/data/processed/test003/sample3/backup/sample3.csv
#
#
# echo "my_local_var" && \
# echo t/example/data/processed/test003/analysis && \
# cp t/example/data/raw/test003/sample4/sample4.csv t/example/data/processed/test003/sample4/backup/sample4.csv
#
#
# echo "my_local_var" && \
# echo t/example/data/processed/test003/analysis && \
# cp t/example/data/raw/test003/sample5/sample5.csv t/example/data/processed/test003/sample5/backup/sample5.csv
#
#
#
# wait
#
# #
# # Ending backup
# #
#
#
# #
# #
#
# # Starting grep_VARA
# #
#
#
#
# #
# # Variables
# # Indir: t/example/data/processed/test003/backup
# # Outdir: t/example/data/processed/test003/grep_VARA
# # Local Variables:
# # LOCAL_VAR: my_local_new_var
# # outdir: t/example/data/processed/test003/grep_VARA
# # indir: t/example/data/processed/test003/backup
# #
#
# echo "my_local_new_var" && \
# echo "Working on t/example/data/processed/test003/sample1/backup/sample1.csv"
# grep -i "VARA" t/example/data/processed/test003/sample1/backup/sample1.csv >> t/example/data/processed/test003/sample1/grep_VARA/sample1.grep_VARA.csv
#
#
# echo "my_local_new_var" && \
# echo "Working on t/example/data/processed/test003/sample2/backup/sample2.csv"
# grep -i "VARA" t/example/data/processed/test003/sample2/backup/sample2.csv >> t/example/data/processed/test003/sample2/grep_VARA/sample2.grep_VARA.csv
#
#
# echo "my_local_new_var" && \
# echo "Working on t/example/data/processed/test003/sample3/backup/sample3.csv"
# grep -i "VARA" t/example/data/processed/test003/sample3/backup/sample3.csv >> t/example/data/processed/test003/sample3/grep_VARA/sample3.grep_VARA.csv
#
#
# echo "my_local_new_var" && \
# echo "Working on t/example/data/processed/test003/sample4/backup/sample4.csv"
# grep -i "VARA" t/example/data/processed/test003/sample4/backup/sample4.csv >> t/example/data/processed/test003/sample4/grep_VARA/sample4.grep_VARA.csv
#
#
# echo "my_local_new_var" && \
# echo "Working on t/example/data/processed/test003/sample5/backup/sample5.csv"
# grep -i "VARA" t/example/data/processed/test003/sample5/backup/sample5.csv >> t/example/data/processed/test003/sample5/grep_VARA/sample5.grep_VARA.csv
#
#
#
# wait
#
# #
# # Ending grep_VARA
# #
#
#
# #
# #
#
# # Starting grep_VARB
# #
#
#
#
# #
# # Variables
# # Indir: t/example/data/processed/test003/grep_VARA
# # Outdir: t/example/data/processed/test003/grep_VARB
# #
#
# echo "This should be overwritten" && \
# grep -i "VARB" t/example/data/processed/test003/sample1/grep_VARA/sample1.grep_VARA.csv >> t/example/data/processed/test003/sample1/grep_VARB/sample1.grep_VARA.grep_VARB.csv
#
#
# echo "This should be overwritten" && \
# grep -i "VARB" t/example/data/processed/test003/sample2/grep_VARA/sample2.grep_VARA.csv >> t/example/data/processed/test003/sample2/grep_VARB/sample2.grep_VARA.grep_VARB.csv
#
#
# echo "This should be overwritten" && \
# grep -i "VARB" t/example/data/processed/test003/sample3/grep_VARA/sample3.grep_VARA.csv >> t/example/data/processed/test003/sample3/grep_VARB/sample3.grep_VARA.grep_VARB.csv
#
#
# echo "This should be overwritten" && \
# grep -i "VARB" t/example/data/processed/test003/sample4/grep_VARA/sample4.grep_VARA.csv >> t/example/data/processed/test003/sample4/grep_VARB/sample4.grep_VARA.grep_VARB.csv
#
#
# echo "This should be overwritten" && \
# grep -i "VARB" t/example/data/processed/test003/sample5/grep_VARA/sample5.grep_VARA.csv >> t/example/data/processed/test003/sample5/grep_VARB/sample5.grep_VARA.grep_VARB.csv
#
#
#
# wait
#
# #
# # Ending grep_VARB
# #
#
# #
# # Ending Workflow
# #
# '
# Looks like you failed 1 test of 3.
# Failed test 'test_006'
# at /opt/perl-5.18.2t/lib/site_perl/5.18.2/Test/Class/Moose/Role/Executor.pm line 103.
# Looks like you failed 1 test of 2.
# Failed test 'TestsFor::BioX::Workflow::Test003'
# at /opt/perl-5.18.2t/lib/site_perl/5.18.2/x86_64-linux-thread-multi/Moose/Meta/Method/Delegation.pm line 110.
# Looks like you failed 3 tests of 3.
t/test_class_tests.t ...
Dubious, test returned 3 (wstat 768, 0x300)
Failed 3/3 subtests
Test Summary Report
-------------------
t/test_class_tests.t (Wstat: 768 Tests: 3 Failed: 3)
Failed tests: 1-3
Non-zero exit status: 3
Files=3, Tests=4, 3 wallclock secs ( 0.03 usr 0.03 sys + 1.77 cusr 0.29 csys = 2.12 CPU)
Result: FAIL
Failed 1/3 test programs. 3/4 subtests failed.
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
-------------------------------- -------- --------
BioX::Wrapper 0 1.3
Carp::Always 0 0.13
Class::Load 0 0.23
Cwd 0 3.60
Data::Dumper 0 2.151
Data::Pairs 0 0.07
DateTime 0 1.21
File::Basename 0 2.84
File::Find::Rule 0 0.33
File::Path 0 2.12
Interpolation 0 0.74
IO::File 0 1.16
List::Compare 0 0.51
Moose 0 2.1604
MooseX::Getopt 0 0.68
MooseX::Getopt::Usage 0 0.24
MooseX::Getopt::Usage::Role::Man 0 0.24
MooseX::Object::Pluggable 0 0.0014
MooseX::SimpleConfig 0 0.10
perl 5.008005 5.018002
Storable 0 2.51
String::CamelCase 0 0.02
Text::Template 0 1.46
YAML::XS 0 0.59
build_requires:
Module Need Have
-------------------------------- -------- --------
Module::Build 0.28 0.4214
Test::Class::Moose 0 0.67
Test::More 0 1.001014
configure_requires:
Module Need Have
-------------------------------- -------- --------
Module::Build 0.28 0.4214
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
LANG = C
LC_ALL = de_DE.UTF-8
PATH = /usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/eserte/bin/linux-gnu:/home/eserte/bin/sh:/home/eserte/bin:/usr/games:/home/eserte/devel:/home/eserte/src/srezic-misc/scripts
PERL5LIB = /home/eserte/.cpan/build/2015120918/Mojo-Webqq-1.6.6-TcO_yD/blib/arch:/home/eserte/.cpan/build/2015120918/Mojo-Webqq-1.6.6-TcO_yD/blib/lib:/home/eserte/.cpan/build/2015120918/Net-SSL-ExpireDate-1.15-p2fkgm/blib/arch:/home/eserte/.cpan/build/2015120918/Net-SSL-ExpireDate-1.15-p2fkgm/blib/lib:/home/eserte/.cpan/build/2015120918/Dist-Zilla-Plugin-Rinci-AbstractFromMeta-0.09-q5SaS4/blib/arch:/home/eserte/.cpan/build/2015120918/Dist-Zilla-Plugin-Rinci-AbstractFromMeta-0.09-q5SaS4/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 9196
PERL5_CPAN_IS_RUNNING = 9196
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 9141,9196
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1001/2015120918/cpanreporter_000_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_PARALLEL_SMOKER = yes
SHELL = /bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1001/2015120918
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /bbbike/perl-5.18.2t/bin/perl
$UID/$EUID = 1001 / 1001
$GID = 1001 109 1001
$EGID = 1001 109 1001
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.05
CPAN::Meta 2.150005
Cwd 3.60
ExtUtils::CBuilder 0.280223
ExtUtils::Command 1.18
ExtUtils::Install 2.04
ExtUtils::MakeMaker 7.04
ExtUtils::Manifest 1.68
ExtUtils::ParseXS 3.24
File::Spec 3.60
JSON 2.90
JSON::PP 2.27300
Module::Build 0.4214
Module::Signature 0.78
Parse::CPAN::Meta 1.4414
Test::Harness 3.35
Test::More 1.001014
YAML 1.15
YAML::Syck 1.29
version 0.9912
--
Summary of my perl5 (revision 5 version 18 subversion 2) configuration:
Platform:
osname=linux, osvers=3.2.0-4-amd64, archname=x86_64-linux-thread-multi
uname='linux eserte 3.2.0-4-amd64 #1 smp debian 3.2.57-3 x86_64 gnulinux '
config_args='-ds -e -Dprefix=/opt/perl-5.18.2t -Dusethreads'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2',
cppflags='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='4.7.2', 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 =' -fstack-protector -L/usr/local/lib'
libpth=/usr/local/lib /lib/x86_64-linux-gnu /lib/../lib /usr/lib/x86_64-linux-gnu /usr/lib/../lib /lib /usr/lib
libs=-lnsl -ldb -ldl -lm -lcrypt -lutil -lpthread -lc
perllibs=-lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
libc=, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.13'
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 MULTIPLICITY PERLIO_LAYERS
PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
PERL_PRESERVE_IVUV PERL_SAWAMPERSAND USE_64_BIT_ALL
USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
USE_LOCALE USE_LOCALE_COLLATE USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC USE_PERLIO USE_PERL_ATOF
USE_REENTRANT_API
Built under linux
Compiled at May 14 2014 07:16:29
%ENV:
PERL5LIB="/home/eserte/.cpan/build/2015120918/Mojo-Webqq-1.6.6-TcO_yD/blib/arch:/home/eserte/.cpan/build/2015120918/Mojo-Webqq-1.6.6-TcO_yD/blib/lib:/home/eserte/.cpan/build/2015120918/Net-SSL-ExpireDate-1.15-p2fkgm/blib/arch:/home/eserte/.cpan/build/2015120918/Net-SSL-ExpireDate-1.15-p2fkgm/blib/lib:/home/eserte/.cpan/build/2015120918/Dist-Zilla-Plugin-Rinci-AbstractFromMeta-0.09-q5SaS4/blib/arch:/home/eserte/.cpan/build/2015120918/Dist-Zilla-Plugin-Rinci-AbstractFromMeta-0.09-q5SaS4/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="9196"
PERL5_CPAN_IS_RUNNING="9196"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="9141,9196"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1001/2015120918/cpanreporter_000_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_PARALLEL_SMOKER="yes"
@INC:
/home/eserte/.cpan/build/2015120918/Mojo-Webqq-1.6.6-TcO_yD/blib/arch
/home/eserte/.cpan/build/2015120918/Mojo-Webqq-1.6.6-TcO_yD/blib/lib
/home/eserte/.cpan/build/2015120918/Net-SSL-ExpireDate-1.15-p2fkgm/blib/arch
/home/eserte/.cpan/build/2015120918/Net-SSL-ExpireDate-1.15-p2fkgm/blib/lib
/home/eserte/.cpan/build/2015120918/Dist-Zilla-Plugin-Rinci-AbstractFromMeta-0.09-q5SaS4/blib/arch
/home/eserte/.cpan/build/2015120918/Dist-Zilla-Plugin-Rinci-AbstractFromMeta-0.09-q5SaS4/blib/lib
/opt/perl-5.18.2t/lib/site_perl/5.18.2/x86_64-linux-thread-multi
/opt/perl-5.18.2t/lib/site_perl/5.18.2
/opt/perl-5.18.2t/lib/5.18.2/x86_64-linux-thread-multi
/opt/perl-5.18.2t/lib/5.18.2
.