[Debian-med-packaging] Failed tests in Ruffus
Andreas Tille
andreas at an3as.eu
Wed Feb 11 21:54:54 UTC 2015
Hi Leo,
I'm writing you on behalf of the Debian Med team who tries to package
biological and medical software for official Debian. We also have
packaged several biological development tools and are working on
Ruffus as well:
http://blends.debian.org/med/tasks/bio-dev#python-ruffus
When doing the packaging we are also trying to run the available test
suites. I did so by running run-unit-test-wrapper from here
http://anonscm.debian.org/cgit/debian-med/python-ruffus.git/tree/debian/tests
Unfortunately not all tests are passing. I attached the output to this
mail. I would be happy, if you could have a look and tell us, whether
the tests are known to fail or if something is wrong in our setup.
Kind regards
Andreas.
--
http://fam-tille.de
-------------- next part --------------
------------> python2.7 test_N_x_M_and_collate.py ===> OK
------------> python2.7 test_active_if.py ===> OK
------------> python2.7 test_branching_dependencies.py ===> OK
------------> python2.7 test_cmdline.py ===> OK
------------> python2.7 test_collate.py ===> OK
------------> python2.7 test_combinatorics.py ===> OK
------------> python2.7 test_ctrl_c_exceptions.py ===> OK
---> skipping test_drmaa.py since no cluster is setup automatically <---
------------> python2.7 test_empty_files_decorator.py ===> OK
------------> python2.7 test_exceptions.py ===> OK
------------> python2.7 test_file_name_parameters.py ===> failed
................FF......
======================================================================
FAIL: test_glob (__main__.Test_split_param_factory)
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_file_name_parameters.py", line 491, in test_glob
'DIR/ruffus_version.py'
AssertionError: Tuples differ: (['DIR/f0.output', 'DIR/f0.tes... != (['DIR/f0.output', 'DIR/f0.tes...
First differing element 1:
[]
['DIR/adjacent_pairs_iterate.py', 'DIR/ruffus_exceptions.py', 'DIR/ruffus_utility.py', 'DIR/ruffus_version.py']
(['DIR/f0.output',
'DIR/f0.test',
'DIR/f1.output',
'DIR/f1.test',
'DIR/f2.output',
'DIR/f2.test'],
- [])
+ ['DIR/adjacent_pairs_iterate.py',
+ 'DIR/ruffus_exceptions.py',
+ 'DIR/ruffus_utility.py',
+ 'DIR/ruffus_version.py'])
======================================================================
FAIL: test_tasks (__main__.Test_split_param_factory)
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_file_name_parameters.py", line 529, in test_tasks
6))
AssertionError: Tuples differ: ([5, ['output4.test', 'output.... != ([5, ['output4.test', 'output....
First differing element 1:
['extra.file']
['DIR/adjacent_pairs_iterate.py', 'DIR/ruffus_exceptions.py', 'DIR/ruffus_utility.py', 'DIR/ruffus_version.py', 'extra.file']
([5,
['output4.test', 'output.ignored'],
'output1.test',
'output2.test',
'output3.test',
'output.ignored',
(2, 'output5.test'),
'DIR/f0.output',
'DIR/f0.test',
'DIR/f1.output',
'DIR/f1.test',
'DIR/f2.output',
'DIR/f2.test'],
+ ['DIR/adjacent_pairs_iterate.py',
+ 'DIR/ruffus_exceptions.py',
+ 'DIR/ruffus_utility.py',
+ 'DIR/ruffus_version.py',
- ['extra.file'],
? ^
+ 'extra.file'],
? ^
6)
----------------------------------------------------------------------
Ran 24 tests in 2.152s
FAILED (failures=2)
------------> python2.7 test_files_decorator.py ===> OK
------------> python2.7 test_files_post_merge.py ===> OK
------------> python2.7 test_filesre_combine.py ===> OK
------------> python2.7 test_filesre_split_and_combine.py ===> OK
------------> python2.7 test_follows_mkdir.py ===> OK
------------> python2.7 test_graphviz.py ===> OK
------------> python2.7 test_inputs_with_multiple_args_raising_exception.py ===> OK
------------> python2.7 test_job_completion_checksums.py ===> OK
------------> python2.7 test_job_history_with_exceptions.py ===> OK
------------> python2.7 test_mkdir.py ===> OK
------------> python2.7 test_pausing.py ===> OK
------------> python2.7 test_regex_error_messages.py ===> OK
------------> python2.7 test_ruffus_utility.py ===> failed
................F.
======================================================================
FAIL: test_shorten_filenames_encoder (__main__.Test_shorten_filenames_encoder)
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_ruffus_utility.py", line 938, in test_shorten_filenames_encoder
'../test1/something.py')
AssertionError: '/tmp/test1/something.py' != '../test1/something.py'
----------------------------------------------------------------------
Ran 18 tests in 0.004s
FAILED (failures=1)
------------> python2.7 test_softlink_uptodate.py ===> OK
------------> python2.7 test_split_and_combine.py ===> OK
------------> python2.7 test_split_regex_and_collate.py ===> OK
------------> python2.7 test_task_file_dependencies.py ===> OK
------------> python2.7 test_task_misc.py ===> OK
------------> python2.7 test_transform_add_inputs.py ===> failed
Ruffus Version = 2.5
F
======================================================================
FAIL: test_task (__main__.Test_task)
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_transform_add_inputs.py", line 212, in test_task
self.assertTrue(correct_output == real_output_str)
AssertionError: False is not true
----------------------------------------------------------------------
Ran 1 test in 1.449s
FAILED (failures=1)
------------> python2.7 test_transform_inputs.py ===> failed
Ruffus Version = 2.5
F
======================================================================
FAIL: test_task (__main__.Test_task)
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_transform_inputs.py", line 196, in test_task
self.assertTrue(correct_output == real_output)
AssertionError: False is not true
----------------------------------------------------------------------
Ran 1 test in 1.517s
FAILED (failures=1)
------------> python2.7 test_transform_with_no_re_matches.py ===> OK
------------> python2.7 test_tutorial7.py ===> OK
------------> python2.7 test_unicode_filenames.py ===> OK
------------> python2.7 test_verbosity.py ===> failed
F.....
======================================================================
FAIL: test_printout_abbreviated_path0 (__main__.Test_verbosity)
Input file exists, output doesn't exist
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_verbosity.py", line 117, in test_printout_abbreviated_path0
self.assertTrue('/ruffus/test/job2.b.start]' in ret)
AssertionError: False is not true
----------------------------------------------------------------------
Ran 6 tests in 0.028s
FAILED (failures=1)
------------> python3.4 test_N_x_M_and_collate.py ===> OK
------------> python3.4 test_active_if.py ===> OK
------------> python3.4 test_branching_dependencies.py ===> OK
------------> python3.4 test_cmdline.py ===> OK
------------> python3.4 test_collate.py ===> OK
------------> python3.4 test_combinatorics.py ===> OK
------------> python3.4 test_ctrl_c_exceptions.py ===> OK
---> skipping test_drmaa.py since no cluster is setup automatically <---
------------> python3.4 test_empty_files_decorator.py ===> OK
------------> python3.4 test_exceptions.py ===> OK
------------> python3.4 test_file_name_parameters.py ===> failed
................FF......
======================================================================
FAIL: test_glob (__main__.Test_split_param_factory)
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_file_name_parameters.py", line 491, in test_glob
'DIR/ruffus_version.py'
AssertionError: Tuples differ: (['DI[90 chars]'], []) != (['DI[90 chars]'], ['DIR/adjacent_pairs_iterate.py', 'DIR/ruf[65 chars]py'])
First differing element 1:
[]
['DIR/adjacent_pairs_iterate.py', 'DIR/ruffus_exceptions.py', 'DIR/ruffus_utility.py', 'DIR/ruffus_version.py']
(['DIR/f0.output',
'DIR/f0.test',
'DIR/f1.output',
'DIR/f1.test',
'DIR/f2.output',
'DIR/f2.test'],
- [])
+ ['DIR/adjacent_pairs_iterate.py',
+ 'DIR/ruffus_exceptions.py',
+ 'DIR/ruffus_utility.py',
+ 'DIR/ruffus_version.py'])
======================================================================
FAIL: test_tasks (__main__.Test_split_param_factory)
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_file_name_parameters.py", line 529, in test_tasks
6))
AssertionError: Tuples differ: ([5, [217 chars]], ['extra.file'], 6) != ([5, [217 chars]], ['DIR/adjacent_pairs_iterate.py', 'DIR/ruff[81 chars]], 6)
First differing element 1:
['extra.file']
['DIR/adjacent_pairs_iterate.py', 'DIR/ruffus_exceptions.py', 'DIR/ruffus_utility.py', 'DIR/ruffus_version.py', 'extra.file']
([5,
['output4.test', 'output.ignored'],
'output1.test',
'output2.test',
'output3.test',
'output.ignored',
(2, 'output5.test'),
'DIR/f0.output',
'DIR/f0.test',
'DIR/f1.output',
'DIR/f1.test',
'DIR/f2.output',
'DIR/f2.test'],
+ ['DIR/adjacent_pairs_iterate.py',
+ 'DIR/ruffus_exceptions.py',
+ 'DIR/ruffus_utility.py',
+ 'DIR/ruffus_version.py',
- ['extra.file'],
? ^
+ 'extra.file'],
? ^
6)
----------------------------------------------------------------------
Ran 24 tests in 2.171s
FAILED (failures=2)
------------> python3.4 test_files_decorator.py ===> OK
------------> python3.4 test_files_post_merge.py ===> OK
------------> python3.4 test_filesre_combine.py ===> OK
------------> python3.4 test_filesre_split_and_combine.py ===> OK
------------> python3.4 test_follows_mkdir.py ===> OK
------------> python3.4 test_graphviz.py ===> OK
------------> python3.4 test_inputs_with_multiple_args_raising_exception.py ===> OK
------------> python3.4 test_job_completion_checksums.py ===> OK
------------> python3.4 test_job_history_with_exceptions.py ===> OK
------------> python3.4 test_mkdir.py ===> OK
------------> python3.4 test_pausing.py ===> OK
------------> python3.4 test_regex_error_messages.py ===> OK
------------> python3.4 test_ruffus_utility.py ===> failed
................F.
======================================================================
FAIL: test_shorten_filenames_encoder (__main__.Test_shorten_filenames_encoder)
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_ruffus_utility.py", line 938, in test_shorten_filenames_encoder
'../test1/something.py')
AssertionError: '/tmp/test1/something.py' != '../test1/something.py'
- /tmp/test1/something.py
? ^^^^
+ ../test1/something.py
? ^^
----------------------------------------------------------------------
Ran 18 tests in 0.005s
FAILED (failures=1)
------------> python3.4 test_softlink_uptodate.py ===> OK
------------> python3.4 test_split_and_combine.py ===> OK
------------> python3.4 test_split_regex_and_collate.py ===> OK
------------> python3.4 test_task_file_dependencies.py ===> OK
------------> python3.4 test_task_misc.py ===> OK
------------> python3.4 test_transform_add_inputs.py ===> failed
Ruffus Version = 2.5
F
======================================================================
FAIL: test_task (__main__.Test_task)
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_transform_add_inputs.py", line 212, in test_task
self.assertTrue(correct_output == real_output_str)
AssertionError: False is not true
----------------------------------------------------------------------
Ran 1 test in 1.570s
FAILED (failures=1)
------------> python3.4 test_transform_inputs.py ===> failed
Ruffus Version = 2.5
F
======================================================================
FAIL: test_task (__main__.Test_task)
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_transform_inputs.py", line 196, in test_task
self.assertTrue(correct_output == real_output)
AssertionError: False is not true
----------------------------------------------------------------------
Ran 1 test in 1.737s
FAILED (failures=1)
------------> python3.4 test_transform_with_no_re_matches.py ===> OK
------------> python3.4 test_tutorial7.py ===> OK
------------> python3.4 test_unicode_filenames.py ===> OK
------------> python3.4 test_verbosity.py ===> failed
F.....
======================================================================
FAIL: test_printout_abbreviated_path0 (__main__.Test_verbosity)
Input file exists, output doesn't exist
----------------------------------------------------------------------
Traceback (most recent call last):
File "test_verbosity.py", line 117, in test_printout_abbreviated_path0
self.assertTrue('/ruffus/test/job2.b.start]' in ret)
AssertionError: False is not true
----------------------------------------------------------------------
Ran 6 tests in 0.030s
FAILED (failures=1)
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