Your message dated Fri, 15 Jan 2016 16:07:07 +0000
with message-id <[email protected]>
and subject line Bug#811002: fixed in python-ruffus 2.6.3+dfsg-2
has caused the Debian Bug report #811002,
regarding python-ruffus: FTBFS: sre_constants.error: unbalanced parenthesis at
position 2
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
811002: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811002
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: python-ruffus
Version: 2.6.3+dfsg-1
Severity: serious
Justification: fails to build from source
User: [email protected]
Usertags: ftbfs
X-Debbugs-Cc: [email protected]
Dear Maintainer,
python-ruffus fails to build from source in unstable/amd64:
[..]
Running test_mkdir.py
. Loose cannon!
. Loose cannon!
.
----------------------------------------------------------------------
Ran 3 tests in 2.782s
OK
Running test_posttask_merge.py
..
----------------------------------------------------------------------
Ran 2 tests in 9.936s
OK
Running test_cmdline.py
....
----------------------------------------------------------------------
Ran 4 tests in 0.007s
OK
Running test_graphviz.py
..
----------------------------------------------------------------------
Ran 2 tests in 0.003s
OK
Running test_ruffus_utility_parse_task_arguments.py
.....
----------------------------------------------------------------------
Ran 5 tests in 0.003s
OK
Running test_split_subdivide_checkpointing.py
Run pipeline normally...
Check that running again does nothing. (All up to date).
Running again with forced tasks to generate more files...
Check that running again does nothing. (All up to date).
Running again with forced tasks to generate even more files...
Check that running again does nothing. (All up to date).
. Run pipeline normally...
Check that running again does nothing. (All up to date).
Running again with forced tasks to generate more files...
Check that running again does nothing. (All up to date).
Running again with forced tasks to generate even more files...
Check that running again does nothing. (All up to date).
.
----------------------------------------------------------------------
Ran 2 tests in 4.496s
OK
Running test_pipeline_printout_graph.py
..
----------------------------------------------------------------------
Ran 2 tests in 0.010s
OK
Run pipeline normally...
Run pipeline normally...
Running test_follows_mkdir.py
..
----------------------------------------------------------------------
Ran 2 tests in 1.570s
OK
Running test_N_x_M_and_collate.py
.
OK
.
----------------------------------------------------------------------
Ran 2 tests in 2.158s
OK
OK
Running test_unicode_filenames.py
..
----------------------------------------------------------------------
Ran 2 tests in 1.677s
OK
Running test_subpipeline.py
.
----------------------------------------------------------------------
Ran 1 test in 2.942s
OK
Running test_regex_error_messages.py
............
----------------------------------------------------------------------
Ran 12 tests in 4.090s
OK
Running test_newstyle_regex_error_messages.py
............
----------------------------------------------------------------------
Ran 12 tests in 3.990s
OK
Running test_combinatorics.py
.................
----------------------------------------------------------------------
Ran 17 tests in 8.407s
OK
Running test_newstyle_combinatorics.py
.................
----------------------------------------------------------------------
Ran 17 tests in 8.737s
OK
Running test_job_completion_checksums.py
..................
----------------------------------------------------------------------
Ran 18 tests in 6.896s
OK
Running test_transform_formatter.py
..
----------------------------------------------------------------------
Ran 2 tests in 0.384s
OK
DONE!!!
Running test_file_name_parameters.py
........................
----------------------------------------------------------------------
Ran 24 tests in 2.247s
OK
Running test_with_logger.py
..
----------------------------------------------------------------------
Ran 2 tests in 6.924s
OK
Running script test_with_logger.py
..
----------------------------------------------------------------------
Ran 2 tests in 6.896s
OK
Running test_proxy_logger.py
.
----------------------------------------------------------------------
Ran 1 test in 0.011s
OK
Running test_exceptions.py
..
----------------------------------------------------------------------
Ran 2 tests in 0.794s
OK
Running test_task_file_dependencies.py
.
----------------------------------------------------------------------
Ran 1 test in 0.135s
OK
Running test_task_misc.py
.
----------------------------------------------------------------------
Ran 1 test in 0.001s
OK
Running test_inputs_with_multiple_args_raising_exception.py
. Expected exception thrown 2
Expected exception thrown 2
.
----------------------------------------------------------------------
Ran 2 tests in 0.016s
OK
Running test_collate.py
..
----------------------------------------------------------------------
Ran 2 tests in 1.370s
OK
Running test_empty_files_decorator.py
Warning printed out correctly
.
Warning printed out correctly
.
----------------------------------------------------------------------
Ran 2 tests in 0.257s
OK
Running test_transform_with_no_re_matches.py
Ruffus Version = 2.6.3
Warning printed out correctly
. In Task 'test::test_transform_with_no_re_matches.task_2':
No jobs were run because no file names matched.
Please make sure that the regular expression is correctly specified.
Warning printed out correctly
.
----------------------------------------------------------------------
Ran 2 tests in 0.864s
OK
In Task 'test_transform_with_no_re_matches.task_2':
No jobs were run because no file names matched.
Please make sure that the regular expression is correctly specified.
Running test_transform_inputs.py
..
----------------------------------------------------------------------
Ran 2 tests in 2.081s
OK
Running test_files_decorator.py
..
----------------------------------------------------------------------
Ran 2 tests in 1.875s
OK
Running test_verbosity.py
......
----------------------------------------------------------------------
Ran 6 tests in 0.090s
OK
Running test_transform_add_inputs.py
Ruffus Version = 2.6.3
..
----------------------------------------------------------------------
Ran 2 tests in 1.969s
OK
Running test_split_regex_and_collate.py
Split into 5 files each
Sequences aligned
%Identity calculated
Results recombined
. Split into 5 files each
Sequences aligned
%Identity calculated
Results recombined
.
----------------------------------------------------------------------
Ran 2 tests in 4.194s
OK
Running test_tutorial7.py
.
----------------------------------------------------------------------
Ran 1 test in 1.180s
OK
hooray
hooray again
whoppee again
Running test_ruffus_utility.py
...F..............
======================================================================
FAIL: test_compile_regex (test_ruffus_utility.Test_compile_regex)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/lamby/temp/cdt.20160114185942.aDc70PbmhT/python-ruffus-2.6.3+dfsg/ruffus/ruffus_utility.py",
line 1284, in compile_regex
matching_regex = re.compile(regex.args[0])
sre_constants.error: unbalanced parenthesis at position 2
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/home/lamby/temp/cdt.20160114185942.aDc70PbmhT/python-ruffus-2.6.3+dfsg/ruffus/test/test_ruffus_utility.py",
line 260, in test_compile_regex
compile_regex("Dummy Task", regex(".*)"), Exception, "test1")
Exception: ('Dummy Task', "test1: regular expression regex('.*)') is
malformed\n[sre_constants.error: (unbalanced parenthesis at position 2)]")
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/home/lamby/temp/cdt.20160114185942.aDc70PbmhT/python-ruffus-2.6.3+dfsg/ruffus/test/test_ruffus_utility.py",
line 262, in test_compile_regex
self.assertEqual(e.args, ('Dummy Task', "test1: regular expression
regex('.*)') is malformed\n[sre_constants.error: (unbalanced parenthesis)]"))
AssertionError: Tuples differ: ('Dum[64 chars][sre_constants.error:
(unbalanced parenthesis at position 2)]") != ('Dum[64
chars][sre_constants.error: (unbalanced parenthesis)]")
First differing element 1:
test1: regular expression regex('.*)') is malformed
[sre_constants.error: (unbalanced parenthesis at position 2)]
test1: regular expression regex('.*)') is malformed
[sre_constants.error: (unbalanced parenthesis)]
('Dummy Task',
"test1: regular expression regex('.*)') is malformed\n"
- '[sre_constants.error: (unbalanced parenthesis at position 2)]')
? --------------
+ '[sre_constants.error: (unbalanced parenthesis)]')
----------------------------------------------------------------------
Ran 18 tests in 0.008s
FAILED (failures=1)
debian/rules:28: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 1
make[1]: Leaving directory
'/home/lamby/temp/cdt.20160114185942.aDc70PbmhT/python-ruffus-2.6.3+dfsg'
debian/rules:13: recipe for target 'build' failed
make: *** [build] Error 2
[..]
The full build log is attached.
Regards,
--
,''`.
: :' : Chris Lamb
`. `'` [email protected] / chris-lamb.co.uk
`-
python-ruffus.2.6.3+dfsg-1.unstable.amd64.log.txt.gz
Description: Binary data
--- End Message ---
--- Begin Message ---
Source: python-ruffus
Source-Version: 2.6.3+dfsg-2
We believe that the bug you reported is fixed in the latest version of
python-ruffus, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated python-ruffus package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Fri, 15 Jan 2016 15:15:35 +0100
Source: python-ruffus
Binary: python-ruffus python3-ruffus python-ruffus-doc
Architecture: source all
Version: 2.6.3+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
python-ruffus - Python computation pipeline library widely used in
bioinformatics
python-ruffus-doc - documentation for python-ruffus computation pipeline
library
python3-ruffus - Python3 computation pipeline library widely used in
bioinformatic
Closes: 811002
Changes:
python-ruffus (2.6.3+dfsg-2) unstable; urgency=medium
.
* Fix issue in test when using Python 3.5 (Thanks for the hints to
Dmitry Shachnev <[email protected]>)
Closes: #811002
* Use Debian packaged mathjax (Thanks to Dmitry Shachnev <[email protected]>
for the hint)
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python-ruffus_2.6.3+dfsg-2.dsc
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python-ruffus_2.6.3+dfsg.orig.tar.xz
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python-ruffus_2.6.3+dfsg-2.debian.tar.xz
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python-ruffus-doc_2.6.3+dfsg-2_all.deb
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python-ruffus_2.6.3+dfsg-2_all.deb
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