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Please help tracking down this issue in test suite [Was: Bug#811002: python-ruffus: FTBFS: sre_constants.error: unbalanced parenthesis at position 2]

Started byAndreas Tille <andreas@an3as.eu>
First post2016-01-14 21:50 +0100
Last post2016-01-17 23:50 +0100
Articles 4 — 4 participants

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  Please help tracking down this issue in test suite [Was: Bug#811002:  python-ruffus: FTBFS: sre_constants.error: unbalanced parenthesis at  position 2] Andreas Tille <andreas@an3as.eu> - 2016-01-14 21:50 +0100
    Bug#811002: Please help tracking down this issue in test suite [Was: Bug#811002: python-ruffus: FTBFS: sre_constants.error: unbalanced parenthesis at position 2] Dmitry Shachnev <mitya57@debian.org> - 2016-01-15 11:10 +0100
      Re: Please help tracking down this issue in test suite [Was:  Bug#811002: python-ruffus: FTBFS: sre_constants.error: unbalanced  parenthesis at position 2] Andreas Tille <tille@debian.org> - 2016-01-15 13:00 +0100
      Bug#811002: Please help tracking down this issue in test suite [Was: Bug#811002: python-ruffus: FTBFS: sre_constants.error: unbalanced parenthesis at position 2] Leo Goodstadt 顧維斌 <llewgoodstadt@gmail.com> - 2016-01-17 23:50 +0100

#8098 — Please help tracking down this issue in test suite [Was: Bug#811002: python-ruffus: FTBFS: sre_constants.error: unbalanced parenthesis at position 2]

FromAndreas Tille <andreas@an3as.eu>
Date2016-01-14 21:50 +0100
SubjectPlease help tracking down this issue in test suite [Was: Bug#811002: python-ruffus: FTBFS: sre_constants.error: unbalanced parenthesis at position 2]
Message-ID<qQX0e-3S8-13@gated-at.bofh.it>
Hi,

I'm forwarding this issue of the test suite to upstream and Debian
Python mailing list since I admit I have no idea what might be wrong
here.

Any help is welcome

     Andreas.

----- Forwarded message from Chris Lamb <lamby@debian.org> -----

Date: Thu, 14 Jan 2016 18:04:32 +0000
From: Chris Lamb <lamby@debian.org>
To: submit@bugs.debian.org
Subject: Bug#811002: python-ruffus: FTBFS: sre_constants.error: unbalanced parenthesis at position 2
X-Debian-PR-Message: report 811002
X-Debian-PR-Package: src:python-ruffus
X-Debian-PR-Keywords: 
X-Debian-PR-Source: python-ruffus

Source: python-ruffus
Version: 2.6.3+dfsg-1
Severity: serious
Justification: fails to build from source
User: reproducible-builds@lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-builds@lists.alioth.debian.org

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
     `. `'`      lamby@debian.org / chris-lamb.co.uk
       `-


_______________________________________________
Debian-med-packaging mailing list
Debian-med-packaging@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging


----- End forwarded message -----

-- 
http://fam-tille.de

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#8100 — Bug#811002: Please help tracking down this issue in test suite [Was: Bug#811002: python-ruffus: FTBFS: sre_constants.error: unbalanced parenthesis at position 2]

FromDmitry Shachnev <mitya57@debian.org>
Date2016-01-15 11:10 +0100
SubjectBug#811002: Please help tracking down this issue in test suite [Was: Bug#811002: python-ruffus: FTBFS: sre_constants.error: unbalanced parenthesis at position 2]
Message-ID<qR9kK-4iA-21@gated-at.bofh.it>
In reply to#8098

[Multipart message — attachments visible in raw view] — view raw

Hi Andreas,

On Fri, Jan 15, 2016 at 10:15:14AM +0100, Andreas Tille wrote:
> Hmmm, I think I misunderstood your hint since my attempt to fix the
> issue[1] did not worked but rather endet up in:
>
> [...]
>
> What am I doing wrong?

Now you are getting an error with Python 3.4 which doesn't have this change :)

How about something like this?

    self.assertEqual(e.args[0], 'Dummy Task')
    self.assertIn("test1: regular expression regex('.*)') is malformed\n[sre_constants.error: (unbalanced parenthesis", e.args[1])

--
Dmitry Shachnev

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#8101 — Re: Please help tracking down this issue in test suite [Was: Bug#811002: python-ruffus: FTBFS: sre_constants.error: unbalanced parenthesis at position 2]

FromAndreas Tille <tille@debian.org>
Date2016-01-15 13:00 +0100
SubjectRe: Please help tracking down this issue in test suite [Was: Bug#811002: python-ruffus: FTBFS: sre_constants.error: unbalanced parenthesis at position 2]
Message-ID<qRbcT-5yd-19@gated-at.bofh.it>
In reply to#8100
Hi Dmitry,

On Fri, Jan 15, 2016 at 12:56:50PM +0300, Dmitry Shachnev wrote:
> 
> Now you are getting an error with Python 3.4 which doesn't have this change :)

This is what I suspected.
 
> How about something like this?
> 
>     self.assertEqual(e.args[0], 'Dummy Task')
>     self.assertIn("test1: regular expression regex('.*)') is malformed\n[sre_constants.error: (unbalanced parenthesis", e.args[1])

Thanks - this works nicely.  Patch commited to Git.

Before I upload I would like to ask for some proper advise how to
deal with

   privacy-breach-uses-embedded-file ... You may use libjs-mathjax package.

lintian errors.  I have done this in d/rules by

   find debian/$(docpkg)/usr/share/doc/$(docpkg)/html -type f -name "*.html" -exec sed -i 's?http://cdn.mathjax.org/mathjax/latest/?/usr/share/javascript/mathjax?g' \{\} \;

which is not reliable since probably due to some change in sphinx the
expression has changed.  I wonder whether I could elegantly patch the
file doc/conf.py which has:

# Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo',
              'sphinx.ext.coverage', 'sphinx.ext.pngmath', 'sphinx.ext.mathjax', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode']


Is there anything I could do here to use local mathjax from beginning
instead of patching the resulting docs afterwards?

Kind regards

         Andreas.

-- 
http://fam-tille.de

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#8102 — Bug#811002: Please help tracking down this issue in test suite [Was: Bug#811002: python-ruffus: FTBFS: sre_constants.error: unbalanced parenthesis at position 2]

FromLeo Goodstadt 顧維斌 <llewgoodstadt@gmail.com>
Date2016-01-17 23:50 +0100
SubjectBug#811002: Please help tracking down this issue in test suite [Was: Bug#811002: python-ruffus: FTBFS: sre_constants.error: unbalanced parenthesis at position 2]
Message-ID<qS4j0-jf-5@gated-at.bofh.it>
In reply to#8100

[Multipart message — attachments visible in raw view] — view raw

I am the developer of ruffus. I am sorry that I have only just see this. I
will get the patches in Ruffus itself to allow the tests to run on 3.5.
Thanks again.
Leo

On 15 January 2016 at 09:56, Dmitry Shachnev <mitya57@debian.org> wrote:

> Hi Andreas,
>
> On Fri, Jan 15, 2016 at 10:15:14AM +0100, Andreas Tille wrote:
> > Hmmm, I think I misunderstood your hint since my attempt to fix the
> > issue[1] did not worked but rather endet up in:
> >
> > [...]
> >
> > What am I doing wrong?
>
> Now you are getting an error with Python 3.4 which doesn't have this
> change :)
>
> How about something like this?
>
>     self.assertEqual(e.args[0], 'Dummy Task')
>     self.assertIn("test1: regular expression regex('.*)') is
> malformed\n[sre_constants.error: (unbalanced parenthesis", e.args[1])
>
> --
> Dmitry Shachnev
>

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