Hi,

At first, I suggest you should use newer version of sphinx.
And in such case you will get more information with using -vvvv option like:
make html SPHINXOPTS=-vvvv   #unix

Regards,
--
Takayuki SHIMIZUKAWA
http://about.me/shimizukawa

2015年9月11日(金) 0:40 Nick Schurch <[email protected]>:

> ok, I think I found the problem. Having a function with the same name as
> the module appears to break things quite a lot. Change function name,
> problem fixed...
>
>
> On Wednesday, 9 September 2015 23:36:36 UTC+1, Nick Schurch wrote:
>>
>> When building a set of sphinx documentation for a project, I am getting
>> the following traceback:
>>
>> # Sphinx version: 1.2b2
>> # Python version: 2.7.3
>> # Docutils version: 0.11 release
>> # Jinja2 version: 2.7.1
>> Traceback (most recent call last):
>>   File
>> "/cluster/gjb_lab/software/centos6.3/opt/python/2.7.3/lib/python2.7/site-packages/sphinx/cmdline.py",
>> line 247, in main
>>     app.build(force_all, filenames)
>>   File
>> "/cluster/gjb_lab/software/centos6.3/opt/python/2.7.3/lib/python2.7/site-packages/sphinx/application.py",
>> line 212, in build
>>     self.builder.build_update()
>>   File
>> "/cluster/gjb_lab/software/centos6.3/opt/python/2.7.3/lib/python2.7/site-packages/sphinx/builders/__init__.py",
>> line 214, in build_update
>>     'out of date' % len(to_build))
>>   File
>> "/cluster/gjb_lab/software/centos6.3/opt/python/2.7.3/lib/python2.7/site-packages/sphinx/builders/__init__.py",
>> line 234, in build
>>     purple, length):
>>   File
>> "/cluster/gjb_lab/software/centos6.3/opt/python/2.7.3/lib/python2.7/site-packages/sphinx/builders/__init__.py",
>> line 142, in status_iterator
>>     self.info(s, nonl=1)
>>   File
>> "/cluster/gjb_lab/software/centos6.3/opt/python/2.7.3/lib/python2.7/site-packages/sphinx/application.py",
>> line 252, in info
>>     self._log(message, self._status, nonl)
>>   File
>> "/cluster/gjb_lab/software/centos6.3/opt/python/2.7.3/lib/python2.7/site-packages/sphinx/application.py",
>> line 235, in _log
>>     wfile.flush()
>> IOError: [Errno 9] Bad file descriptor
>>
>> The culprit would appear to be a .. automodule:: call for a module
>> called sort_and_index_bams.py. Unfortunately the error doesn't seem to give
>> me any real information at all to go on about what exactly the problem is.
>> The docs build fine without the automodule call but with the autofunction
>> calls for the two functions in this module, and removing the main docstring
>> and trying to rebuild the docs with the automodule call in causes the same
>> error. Anyone have any insights?
>>
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