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'out of date' % len(to_build))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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