On OS X 10.7, building the documentation for 2.18.1, I get the following failure for the man file (the html target succeeds):
make -j1 -C docs man
sphinx-build -b man -d _build/doctrees . _build/man
Making output directory...
Running Sphinx v1.1.3
loading pickled environment... done
loading intersphinx inventory from http://docs.python.org/objects.inv...
building [man]: all manpages
updating environment: 0 added, 48 changed, 0 removed
reading sources... [100%] index
/sw/build.build/bedtools-2.18.1-1/bedtools2/docs/content/bedtools-suite.rst:16: WARNING: toctree contains reference to nonexisting document u'content/tools/igv'
/sw/build.build/bedtools-2.18.1-1/bedtools2/docs/content/general-usage.rst:25: WARNING: Enumerated list ends without a blank line; unexpected unindent.
[ a bunch more warnings ]
/sw/build.build/bedtools-2.18.1-1/bedtools2/docs/content/general-usage.rst:166: ERROR: Unexpected indentation.
/sw/build.build/bedtools-2.18.1-1/bedtools2/docs/content/general-usage.rst:184: ERROR: Unexpected indentation.
/sw/build.build/bedtools-2.18.1-1/bedtools2/docs/content/general-usage.rst:161: ERROR: Unknown target name: "aza-z0-9".
/sw/build.build/bedtools-2.18.1-1/bedtools2/docs/content/related-tools.rst:3: WARNING: Duplicate explicit target name: "here".
=======================================================================================
``-both`` Report both the count of hits and the fraction covered from the annotation files
=======================================================================================
/sw/build.build/bedtools-2.18.1-1/bedtools2/docs/content/tools/bamtobed.rst:149: ERROR: Unexpected indentation.
/sw/build.build/bedtools-2.18.1-1/bedtools2/docs/content/tools/bed12tobed6.rst:14: ERROR: Unexpected indentation.
/sw/build.build/bedtools-2.18.1-1/bedtools2/docs/content/tools/bed12tobed6.rst:30: ERROR: Unexpected indentation.
/sw/build.build/bedtools-2.18.1-1/bedtools2/docs/content/tools/bedtobam.rst:12: ERROR: Unexpected indentation.
/sw/build.build/bedtools-2.18.1-1/bedtools2/docs/content/tools/bedtobam.rst:30: ERROR: Unexpected indentation.
/sw/build.build/bedtools-2.18.1-1/bedtools2/docs/content/tools/bedtobam.rst:57: ERROR: Unexpected indentation.
[ tons more similar errors ]
/sw/build.build/bedtools-2.18.1-1/bedtools2/docs/content/tools/unionbedg.rst:148: ERROR: Unexpected indentation.
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
writing... bedtools.1 { content/overview content/installation content/quick-start content/general-usage content/bedtools-suite content/tools/annotate content/tools/bamtobed content/tools/bamtofastq content/tools/bed12tobed6 content/tools/bedpetobam content/tools/bedtobam content/tools/closest content/tools/cluster content/tools/complement content/tools/coverage content/tools/expand content/tools/flank content/tools/genomecov content/tools/getfasta content/tools/groupby content/tools/intersect content/tools/jaccard content/tools/links content/tools/makewindows content/tools/map content/tools/maskfasta content/tools/merge content/tools/multicov content/tools/multiinter content/tools/nuc content/tools/overlap content/tools/pairtobed content/tools/pairtopair content/tools/random content/tools/reldist content/tools/shuffle content/tools/slop content/tools/sort content/tools/subtract content/tools/tag content/tools/unionbedg content/tools/window content/example-usage content/advanced-usage content/tips-and-tricks content/faq content/related-tools }
Exception occurred:
File "/sw/lib/python2.7/site-packages/docutils/writers/manpage.py", line 865, in dedent
self._indent.pop()
IndexError: pop from empty list
# Sphinx version: 1.1.3
# Python version: 2.7.6
# Docutils version: 0.10 release
# Jinja2 version: 2.7.1
Traceback (most recent call last):
File "/sw/lib/python2.7/site-packages/sphinx/cmdline.py", line 189, in main
app.build(force_all, filenames)
File "/sw/lib/python2.7/site-packages/sphinx/application.py", line 204, in build
self.builder.build_update()
File "/sw/lib/python2.7/site-packages/sphinx/builders/__init__.py", line 191, in build_update
self.build(['__all__'], to_build)
File "/sw/lib/python2.7/site-packages/sphinx/builders/__init__.py", line 252, in build
self.write(docnames, list(updated_docnames), method)
File "/sw/lib/python2.7/site-packages/sphinx/builders/manpage.py", line 88, in write
docwriter.write(largetree, destination)
File "/sw/lib/python2.7/site-packages/docutils/writers/__init__.py", line 80, in write
self.translate()
File "/sw/lib/python2.7/site-packages/sphinx/writers/manpage.py", line 35, in translate
self.document.walkabout(visitor)
File "/sw/lib/python2.7/site-packages/docutils/nodes.py", line 174, in walkabout
if child.walkabout(visitor):
File "/sw/lib/python2.7/site-packages/docutils/nodes.py", line 174, in walkabout
if child.walkabout(visitor):
File "/sw/lib/python2.7/site-packages/docutils/nodes.py", line 174, in walkabout
if child.walkabout(visitor):
File "/sw/lib/python2.7/site-packages/docutils/nodes.py", line 174, in walkabout
if child.walkabout(visitor):
File "/sw/lib/python2.7/site-packages/docutils/nodes.py", line 174, in walkabout
if child.walkabout(visitor):
File "/sw/lib/python2.7/site-packages/docutils/nodes.py", line 174, in walkabout
if child.walkabout(visitor):
File "/sw/lib/python2.7/site-packages/docutils/nodes.py", line 174, in walkabout
if child.walkabout(visitor):
File "/sw/lib/python2.7/site-packages/docutils/nodes.py", line 187, in walkabout
visitor.dispatch_departure(self)
File "/sw/lib/python2.7/site-packages/docutils/nodes.py", line 1640, in dispatch_departure
return method(node)
File "/sw/lib/python2.7/site-packages/docutils/writers/manpage.py", line 411, in depart_admonition
self.depart_block_quote(node)
File "/sw/lib/python2.7/site-packages/docutils/writers/manpage.py", line 449, in depart_block_quote
self.dedent()
File "/sw/lib/python2.7/site-packages/docutils/writers/manpage.py", line 865, in dedent
self._indent.pop()
IndexError: pop from empty list