Documentation problems

[Andrew Mathas]

Hi,

I wanted to check if I am doing something wrong because I am frequently having problems building the sage documentation when I want to check it for patches that I am writing or reviewing. My problem is that large sections of the reference guide, for example, regularly fail to build. I think that the problem may be that building the documentation does not play well with the (sage-combinat) patch queue, although I have no real evidence for this. Equally likely, it is something that I a doing or not doing.

To build the documentation I typically use something like

sage -b && sage --docbuild reference html

Often this works without a hitch and just as often I get numerous warnings like

categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/commutative_additive_monoids'

and the corresponding pages are missing. In such cases, sage reports that the documentation
builds "successfully" but the corresponding pages are missing.

Is there anything obvious that I am doing wrong?  Just in case it helps, I'll
put the output of a "successful" documentation build failure below.

Cheers,
Andrew

----
MacAndrew-62-(sage)-combinat: sage --docbuild reference html
sphinx-build -b html -d /usr/local/src/sage/sage-5.4/devel/sage/doc/output/doctrees/en/reference    /usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference /usr/local/src/sage/sage-5.4/devel/sage/doc/output/html/en/reference
Running Sphinx v1.1.2
loading pickled environment... done
loading intersphinx inventory from /usr/local/src/sage/sage-5.4/devel/sage/doc/common/python.inv...
building [html]: targets for 0 source files that are out of date
updating environment: 0 added, 14 changed, 0 removed
reading sources... [  7%] categories
reading sources... [ 14%] combinat/algebra
reading sources... [ 21%] combinat/developer
reading sources... [ 28%] combinat/index
reading sources... [ 35%] combinat/root_systems
reading sources... [ 42%] combinat/tableaux
reading sources... [ 50%] combinat/words
reading sources... [ 57%] databases
reading sources... [ 64%] libs
reading sources... [ 71%] modules
reading sources... [ 78%] parallel
reading sources... [ 85%] plotting
reading sources... [ 92%] rings_standard
reading sources... [100%] structure

/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:6: WARNING: toctree contains reference to nonexisting document u'sage/categories/primer'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:6: WARNING: toctree contains reference to nonexisting document u'sage/categories/tutorial'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:6: WARNING: toctree contains reference to nonexisting document u'sage/categories/category'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:6: WARNING: toctree contains reference to nonexisting document u'sage/categories/category_types'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:6: WARNING: toctree contains reference to nonexisting document u'sage/categories/map'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:6: WARNING: toctree contains reference to nonexisting document u'sage/categories/homset'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:6: WARNING: toctree contains reference to nonexisting document u'sage/categories/morphism'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:6: WARNING: toctree contains reference to nonexisting document u'sage/categories/functor'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:6: WARNING: toctree contains reference to nonexisting document u'sage/categories/pushout'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:22: WARNING: toctree contains reference to nonexisting document u'sage/categories/covariant_functorial_construction'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:22: WARNING: toctree contains reference to nonexisting document u'sage/categories/cartesian_product'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:22: WARNING: toctree contains reference to nonexisting document u'sage/categories/tensor'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:22: WARNING: toctree contains reference to nonexisting document u'sage/categories/dual'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:22: WARNING: toctree contains reference to nonexisting document u'sage/categories/algebra_functor'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:22: WARNING: toctree contains reference to nonexisting document u'sage/categories/subquotients'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:22: WARNING: toctree contains reference to nonexisting document u'sage/categories/quotients'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:22: WARNING: toctree contains reference to nonexisting document u'sage/categories/subobjects'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:22: WARNING: toctree contains reference to nonexisting document u'sage/categories/isomorphic_objects'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:22: WARNING: toctree contains reference to nonexisting document u'sage/categories/realizations'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:22: WARNING: toctree contains reference to nonexisting document u'sage/categories/with_realizations'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/additive_magmas'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/algebra_ideals'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/algebra_modules'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/algebras'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/algebras_with_basis'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/bialgebras'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/bialgebras_with_basis'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/bimodules'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/classical_crystals'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/coalgebras'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/coalgebras_with_basis'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/commutative_additive_groups'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/commutative_additive_monoids'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/commutative_additive_semigroups'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/commutative_algebra_ideals'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/commutative_algebras'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/commutative_ring_ideals'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/commutative_rings'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/coxeter_groups'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/crystals'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/division_rings'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/domains'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/enumerated_sets'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/euclidean_domains'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/fields'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/finite_crystals'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/finite_coxeter_groups'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/finite_dimensional_algebras_with_basis'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/finite_dimensional_bialgebras_with_basis'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/finite_dimensional_coalgebras_with_basis'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/finite_dimensional_hopf_algebras_with_basis'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/finite_dimensional_modules_with_basis'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/finite_enumerated_sets'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/finite_fields'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/finite_posets'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/finite_lattice_posets'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/finite_monoids'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/finite_permutation_groups'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/finite_semigroups'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/finite_weyl_groups'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/gcd_domains'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/graded_algebras'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/graded_algebras_with_basis'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/graded_bialgebras'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/graded_bialgebras_with_basis'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/graded_coalgebras'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/graded_coalgebras_with_basis'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/graded_hopf_algebras'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/graded_hopf_algebras_with_basis'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/graded_modules'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/graded_modules_with_basis'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/groupoid'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/groups'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/g_sets'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/hecke_modules'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/highest_weight_crystals'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/hopf_algebras'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/hopf_algebras_with_basis'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/infinite_enumerated_sets'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/integral_domains'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/lattice_posets'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/left_modules'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/magmas'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/matrix_algebras'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/modular_abelian_varieties'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/modules'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/modules_with_basis'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/monoid_algebras'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/monoids'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/number_fields'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/objects'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/partially_ordered_monoids'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/posets'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/pointed_sets'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/principal_ideal_domains'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/quotient_fields'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/right_modules'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/ring_ideals'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/rings'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/rngs'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/schemes'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/semigroups'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/semirings'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/sets_cat'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/unique_factorization_domains'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/vector_spaces'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:44: WARNING: toctree contains reference to nonexisting document u'sage/categories/weyl_groups'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:138: WARNING: toctree contains reference to nonexisting document u'sage/categories/facade_sets'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:146: WARNING: toctree contains reference to nonexisting document u'sage/categories/examples/algebras_with_basis'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:146: WARNING: toctree contains reference to nonexisting document u'sage/categories/examples/commutative_additive_monoids'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:146: WARNING: toctree contains reference to nonexisting document u'sage/categories/examples/commutative_additive_semigroups'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:146: WARNING: toctree contains reference to nonexisting document u'sage/categories/examples/coxeter_groups'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:146: WARNING: toctree contains reference to nonexisting document u'sage/categories/examples/crystals'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:146: WARNING: toctree contains reference to nonexisting document u'sage/categories/examples/finite_coxeter_groups'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:146: WARNING: toctree contains reference to nonexisting document u'sage/categories/examples/finite_enumerated_sets'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:146: WARNING: toctree contains reference to nonexisting document u'sage/categories/examples/finite_monoids'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:146: WARNING: toctree contains reference to nonexisting document u'sage/categories/examples/finite_semigroups'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:146: WARNING: toctree contains reference to nonexisting document u'sage/categories/examples/finite_weyl_groups'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:146: WARNING: toctree contains reference to nonexisting document u'sage/categories/examples/hopf_algebras_with_basis'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:146: WARNING: toctree contains reference to nonexisting document u'sage/categories/examples/infinite_enumerated_sets'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:146: WARNING: toctree contains reference to nonexisting document u'sage/categories/examples/monoids'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:146: WARNING: toctree contains reference to nonexisting document u'sage/categories/examples/semigroups'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:146: WARNING: toctree contains reference to nonexisting document u'sage/categories/examples/semigroups_cython'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:146: WARNING: toctree contains reference to nonexisting document u'sage/categories/examples/sets_cat'
/usr/local/src/sage/sage-5.4/devel/sage/doc/en/reference/categories.rst:146: WARNING: toctree contains reference to nonexisting document u'sage/categories/examples/with_realizations'
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looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  6%] categories
writing output... [ 13%] combinat/algebra
writing output... [ 20%] combinat/developer
writing output... [ 26%] combinat/index
writing output... [ 33%] combinat/root_systems
writing output... [ 40%] combinat/tableaux
writing output... [ 46%] combinat/words
writing output... [ 53%] databases
writing output... [ 60%] index
writing output... [ 66%] libs
writing output... [ 73%] modules
writing output... [ 80%] parallel
writing output... [ 86%] plotting
writing output... [ 93%] rings_standard
writing output... [100%] structure

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writing additional files... genindex py-modindex search
copying static files... done
dumping search index... done
dumping object inventory... done
build succeeded, 1056 warnings.
Build finished.  The built documents can be found in /usr/local/src/sage/sage-5.4/devel/sage/doc/output/html/en/reference

[Travis Scrimshaw]

Hey Andrew,

   Short version, the docbuild does not automatically update files as we expect it to. The surefire way to make sure the doc builds cleanly is to nuke the output/html directory and then rebuild the doc. I suspect we could delete key files in the output/html and get a partial rebuild. From what I recall, merely changing .rst (or touching them) won't rebuild the corresponding sections of the doc, be nice if it did...

Best,

Travis

[Nicolas M. Thiery]

On Fri, Nov 16, 2012 at 08:29:16PM -0800, Andrew Mathas wrote:
> To build the documentation I typically use something like
> sage -b && sage --docbuild reference html
> Often this works without a hitch and just as often I get numerous warnings
> like
> categories.rst:44: WARNING: toctree contains reference to nonexisting
> document u'sage/categories/commutative_additive_monoids'
> and the corresponding pages are missing. In such cases, sage reports that
> the documentation
> builds "successfully" but the corresponding pages are missing.

Yeah, the documentation builder does not play nicely with applying and
unapplying patches, as it does not keep track properly of added /
removed files. As Travis said, the only really safe option is to nuke
the doc output.

Cheers,
Nicolas
--
Nicolas M. Thi�ry "Isil" <nth...@users.sf.net>
http://Nicolas.Thiery.name/

[John H Palmieri]

On Friday, November 30, 2012 8:11:11 AM UTC-8, Nicolas M. Thiéry wrote:

On Fri, Nov 16, 2012 at 08:29:16PM -0800, Andrew Mathas wrote:
>    To build the documentation I typically use something like
>    sage -b && sage --docbuild reference html
>    Often this works without a hitch and just as often I get numerous warnings
>    like
>    categories.rst:44: WARNING: toctree contains reference to nonexisting
>    document u'sage/categories/commutative_additive_monoids'
>    and the corresponding pages are missing. In such cases, sage reports that
>    the documentation
>    builds "successfully" but the corresponding pages are missing.

Yeah, the documentation builder does not play nicely with applying and
unapplying patches, as it does not keep track properly of added /
removed files. As Travis said, the only really safe option is to nuke
the doc output.

I suppose it might also be necessary, occasionally, to delete the auto-generated files in devel/sage/doc/en/reference/sage. Deleting that entire directory would be an option if deleting the output directory doesn't fix things.

--
John