Your build may be picking up on the wrong version of pygments. Vanilla Sage uses pygments-2.3.1.p0.
./sage -f pygments may fix the issue. On my sage-on-gentoo build, which uses a system pygments, I see the same lex literal_block as "python" Warning with pygments-2.5.2. But pygments-2.4.2 is fine. On Wednesday, January 22, 2020 at 9:32:52 AM UTC-6, David Coudert wrote: > > sage: *import* *sphinx* > sage: sphinx.version_info > (2, 3, 1, 'final', 0) > > after ./sage -f sphinx I can compile part of the doc (I did a make > doc-clean before), until the following error > > [dochtml] > [dochtml] Building en/thematic_tutorials. > [dochtml] > [dochtml] [thematic_] building [html]: targets for 85 source files that > are out of date > [dochtml] [thematic_] updating environment: 85 added, 0 changed, 0 removed > [dochtml] [thematic_] > /Users/dcoudert/sage/local/lib/python3.7/site-packages/sphinx/util/nodes.py:94: > > FutureWarning: > [dochtml] [thematic_] The iterable returned by Node.traverse() > [dochtml] [thematic_] will become an iterator instead of a list in > Docutils > 0.16. > [dochtml] [thematic_] for classifier in > reversed(node.parent.traverse(nodes.classifier)): > [dochtml] [thematic_] Merging environment/index files... > [dochtml] [thematic_] ... done (3 todos, 85 index, 66 citations, 0 modules) > [dochtml] [thematic_] pickling environment... fait > [dochtml] [thematic_] checking consistency... fait > [dochtml] [thematic_] preparing documents... fait > [dochtml] [thematic_] > /Users/dcoudert/sage/local/lib/python3.7/site-packages/sphinx/writers/html.py:462: > > FutureWarning: > [dochtml] [thematic_] The iterable returned by Node.traverse() > [dochtml] [thematic_] will become an iterator instead of a list in > Docutils > 0.16. > [dochtml] [thematic_] target_node = image_nodes and image_nodes[0] or > node.parent > [dochtml] [thematic_] > /Users/dcoudert/sage/src/doc/en/thematic_tutorials/structures_in_coding_theory.rst:722: > > WARNING: Could not lex literal_block as "python". Highlighting skipped. > [dochtml] [thematic_] Merging js index files... > [dochtml] [thematic_] ... done (4882 js index entries) > [dochtml] [thematic_] copying extra files... fait > [dochtml] [thematic_] dumping search index in English (code: en) ... fait > [dochtml] [thematic_] dumping object inventory... fait > [dochtml] [thematic_] build réussi, 6 warnings. > [dochtml] [thematic_] The HTML pages are in > local/share/doc/sage/html/en/thematic_tutorials. > [dochtml] Error building the documentation. > [dochtml] Traceback (most recent call last): > [dochtml] File "/Users/dcoudert/sage/local/lib/python3.7/runpy.py", line > 193, in _run_module_as_main > [dochtml] "__main__", mod_spec) > [dochtml] File "/Users/dcoudert/sage/local/lib/python3.7/runpy.py", line > 85, in _run_code > [dochtml] exec(code, run_globals) > [dochtml] File > "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__main__.py", > > line 2, in <module> > [dochtml] main() > [dochtml] File > "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", > > line 1720, in main > [dochtml] builder() > [dochtml] File > "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", > > line 336, in _wrapper > [dochtml] build_many(build_other_doc, L) > [dochtml] File > "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", > > line 280, in build_many > [dochtml] _build_many(target, args, processes=NUM_THREADS) > [dochtml] File > "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py", > > line 283, in build_many > [dochtml] raise worker_exc.original_exception > [dochtml] OSError: > /Users/dcoudert/sage/src/doc/en/thematic_tutorials/structures_in_coding_theory.rst:722: > > WARNING: Could not lex literal_block as "python". Highlighting skipped. > [dochtml] > [dochtml] Note: incremental documentation builds sometimes cause > spurious > [dochtml] error messages. To be certain that these are real errors, run > [dochtml] "make doc-clean" first and try again. > make[3]: *** [doc-html] Error 1 > make[2]: *** [all-start] Error 2 > > > > Le 22 janv. 2020 à 11:01, Dima Pasechnik <dim...@gmail.com <javascript:>> > a écrit : > > On Wed, Jan 22, 2020 at 9:39 AM David Coudert <david....@gmail.com > <javascript:>> wrote: > > > Le 22 janv. 2020 à 10:27, Dima Pasechnik <dim...@gmail.com <javascript:>> > a écrit : > > On Wed, Jan 22, 2020 at 7:53 AM David Coudert <david....@gmail.com > <javascript:>> wrote: > > > I cannot build the doc, even after a doc-clean. > > > cd ../.. && sage-logger -p './sage --docbuild --no-pdf-links all html ' > logs/dochtml.log > [dochtml] > [dochtml] Building reference manual, first pass. > [dochtml] > [dochtml] [reference] Sphinx v2.3.1 en cours d'exécution > > > we are still on sphinx 1.8.5. > cf e.g. https://trac.sagemath.org/ticket/28856 > > you probably installed a new sphinx via pip or something like that, and, > oops… > > > I have not installed a new sphinx (or it’s a side effect of something > else, but what ??) > > > check e.g. the following > > sage: import sphinx > sage: sphinx.version_info > (1, 8, 5, 'final', 0) > > if it's not 1.8.5, I'd just do > > ./sage -f sphinx > > as to the root couse of this, I'd first look at > > ./sage --python -m pip list > > to see the list of all pip-install packages with versions. > > Or even more details: > > $ ./sage --python > Python 3.7.3 (default, Jan 20 2020, 14:52:21) > [GCC 8.3.0] on linux > Type "help", "copyright", "credits" or "license" for more information. > > > import pkg_resources, os, time > for package in pkg_resources.working_set: > > ... print("%s: %s" % (package, > time.ctime(os.path.getctime(package.location)))) > ... > zope.interface 4.6.0: Tue Jan 21 22:21:30 2020 > widgetsnbextension 3.4.2: Tue Jan 21 22:21:30 2020 > > etc. > > > D. > > [dochtml] [reference] > /Users/dcoudert/sage/local/lib/python3.7/site-packages/sphinx/util/docutils.py:285: > > RemovedInSphinx30Warning: function based directive support is now > deprecated. Use class based directive instead. > [dochtml] [reference] RemovedInSphinx30Warning) > [dochtml] [reference] WARNING: l'entrée html_static_path > '/Users/dcoudert/sage/src/doc/common/static' n'existe pas > [dochtml] [reference] WARNING: l'entrée html_static_path 'static' n'existe > pas > [dochtml] [reference] WARNING: le fichier de favicon 'favicon.ico' > n'existe pas > [dochtml] [reference] construction en cours [mo]:cibles pour les fichiers > po 0 qui sont périmées > [dochtml] [reference] construction [inventory]:cibles pour les fichiers > sources 1 qui sont périmées > [dochtml] [reference] mise-à-jour de l'environnement :[nouvelle > configuration] 1 ajouté, 0 modifié, 0 supprimé > [dochtml] [reference] lecture des sources... [100%] index > [dochtml] [reference] recherche des fichiers périmés... aucun résultat > [dochtml] [reference] environnement de sérialisation... fait > [dochtml] [reference] > /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:36: WARNING: > La citation [AAGMRZ2019] n'est pas référencée > [dochtml] [reference] > /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:40: WARNING: > La citation [Ab1995] n'est pas référencée > [dochtml] [reference] > /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:46: WARNING: > La citation [AB2007] n'est pas référencée > [dochtml] [reference] > /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:50: WARNING: > La citation [AB2008] n'est pas référencée > ... > ... > [dochtml] [reference] > /Users/dcoudert/sage/src/doc/en/reference/references/index.rst:5429: > WARNING: La citation [ZZ2005] n'est pas référencée > [dochtml] [reference] vérification de la cohérence... fait > [dochtml] [reference] document en préparation... fait > [dochtml] [reference] écriture... [100%] index > [dochtml] [reference] dumping object inventory... fait > [dochtml] [reference] build a réussi, 1284 warnings. > [dochtml] [reference] The inventory files are in > local/share/doc/sage/inventory/en/reference/references. > [dochtml] Error building the documentation. > [dochtml] Traceback (most recent call last): > [dochtml] File "/Users/dcoudert/sage/local/lib/python3.7/runpy.py", line > 193, in _run_module_as_main > [dochtml] "__main__", mod_spec) > [dochtml] File "/Users/dcoudert/sage/local/lib/python3.7/runpy.py", line > 85, in _run_code > [dochtml] exec(code, run_globals) > [dochtml] File > "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__main__.py", > > line 2, in <module> > [dochtml] main() > [dochtml] File > "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", > > line 1720, in main > [dochtml] builder() > [dochtml] File > "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", > > line 327, in _wrapper > [dochtml] getattr(get_builder(document), 'inventory')(*args, **kwds) > [dochtml] File > "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", > > line 550, in _wrapper > [dochtml] self._build_bibliography(lang, format, *args, **kwds) > [dochtml] File > "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", > > line 527, in _build_bibliography > [dochtml] build_many(build_ref_doc, references) > [dochtml] File > "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/__init__.py", > > line 280, in build_many > [dochtml] _build_many(target, args, processes=NUM_THREADS) > [dochtml] File > "/Users/dcoudert/sage/local/lib/python3.7/site-packages/sage_setup/docbuild/utils.py", > > line 283, in build_many > [dochtml] raise worker_exc.original_exception > [dochtml] OSError: WARNING: l'entrée html_static_path > '/Users/dcoudert/sage/src/doc/common/static' n'existe pas > make[3]: *** [doc-html] Error 1 > make[2]: *** [all-start] Error 2 > > real 0m20.334s > user 0m10.723s > sys 0m4.168s > *************************************************************** > Error building Sage. > > The following package(s) may have failed to build (not necessarily > during this run of 'make all-start'): > > * documentation: dochtml > log file: /Users/dcoudert/sage/logs/pkgs/../dochtml.log > > The build directory may contain configuration files and other potentially > helpful information. WARNING: if you now run 'make' again, the build > directory will, by default, be deleted. Set the environment variable > SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this. > > make[1]: *** [all-start] Error 1 > make: *** [all] Error 2 > > > > Le 22 janv. 2020 à 00:41, Volker Braun <vbrau...@gmail.com <javascript:>> > a écrit : > > As always, you can get the latest beta version from the "develop" git > branch. Alternatively, the self-contained source tarball is at > http://www.sagemath.org/download-latest.html > > > dde78cbd22 (tag: 9.1.beta1, trac/develop) Updated SageMath version to > 9.1.beta1 > 4fd5d56ece Trac #29029: some cleaning in power series pyx files > 4cb8a7b996 Trac #29020: remove some deprecated stuff in modular > ed52d73c0d Trac #29014: cvxopt: use pkg-config for blas libdir in > spkg-install > 64438cef9b Trac #29010: Split off sage.rings.number_field.homset from > sage.rings.number_field.morphism > 6612330a9f Trac #29008: Move sage.rings.homset to the "new" coercion model > 66cfbfcedc Trac #29001: PKG_CHECK_VAR missing on pkgconfig < 0.28 > 03886d35eb Trac #28995: little tweak to our lgtm config file > 6d8d080aa2 Trac #28990: some fixes in sage_bootstrap and mac-app > 9a911b0056 Trac #28978: Change "high mem" to "memlimit" when referring to > doctesting tags > c18ebf94f0 Trac #28967: implement easy cases of inverse_mod for general > commutative rings > 437b96dd6a Trac #29030: Fix deprecation warnings with ipython 7 > 4579b22408 Trac #29027: MR40: add missing # long time tags > 4200a9a134 Trac #29025: numpy: site.cfg needs a [DEFAULT] section > d5521bf8c8 Trac #29021: Bug in setting the calculus method on manifolds > 5534ecd1ce Trac #29019: Make patch to pillow more robust (do not depend on > "Py_MACOS_SYSROOT") and fix zlib problem on macOS > 0c037c69c1 Trac #29017: Coercion map to a quotient of a polynomial ring > has incorrect parent > d337302be4 Trac #29016: spkg-legacy-uninstall for R > fb6146ade2 Trac #29004: Fix broken link with hall_polynomial in HallAlgebra > 89447f97ca Trac #29003: Install Sage-specific .pc files when running make, > not configure > b6f7be5e5b Trac #28997: Update sage-numerical-backends-gurobi to 9.0.0 > 24dbe7fe89 Trac #28994: pyflakes cleanup in categories > 8966c95bd5 Trac #28993: Adding keyword `prec` to the element constructor > of Laurent series > e98af516aa Trac #28988: Support rpy 3.x > 1f0508d28a Trac #28985: spkg-configure for gfan > 1f76e74068 Trac #28973: Automorphism Fields: Notation of Inverse > 6c59de24f0 Trac #28968: further improvements to GroupLibGAP > 5a115e0502 Trac #28965: enhance GroupLibGAP > 25b20e31be Trac #28961: Better class hierarchy for classical matrix Lie > algebras > 305ed5a09b Trac #28958: spkg-configure.m4 for nauty > f0b2140404 Trac #28954: polynomial degree is broken for weighted block > orders > d12132f98f Trac #28611: Genus Representative > 295bd69e58 Trac #28473: decomposition by clique minimal separators > d63a3bc1d3 Trac #28239: Precision of Laurent series is restricted to be > positive > 878ff06b8e Trac #28045: spkg-configure.m4 for libatomic > ba57ab1cca Trac #28969: fix typo in error message of > IntegerMod_abstract.__abs__ > 34d6e53bf6 Trac #28975: return is not a function > e13339bda5 Trac #28972: some details about all(...) and return > 6fa6de600d Trac #28952: Rational representative for a genus > 266a6aaa9c Trac #28908: spkg-configure for cbc > f8430c4d06 Trac #28934: remove stuff about python 2.4 compatibility > 582712b85d Trac #28932: fix QuadraticField constructor if embedding=False > 2f6e2f2219 Trac #28931: some cleanup for contour plot > 75f1dccb81 Trac #28907: remove the method MathematicaElement.N() > 0e4041927e Trac #28902: Cythonize hypergeometric trace formula > b40e3a3ad7 Trac #28901: some details in matrix/ > 6c520b21de Trac #28772: Kneading sequences for the doubling map > 0e19bcb7e6 Trac #28695: gcc: mismatch of assembler / linker during > configure > 495254a7fd Trac #28956: correct AC_CHECK_PROG call in spkg-configure for > bzip2 > 85c95a6959 Trac #28955: Bug in quadratic_form_from_invariants > 93ed1bbb25 Trac #28942: Maximal even overlattice > 8a0e0ebfe1 Trac #28921: Mixed Forms - Zero Treatment for Scalar > Multiplication > fb8d83d885 Trac #28916: MixedFormAlgebra - More Flexible Coercions > 708ab81536 Trac #28886: Update FP(Y)LLL > af6498344d Trac #27086: Simplicity and simpliciality for > CombinatorialPolyhedron > af2f949780 Trac #19803: difference of behavior in polyhedra with different > backends > b8f53f72e8 (tag: 9.1.beta0) Updated SageMath version to 9.1.beta0 > > > -- > You received this message because you are subscribed to the Google Groups > "sage-release" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-r...@googlegroups.com <javascript:>. > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-release/fea3c91d-a208-4bc2-b846-3645ce7dcb86%40googlegroups.com > . > > > -- > You received this message because you are subscribed to the Google Groups > "sage-release" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-r...@googlegroups.com <javascript:>. > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-release/D5D0139C-7A98-4797-A7B2-AE5AEA4875DF%40gmail.com > . > > > -- > You received this message because you are subscribed to the Google Groups > "sage-release" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-r...@googlegroups.com <javascript:>. > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-release/CAAWYfq0v6NwzSA8Pb9_VTQmxX3csnxrdJ%3D-rvmFCCjDiZ5s%2B5g%40mail.gmail.com > . > > > -- > You received this message because you are subscribed to the Google Groups > "sage-release" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-r...@googlegroups.com <javascript:>. > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-release/CBF8B41A-2994-4989-839F-52E050FB1C1C%40gmail.com > . > > > -- > You received this message because you are subscribed to the Google Groups > "sage-release" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-r...@googlegroups.com <javascript:>. > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-release/CAAWYfq3pZDx23CAg7QdrTupZhA--3VShPw-QKvQtej7xH5J4YQ%40mail.gmail.com > . > > > -- You received this message because you are subscribed to the Google Groups "sage-release" group. 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