Sage 9.6.beta7 released

[Volker Braun]

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

78bfb6c7ad (tag: 9.6.beta7, trac/develop) Updated SageMath version to 9.6.beta7
199ee74bdd Trac #33563: fix some tests of emptiness
596c5ebe69 Trac #33552: adjust error messages in toric/
36ffa34de1 Trac #33551: various details in pyx files
b9c0c5cb3e Trac #33545: fix W391 in rings
160a503a46 Trac #33539: sage.manifolds, sage.tensor: Fix spelling errors
26c9c81022 Trac #33519: fix indentation in integration.pyx
6312320fb8 Trac #33517: fix W391 in categories
eb33795b51 Trac #33516: fix W391 in schemes
2258189a8d Trac #33510: clean build/sage_bootstrap
23ac99956a Trac #33506: spaces around some % in combinat/
5b4fe73af3 Trac #33503: adjust a few more error messages
aba82b3e94 Trac #33422: Bug in equivalence_decomposition of inductive valuation
f516aabdee Trac #33400: Add pictures to various 3d graphics manual pages
f4a39b12e3 Trac #29775: Add a bit of typing to manifold code
a45aa86091 Trac #33604: Remove random_DAG from global namespace
c55624e4dc Trac #33603: Fix Conic doctests
76167599cc Trac #33602: Deprecate the import of some element classes in sage/ring/all.py
9b8d0ef4f1 Trac #33595: fix indentation (E111) in some pyx files, mostly in rings/
aa11173798 Trac #33594: fix W391 in manifolds, geometry and graphs
4a8c685227 Trac #33583: Move integration and volume to Polyhedron_base7
8f750d97b3 Trac #33581: small cleanup for mathics.py
a79b1b8baa Trac #33573: extend method cores to accept graphs with multiple edges
9543d076d5 Trac #33570: Add CONTRIBUTING.md to the repository
86d9846846 Trac #33569: Speed up methods allow_multiple_edges and  multiple_edges
08a942330a Trac #33507: sagemath_doc_html: Use jupyter-sphinx for 3D graphics
3dd4e6b470 Trac #33568: Add method `is_integral_domain` for polynomial quotient rings
76d0d33770 Trac #33567: finer category for cubic braid group quotients
328de7a17c Trac #33564: add one test in TestSuite of Coxeter groups
08854a8167 Trac #33559: Fix bug in sage.graphs.graph_coloring.vertex_coloring
1762a6ca6d Trac #33558: get rid of __nonzero__ and use __bool__ instead
fbc8bd05e9 Trac #33555: refresh the file subword.py
42a088a131 Trac #33553: README Build from Source: m4 (step 5) is needed to run `make configure` (step 3)
ce74d3217f Trac #33540: remove class inheritance of object in combinat
d8f2ce96a0 Trac #33538: More doctests fix in sage_docbuild
a5446dbaa4 Trac #33536: Some changes suggested by lgtm
b9cdb7c713 Trac #33529: Remove old thebe package
211da0e7d1 Trac #33214: Vélu isogeny formulas use incorrect a-invariants when pre-isomorphism is set
64bd36ebc8 Trac #32687: error in height difference bound
f6ce4103f3 Trac #8784: remove quit_sage() command from all.py top level
3c6f5086b7 Trac #33585: doctest failure when doc html not built/installed but sphinx is available in PYTHONPATH
afa0d9633b Trac #33584: Adapt Mathics interface to SymPy upgrade from 1.8 to 1.10 (resp.1.9)
58bf1ba6bb Trac #33520: scipy, networkx: Update install-requires.txt
d20cc4945d Trac #33139: Fix sagemath_doc_html build failure on Cygwin
e39a3a2736 Trac #31924: sage -t: Do not run pytest on individual Python files unless they match the pytest file pattern
a275e1f383 Trac #33607: jupyterlab: Use jupyterlab-server < 2.11
949bb36dd0 Trac #33523: Fix crosslinks in algebras catalog
e3fce642a0 Trac #33469: %matplotlib widget does not work in the scope of %display latex
baf6b19517 Trac #33443: slow doctest improvements (isogeny_small_degree, function_field, doctest/test.py)
b11471b30b Trac #33393: Implement Krawtchouk, Meixner, and Hahn polynomials
a54d7ce44a Trac #33114: Feature.require vs. is_present, is_functional
c399fc096b Trac #32364: every quaternion lies in every quaternion order
5166ac1413 Trac #20343: Add file `sage/misc/latex_standalone.py` and class `TikzPicture`
0991f82d57 Trac #33547: Update sympy to 1.10.1
0d0bb77fb2 Trac #33508: OpenSSL 3.0.2 security update
56d233b1f6 Trac #33227: SystemError: calling remove_from_pari_stack() inside sig_on() in expression.pyx
43474c96d5 (tag: 9.6.beta6) Updated SageMath version to 9.6.beta6

[Volker Braun]

Also, we should make a new release soon. So if you have anything that you want to be in 9.6 then now is the time to wrap it up ;)

[Matthias Köppe]

+1 on getting a release out. We have lots of improvements over 9.5

[Emmanuel Charpentier]

On Debian testing running on core i7 + 16 GB RAM, upgrading 9.6.beta6 to 9.6.beta7 and running ptestlong gives one transient failure :

HTH,

which passes when ran standalone. Original failure (in ptestlong.log) :

sage -t --long --warn-long 207.5 --random-seed=104190692585737511304860911887747877058 src/sage/schemes/cyclic_covers/cycliccover_finite_field.py  # 1 doctest failed

Original failure in ptestlong.log :

sage -t --long --warn-long 207.5 --random-seed=104190692585737511304860911887747877058 src/sage/plot/plot3d/base.pxd
    [0 tests, 0.00 s]
sage -t --long --warn-long 207.5 --random-seed=104190692585737511304860911887747877058 src/sage/schemes/cyclic_covers/cycliccover_finite_field.py
**********************************************************************
File "src/sage/schemes/cyclic_covers/cycliccover_finite_field.py", line 1139, in sage.schemes.cyclic_covers.cycliccover_finite_field.CyclicCover_finite_field.frobenius_polynomial
Failed example:
    CyclicCover(11, PolynomialRing(GF(1129), 'x')([-1] + [0]*(5-1) + [1])).frobenius_polynomial() # long time
Exception raised:
    Traceback (most recent call last):
      File "sage/misc/cachefunc.pyx", line 1943, in sage.misc.cachefunc.CachedMethodCaller.__call__ (build/cythonized/sage/misc/cachefunc.c:10414)
        return cache[k]
    KeyError: ((11,), ())

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/doctest/forker.py", line 695, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/doctest/forker.py", line 1093, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.schemes.cyclic_covers.cycliccover_finite_field.CyclicCover_finite_field.frobenius_polynomial[23]>", line 1, in <module>
        CyclicCover(Integer(11), PolynomialRing(GF(Integer(1129)), 'x')([-Integer(1)] + [Integer(0)]*(Integer(5)-Integer(1)) + [Integer(1)])).frobenius_polynomial() # long time
      File "sage/misc/cachefunc.pyx", line 2310, in sage.misc.cachefunc.CachedMethodCallerNoArgs.__call__ (build/cythonized/sage/misc/cachefunc.c:13024)
        self.cache = f(self._instance)
      File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/schemes/cyclic_covers/cycliccover_finite_field.py", line 1234, in frobenius_polynomial
        F = self.frobenius_matrix(self._N0)
      File "sage/misc/cachefunc.pyx", line 1948, in sage.misc.cachefunc.CachedMethodCaller.__call__ (build/cythonized/sage/misc/cachefunc.c:10550)
        w = self._instance_call(*args, **kwds)
      File "sage/misc/cachefunc.pyx", line 1824, in sage.misc.cachefunc.CachedMethodCaller._instance_call (build/cythonized/sage/misc/cachefunc.c:10016)
        return self.f(self._instance, *args, **kwds)
      File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/schemes/cyclic_covers/cycliccover_finite_field.py", line 1072, in frobenius_matrix
        FrobP = _frobenius_matrix_p(self._N0)
      File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/schemes/cyclic_covers/cycliccover_finite_field.py", line 1068, in _frobenius_matrix_p
        ] = self._frob(i, j + self._epsilon * self._r, N0)
      File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/schemes/cyclic_covers/cycliccover_finite_field.py", line 994, in _frob
        self._initialize_fat_horizontal(
      File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/schemes/cyclic_covers/cycliccover_finite_field.py", line 738, in _initialize_fat_horizontal
        DH = [elt[0, 0] for elt in interval_products(D0, D1, targets)]
      File "sage/schemes/hyperelliptic_curves/hypellfrob.pyx", line 140, in sage.schemes.hyperelliptic_curves.hypellfrob.interval_products (build/cythonized/sage/schemes/hyperelliptic_curves/hypellfrob.cpp:4007)
        sig_on()
    SystemError: calling remove_from_pari_stack() inside sig_on()
**********************************************************************
File "src/sage/schemes/cyclic_covers/cycliccover_finite_field.py", line 1142, in sage.schemes.cyclic_covers.cycliccover_finite_field.CyclicCover_finite_field.frobenius_polynomial
Warning, slow doctest:
    CyclicCover(3, PolynomialRing(GF(1009^2), 'x')([-1] + [0]*(5-1) + [1])).frobenius_polynomial() # long time
Test ran for 261.78 s, check ran for 0.00 s
**********************************************************************
1 item had failures:
   1 of  60 in sage.schemes.cyclic_covers.cycliccover_finite_field.CyclicCover_finite_field.frobenius_polynomial
    [168 tests, 1 failure, 402.34 s]

HTH,

​

[G. M.-S.]

Thanks, Volker.

This is on Apple Silicon M1 Macs with Homebrew up to date.

For SageMath 9.6.beta7 plus make pytest and nothing else.

macOS 11.6.5 (Big Sur) with Xcode 13.2.1:  make ptestlong gives the usual:

----------------------------------------------------------------------
sage -t --long --warn-long 47.2 --random-seed=204316541266034313354224566486337275355 src/sage/matrix/matrix_gf2e_dense.pyx  # 1 doctest failed
----------------------------------------------------------------------

(see https://trac.sagemath.org/ticket/33212 and https://bitbucket.org/malb/m4rie/issues/23/trying-to-compile-on-apple-m1).

macOS 12.3.1 (Monterey) with Xcode 13.3:  make ptestlong gives no errors.

On Monterey there was only one alert "Pyhton quit unexpectedly", which was ignored.

Guillermo

[Sébastien Labbé]

Thanks for the release. I am quite happy that #20343 is now in!

Testing on Ubuntu 18.04 with few optional and external packages, I get:

----------------------------------------------------------------------
sage -t --long --random-seed=290149003222784740688944140527868655673 src/sage/combinat/designs/incidence_structures.py  # 1 doctest failed
sage -t --long --random-seed=290149003222784740688944140527868655673 src/sage/geometry/polyhedron/base.py  # 1 doctest failed
sage -t --long --random-seed=290149003222784740688944140527868655673 src/sage/graphs/generic_graph.py  # 2 doctests failed
sage -t --long --random-seed=290149003222784740688944140527868655673 src/sage/graphs/graph.py  # 3 doctests failed
sage -t --long --random-seed=290149003222784740688944140527868655673 src/sage/interfaces/expect.py  # 2 doctests failed
sage -t --long --random-seed=290149003222784740688944140527868655673 src/sage/interfaces/mathematica.py  # 1 doctest failed
sage -t --long --random-seed=290149003222784740688944140527868655673 src/sage/numerical/backends/glpk_backend.pyx  # 4 doctests failed
sage -t --long --random-seed=290149003222784740688944140527868655673 src/sage/numerical/mip.pyx  # 8 doctests failed
sage -t --long --random-seed=290149003222784740688944140527868655673 src/sage/tests/books/computational-mathematics-with-sagemath/lp_doctest.py  # 2 doctests failed
sage -t --long --random-seed=290149003222784740688944140527868655673 src/sage/tests/cmdline.py  # 1 doctest failed
----------------------------------------------------------------------
Features detected for doctesting: dvipng,ffmpeg,graphviz,imagemagick,internet,latex,latex_package_tkz_graph,lualatex,nauty,octave,palp,pandoc,pdf2svg,pdflatex,pdftocairo,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.plot,sage.rings.number_field,sage.rings.padics,sage.rings.real_double,sage.symbolic,sagemath_doc_html,sphinx,xelatex

Rerunning failed doctests, I get:

----------------------------------------------------------------------
sage -t --long --random-seed=253857822428465768945439832358430332549 src/sage/combinat/designs/incidence_structures.py  # 1 doctest failed
sage -t --long --random-seed=253857822428465768945439832358430332549 src/sage/geometry/polyhedron/base.py  # 1 doctest failed
sage -t --long --random-seed=253857822428465768945439832358430332549 src/sage/graphs/generic_graph.py  # 2 doctests failed
sage -t --long --random-seed=253857822428465768945439832358430332549 src/sage/graphs/graph.py  # 3 doctests failed
sage -t --long --random-seed=253857822428465768945439832358430332549 src/sage/numerical/backends/glpk_backend.pyx  # 4 doctests failed
sage -t --long --random-seed=253857822428465768945439832358430332549 src/sage/numerical/mip.pyx  # 8 doctests failed
sage -t --long --random-seed=253857822428465768945439832358430332549 src/sage/tests/books/computational-mathematics-with-sagemath/lp_doctest.py  # 2 doctests failed
sage -t --long --random-seed=253857822428465768945439832358430332549 src/sage/tests/cmdline.py  # 1 doctest failed
----------------------------------------------------------------------
Features detected for doctesting: graphviz,internet,latex,pandoc,sage.combinat,sage.graphs,sage.groups,sage.rings.number_field,sage.symbolic


As you see, failures with interfaces/mathmematica.py and interfaces/expect.py did not reproduce. I copy the non-reproducible failures below.


sage -t --long --random-seed=290149003222784740688944140527868655673 src/sage/interfaces/mathematica.py
**********************************************************************
File "src/sage/interfaces/mathematica.py", line 1228, in sage.interfaces.mathematica.parse_moutput_from_json
Failed example:
    sorted(L)                                             # optional internet
Expected:
    ['-Cos[x]', '{x == 0}', '{x == Pi C[1], Element[C[1], Integers]}']
Got:
    ['-Cos[x]']

**********************************************************************
1 item had failures:

   1 of  10 in sage.interfaces.mathematica.parse_moutput_from_json
    121 mathematica tests not run
    3 mathematicafrontend tests not run
    0 tests not run because we ran out of time
    [35 tests, 1 failure, 9.63 s]

sage -t --long --random-seed=290149003222784740688944140527868655673 src/sage/interfaces/expect.py
**********************************************************************
File "src/sage/interfaces/expect.py", line 920, in sage.interfaces.expect.Expect._eval_line
Failed example:
    singular.interrupt()
Expected:
    True
Got:
    False
**********************************************************************
File "src/sage/interfaces/expect.py", line 926, in sage.interfaces.expect.Expect._eval_line
Failed example:
    singular('2+3')
Expected:
    Singular crashed -- automatically restarting.
    5
Got:
    5

**********************************************************************
1 item had failures:

   2 of  16 in sage.interfaces.expect.Expect._eval_line
    0 tests not run because we ran out of time
    [102 tests, 2 failures, 18.49 s]


Other failures are already tracked at: https://trac.sagemath.org/ticket/25536

In particular, I figured out the problem with failures because "Long-step dual simplex will be used" gets printed which involves 4 of the files above. It is because such warnings are not ignored with the presence of # abs tol comments.

See https://trac.sagemath.org/ticket/33588

[Kenji Iohara]

Thanks for the release. On my MacBookPro with Intelcore, OS 12.3, XCode 13.3 and Homebrew,

I could compile sage9.6.beta6 from the firt built but for beta7, I cannot compile it because of

    gmpy2-2.1.1    cysignals-1.11.2   and matplotlib-3.5.1

even if they are pre-installed on the machine via pip3. Here are the log-files:

[Kazuyoshi Furutaka]

The build failed on Fedora-35/python-3.10.4.

Logs attached; excerpts below...

Kazuyoshi

...

[sagemath_doc_html-none] Build finished. The built documents can be found in /home/furutaka/work/sage/sage-9.6.beta7-gcc/local/share/doc/sage/inventory/en/reference/coercion
[sagemath_doc_html-none] [repl     ] executing interact
[sagemath_doc_html-none] [repl     ] /home/furutaka/work/sage/sage-9.6.beta7-gcc/local/var/lib/sage/venv-python3.10/lib64/python3.10/site-packages/jsonschema/validators.py:188: DeprecationWarning: Passing a schema to Validator.iter_errors is deprecated and will be removed in a future release. Call validator.evolve(schema=new_schema).iter_errors(...) instead.
[sagemath_doc_html-none] [repl     ]   warnings.warn(
[sagemath_doc_html-none] [repl     ] /home/furutaka/work/sage/sage-9.6.beta7-gcc/local/var/lib/sage/venv-python3.10/lib64/python3.10/site-packages/nbclient/util.py:47: DeprecationWarning: There is no current event loop
[sagemath_doc_html-none] [repl     ]   loop = asyncio.get_event_loop()
[sagemath_doc_html-none] [repl     ] Extension error:
[sagemath_doc_html-none] [repl     ] Notebook execution failed (exception: [Errno 2] No such file or directory: '/home/furutaka/work/sage/sage-9.0-git-bld/local/bin/sage')
[sagemath_doc_html-none] Build finished. The built documents can be found in /home/furutaka/work/sage/sage-9.6.beta7-gcc/local/share/doc/sage/inventory/en/reference/repl
...
[sagemath_doc_html-none] Build finished. The built documents can be found in /home/furutaka/work/sage/sage-9.6.beta7-gcc/local/share/doc/sage/inventory/en/reference/combinat
[sagemath_doc_html-none] [plot3d   ] executing plot3d
[sagemath_doc_html-none] [plot3d   ] /home/furutaka/work/sage/sage-9.6.beta7-gcc/local/var/lib/sage/venv-python3.10/lib64/python3.10/site-packages/jsonschema/validators.py:188: DeprecationWarning: Passing a schema to Validator.iter_errors is deprecated and will be removed in a future release. Call validator.evolve(schema=new_schema).iter_errors(...) instead.
[sagemath_doc_html-none] [plot3d   ]   warnings.warn(
[sagemath_doc_html-none] [plot3d   ] /home/furutaka/work/sage/sage-9.6.beta7-gcc/local/var/lib/sage/venv-python3.10/lib64/python3.10/site-packages/nbclient/util.py:47: DeprecationWarning: There is no current event loop
[sagemath_doc_html-none] [plot3d   ]   loop = asyncio.get_event_loop()
[sagemath_doc_html-none] [plot3d   ] Extension error:
[sagemath_doc_html-none] [plot3d   ] Notebook execution failed (exception: [Errno 2] No such file or directory: '/home/furutaka/work/sage/sage-9.0-git-bld/local/bin/sage')
[sagemath_doc_html-none] Build finished. The built documents can be found in /home/furutaka/work/sage/sage-9.6.beta7-gcc/local/share/doc/sage/inventory/en/reference/plot3d
[sagemath_doc_html-none] /home/furutaka/work/sage/sage-9.6.beta7-gcc/local/var/lib/sage/venv-python3.10/lib64/python3.10/site-packages/nbclient/util.py:47: DeprecationWarning: There is no current event loop
[sagemath_doc_html-none]   loop = asyncio.get_event_loop()

...

[sagemath_doc_html-none] [reference] /home/furutaka/work/sage/sage-9.6.beta7-gcc/src/doc/en/reference/index.rst:17: WARNING: unknown document: repl/index
[sagemath_doc_html-none] [reference] /home/furutaka/work/sage/sage-9.6.beta7-gcc/src/doc/en/reference/index.rst:24: WARNING: unknown document: plot3d/index
[sagemath_doc_html-none] [reference] The inventory files are in local/share/doc/sage/inventory/en/reference.
[sagemath_doc_html-none] Error building the documentation.
[sagemath_doc_html-none] Traceback (most recent call last):
[sagemath_doc_html-none]   File "/usr/lib64/python3.10/runpy.py", line 196, in _run_module_as_main
[sagemath_doc_html-none]     return _run_code(code, main_globals, None,
[sagemath_doc_html-none]   File "/usr/lib64/python3.10/runpy.py", line 86, in _run_code
[sagemath_doc_html-none]     exec(code, run_globals)
[sagemath_doc_html-none]   File "/home/furutaka/work/sage/sage-9.6.beta7-gcc/local/var/lib/sage/venv-python3.10/lib64/python3.10/site-packages/sage_docbuild/__main__.py", line 2, in <module>
[sagemath_doc_html-none]     main()
[sagemath_doc_html-none]   File "/home/furutaka/work/sage/sage-9.6.beta7-gcc/local/var/lib/sage/venv-python3.10/lib64/python3.10/site-packages/sage_docbuild/__init__.py", line 1762, in main
[sagemath_doc_html-none]     builder()
[sagemath_doc_html-none]   File "/home/furutaka/work/sage/sage-9.6.beta7-gcc/local/var/lib/sage/venv-python3.10/lib64/python3.10/site-packages/sage_docbuild/__init__.py", line 145, in f
[sagemath_doc_html-none]     runsphinx()
[sagemath_doc_html-none]   File "/home/furutaka/work/sage/sage-9.6.beta7-gcc/local/var/lib/sage/venv-python3.10/lib64/python3.10/site-packages/sage_docbuild/sphinxbuild.py", line 326, in runsphinx
[sagemath_doc_html-none]     sys.stderr.raise_errors()
[sagemath_doc_html-none]   File "/home/furutaka/work/sage/sage-9.6.beta7-gcc/local/var/lib/sage/venv-python3.10/lib64/python3.10/site-packages/sage_docbuild/sphinxbuild.py", line 262, in raise_errors
[sagemath_doc_html-none]     raise OSError(self._error)
[sagemath_doc_html-none] OSError: /home/furutaka/work/sage/sage-9.6.beta7-gcc/src/doc/en/reference/index.rst:17: WARNING: unknown document: repl/index
[sagemath_doc_html-none]
[sagemath_doc_html-none]     Note: incremental documentation builds sometimes cause spurious
[sagemath_doc_html-none]     error messages. To be certain that these are real errors, run
[sagemath_doc_html-none]     "make doc-clean doc-uninstall" first and try again.
[sagemath_doc_html-none] make[6]: *** [Makefile:20: doc-inventory--reference_top] Error 1
[sagemath_doc_html-none] make[5]: *** [Makefile:38: doc-inventory-reference] Error 2
make[4]: *** [Makefile:2910: sagemath_doc_html-SAGE_DOCS-no-deps] Error 2
make[3]: *** [Makefile:2910: /home/furutaka/work/sage/sage-9.6.beta7-gcc/local/var/lib/sage/installed/sagemath_doc_html-none] Error 2
make[2]: *** [Makefile:2471: all-start] Error 2
make[2]: Leaving directory '/home/furutaka/work/sage/sage-9.6.beta7-gcc/build/make'

real    21m52.324s
user    152m48.760s
sys     8m20.897s
***************************************************************
Error building Sage.

The following package(s) may have failed to build (not necessarily
during this run of 'make all-start'):

It is safe to delete any log files and build directories, but they
contain information that is helpful for debugging build problems.
WARNING: If you now run 'make' again, the build directory of the
same version of the package will, by default, be deleted. Set the
environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.

make[1]: *** [Makefile:39: all-start] Error 1
make[1]: Leaving directory '/home/furutaka/work/sage/sage-9.6.beta7-gcc'
make: *** [Makefile:13: all] Error 2

2022年4月3日(日) 4:12 Volker Braun <vbrau...@gmail.com>:

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Kazuyoshi Furutaka

[Dima Pasechnik]

Errors such as

sagemath_doc_html-none] [repl ] Notebook execution failed
(exception: [Errno 2] No such file or directory:
'/home/furutaka/work/sage/sage-9.0-git-bld/local/bin/sage')

indicate that you have remains of Sage 9.0 (still instaleld in
/home/furutaka/work/sage/sage-9.0-git-bld ?) pollutng the build.
Perhaps it's in your PATH.

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CANjERvfFtWRp%2B-3BWrKLj0N1Nz-8tSunkG-S6_treEyTtVDuxg%40mail.gmail.com.

[Eric Gourgoulhon]

Thanks for the new release.

On Ubuntu 20.04 running on Xeon E5-2623 + 16 GB RAM:

- incremental build (-j16) from Sage 9.6.beta6 with system python (3.8.10): OK

- make ptestlong --> "All tests passed!"

Eric.

[Dima Pasechnik]

More precisely, a very similarly looking error was mentioned in https://trac.sagemath.org/ticket/33507#comment:75

- and it turns out that there was a stale Sagemath Jupyter kernel, i.e. a file named kernel.json, in a directory

with name ending on sagemath, i.e. something like foo/bar/sagemath/kernel.json.

In that particular case it was (on macOS) ~/Library/Jupyter/sagemath/kernel.json with the obsolete path to sage (version 9.4.beta3)

In your case it would be pointing to sage 9.0.

[Antonio Rojas]

Running 'sage -t --installed' gives one new failure here:

sage -t --long --random-seed=169358931466360395563136887940502246251 /usr/share/doc/sage/html/en/reference/jupyter_execute/sage/plot/plot3d/plot3d.py
   SyntaxError in doctesting framework
**********************************************************************

Traceback (most recent call last):

 File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 2490, in __call__
   doctests, extras = self._run(runner, options, results)
 File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 2538, in _run
   doctests, extras = self.source.create_doctests(sage_namespace)
 File "/usr/lib/python3.10/site-packages/sage/doctest/sources.py", line 751, in create_doctests
   load(filename, namespace) # errors raised here will be caught in DocTestTask
 File "/usr/lib/python3.10/site-packages/sage/repl/load.py", line 251, in load
   code = compile(f.read(), fpath, 'exec')
 File "./plot3d.py", line 278
   cylindrical(r, theta, z) = [r*cos(theta), r*sin(theta), z]
   ^^^^^^^^^^^^^^^^^^^^^^^^
SyntaxError: cannot assign to function call here. Maybe you meant '==' instead of '='?

[Kazuyoshi Furutaka]

Hi,

The build finished successfully after deleting ~/.local/share/jupyter/kernels/sagemath/kernel.json.

Thanks,

Kazuyoshi

2022年4月6日(水) 6:05 Dima Pasechnik <dim...@gmail.com>:

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/e0838435-0604-4c95-b774-ac7e51264d0cn%40googlegroups.com.

[John H Palmieri]

I'm getting a doctest failure (OS X, iMac Pro):

sage -t --random-seed=282087015394155253226119703033530733169 src/sage/libs/pari/tests.py
**********************************************************************
File "src/sage/libs/pari/tests.py", line 786, in sage.libs.pari.tests
Failed example:
    pari('x+O(x^8)').cosh()
Expected:
    1 + 1/2*x^2 + 1/24*x^4 + 1/720*x^6 + O(x^8)
Got:
    1 + 1/2*x^2 + 1/24*x^4 + 1/720*x^6 + 1/40320*x^8 + O(x^9)
**********************************************************************

This is using pari from homebrew, pari updated this morning to version 2.13.4.

[arojas]

https://trac.sagemath.org/ticket/33647

[John H Palmieri]

Quick work, thanks!

[Thierry Dumont]

A cur(l)ious problem...

As I did not succeed to upgrade from 9.7beta4 to beta5, I restarted from
scratch, from a fresh clone of the repository.

My OS: Ubuntu 22-04, up to date.

Compilation crashes when trying to install... curl.

curl is installed on my machine (and also libcurl4, libcurl4-gnutls)

log file :
Attempting to download package curl-7.62.0.tar.bz2 from mirrors
https://www-ftp.lip6.fr/pub/math/sagemath/spkg/upstream/curl/curl-7.62.0.tar.bz2
[......................................................................]
curl-7.62.0.p0
====================================================
Setting up build directory for curl-7.62.0.p0
Finished extraction
No patch files found in ../patches
****************************************************

....
openldap.c:82:17: error: conflicting types for 'ldap_connect'; have
'CURLcode(struct connectdata *, _Bool *)'
82 | static CURLcode ldap_connect(struct connectdata *conn, bool *done);
| ^~~~~~~~~~~~
In file included from openldap.c:39:
/usr/include/ldap.h:1555:1: note: previous declaration of 'ldap_connect'
with type 'int(LDAP *)' {aka 'int(struct ldap *)'}

[Dima Pasechnik]

what does top level config.log say about curl?

why the system one was not good?

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[Thierry Dumont]

Le 13/07/2022 à 09:57, Dima Pasechnik a écrit :
> what does top level config.log say about curl?
>
> why the system one was not good?

Note that curl was downloaded (source) and its compilation failed.
This is a part of install.log (full logfile is joined):

curl-7.62.0.p0] Attempting to download package curl-7.62.0.tar.bz2 from
mirrors
[curl-7.62.0.p0]
https://www-ftp.lip6.fr/pub/math/sagemath/spkg/upstream/curl/curl-7.62.0.tar.bz2

and
curl-7.62.0.p0] curl-7.62.0.p0
[curl-7.62.0.p0] ====================================================
[curl-7.62.0.p0] Setting up build directory for curl-7.62.0.p0
....

curl-7.62.0.p0] Finished extraction
[curl-7.62.0.p0] No patch files found in ../patches
....

curl-7.62.0.p0] /usr/bin/bash ../libtool --tag=CC --mode=compile gcc
-DHAVE_CONFIG_H -I../include -I../lib -I../lib -DBUILDING_LIBCURL
-DCURL_HIDDEN_SYMBOLS -fvisibility=hidden -O2
-Werror-implicit-function-declaration -Wno-system-headers -c -o
libcurl_la-openldap.lo `test -f 'openldap.c' || echo './'`openldap.c
[curl-7.62.0.p0] libtool: compile: gcc -DHAVE_CONFIG_H -I../include
-I../lib -I../lib -DBUILDING_LIBCURL -DCURL_HIDDEN_SYMBOLS
-fvisibility=hidden -O2 -Werror-implicit-function-declaration
-Wno-system-headers -c openldap.c -fPIC -DPIC -o
.libs/libcurl_la-openldap.o
[curl-7.62.0.p0] openldap.c:82:17: error: conflicting types for

'ldap_connect'; have 'CURLcode(struct connectdata *, _Bool *)'

[curl-7.62.0.p0] 82 | static CURLcode ldap_connect(struct connectdata
*conn, bool *done);
[curl-7.62.0.p0] | ^~~~~~~~~~~~
[curl-7.62.0.p0] In file included from openldap.c:39:
[curl-7.62.0.p0] /usr/include/ldap.h:1555:1: note: previous declaration

of 'ldap_connect' with type 'int(LDAP *)' {aka 'int(struct ldap *)'}

[curl-7.62.0.p0] 1555 | ldap_connect( LDAP *ld );
[curl-7.62.0.p0] | ^~~~~~~~~~~~
[curl-7.62.0.p0] make[7]: *** [Makefile:2107: libcurl_la-openldap.lo]
Error 1
[curl-7.62.0.p0] make[6]: *** [Makefile:1028: all] Error 2
[curl-7.62.0.p0] make[5]: *** [Makefile:929: all-recursive] Error 1
[curl-7.62.0.p0]
********************************************************************************

> <mailto:sage-release%2Bunsu...@googlegroups.com>.

> To view this discussion on the web visit
> https://groups.google.com/d/msgid/sage-release/5cc232e7-70c5-0b53-eb65-0317f7e48656%40math.univ-lyon1.fr

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>
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> To view this discussion on the web visit

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[Dima Pasechnik]

On Wed, 13 Jul 2022, 09:25 Thierry Dumont, <tdu...@math.univ-lyon1.fr> wrote:

Le 13/07/2022 à 09:57, Dima Pasechnik a écrit :
> what does top level config.log say about curl?
>
> why the system one was not good?

Note that curl was downloaded (source) and its compilation failed.

you have a header clash between the Sage's curl and system curl.

why does configure reject the system curl?

(this can be found by inspecting config.log)

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[Thierry Dumont]

Le 13/07/2022 à 10:29, Dima Pasechnik a écrit :
>
>
> On Wed, 13 Jul 2022, 09:25 Thierry Dumont, <tdu...@math.univ-lyon1.fr
> <mailto:tdu...@math.univ-lyon1.fr>> wrote:
>
>
>
> Le 13/07/2022 à 09:57, Dima Pasechnik a écrit :
> > what does top level config.log say about curl?
> >
> > why the system one was not good?
>
> Note that curl was downloaded (source) and its compilation failed.
>
>
> you have a header clash between the Sage's curl and system curl.
>
> why does configure reject the system curl?
> (this can be found by inspecting config.log)
>

This is a part of config.log.
The ubuntu packages libcurl*.dev are not installed (and the
configuration procedure did not mention this):

# Checking whether SageMath should install SPKG curl... ##
## ----------------------------------------------------- ##
configure:20300: checking for curl 7.22
configure:20343: result:
configure:20389: checking for gawk
configure:20421: result: gawk
configure:20488: checking for curl-config
configure:20526: result: no
configure:20604: checking whether libcurl is usable
configure:20639: g++ -std=gnu++11 -o conftest conftest.cpp -lcurl
-lbz2 -lflint -lmpfr -lgmp -lm -lntl >&5
conftest.cpp:28:10: fatal error: curl/curl.h: No such file or directory
28 | #include <curl/curl.h>
| ^~~~~~~~~~~~~
compilation terminated.
configure:20639: $? = 1
configure: failed program was:
| /* confdefs.h */

[Dima Pasechnik]

On Wed, Jul 13, 2022 at 9:40 AM Thierry Dumont

<tdu...@math.univ-lyon1.fr> wrote:
>
>
>
> Le 13/07/2022 à 10:29, Dima Pasechnik a écrit :
> >
> >
> > On Wed, 13 Jul 2022, 09:25 Thierry Dumont, <tdu...@math.univ-lyon1.fr
> > <mailto:tdu...@math.univ-lyon1.fr>> wrote:
> >
> >
> >
> > Le 13/07/2022 à 09:57, Dima Pasechnik a écrit :
> > > what does top level config.log say about curl?
> > >
> > > why the system one was not good?
> >
> > Note that curl was downloaded (source) and its compilation failed.
> >
> >
> > you have a header clash between the Sage's curl and system curl.
> >
> > why does configure reject the system curl?
> > (this can be found by inspecting config.log)
> >
>
> This is a part of config.log.
> The ubuntu packages libcurl*.dev are not installed (and the
> configuration procedure did not mention this):
>

./configure should print an advice to install libcurl4-openssl-dev
somewhere at the end of its run.

> # Checking whether SageMath should install SPKG curl... ##
> ## ----------------------------------------------------- ##
> configure:20300: checking for curl 7.22
> configure:20343: result:
> configure:20389: checking for gawk
> configure:20421: result: gawk
> configure:20488: checking for curl-config
> configure:20526: result: no
> configure:20604: checking whether libcurl is usable
> configure:20639: g++ -std=gnu++11 -o conftest conftest.cpp -lcurl
> -lbz2 -lflint -lmpfr -lgmp -lm -lntl >&5
> conftest.cpp:28:10: fatal error: curl/curl.h: No such file or directory
> 28 | #include <curl/curl.h>
> | ^~~~~~~~~~~~~
> compilation terminated.
> configure:20639: $? = 1
> configure: failed program was:
> | /* confdefs.h */
>

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[Thierry Dumont]

Le 13/07/2022 à 10:57, Dima Pasechnik a écrit :
> On Wed, Jul 13, 2022 at 9:40 AM Thierry Dumont
> <tdu...@math.univ-lyon1.fr> wrote:
>>
>>
>>
>> Le 13/07/2022 à 10:29, Dima Pasechnik a écrit :
>>>
>>>
>
> ./configure should print an advice to install libcurl4-openssl-dev
> somewhere at the end of its run.
>
>

Yes. But it did not.
This problem seems to appear with this beta7 version.
Also: in Ubuntu there are different versions of libcurl*.dev
libcurl4-gnutls.dev
libcurl4-nss.dev
libcurl4-openssl.dev
In my case only the gnutls version could be installed (others give
conflicts). May be the advice will be a bit complicated.
So I installed it. Then config.log is ok with curl.
I am now recompiling.
t.d

>

[Dima Pasechnik]

On Wed, Jul 13, 2022 at 10:08 AM Thierry Dumont

<tdu...@math.univ-lyon1.fr> wrote:
>
>
>
> Le 13/07/2022 à 10:57, Dima Pasechnik a écrit :
> > On Wed, Jul 13, 2022 at 9:40 AM Thierry Dumont
> > <tdu...@math.univ-lyon1.fr> wrote:
> >>
> >>
> >>
> >> Le 13/07/2022 à 10:29, Dima Pasechnik a écrit :
> >>>
> >>>
> >
> > ./configure should print an advice to install libcurl4-openssl-dev
> > somewhere at the end of its run.
> >
> >
> Yes. But it did not.
> This problem seems to appear with this beta7 version.

9.7.beta5, you mean?

I suppose Sage's curl is getting old, and less compatible.
For some reason, Ubuntu is behind Debian in versions (Debian's curl is
7.84, the latest)
https://curl.se/download.html

I've opened a ticket to update curl: https://trac.sagemath.org/ticket/34176

> Also: in Ubuntu there are different versions of libcurl*.dev
> libcurl4-gnutls.dev
> libcurl4-nss.dev
> libcurl4-openssl.dev
> In my case only the gnutls version could be installed (others give
> conflicts). May be the advice will be a bit complicated.

yeah. (I don't understand why people want to use gnutls, in view of
https://cve.mitre.org/cgi-bin/cvekey.cgi?keyword=gnutls
it's no better than openssl, if not worse)

> So I installed it. Then config.log is ok with curl.
> I am now recompiling.
> t.d
>
> >
>

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