Sage 9.2.beta13 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 

Again, if there is anything that should be merged in this beta cycle then a positively-reviewed patch has to materialize real soon ;-)

468f23815a (tag: 9.2.beta13, trac/develop) Updated SageMath version to 9.2.beta13

85a3dc5389 Trac #30600: fix ecm on macOS Xcode 12

a7608327d4 Trac #30053: Python 3.7+: setlocale: LC_ALL: cannot change locale (C.UTF-8) from build/bin/sage-spkg and in doctests; disable use of system Python 3.6

99faab8cbe Trac #30593: gf2x build with Xcode 12

2e265be7d0 Trac #30594: ecl build with Xcode 12

b66986d09b Trac #30491: add check parameter for lattice posets

114ee7373b Trac #30467: src/tox.ini: Check patchbot plugin patterns and common typo patterns

f2e15e2be5 Trac #30465: faster and memory efficient implementation of Szeged index

868adde689 Trac #30444: Mention anonymous hyperlinks in developer doc

ee5f4f3c6d Trac #30437: Special Implementation of random_element() for Laurent Series Rings

2eebb6c71e Trac #30425: Upgrade: misc pip upgrades 2020-08: SymPy, pip, six

fc5bfc7617 Trac #29363: At the end of configure, indicate which optional/experimental packages are configured to be installed

87116edf2a Trac #28864: 17 internet doctest failing in findstat.py

c58024ef03 Trac #30568: Fix computation of eigenvectors using arb

5e159a4298 Trac #30560: Make openssl an optional dependency of python3

6525ae113e Trac #30557: Add spkg-configure.m4 for openssl

fda96c41ac Trac #28838: Resurrect "sage -sws2rst" via a pip-installable package sage_sws2rst

da78a68d07 Trac #30396: cygwin-standard: sagelib build fails

d5b9e06998 Trac #30403: Standard package zlib cannot be installed on some platforms, breaking Docker build

907912f7ff Trac #30405: Graphs: fast implementation to compute antipodal graph

5adec5bd66 Trac #30329: Graphs: last unbounded diameter distance-regular graphs

51ea8fa1cb Trac #30320: set_default_frame() too restrictive on parallelizable manifolds

e8c87f3cd3 Trac #30312: Graphs: more classical parameters distance regular graphs

42f81f6f5c Trac #30275: Replace AssertionError with ValueError

57cd152782 Trac #30216: GH Actions: Test Windows with WSL

762de29268 Trac #30187: Words: improve `count` consistency across datatype representation

0ffff2c41b Trac #30041: coefficients of a polynomial yielding an element in an extension of a p-adic field

dff7c61f3a Trac #29541: spkg-configure.m4 for giac

70ea8fedf0 Trac #28136: Add number_of_subgroups() method to AbelianGroup

395be93987 Trac #28012: py3: import certain things from collections.abc

d9c15ae9c9 Trac #30550: conda-forge-ubuntu-standard: Pillow fails to install

d73ae6d0f4 Trac #30543: Document spkg-configure.m4 and distros directory

488f5076f7 Trac #30535: conda-forge-macos-standard: sagelib build fails with linbox-related error

53cf5c2aed Trac #29743: is_unit() fails for power-series-ring element: O(t^0)

72a76b31a5 Trac #28991: spkg-configure.m4 for gc

0e79ab3e4c Trac #28814: Conversion of scientific notation floats/RDF,etc... incorrect in Mathematica interface

0192e3a95c Trac #11736: Linear time implementation of lex_BFS()

f100b1886d Trac #30536: configure: No longer prefer gfortran-9; homebrew: Recommend gcc instead of gcc@9

736554330f Trac #30519: Fix check of orientation in volume form

cd65699176 Trac #30340: tox.yml (dist): Do not fail when the tag already exists

07a863dd16 Trac #28022: Downgrade rubiks to optional

363f8586eb Trac #16809: leak in maxima interface

5ec24db181 (tag: 9.2.beta12) Updated SageMath version to 9.2.beta12

[Kenji Iohara]

I have compiled it completely (not an update) on Mac OS 10.15.6 with XCode 12 and execute make -k, it failed for 3 packages:

openblas-0.3.9

readline-6.3.008.p0

symmetrica-2.0.p11

. 

[John H Palmieri]

For openblas and readline, I suggest using homebrew's versions of those packages. For symmetrica, there is an upgrade at https://trac.sagemath.org/ticket/29061 which seems to fix the problem. For scipy (which you probably haven't reached in your build and which will probably fail when you do), there is a fix at https://trac.sagemath.org/ticket/30604.

If you don't use homebrew, there is a proposed fix for readline at https://trac.sagemath.org/ticket/30603, although it hasn't been tested very much. There are no fixes yet for openblas.

[John H Palmieri]

On Monday, September 21, 2020 at 10:32:05 PM UTC-7, John H Palmieri wrote:

For openblas and readline, I suggest using homebrew's versions of those packages. For symmetrica, there is an upgrade at https://trac.sagemath.org/ticket/29061 which seems to fix the problem. For scipy (which you probably haven't reached in your build and which will probably fail when you do), there is a fix at https://trac.sagemath.org/ticket/30604.

If you don't use homebrew, there is a proposed fix for readline at https://trac.sagemath.org/ticket/30603, although it hasn't been tested very much. There are no fixes yet for openblas.

Actually, after running configure, you should have seen a message saying

hint: installing the following system packages is recommended and may avoid building some of the above SPKGs from source:
$ brew install bdw-gc gcc gsl libatomic_ops openblas openssl r readline suite-sparse

You should follow those directions: it will speed up the Sage build (especially building gcc, which can take quite a while), as well as avoiding some of these Xcode 12 problems.

[Eric Gourgoulhon]

On Ubuntu 18.04 running on a bi-Xeon E5-2623 (8 cores) + 16 GB RAM computer:

  - incremental build (with -j16) from 9.2.beta12: OK

  - make ptestlong: all tests passed.

Eric.

[Emmanuel Charpentier]

Results similar (but not identical !) to those obtained on the same machine with 9.2.beta12 :

On Debian testing running on core i7 + 16 GB RAM, upgrading 9.2.beta12 to 9.10.beta13 and running ptestlong gets 7 permanent and 1 transient failures :

File	Result	P/T
src/sage/schemes/hyperelliptic_curves/monsky_washnitzer.py	Killed due to abort	P
src/sage/tests/parigp.py	Timed out	T
src/sage/rings/complex_arb.pyx	6 doctests failed	P
src/sage/modules/fg_pid/fgp_module.py	3 doctests failed	P
src/doc/en/constructions/algebraic_geometry.rst	1 doctest failed	P
src/doc/en/developer/coding_in_other.rst	1 doctest failed	P
src/sage/rings/real_arb.pyx	2 doctests failed	P
src/sage/modules/free_module_morphism.py	3 doctests failed	P

Of note :

• ./configure --enable-download-from-upstream-url suggested the installation of libnauty-dev, which I did ; apt installed libnauty2-dev instead, which was not recognized by ./config.status --recheck.

HTH,

​

[Dima Pasechnik]

for arb-related errors (you are probably using arb 2.18) there is a fix, not yet in beta.

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[Thierry Dumont]

Ubuntu 20-04. Migration from beta 12 to beta 13 ok.make ptestlong: all
test passed.
t.d.

[Sébastien Labbé]

On Ubuntu 18.04, Running tests with few optional and external packages (including internet this time), I obtain

Using --optional=4ti2,ccache,cryptominisat,dot2tex,e_antic,external,fricas,glucose,latte_int,libnauty,lidia,lrslib,memlimit,normaliz,notedown,openssl,pandoc_attributes,pycosat,pynormaliz,rst2ipynb,sage,sage_numerical_backends_coin

----------------------------------------------------------------------
sage -t --long --random-seed=0 src/doc/en/constructions/interface_issues.rst  # 1 doctest failed
sage -t --long --random-seed=0 src/sage/arith/misc.py  # 1 doctest failed
sage -t --long --random-seed=0 src/sage/combinat/designs/incidence_structures.py  # 1 doctest failed
sage -t --long --random-seed=0 src/sage/databases/oeis.py  # 1 doctest failed
sage -t --long --random-seed=0 src/sage/graphs/generic_graph.py  # 2 doctests failed
sage -t --long --random-seed=0 src/sage/graphs/graph.py  # 3 doctests failed
sage -t --long --random-seed=0 src/sage/lfunctions/sympow.py  # 4 doctests failed
sage -t --long --random-seed=0 src/sage/misc/package.py  # 2 doctests failed
sage -t --long --random-seed=0 src/sage/misc/remote_file.py  # 1 doctest failed
sage -t --long --random-seed=0 src/sage/schemes/elliptic_curves/ell_rational_field.py  # 2 doctests failed
sage -t --long --random-seed=0 src/sage/symbolic/integration/external.py  # 1 doctest failed
sage -t --long --random-seed=0 src/sage/symbolic/integration/integral.py  # 1 doctest failed
----------------------------------------------------------------------
External software detected for doctesting: ffmpeg,graphviz,imagemagick,internet,latex,octave,pandoc


Rerunning the failed tests, I get the same.


I copy paste below the failures:


sage -t --long --random-seed=0 src/sage/schemes/elliptic_curves/ell_rational_field.py
**********************************************************************
File "src/sage/schemes/elliptic_curves/ell_rational_field.py", line 1496, in sage.schemes.elliptic_curves.ell_rational_field.EllipticCurve_rational_field.analytic_rank
Failed example:
    E.analytic_rank(algorithm='sympow')
Exception raised:
    Traceback (most recent call last):
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 720, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 1145, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.schemes.elliptic_curves.ell_rational_field.EllipticCurve_rational_field.analytic_rank[3]>", line 1, in <module>
        E.analytic_rank(algorithm='sympow')
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/schemes/elliptic_curves/ell_rational_field.py", line 1551, in analytic_rank
        return sympow.analytic_rank(self)[0]
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/lfunctions/sympow.py", line 299, in analytic_rank
        raise RuntimeError("failed to compute analytic rank")
    RuntimeError: failed to compute analytic rank
**********************************************************************
File "src/sage/schemes/elliptic_curves/ell_rational_field.py", line 1502, in sage.schemes.elliptic_curves.ell_rational_field.EllipticCurve_rational_field.analytic_rank
Failed example:
    E.analytic_rank(algorithm='all')
Exception raised:
    Traceback (most recent call last):
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 720, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 1145, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.schemes.elliptic_curves.ell_rational_field.EllipticCurve_rational_field.analytic_rank[5]>", line 1, in <module>
        E.analytic_rank(algorithm='all')
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/schemes/elliptic_curves/ell_rational_field.py", line 1567, in analytic_rank
        self.analytic_rank('rubinstein'), self.analytic_rank('sympow')])
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/schemes/elliptic_curves/ell_rational_field.py", line 1551, in analytic_rank
        return sympow.analytic_rank(self)[0]
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/lfunctions/sympow.py", line 299, in analytic_rank
        raise RuntimeError("failed to compute analytic rank")
    RuntimeError: failed to compute analytic rank
**********************************************************************
1 item had failures:
   2 of  14 in sage.schemes.elliptic_curves.ell_rational_field.EllipticCurve_rational_field.analytic_rank
    1 database_cremona_ellcurve test not run
    8 magma tests not run
    1 webbrowser test not run
    0 tests not run because we ran out of time
    [849 tests, 2 failures, 86.03 s]
sage -t --long --random-seed=0 src/sage/arith/misc.py
**********************************************************************
File "src/sage/arith/misc.py", line 2019, in sage.arith.misc.xkcd
Failed example:
    xkcd(353)  # optional - internet
Expected:
    <h1>Python</h1><img src="https://imgs.xkcd.com/comics/python.png" title="I wrote 20 short programs in Python yesterday.  It was wonderful.  Perl, I'm leaving you."><div>Source: <a href="http://xkcd.com/353" target="_blank">http://xkcd.com/353</a></div>
Got:
    <script> alert("Error: -41"); </script>
**********************************************************************
1 item had failures:
   1 of   2 in sage.arith.misc.xkcd
    1 kash test not run
    2 magma tests not run
    1 not tested test not run
    0 tests not run because we ran out of time
    [1066 tests, 1 failure, 22.54 s]
sage -t --long --random-seed=0 src/sage/symbolic/integration/external.py
**********************************************************************
File "src/sage/symbolic/integration/external.py", line 260, in sage.symbolic.integration.external.parse_moutput_from_json
Failed example:
    sorted(L)                                             # optional internet
Expected:
    [u'-Cos[x]', u'{{x == Pi C[1], Element[C[1], Integers]}}']
Got:
    ['-Cos[x]', '{{x == 0}}', '{{x == Pi C[1], Element[C[1], Integers]}}']
**********************************************************************
1 item had failures:
   1 of  10 in sage.symbolic.integration.external.parse_moutput_from_json
    0 tests not run because we ran out of time
    [48 tests, 1 failure, 24.69 s]
sage -t --long --random-seed=0 src/sage/lfunctions/sympow.py
**********************************************************************
File "src/sage/lfunctions/sympow.py", line 277, in sage.lfunctions.sympow.Sympow.analytic_rank
Failed example:
    sympow.analytic_rank(EllipticCurve('11a'))
Exception raised:
    Traceback (most recent call last):
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 720, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 1145, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.lfunctions.sympow.Sympow.analytic_rank[0]>", line 1, in <module>
        sympow.analytic_rank(EllipticCurve('11a'))
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/lfunctions/sympow.py", line 299, in analytic_rank
        raise RuntimeError("failed to compute analytic rank")
    RuntimeError: failed to compute analytic rank
**********************************************************************
File "src/sage/lfunctions/sympow.py", line 281, in sage.lfunctions.sympow.Sympow.analytic_rank
Failed example:
    sympow.analytic_rank(EllipticCurve('389a'))
Exception raised:
    Traceback (most recent call last):
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 720, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 1145, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.lfunctions.sympow.Sympow.analytic_rank[2]>", line 1, in <module>
        sympow.analytic_rank(EllipticCurve('389a'))
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/lfunctions/sympow.py", line 299, in analytic_rank
        raise RuntimeError("failed to compute analytic rank")
    RuntimeError: failed to compute analytic rank
**********************************************************************
File "src/sage/lfunctions/sympow.py", line 285, in sage.lfunctions.sympow.Sympow.analytic_rank
Failed example:
    sympow.analytic_rank(EllipticCurve([1, -1, 0, -79, 289]))
Exception raised:
    Traceback (most recent call last):
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 720, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 1145, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.lfunctions.sympow.Sympow.analytic_rank[4]>", line 1, in <module>
        sympow.analytic_rank(EllipticCurve([Integer(1), -Integer(1), Integer(0), -Integer(79), Integer(289)]))
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/lfunctions/sympow.py", line 299, in analytic_rank
        raise RuntimeError("failed to compute analytic rank")
    RuntimeError: failed to compute analytic rank
**********************************************************************
File "src/sage/lfunctions/sympow.py", line 289, in sage.lfunctions.sympow.Sympow.analytic_rank
Failed example:
    sympow.analytic_rank(EllipticCurve([1, 1, 0, -2582, 48720]))  # long time
Exception raised:
    Traceback (most recent call last):
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 720, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 1145, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.lfunctions.sympow.Sympow.analytic_rank[6]>", line 1, in <module>
        sympow.analytic_rank(EllipticCurve([Integer(1), Integer(1), Integer(0), -Integer(2582), Integer(48720)]))  # long time
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/lfunctions/sympow.py", line 299, in analytic_rank
        raise RuntimeError("failed to compute analytic rank")
    RuntimeError: failed to compute analytic rank
**********************************************************************
1 item had failures:
   4 of   9 in sage.lfunctions.sympow.Sympow.analytic_rank
    5 not tested tests not run
    0 tests not run because we ran out of time
    [13 tests, 4 failures, 3.39 s]
sage -t --long --random-seed=0 src/sage/symbolic/integration/integral.py
**********************************************************************
File "src/sage/symbolic/integration/integral.py", line 72, in sage.symbolic.integration.integral.IndefiniteIntegral.__init__
Failed example:
    (f*f).integrate(x, algorithm="mathematica_free") # optional -- internet
Expected:
    -b*log(e^(-(a - x)/b) + 1) + x + b/(e^(-(a - x)/b) + 1)
Got:
    -b*log(e^(a/b) + e^(x/b)) + x + b/(e^(-(a - x)/b) + 1)
**********************************************************************
1 item had failures:
   1 of  12 in sage.symbolic.integration.integral.IndefiniteIntegral.__init__
    3 tests not run due to known bugs
    2 maple tests not run
    3 mathematica tests not run
    0 tests not run because we ran out of time
    [216 tests, 1 failure, 26.14 s]
sage -t --long --random-seed=0 src/sage/misc/remote_file.py
**********************************************************************
File "src/sage/misc/remote_file.py", line 27, in sage.misc.remote_file.get_remote_file
Failed example:
    with open(g) as f: print(f.read())           # optional - internet
Expected:
    print("hi from the net")
    <BLANKLINE>
    print(2+3)
Got:
    print("hi from the net")
    <BLANKLINE>
    print(2 + 3)
    <BLANKLINE>
**********************************************************************
1 item had failures:
   1 of   4 in sage.misc.remote_file.get_remote_file
    0 tests not run because we ran out of time
    [3 tests, 1 failure, 0.26 s]
sage -t --long --random-seed=0 src/doc/en/constructions/interface_issues.rst
**********************************************************************
File "src/doc/en/constructions/interface_issues.rst", line 432, in doc.en.constructions.interface_issues
Failed example:
    octave("atanh(1.1)")   ## optional - octave
Expected:
    (1.52226,-1.5708)
Got:
     (1.52226,1.5708)
**********************************************************************
1 item had failures:
   1 of  22 in doc.en.constructions.interface_issues
    0 tests not run because we ran out of time
    [17 tests, 1 failure, 1.98 s]
sage -t --long --random-seed=0 src/sage/graphs/graph.py
**********************************************************************
File "src/sage/graphs/graph.py", line 4507, in sage.graphs.graph.Graph.has_homomorphism_to
Failed example:
    g.has_homomorphism_to(graphs.CycleGraph(4)) is not False
Expected:
    False
Got:
    True
**********************************************************************
File "src/sage/graphs/graph.py", line 4902, in sage.graphs.graph.Graph.minor
Failed example:
    L = g.minor(graphs.CompleteGraph(3))
Expected:
    Traceback (most recent call last):
    ...
    ValueError: This graph has no minor isomorphic to H !
Got:
    <BLANKLINE>
**********************************************************************
File "src/sage/graphs/graph.py", line 6112, in sage.graphs.graph.Graph.topological_minor
Failed example:
    g.topological_minor(graphs.CycleGraph(3))
Expected:
    False
Got:
    Subgraph of (Subgraph of (RandomGNP(15,0.300000000000000))): Graph on 0 vertices
**********************************************************************
3 items had failures:
   1 of  10 in sage.graphs.graph.Graph.has_homomorphism_to
   1 of  14 in sage.graphs.graph.Graph.minor
   1 of   7 in sage.graphs.graph.Graph.topological_minor
    2 mcqd tests not run
    2 not tested tests not run
    13 python_igraph tests not run
    0 tests not run because we ran out of time
    [1238 tests, 3 failures, 26.85 s]
sage -t --long --random-seed=0 src/sage/combinat/designs/incidence_structures.py
**********************************************************************
File "src/sage/combinat/designs/incidence_structures.py", line 2027, in sage.combinat.designs.incidence_structures.IncidenceStructure.coloring
Failed example:
    len(designs.steiner_triple_system(7).coloring())
Expected:
    3
Got:
    2
**********************************************************************
1 item had failures:
   1 of   6 in sage.combinat.designs.incidence_structures.IncidenceStructure.coloring
    8 gap_packages tests not run
    3 not tested tests not run
    0 tests not run because we ran out of time
    [337 tests, 1 failure, 1.58 s]
sage -t --long --random-seed=0 src/sage/databases/oeis.py
**********************************************************************
File "src/sage/databases/oeis.py", line 527, in sage.databases.oeis.OEIS.find_by_subsequence
Failed example:
    oeis.find_by_subsequence([2, 3, 5, 8, 13, 21, 34, 55, 89, 144, 233, 377]) # optional -- internet
Expected:
    0: A000045: Fibonacci numbers: F(n) = F(n-1) + F(n-2) with F(0) = 0 and F(1) = 1.
    1: A212804: Expansion of (1-x)/(1-x-x^2).
    2: A177194: Fibonacci numbers whose decimal expansion does not contain any digit 0.
Got:
    0: A000045: Fibonacci numbers: F(n) = F(n-1) + F(n-2) with F(0) = 0 and F(1) = 1.
    1: A212804: Expansion of (1 - x)/(1 - x - x^2).
    2: A177194: Fibonacci numbers whose decimal expansion does not contain any digit 0.
**********************************************************************
1 item had failures:
   1 of   3 in sage.databases.oeis.OEIS.find_by_subsequence
    5 webbrowser tests not run
    0 tests not run because we ran out of time
    [287 tests, 1 failure, 32.50 s]
sage -t --long --random-seed=0 src/sage/graphs/generic_graph.py
**********************************************************************
File "src/sage/graphs/generic_graph.py", line 8909, in sage.graphs.generic_graph.GenericGraph.nowhere_zero_flow
Failed example:
    h = g.nowhere_zero_flow(k=3)
Expected:
    Traceback (most recent call last):
    ...
    EmptySetError: the problem has no feasible solution
Got:
    <BLANKLINE>
**********************************************************************
File "src/sage/graphs/generic_graph.py", line 9530, in sage.graphs.generic_graph.GenericGraph.disjoint_routed_paths
Failed example:
    p1,p2 = g.disjoint_routed_paths([((0, 0), (4, 4)), ((0, 4), (4, 0))])
Expected:
    Traceback (most recent call last):
    ...
    EmptySetError: the disjoint routed paths do not exist
Got:
    <BLANKLINE>
**********************************************************************
2 items had failures:
   1 of   5 in sage.graphs.generic_graph.GenericGraph.disjoint_routed_paths
   1 of  29 in sage.graphs.generic_graph.GenericGraph.nowhere_zero_flow
    17 bliss tests not run
    6 not tested tests not run
    39 python_igraph tests not run
    0 tests not run because we ran out of time
    [3513 tests, 2 failures, 36.86 s]
sage -t --long --random-seed=0 src/sage/misc/package.py
**********************************************************************
File "src/sage/misc/package.py", line 103, in sage.misc.package.pip_remote_version
Failed example:
    pip_remote_version(nap, pypi_url=pypi, ignore_URLError=True) # optional - internet
Expected:
    doctest:...: UserWarning: failed to fetch the version of
    pkg='hey_this_is_NOT_a_python_package' at http://this.is.not.pypi.com/
Got:
    doctest:warning
      File "/home/slabbe/GitBox/sage/src/bin/sage-runtests", line 182, in <module>
        err = DC.run()
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/control.py", line 1230, in run
        self.run_doctests()
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/control.py", line 931, in run_doctests
        self.dispatcher.dispatch()
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 2052, in dispatch
        self.parallel_dispatch()
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 1947, in parallel_dispatch
        w.start()  # This might take some time
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 2219, in start
        super(DocTestWorker, self).start()
      File "/usr/lib/python3.8/multiprocessing/process.py", line 121, in start
        self._popen = self._Popen(self)
      File "/usr/lib/python3.8/multiprocessing/context.py", line 224, in _Popen
        return _default_context.get_context().Process._Popen(process_obj)
      File "/usr/lib/python3.8/multiprocessing/context.py", line 276, in _Popen
        return Popen(process_obj)
      File "/usr/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
        self._launch(process_obj)
      File "/usr/lib/python3.8/multiprocessing/popen_fork.py", line 75, in _launch
        code = process_obj._bootstrap(parent_sentinel=child_r)
      File "/usr/lib/python3.8/multiprocessing/process.py", line 313, in _bootstrap
        self.run()
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 2191, in run
        task(self.options, self.outtmpfile, msgpipe, self.result_queue)
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 2520, in __call__
        doctests, extras = self._run(runner, options, results)
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 2567, in _run
        result = runner.run(test)
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 918, in run
        return self._run(test, compileflags, out)
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 720, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 1145, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.misc.package.pip_remote_version[3]>", line 1, in <module>
        pip_remote_version(nap, pypi_url=pypi, ignore_URLError=True) # optional - internet
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/misc/package.py", line 120, in pip_remote_version
        warnings.warn("failed to fetch the version of pkg={!r} at {}".format(pkg, url))
      File "/usr/lib/python3.8/warnings.py", line 109, in _showwarnmsg
        sw(msg.message, msg.category, msg.filename, msg.lineno,
    :
    UserWarning: failed to fetch the version of pkg='hey_this_is_NOT_a_python_package' at http://this.is.not.pypi.com//hey_this_is_NOT_a_python_package/json
**********************************************************************

[Emmanuel Charpentier]

Le mardi 22 septembre 2020 à 16:09:50 UTC+2, Dima Pasechnik a écrit :

for arb-related errors (you are probably using arb 2.18)

Indeed.

 

there is a fix, not yet in beta.

Thank you !

[Sébastien Labbé]

I copy paste below the failures:

Just created tickets #30632 to #30638 to deal with the doctest failures I reported earlier.

Follow up at https://trac.sagemath.org/ticket/25536

[jonatha...@googlemail.com]

On ubuntu bionic incremental build  of  and dateutils fail.

Those are the logs:

 Found local metadata for zipp-0.5.2
   2 Attempting to download package zipp-0.5.2.tar.gz from mirrors
   3 https://mirror.koddos.net/sagemath/spkg/upstream/zipp/zipp-0.5.2.tar.gz
   4 [......................................................................]
   5 zipp-0.5.2
   6 ====================================================
   7 Setting up build directory for zipp-0.5.2
   8 Finished extraction
   9 No patch files found in ../patches
  10 ****************************************************
  11 Host system:
  12 Linux kliem-ThinkPad-L570 4.15.0-115-generic #116-Ubuntu SMP Wed Aug 26 14:04:49 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
  13 ****************************************************
  14 C compiler: gcc
  15 C compiler version:
  16 Using built-in specs.
  17 COLLECT_GCC=gcc
  18 COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper
  19 OFFLOAD_TARGET_NAMES=nvptx-none
  20 OFFLOAD_TARGET_DEFAULT=1
  21 Target: x86_64-linux-gnu
  22 Configured with: ../src/configure -v --with-pkgversion='Ubuntu 7.5.0-3ubuntu1~18.04' --with-bugurl=file:///usr/share/doc/gcc-7/README.Bugs --enable-languages=c,ada,c++,go,brig     +++,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-7 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexe     +++cdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-lib     +++stdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib      +++--with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib -     +++-with-tune=generic --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linu     +++x-gnu
  23 Thread model: posix
  24 gcc version 7.5.0 (Ubuntu 7.5.0-3ubuntu1~18.04)
  25 ****************************************************
  26 Package 'zipp' is currently not installed
  27 No legacy uninstaller found for 'zipp'; nothing to do
  28 Installing zipp-0.5.2
  29 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSCo     +++nnection object at 0x7fd0fc6899d0>, 'Connection to 192.0.2.0 timed out. (connect timeout=15)')': /simple/setuptools-scm/
  30 WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSCo     +++nnection object at 0x7fd0fc6b4150>, 'Connection to 192.0.2.0 timed out. (connect timeout=15)')': /simple/setuptools-scm/
  31 WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSCo     +++nnection object at 0x7fd0fc6b42d0>, 'Connection to 192.0.2.0 timed out. (connect timeout=15)')': /simple/setuptools-scm/
  32 WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSCo     +++nnection object at 0x7fd0fc6b4490>, 'Connection to 192.0.2.0 timed out. (connect timeout=15)')': /simple/setuptools-scm/
  33 WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSCo     +++nnection object at 0x7fd0fc6b4650>, 'Connection to 192.0.2.0 timed out. (connect timeout=15)')': /simple/setuptools-scm/
  34 ERROR: Could not find a version that satisfies the requirement setuptools_scm>=1.15.0 (from versions: none)
  35 ERROR: No matching distribution found for setuptools_scm>=1.15.0
  36 Traceback (most recent call last):
  37   File "/home/jonathan/Applications/sage/local/lib/python3.7/site-packages/setuptools/installer.py", line 128, in fetch_build_egg
  38     subprocess.check_call(cmd)
  39   File "/usr/lib/python3.7/subprocess.py", line 363, in check_call
  40     raise CalledProcessError(retcode, cmd)
  41 subprocess.CalledProcessError: Command '['/home/jonathan/Applications/sage/local/bin/python3', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tm     +++ph9pgk8lv', '--quiet', 'setuptools_scm>=1.15.0']' returned non-zero exit status 1.
  42
  43 The above exception was the direct cause of the following exception:
  44
  45 Traceback (most recent call last):
  46   File "setup.py", line 6, in <module>
  47     setuptools.setup(use_scm_version=True)
  48   File "/home/jonathan/Applications/sage/local/lib/python3.7/site-packages/setuptools/__init__.py", line 162, in setup
  49     _install_setup_requires(attrs)
  50   File "/home/jonathan/Applications/sage/local/lib/python3.7/site-packages/setuptools/__init__.py", line 157, in _install_setup_requires
  51     dist.fetch_build_eggs(dist.setup_requires)
  52   File "/home/jonathan/Applications/sage/local/lib/python3.7/site-packages/setuptools/dist.py", line 702, in fetch_build_eggs
  53     replace_conflicting=True,
  54   File "/home/jonathan/Applications/sage/local/lib/python3.7/site-packages/pkg_resources/__init__.py", line 781, in resolve
  55     replace_conflicting=replace_conflicting
  56   File "/home/jonathan/Applications/sage/local/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1064, in best_match
  57     return self.obtain(req, installer)
  58   File "/home/jonathan/Applications/sage/local/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1076, in obtain
  59     return installer(requirement)
  60   File "/home/jonathan/Applications/sage/local/lib/python3.7/site-packages/setuptools/dist.py", line 758, in fetch_build_egg
  61     return fetch_build_egg(self, req)
  62   File "/home/jonathan/Applications/sage/local/lib/python3.7/site-packages/setuptools/installer.py", line 130, in fetch_build_egg
  63     raise DistutilsError(str(e)) from e
  64 distutils.errors.DistutilsError: Command '['/home/jonathan/Applications/sage/local/bin/python3', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/     +++tmph9pgk8lv', '--quiet', 'setuptools_scm>=1.15.0']' returned non-zero exit status 1.
  65 Error: could not determine package name
  66 *******************************************************************************************************************************************************************************     +++*****
  67 Error installing zipp-0.5.2
  68 *******************************************************************************************************************************************************************************     +++*****
  69
  70 real    1m38.874s
  71 user    0m1.090s
  72 sys     0m0.118s

631 Found local metadata for dateutil-2.8.1
632 Using cached file /home/jonathan/Applications/sage/upstream/python-dateutil-2.8.1.tar.gz
633 dateutil-2.8.1
634 ====================================================
635 Setting up build directory for dateutil-2.8.1
636 Finished extraction
637 No patch files found in ../patches
638 ****************************************************
639 Host system:
640 Linux kliem-ThinkPad-L570 4.15.0-117-generic #118-Ubuntu SMP Fri Sep 4 20:02:41 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
641 ****************************************************
642 C compiler: gcc
643 C compiler version:
644 Using built-in specs.
645 COLLECT_GCC=gcc
646 COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper
647 OFFLOAD_TARGET_NAMES=nvptx-none
648 OFFLOAD_TARGET_DEFAULT=1
649 Target: x86_64-linux-gnu
650 Configured with: ../src/configure -v --with-pkgversion='Ubuntu 7.5.0-3ubuntu1~18.04' --with-bugurl=file:///usr/share/doc/gcc-7/README.Bugs --enable-languages=c,ada,c++,go,brig,    +++d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-7 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecd    +++ir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstd    +++cxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --wi    +++th-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with    +++-tune=generic --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
651 Thread model: posix
652 gcc version 7.5.0 (Ubuntu 7.5.0-3ubuntu1~18.04)
653 ****************************************************
654 Package 'dateutil' is currently not installed
655 No legacy uninstaller found for 'dateutil'; nothing to do
656 Installing dateutil-2.8.1
657 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSCon    +++nection object at 0x7ffa11077150>, 'Connection to 192.0.2.0 timed out. (connect timeout=15)')': /simple/setuptools-scm/
658 WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSCon    +++nection object at 0x7ffa11077950>, 'Connection to 192.0.2.0 timed out. (connect timeout=15)')': /simple/setuptools-scm/
659 WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSCon    +++nection object at 0x7ffa11077a10>, 'Connection to 192.0.2.0 timed out. (connect timeout=15)')': /simple/setuptools-scm/
660 WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSCon    +++nection object at 0x7ffa110779d0>, 'Connection to 192.0.2.0 timed out. (connect timeout=15)')': /simple/setuptools-scm/
661 WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSCon    +++nection object at 0x7ffa11077dd0>, 'Connection to 192.0.2.0 timed out. (connect timeout=15)')': /simple/setuptools-scm/
662 ERROR: Could not find a version that satisfies the requirement setuptools_scm (from versions: none)
663 ERROR: No matching distribution found for setuptools_scm
664 Traceback (most recent call last):
665   File "/home/jonathan/Applications/sage/local/lib/python3.7/site-packages/setuptools/installer.py", line 128, in fetch_build_egg
666     subprocess.check_call(cmd)
667   File "/usr/lib/python3.7/subprocess.py", line 363, in check_call
668     raise CalledProcessError(retcode, cmd)
669 subprocess.CalledProcessError: Command '['/home/jonathan/Applications/sage/local/bin/python3', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmp    +++tokz6a75', '--quiet', 'setuptools_scm']' returned non-zero exit status 1.
                                                                                                                                                                  597,29        92%

670
671 The above exception was the direct cause of the following exception:
672
673 Traceback (most recent call last):
674   File "setup.py", line 56, in <module>
675     "test": Unsupported
676   File "/home/jonathan/Applications/sage/local/lib/python3.7/site-packages/setuptools/__init__.py", line 162, in setup
677     _install_setup_requires(attrs)
678   File "/home/jonathan/Applications/sage/local/lib/python3.7/site-packages/setuptools/__init__.py", line 157, in _install_setup_requires
679     dist.fetch_build_eggs(dist.setup_requires)
680   File "/home/jonathan/Applications/sage/local/lib/python3.7/site-packages/setuptools/dist.py", line 702, in fetch_build_eggs
681     replace_conflicting=True,
682   File "/home/jonathan/Applications/sage/local/lib/python3.7/site-packages/pkg_resources/__init__.py", line 781, in resolve
683     replace_conflicting=replace_conflicting
684   File "/home/jonathan/Applications/sage/local/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1064, in best_match
685     return self.obtain(req, installer)
686   File "/home/jonathan/Applications/sage/local/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1076, in obtain
687     return installer(requirement)
688   File "/home/jonathan/Applications/sage/local/lib/python3.7/site-packages/setuptools/dist.py", line 758, in fetch_build_egg
689     return fetch_build_egg(self, req)
690   File "/home/jonathan/Applications/sage/local/lib/python3.7/site-packages/setuptools/installer.py", line 130, in fetch_build_egg
691     raise DistutilsError(str(e)) from e
692 distutils.errors.DistutilsError: Command '['/home/jonathan/Applications/sage/local/bin/python3', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/t    +++mptokz6a75', '--quiet', 'setuptools_scm']' returned non-zero exit status 1.
693 Error: could not determine package name
694 ********************************************************************************************************************************************************************************    +++****
695 Error installing dateutil-2.8.1
696 ********************************************************************************************************************************************************************************    +++****
697
698 real    1m39.559s
699 user    0m1.487s
700 sys     0m0.162s
701 ************************************************************************
702 Error installing package dateutil-2.8.1
703 ************************************************************************
704 Please email sage-devel (http://groups.google.com/group/sage-devel)
705 explaining the problem and including the log file
706   /home/jonathan/Applications/sage/logs/pkgs/dateutil-2.8.1.log
707 Describe your computer, operating system, etc.
708 If you want to try to fix the problem yourself, *don't* just cd to
709 /home/jonathan/Applications/sage/local/var/tmp/sage/build/dateutil-2.8.1 and type 'make' or whatever is appropriate.
710 Instead, the following commands setup all environment variables
711 correctly and load a subshell for you to debug the error:
712   (cd '/home/jonathan/Applications/sage/local/var/tmp/sage/build/dateutil-2.8.1' && '/home/jonathan/Applications/sage/sage' --buildsh)
713 When you are done debugging, you can type "exit" to leave the subshell.
714 ************************************************************************
                                                                                                                                                                  714,29        Bot

[Dima Pasechnik]

yes, for some reason incremental build of dateutils fails.

rebuild from scratch works.

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[Thierry]

Hi,

On Wed, Sep 23, 2020 at 02:58:38AM -0700, 'jonatha...@googlemail.com' via sage-release wrote:
> On ubuntu bionic incremental build of and dateutils fail.

Indeed, apparently dateutil breaks most patchbots too, see
https://patchbot.sagemath.org/ticket/0/

Ciao,
Thierry

[Steven Trogdon]

On Gentoo, incremental build from beta12 -> beta13, I see the following failure

sage -t --long --warn-long 209.7 --random-seed=0 src/sage/interfaces/singular.py  # Killed due to segmentation fault

which is identical to the failure on ubuntu-groovy with beta12

https://github.com/sagemath/sage/runs/1078907777

The Cython backtrace starts as

Cython backtrace

----------------

#0  0x00007f2640f8daa0 in wait4 ()

#1  0x00007f2637f989ed in print_enhanced_backtrace ()

#2  0x00007f2637f98b89 in sigdie ()

#3  0x00007f2637f97f1c in sigdie_for_sig ()

#4  0x00007f2637f980b4 in cysigs_signal_handler ()

#5  0x0000000000000000 in ?? ()

#6  0x00007f2512e72710 in __pyx_f_9cysignals_7signals_verify_exc_value ()

#7  0x00007f261f11e0f9 in sig_occurred () at /local/sage-git/sage/build/pkgs/sagelib/src/sage/graphs/base/boost_graph.pyx:0

     1    r"""

     2    Interface to run Boost algorithms

     3

     4    Wrapper for a Boost graph. The Boost graphs are Cython C++ variables, and they

#8  0x00007f261f11caa4 in fast_tp_dealloc () at /local/sage-git/sage/build/pkgs/sagelib/src/sage/rings/integer.pyx:0

     1    r"""

     2    Elements of the ring `\ZZ` of integers

     3

     4    Sage has highly optimized and extensive functionality for arithmetic with integers

#9  0x00007f26412ebe40 in _PyEval_EvalFrameDefault ()

#10 0x00007f26413c8ab0 in _PyEval_EvalCodeWithName ()

#11 0x00007f26413c95d0 in PyEval_EvalCodeEx ()

#12 0x00007f26413c9620 in PyEval_EvalCode ()

The doctest always fails when run individually; although, occasionally it will pass when run from the full testsuite.

[Matthias Köppe]

This is likely from the most recent setuptools upgrade.

Try if https://trac.sagemath.org/ticket/29500 fixes this for you.

[Matthias Köppe]

I just encountered this problem on my system as well. Somehow the installation of `setuptools_scm` had disappeared even though the installation record in local/var/lib/sage/installed was still there. `sage -f setuptools_scm` corrected this.

[Kenji Iohara]

I have recompiled from the very beginning on Mac OS 10.15.7 with XCode 12,

and I couldn’t compile 

openblas-0.3.9

readline-6.3.008.p0

symmetrica-2.0.p11

.

2020/09/23 23:41、Matthias Köppe <matthia...@gmail.com>のメール:

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[Dima Pasechnik]

On Sat, Sep 26, 2020 at 9:29 PM Kenji Iohara <simplye...@gmail.com> wrote:
>
> I have recompiled from the very beginning on Mac OS 10.15.7 with XCode 12,
> and I couldn’t compile
>
> openblas-0.3.9
> readline-6.3.008.p0
> symmetrica-2.0.p11

there is work being done on these issues on
https://trac.sagemath.org/ticket/30494
In particular,

symmetrica is fixed by https://trac.sagemath.org/ticket/29061
readline by https://trac.sagemath.org/ticket/30603
openblas by https://trac.sagemath.org/ticket/30610

HTH
Dima

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