Sage 9.2.beta12 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 ;-)

5ec24db181 (tag: 9.2.beta12, trac/develop) Updated SageMath version to 9.2.beta12

5efa8df9cd Trac #30454: some details in doc of number fields

d1a1a28695 Trac #30443: Simplify setting and getting "edges" of edges, ridges, incidences in `CombinatorialPolyhedron`

f8c4e4b530 Trac #30409: Optional ideal parameter for normalize_coordinates

603aa8806e Trac #28722: update constants for S-unit solver

21f7af35b4 Trac #14735: Bug with Python int division in wigner.py

7d9921cca9 Trac #30490: Reduce doctesting time for polyhedra

11c8e5b6ff Trac #30487: GH Actions: Test also with Xcode 12 beta

80c4c5e916 Trac #30479: deprecate random_DAG

505f3f4065 Trac #30470: Make spanning_trees an iterator

80d9314aef Trac #30455: pep8 cleanup of the file e_one_star

d6b5a59b02 Trac #30452: "sage -startuptime" should accept file names too

9e5a3ba06e Trac #30449: Fix docbuild warning in combinat plus improve formatting

875d7180ca Trac #30442: Implement general table art for tableau-like objects

e8696d8001 Trac #30440: Pyramid for combinatorial polyhedron

dfa0d227a5 Trac #30410: Command "sage -tox"

b8421f50e2 Trac #30401: Unions of subsets of a fixed open set X are not known to be subsets of X

e0b21bfd1d Trac #30395: enhance fricas lists

50d0934dff Trac #30382: More voidlinux.txt

1185b94e8d Trac #30212: Fix tkz-graph and tkz-berge links: altermundus.com is gone

4974b90112 Trac #28982: Use CombinatorialPolyhedron to obtain faces lattice of polyhedra

dcf19afbfc Trac #27952: upgrade Normaliz to 3.8.8, PyNormaliz to 2.12, add script package libnauty

a5f5293ca6 Trac #30496: fix conversion of GAP univariate rat functions, which are polynomial with valuation>0

596988abf2 Trac #30489: Two fixes for test suite for products of polyhedra

b9c5e0bdbd Trac #30488: ci-cygwin: Remove sage_brial

b0465d76c9 Trac #30317: Update pip to 20.2.2, setuptools to 49.6.0

d96db5467d Trac #27754: Upgrade: Python 3.8.5

c353bce995 (tag: 9.2.beta11) Updated SageMath version to 9.2.beta11

[Matthias Köppe]

On Sunday, September 6, 2020 at 4:25:39 PM UTC-7, Volker Braun wrote:

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 

5ec24db181 (tag: 9.2.beta12, trac/develop) Updated SageMath version to 9.2.beta12

Thanks for preparing the new beta.

Testers, please note that this beta contains the Python 3.8 upgrade from https://trac.sagemath.org/ticket/27754, so if previous betas rejected your distribution's python 3.8, it would make sense to do a "make python3-clean" before rebuilding.

Tests have started at https://github.com/sagemath/sage/actions . First results:

ubuntu-{trusty, xenial, focal}: clean

ubunt-{bionic,eoan, groovy}-minimal: clean

ubuntu-bionic-standard (https://github.com/sagemath/sage/runs/1078907737):

  [dochtml]   UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 2661: ordinal not in range(128)

  [dochtml] Full log file: logs/dochtml.log

Makefile:1874: recipe for target 'doc-html' failed

ubuntu-eoan-standard (https://github.com/sagemath/sage/runs/1078907750)

sage -t --random-seed=0 src/sage/libs/eclib/interface.py  # 2 doctests failed

ubuntu-groovy-standard (https://github.com/sagemath/sage/runs/1078907777): 

sage -t --random-seed=0 src/doc/en/constructions/algebraic_geometry.rst  # 1 doctest failed

sage -t --random-seed=0 src/doc/en/developer/coding_in_other.rst  # 1 doctest failed

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

sage -t --random-seed=0 src/sage/modules/fg_pid/fgp_module.py  # 3 doctests failed

sage -t --random-seed=0 src/sage/modules/free_module_morphism.py  # 3 doctests failed

sage -t --random-seed=0 src/sage/rings/complex_arb.pyx  # 6 doctests failed

sage -t --random-seed=0 src/sage/rings/real_arb.pyx  # 2 doctests failed

sage -t --random-seed=0 src/sage/schemes/hyperelliptic_curves/monsky_washnitzer.py  # Killed due to abort

Tests for optional packages are running at https://github.com/sagemath/sage/actions/runs/242113003

As noted in https://trac.sagemath.org/ticket/29900, many optional packages fail to build. I propose that we do a mass downgrade of broken optional packages to experimental status in https://trac.sagemath.org/ticket/30349, based on the test results of this beta.

[Kenji Iohara]

I could compile it on Mac OS 10.15.6 but failed in making ptestlong: 

The following package(s) may have failed to build (not necessarily

during this run of 'make all-start'):

* documentation:         dochtml

  last build time: Sep 7 09:57

  log file:        /Users/iohara/Desktop/sage-9.2.beta12/logs/pkgs/../dochtml.log

here is its logfile:

[Thierry Dumont]

Migration from beta 11 to beta 12 (Ubuntu 20-04):

- compilation ok.

- make ptestlong:

sage -t --long --warn-long 110.2 --random-seed=0

src/sage/interfaces/singular.py # Killed due to segmentation fault

t.d.

[Eric Gourgoulhon]

Hi,

Le lundi 7 septembre 2020 à 07:21:19 UTC+2, matthia...@gmail.com a écrit :

ubuntu-bionic-standard (https://github.com/sagemath/sage/runs/1078907737):

  [dochtml]   UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 2661: ordinal not in range(128)

  [dochtml] Full log file: logs/dochtml.log

Makefile:1874: recipe for target 'doc-html' failed

For the record, I did not experience such an issue on my Ubuntu Bionic (18.04) machine: the incremental build from Sage 9.2.beta11 went well, including for doc-html.

Eric.

[Dima Pasechnik]

please also send the top-level config.log
Otherwise it is not clear how to reproduce this, e.g. what Python is used.

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[Sébastien Labbé]

I now upgraded to Ubuntu 20.04.1 LTS (which may explains why I am reporting errors below I was not reporting before).

Moreover, my config.log confirms that I am using python3.8 from my system:

...
## -------------------------------------------------------- ##
## Checking whether SageMath should install SPKG python3... ##
## -------------------------------------------------------- ##
configure:29385: checking whether any of sqlite libpng bzip2 xz libffi is installed as or will be installed as SPKG
configure:29394: result: no
configure:29404: checking for python3 >= 3.6, < 3.9 with modules sqlite3, ctypes, math, hashlib, crypt, readline, socket, zlib, distutils.core
configure:29410: result:
configure:29425: checking ... whether /usr/bin/python3.8 is good
configure:29618: result: yes
configure:29620: checking for python3 >= 3.6, < 3.9 with modules sqlite3, ctypes, math, hashlib, crypt, readline, socket, zlib, distutils.core
configure:29679: result: /usr/bin/python3.8
configure:29694: will use system package and not install SPKG python3
...

Testing few optional and external packages, I get:

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/doc/en/constructions/linear_algebra.rst  # 1 doctest failed
sage -t --long --random-seed=0 src/doc/en/developer/coding_in_other.rst  # 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/interfaces/octave.py  # 3 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
Doctests interrupted: 2236/4204 files tested
----------------------------------------------------------------------
External software detected for doctesting: graphviz,internet,octave


For some reason that I ignore, the doctests were interrupted while I was in a
webconf on the same machine. I will rerun the tests and post the result later.


Doctests failures are copied below.


sage -t --long --random-seed=0 src/doc/en/constructions/linear_algebra.rst
**********************************************************************
File "src/doc/en/constructions/linear_algebra.rst", line 454, in doc.en.constructions.linear_algebra
Failed example:
    octave.solve_linear_system(A,b)    # optional - octave
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 doc.en.constructions.linear_algebra[4]>", line 1, in <module>
        octave.solve_linear_system(A,b)    # optional - octave
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/interfaces/octave.py", line 519, in solve_linear_system
        return eval(sol)
      File "<string>", line 1
        [-0.333333, 0.666667, 0,
                               ^
    SyntaxError: unexpected EOF while parsing
**********************************************************************
1 item had failures:
   1 of 115 in doc.en.constructions.linear_algebra
    0 tests not run because we ran out of time
    [93 tests, 1 failure, 3.17 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, 2.68 s]
sage -t --long --random-seed=0 src/sage/interfaces/octave.py
**********************************************************************
File "src/sage/interfaces/octave.py", line 159, in sage.interfaces.octave.Octave
Failed example:
    octave.eval("a = [ 1, 1, 2; 3, 5, 8; 13, 21, 33 ]")    # optional - octave
Expected:
    'a =\n\n 1 1 2\n 3 5 8\n 13 21 33\n\n'
Got:
    'a =\n\n 1 1 2\n 3 5 8\n 13 21 33\n'
**********************************************************************
File "src/sage/interfaces/octave.py", line 161, in sage.interfaces.octave.Octave
Failed example:
    octave.eval("b = [ 1; 3; 13]")                         # optional - octave
Expected:
    'b =\n\n 1\n 3\n 13\n\n'
Got:
    'b =\n\n 1\n 3\n 13\n'
**********************************************************************
File "src/sage/interfaces/octave.py", line 496, in sage.interfaces.octave.Octave.solve_linear_system
Failed example:
    octave.solve_linear_system(A,b)    # optional - octave (and output is slightly random in low order bits)
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.interfaces.octave.Octave.solve_linear_system[4]>", line 1, in <module>
        octave.solve_linear_system(A,b)    # optional - octave (and output is slightly random in low order bits)
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/interfaces/octave.py", line 519, in solve_linear_system
        return eval(sol)
      File "<string>", line 1
        [-0.333333, 0.666667, 0,
                               ^
    SyntaxError: unexpected EOF while parsing
**********************************************************************
2 items had failures:
   2 of   8 in sage.interfaces.octave.Octave
   1 of   6 in sage.interfaces.octave.Octave.solve_linear_system
    3 not tested tests not run
    0 tests not run because we ran out of time
    [132 tests, 3 failures, 2.38 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, 33.45 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, 1.59 s]
sage -t --long --random-seed=0 src/doc/en/developer/coding_in_other.rst
**********************************************************************
File "src/doc/en/developer/coding_in_other.rst", line 728, in doc.en.developer.coding_in_other.solve_linear_system
Failed example:
    octave.solve_linear_system(A,b)    # optional - octave
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 doc.en.developer.coding_in_other.solve_linear_system[4]>", line 1, in <module>
        octave.solve_linear_system(A,b)    # optional - octave
      File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/interfaces/octave.py", line 519, in solve_linear_system
        return eval(sol)
      File "<string>", line 1
        [-0.333333, 0.666667, 0,
                               ^
    SyntaxError: unexpected EOF while parsing
**********************************************************************
1 item had failures:
   1 of   6 in doc.en.developer.coding_in_other.solve_linear_system
    0 tests not run because we ran out of time
    [41 tests, 1 failure, 0.84 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, 29.29 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
    [3519 tests, 2 failures, 54.81 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, 34.98 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, 37.14 s]

[jonatha...@googlemail.com]

pynormaliz 2.12 isn't on the mirrors yet

(I can work around that)

[Sébastien Labbé]

Again, the doctests gets interrupted with an error OSError: [Errno 24] Too many open files. Is it related to Python 3.8?

...

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

sage -t --long --random-seed=0 src/sage/graphs/generic_graph.py  # 2 doctests failed
sage -t --long --random-seed=0 src/sage/databases/oeis.py  # 1 doctest failed
sage -t --long --random-seed=0 src/sage/symbolic/integration/integral.py  # 1 doctest failed
sage -t --long --random-seed=0 src/sage/graphs/graph.py  # 3 doctests failed
sage -t --long --random-seed=0 src/sage/symbolic/integration/external.py  # 1 doctest failed
sage -t --long --random-seed=0 src/doc/en/constructions/linear_algebra.rst  # 1 doctest failed
sage -t --long --random-seed=0 src/doc/en/constructions/interface_issues.rst  # 1 doctest failed
sage -t --long --random-seed=0 src/sage/interfaces/octave.py  # 3 doctests failed
sage -t --long --random-seed=0 src/sage/combinat/designs/incidence_structures.py  # 1 doctest failed
sage -t --long --random-seed=0 src/doc/en/developer/coding_in_other.rst  # 1 doctest failed
Doctests interrupted: 1862/4204 files tested
----------------------------------------------------------------------
Total time for all tests: 2372.2 seconds
    cpu time: 12523.8 seconds
    cumulative wall time: 13826.7 seconds

Traceback (most recent call last):

  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 69, in _launch
    child_r, parent_w = os.pipe()
OSError: [Errno 24] Too many open files

[Emmanuel Charpentier]

On Debian testing running on core i5 + 8 GB RAM, upgrading 9.2.beta11 to 9.2.beta12 after make python3-cleanusing all system packages and running ptestlong gives 7 permanent failures :

File	Result	P/T
src/sage/schemes/hyperelliptic_curves/monsky_washnitzer.py	Killed due to abort	P
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/sage/rings/real_arb.pyx	2 doctests failed	P
src/sage/modules/free_module_morphism.py	3 doctests failed	P
src/doc/en/developer/coding_in_other.rst	1 doctest failed	P

These failures have been reported already for 2.9.beta11 on the same machine, except for the failure observed for coding_in_other.rst, which was transient in 2.9.beta11 and is now permanent.

Of note :

• ./configure failed to recognize the system’s Python packages ; notwithstanding this failure,
  • $SAGE_LOCAL/bin/python3.8 is a symlink to /usr/bin/python3.8
  • sage -standard | grep python reports python3 as
    (not_installed)
• gap-packages still no longer installs (complains about multiply-defined symbols).

HTH,

​

[Sébastien Labbé]

On Monday, September 7, 2020 at 2:48:29 PM UTC+2 Sébastien Labbé wrote:

Again, the doctests gets interrupted with an error OSError: [Errno 24] Too many open files. Is it related to Python 3.8?

Running tests only with the optional packages (not the external packages), I managed to complete the doctests of the whole library. I get:

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

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

rerunning failed tests, I get:

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

sage -t --long --random-seed=0 src/sage/combinat/designs/incidence_structures.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

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

failures copied below:

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, 1.29 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, 20.78 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

    [3519 tests, 2 failures, 32.11 s]

 

[Matthias Köppe]

On Sunday, September 6, 2020 at 10:21:19 PM UTC-7, Matthias Köppe wrote:

On Sunday, September 6, 2020 at 4:25:39 PM UTC-7, Volker Braun wrote:

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 

5ec24db181 (tag: 9.2.beta12, trac/develop) Updated SageMath version to 9.2.beta12

Tests have started at https://github.com/sagemath/sage/actions . 

debian-{jessie,stretch,buster} : Clean 

debian-{bullseye,sid}-minimal: Clean

debian-{bullseye,sid}-standard: doctest failures similar to ubuntu-groovy-standard

debian-buster-i386-standard: Clean

linuxmint-17 (https://github.com/sagemath/sage/runs/1078907871): Lots of doctest failures due to setlocale messages. (A lot of discussion at https://trac.sagemath.org/ticket/30053....)

linuxmint-{18,19,19.3}: Clean

fedora-{26, 32}: Clean

fedora-{27,28,29,30,31,33}-minimal: Clean (but some exceed 6h while in doctests)

fedora-{27,29}-standard (https://github.com/sagemath/sage/runs/1078907974): 

sage -t --random-seed=0 src/sage/lfunctions/sympow.py  # 3 doctests failed

sage -t --random-seed=0 src/sage/schemes/elliptic_curves/ell_rational_field.py  # 2 doctests failed

fedora-28-standard (https://github.com/sagemath/sage/runs/1078907994): 

Test failures in cvxopt

sage -t --random-seed=0 src/sage/lfunctions/sympow.py  # 3 doctests failed

sage -t --random-seed=0 src/sage/rings/polynomial/groebner_fan.py  # 3 doctests failed

sage -t --random-seed=0 src/sage/schemes/elliptic_curves/ell_rational_field.py  # 2 doctests failed

fedora-33-standard (https://github.com/sagemath/sage/runs/1078908107):

  [arb-2.16.0.p0]   /sage/local/var/tmp/sage/build/arb-2.16.0.p0/src/fmpr.h:25:10: fatal error: flint/config.h: No such file or directory

  [arb-2.16.0.p0]      25 | #include "flint/config.h"

  [arb-2.16.0.p0]         |          ^~~~~~~~~~~~~~~~

  [arb-2.16.0.p0]   compilation terminated.

centos-{7,8}: Clean

gentoo: Clean

gentoo-python3.7: Clean

archlinux-minimal: Clean

archlinux-standard (https://github.com/sagemath/sage/runs/1078908183): 

sage -t --random-seed=0 src/sage/interfaces/quit.py  # 1 doctest failed

slackware-14.2-minimal (https://github.com/sagemath/sage/runs/1078908190): 

[libs     ] WARNING: autodoc: failed to import module 'giac' from module 'sage.libs'; the following exception was raised:

[libs     ] libsasl2.so.3: cannot open shared object file: No such file or directory

slackware-14.2-standard: Clean

conda-forge-minimal (https://github.com/sagemath/sage/runs/1078908216):

Error building python3, Failures testing package symmetrica

conda-forge-standard (https://github.com/sagemath/sage/runs/1078908224):

sage -t --random-seed=0 src/doc/en/constructions/algebraic_geometry.rst  # 1 doctest failed

sage -t --random-seed=0 src/doc/en/developer/coding_in_other.rst  # 1 doctest failed

sage -t --random-seed=0 src/sage/misc/cython.py  # 3 doctests failed

sage -t --random-seed=0 src/sage/modules/fg_pid/fgp_module.py  # 3 doctests failed

sage -t --random-seed=0 src/sage/modules/free_module_morphism.py  # 3 doctests failed

sage -t --random-seed=0 src/sage/rings/complex_arb.pyx  # 6 doctests failed

sage -t --random-seed=0 src/sage/rings/real_arb.pyx  # 2 doctests failed

sage -t --random-seed=0 src/sage/schemes/hyperelliptic_curves/monsky_washnitzer.py  # Killed due to abort

conda-forge-ubuntu-standard (https://github.com/sagemath/sage/runs/1078909743): 

  [pillow-7.2.0]   In file included from /home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-standard/conda/include/python3.7m/Python.h:11:0,

  [pillow-7.2.0]                    from src/_imagingmorph.c:14:

  [pillow-7.2.0]   /usr/include/limits.h:26:10: fatal error: bits/libc-header-start.h: No such file or directory

  [pillow-7.2.0]    #include <bits/libc-header-start.h>

  [pillow-7.2.0]             ^~~~~~~~~~~~~~~~~~~~~~~~~~

  [pillow-7.2.0]   compilation terminated.

  [pillow-7.2.0]   error: command '/home/runner/work/sage/sage/.tox/local-conda-forge-ubuntu-standard/conda/bin/x86_64-conda-linux-gnu-cc' failed with exit status 1

[Matthias Köppe]

On Sunday, September 6, 2020 at 10:21:19 PM UTC-7, Matthias Köppe wrote:

On Sunday, September 6, 2020 at 4:25:39 PM UTC-7, Volker Braun wrote:

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 

5ec24db181 (tag: 9.2.beta12, trac/develop) Updated SageMath version to 9.2.beta12

Tests have started at https://github.com/sagemath/sage/actions 

Cygwin results:

cygwin-standard (https://github.com/sagemath/sage/runs/1079702566): 

  [sagelib-9.2.beta12]   error: command 'g++' failed with exit status 1

(No g++ error message to be seen; this is https://trac.sagemath.org/ticket/30396)

This needs urgent help by someone who has a Windows development box.

cygwin-minimal (https://github.com/sagemath/sage/runs/1079395893):

Times out in stage-ii-a, stage-ii-c - needs repartitioning

[Kenji Iohara]

I am sorry... here it is. 

2020年9月7日(月) 13:20 Dima Pasechnik <dim...@gmail.com>:

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CAAWYfq04Nan32aWB-agHcONAXQ36Ep594tR3fjCPfK-k_FKHTg%40mail.gmail.com.

[David Coudert]

I have several issues on macOS 10.15.6

I first tried to do incremental upgrade. The compilation completed, but then I realized that I was still with Python 3.7…

So I tried "make python3-clean » and then ./configure and make again but it fails. 

After a make distclean, the compilation failed in the doc (see attached log file).

The main issue is that sage crash at startup (see attached crash report).

I don’t know what to do.

Thanks.

David.

[Dima Pasechnik]

it is a linking problem: what does

otool -L local/lib/python3.8/site-packages/sage/matrix/matrix_integer_dense.cpython-38-darwin.so

say?

>
> I don’t know what to do.
> Thanks.
> David.
>
>
>

> --
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>
> --
> 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-release...@googlegroups.com.

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/617FC0A3-9075-4F92-8006-251D167436E3%40gmail.com.

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CAPCAjE1p23fKTQ7DKJMG9ApcpMqGi-c9gYegj%2BWfhWGbt%2BvJig%40mail.gmail.com.
> <config.log>

>
>
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> To unsubscribe from this group and stop receiving emails from it, send an email to sage-release...@googlegroups.com.

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[David Coudert]

sapristi:sage dcoudert$ otool -L local/lib/python3.8/site-packages/sage/matrix/matrix_integer_dense.cpython-38-darwin.so

local/lib/python3.8/site-packages/sage/matrix/matrix_integer_dense.cpython-38-darwin.so:

/Users/dcoudert/sage/local/lib/liblinbox.0.dylib (compatibility version 1.0.0, current version 1.0.0)

/usr/local/opt/ntl/lib/libntl.43.dylib (compatibility version 44.0.0, current version 44.1.0)

/Users/dcoudert/sage/local/lib/libiml.0.dylib (compatibility version 2.0.0, current version 2.1.0)

/Users/dcoudert/sage/local/lib/libfflas.1.dylib (compatibility version 2.0.0, current version 2.0.0)

/Users/dcoudert/sage/local/lib/libffpack.1.dylib (compatibility version 2.0.0, current version 2.0.0)

/Users/dcoudert/sage/local/lib/libgivaro.9.dylib (compatibility version 11.0.0, current version 11.1.0)

/Users/dcoudert/sage/local/lib/libpari-gmp.dylib (compatibility version 2.11.0, current version 2.11.4)

/Users/dcoudert/sage/local/lib/libflint-13.5.2.dylib (compatibility version 13.5.0, current version 13.5.2)

/usr/local/opt/mpfr/lib/libmpfr.6.dylib (compatibility version 8.0.0, current version 8.0.0)

/usr/local/opt/gmp/lib/libgmp.10.dylib (compatibility version 15.0.0, current version 15.0.0)

/usr/local/opt/gmp/lib/libgmpxx.4.dylib (compatibility version 11.0.0, current version 11.0.0)

/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1281.100.1)

/usr/local/opt/openblas/lib/libopenblas.0.dylib (compatibility version 0.0.0, current version 0.0.0)

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CAAWYfq38%2BcyX4aNCAHVSnbJtD8f2BArN_FsDgTuDhDj6PjZ2SQ%40mail.gmail.com.

[Dima Pasechnik]

hmm, weird.

perhaps try building Sage's NTL rather than using the one from Homebrew

./configure --with-system-ntl=no && make -j8 build

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/71DA0AFD-3389-4E72-A7F8-2B61B9A3DDE7%40gmail.com.

[David Coudert]

Not working :((

[sagelib-9.2.beta12]   0, /*tp_print*/

[sagelib-9.2.beta12]   ^

[sagelib-9.2.beta12] /usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here

[sagelib-9.2.beta12]     Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);

[sagelib-9.2.beta12]     ^

[sagelib-9.2.beta12] /usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'

[sagelib-9.2.beta12] #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))

[sagelib-9.2.beta12]                                                      ^

[sagelib-9.2.beta12] 21 warnings generated.

[sagelib-9.2.beta12] gcc -bundle -undefined dynamic_lookup -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk -L/Users/dcoudert/sage/local/lib -Wl,-rpath,/Users/dcoudert/sage/local/lib build/temp.macosx-10.15-x86_64-3.8/build/cythonized/sage/matrix/matrix_rational_dense.o -L/usr/local/Cellar/openblas/0.3.10_1/lib -L/usr/local/lib -L/usr/local/opt/openssl@1.1/lib -L/usr/local/opt/sqlite/lib -lntl -liml -lpari -lflint -lgmp -lm -lopenblas -o build/lib.macosx-10.15-x86_64-3.8/sage/matrix/matrix_rational_dense.cpython-38-darwin.so -lpari

[sagelib-9.2.beta12] build/cythonized/sage/matrix/matrix_integer_sparse.cpp:12647:18: warning: unused function '__pyx_pw_4sage_9structure_7element_1parent' [-Wunused-function]

[sagelib-9.2.beta12] static PyObject *__pyx_pw_4sage_9structure_7element_1parent(PyObject *__pyx_self, PyObject *__pyx_v_x) {

[sagelib-9.2.beta12]                  ^

[sagelib-9.2.beta12] build/cythonized/sage/matrix/matrix_integer_sparse.cpp:12646:13: warning: unused variable '__pyx_doc_4sage_9structure_7element_parent' [-Wunused-variable]

[sagelib-9.2.beta12] static char __pyx_doc_4sage_9structure_7element_parent[] = "parent(x)\nFile: sage/structure/element.pxd (starting at line 6)\n\n    Return the parent of the element ``x``.\n\n    Usually, this means the mathematical object of which ``x`` is an\n    element.\n\n    INPUT:\n\n    - ``x`` -- an element\n\n    OUTPUT:\n\n    - If ``x`` is a Sage :class:`Element`, return ``x.parent()``.\n\n    - Otherwise, return ``type(x)``.\n\n    .. SEEALSO::\n\n        `Parents, Conversion and Coercion <http://doc.sagemath.org/html/en/tutorial/tour_coercion.html>`_\n        Section in the Sage Tutorial\n\n    EXAMPLES::\n\n        sage: a = 42\n        sage: parent(a)\n        Integer Ring\n        sage: b = 42/1\n        sage: parent(b)\n        Rational Field\n        sage: c = 42.0\n        sage: parent(c)\n        Real Field with 53 bits of precision\n\n    Some more complicated examples::\n\n        sage: x = Partition([3,2,1,1,1])\n        sage: parent(x)\n        Partitions\n        sage: v = vector(RDF, [1,2,3])\n        sage: parent(v)\n        Vector space of dimension 3 over Real Double Field\n\n    The following are not considered to be elements, so the type is\n    returned::\n\n        sage: d = int(42)  # Python int\n        sage: parent(d)\n        <... 'int'>\n        sage: L = list(range(10))\n        sage: parent(L)\n        <... 'list'>\n    ";

[sagelib-9.2.beta12]             ^

[sagelib-9.2.beta12] build/cythonized/sage/matrix/matrix_integer_sparse.cpp:12992:18: warning: unused function '__pyx_pw_4sage_9structure_7element_3have_same_parent' [-Wunused-function]

[sagelib-9.2.beta12] static PyObject *__pyx_pw_4sage_9structure_7element_3have_same_parent(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {

[sagelib-9.2.beta12]                  ^

[sagelib-9.2.beta12] build/cythonized/sage/matrix/matrix_integer_sparse.cpp:12991:13: warning: unused variable '__pyx_doc_4sage_9structure_7element_2have_same_parent' [-Wunused-variable]

[sagelib-9.2.beta12] static char __pyx_doc_4sage_9structure_7element_2have_same_parent[] = "have_same_parent(left, right) -> bool\nFile: sage/structure/element.pxd (starting at line 111)\n\n    Return ``True`` if and only if ``left`` and ``right`` have the\n    same parent.\n\n    .. WARNING::\n\n        This function assumes that at least one of the arguments is a\n        Sage :class:`Element`. When in doubt, use the slower\n        ``parent(left) is parent(right)`` instead.\n\n    EXAMPLES::\n\n        sage: from sage.structure.element import have_same_parent\n        sage: have_same_parent(1, 3)\n        True\n        sage: have_same_parent(1, 1/2)\n        False\n        sage: have_same_parent(gap(1), gap(1/2))\n        True\n\n    These have different types but the same parent::\n\n        sage: a = RLF(2)\n        sage: b = exp(a)\n        sage: type(a)\n        <... 'sage.rings.real_lazy.LazyWrapper'>\n        sage: type(b)\n        <... 'sage.rings.real_lazy.LazyNamedUnop'>\n        sage: have_same_parent(a, b)\n        True\n    ";

[sagelib-9.2.beta12]             ^

[sagelib-9.2.beta12] 15 warnings generated.

[sagelib-9.2.beta12] g++ -bundle -undefined dynamic_lookup -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk -L/Users/dcoudert/sage/local/lib -Wl,-rpath,/Users/dcoudert/sage/local/lib build/temp.macosx-10.15-x86_64-3.8/build/cythonized/sage/matrix/matrix_integer_sparse.o -L/usr/local/Cellar/openblas/0.3.10_1/lib -L/Users/dcoudert/sage/local/lib -L/usr/local/lib -L/usr/local/opt/openssl@1.1/lib -L/usr/local/opt/sqlite/lib -llinbox -lntl -liml -lfflas -lffpack -lgivaro -lflint -lmpfr -lgmp -lgmpxx -lopenblas -o build/lib.macosx-10.15-x86_64-3.8/sage/matrix/matrix_integer_sparse.cpython-38-darwin.so -lpari

[sagelib-9.2.beta12] ld: illegal thread local variable reference to regular symbol __ZN3NTL20ZZXFac_InitNumPrimesE for architecture x86_64

[sagelib-9.2.beta12] clang: error: linker command failed with exit code 1 (use -v to see invocation)

[sagelib-9.2.beta12] error: command 'g++' failed with exit status 1

[sagelib-9.2.beta12] 

[sagelib-9.2.beta12] real 6m3.603s

[sagelib-9.2.beta12] user 10m3.754s

[sagelib-9.2.beta12] sys 0m25.122s

make[4]: *** [sagelib-no-deps] Error 1

make[3]: *** [/Users/dcoudert/sage/local/var/lib/sage/installed/sagelib-9.2.beta12] Error 2

make[2]: *** [all-build] Error 2

real 51m47.566s

user 221m19.747s

sys 24m21.839s

***************************************************************

Error building Sage.

The following package(s) may have failed to build (not necessarily

during this run of 'make all-build'):

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]: *** [all-build] Error 1

make: *** [build] Error 2

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[Matthias Köppe]

On Sunday, September 6, 2020 at 10:21:19 PM UTC-7, Matthias Köppe wrote:

On Sunday, September 6, 2020 at 4:25:39 PM UTC-7, Volker Braun wrote:

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 

5ec24db181 (tag: 9.2.beta12, trac/develop) Updated SageMath version to 9.2.beta12

Tests have started at https://github.com/sagemath/sage/actions 

macOS results:  All runs have a number of timeouts in doctests.

homebrew-macos-{minimal, standard} (= build with homebrew python3.8):

sage -t --random-seed=0 src/sage/interfaces/gap.py  # 1 doctest failed

homebrew-macos-python3_xcode-minimal: Clean

homebrew-macos-python3_xcode-standard:

sage -t --random-seed=0 src/sage/interfaces/gap.py  # 1 doctest failed

homebrew-macos-python3_xcode-nokegonly-standard: Error building R:

configure: error: in `/Users/runner/work/sage/sage/.tox/local-homebrew-macos-python3_xcode-nokegonly-standard/local/var/tmp/sage/build/r-3.6.3/src':

configure: error: linking to Fortran libraries from C fails

Looks like this build is still using gfortran-9

homebrew-macos-python3_pythonorg-minimal:

sage -t --random-seed=0 src/sage/interfaces/gap.py  # 1 doctest failed

homebrew-macos-python3_xcode-gcc_spkg-{minimal,standard}: Various build errors (ignore for Sage 9.2)

homebrew-macos with xcode-12 beta: Various build errors, tracked at https://trac.sagemath.org/ticket/30494 (ignore for Sage 9.2)

conda-forge-macos-minimal: python3 build fails:

configure: error: Cross compiling required --host=HOST-TUPLE and --build=ARCH

conda-forge-macos-standard (https://github.com/sagemath/sage/runs/1078909711): 

  [sagelib-9.2.beta12]   /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-standard/local/include/linbox/algorithms/det-rational.h:96:39: error: no viable overloaded '='

  [sagelib-9.2.beta12]                   void detMul (const Integer& m) {mul = m;}

  [sagelib-9.2.beta12]                                                   ~~~ ^ ~

  [sagelib-9.2.beta12]   /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-standard/conda/include/gmp++/gmp++_int.h:236:34: note: candidate function not viable: 'this' argument has type 'const LinBox::Integer' (aka 'const Givaro::Integer'), but method is not marked const

  [sagelib-9.2.beta12]           giv_all_inlined Integer& operator = (const Integer& n);

  [sagelib-9.2.beta12]                                    ^

  [sagelib-9.2.beta12]   build/cythonized/sage/matrix/matrix_integer_sparse.cpp:12289:35: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'long' [-Wsign-compare]

  [sagelib-9.2.beta12]     for (__pyx_t_12 = 0; __pyx_t_12 < __pyx_t_11; __pyx_t_12+=1) {

  [sagelib-9.2.beta12]                          ~~~~~~~~~~ ^ ~~~~~~~~~~

  [sagelib-9.2.beta12]   1 warning and 2 errors generated.

  [sagelib-9.2.beta12]   error: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 1

I have created https://trac.sagemath.org/ticket/30535 for this

[David Coudert]

If I understand well, I’m facing the case (not completely sure): 

homebrew-macos-python3_xcode-gcc_spkg-{minimal,standard}: Various build errors (ignore for Sage 9.2)

That is: macOS 10.15.6 with clang version 11.0.3 (clang-1103.0.32.62) and all recommended packages installed with homebrew, and unable to compile beta12.

Any idea to get something working is more than welcome ;)

Best,

David.

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[Dima Pasechnik]

On Wed, Sep 9, 2020 at 10:49 AM David Coudert <david....@gmail.com> wrote:
>
> If I understand well, I’m facing the case (not completely sure):
> homebrew-macos-python3_xcode-gcc_spkg-{minimal,standard}: Various build errors (ignore for Sage 9.2)

no, this is for macOS 11, still in beta, and not going to be supported in 9.2

>
> That is: macOS 10.15.6 with clang version 11.0.3 (clang-1103.0.32.62) and all recommended packages installed with homebrew, and unable to compile beta12.
>

Is your xcode up to date?

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/F206C9A0-DF8D-40E1-9C98-F1F4B893E27C%40gmail.com.

[David Coudert]

Le 9 sept. 2020 à 12:04, Dima Pasechnik <dim...@gmail.com> a écrit :

On Wed, Sep 9, 2020 at 10:49 AM David Coudert <david....@gmail.com> wrote:

If I understand well, I’m facing the case (not completely sure):
homebrew-macos-python3_xcode-gcc_spkg-{minimal,standard}: Various build errors (ignore for Sage 9.2)

no, this is for macOS 11, still in beta, and not going  to be supported in 9.2

That is: macOS 10.15.6 with clang version 11.0.3 (clang-1103.0.32.62) and all recommended packages installed with homebrew, and unable to compile beta12.

Is your xcode up to date?

My laptop is 2 months old, and the last Xcode update was on Septembre 3 (Xcode 11.7). No other proposed update on app store.

Last « brew update » yesterday.

David.

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CAAWYfq3uUdwquVe-vb5x-8qi%3D_q%2BokpXywMz9WPOk%2BQyu8udhQ%40mail.gmail.com.

[Dima Pasechnik]

you do

$ source .homebrew-build-env

before builds, right?

Post the top-level config.log

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/E933562E-5D67-432F-BF0B-D54AC020421F%40gmail.com.

[David Coudert]

> Le 9 sept. 2020 à 13:29, Dima Pasechnik <dim...@gmail.com> a écrit :
>
> you do
>
> $ source .homebrew-build-env
>
> before builds, right?

Yes, and I have « source $SAGE_ROOT/.homebrew-build-env » in my .bash_profile

> Post the top-level config.log

Here it is

[Dima Pasechnik]

do you by any chance have g++ and/or gcc being "real" gcc, not just
links to Apple's clang(++) ?
E.g. I have

% g++ -v

Configured with: --prefix=/Library/Developer/CommandLineTools/usr
--with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 11.0.3 (clang-1103.0.32.62)
Target: x86_64-apple-darwin19.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

which is OK. (similar for gcc)

Why is your gfortran version 9?
I have version 10:

% gfortran -v

Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/10.2.0/libexec/gcc/x86_64-apple-darwin19/10.2.0/lto-wrapper
Target: x86_64-apple-darwin19
Configured with: ../configure --build=x86_64-apple-darwin19
--prefix=/usr/local/Cellar/gcc/10.2.0
--libdir=/usr/local/Cellar/gcc/10.2.0/lib/gcc/10 --disable-nls
--enable-checking=release
--enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-10
--with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr
--with-mpc=/usr/local/opt/libmpc --with-isl=/usr/local/opt/isl
--with-system-zlib --with-pkgversion='Homebrew GCC 10.2.0'
--with-bugurl=https://github.com/Homebrew/homebrew-core/issues
--disable-multilib --with-native-system-header-dir=/usr/include
--with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk
SED=/usr/bin/sed
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 10.2.0 (Homebrew GCC 10.2.0)

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[david....@gmail.com]

below are gcc -v, g++ -v, fortran -v and env (after source $SAGE_ROOT/.homebrew-build-env , which is done by default)

sapristi:sage dcoudert$ gcc -v

Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1

Apple clang version 11.0.3 (clang-1103.0.32.62)

Target: x86_64-apple-darwin19.6.0

Thread model: posix

InstalledDir: /Library/Developer/CommandLineTools/usr/bin

sapristi:sage dcoudert$ g++ -v

Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1

Apple clang version 11.0.3 (clang-1103.0.32.62)

Target: x86_64-apple-darwin19.6.0

Thread model: posix

InstalledDir: /Library/Developer/CommandLineTools/usr/bin

sapristi:sage dcoudert$ gfortran -v

Using built-in specs.

COLLECT_GCC=gfortran

COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/10.2.0/libexec/gcc/x86_64-apple-darwin19/10.2.0/lto-wrapper

Target: x86_64-apple-darwin19

Configured with: ../configure --build=x86_64-apple-darwin19 --prefix=/usr/local/Cellar/gcc/10.2.0 --libdir=/usr/local/Cellar/gcc/10.2.0/lib/gcc/10 --disable-nls --enable-checking=release --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-10 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-isl=/usr/local/opt/isl --with-system-zlib --with-pkgversion='Homebrew GCC 10.2.0' --with-bugurl=https://github.com/Homebrew/homebrew-core/issues --disable-multilib --with-native-system-header-dir=/usr/include --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk SED=/usr/bin/sed

Thread model: posix

Supported LTO compression algorithms: zlib

gcc version 10.2.0 (Homebrew GCC 10.2.0) 

sapristi:sage dcoudert$ env

TERM_PROGRAM=Apple_Terminal

TERM=xterm-256color

SHELL=/bin/bash

TMPDIR=/var/folders/5q/t180zjs936d_lt3p1cz3mql4000_hf/T/

LIBRARY_PATH=/usr/local/opt/gcc@9/lib/gcc/9:/usr/local/opt/readline/lib:/usr/local/lib

CPLEX_HOME=/Applications/CPLEX_Studio1210

TERM_PROGRAM_VERSION=433

TERM_SESSION_ID=9758A080-2A8A-4003-9C98-21DB374BE497

DOT_SAGE=/Users/dcoudert/.sage

USER=dcoudert

CPATH=/usr/local/opt/readline/include:/usr/local/include

SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.3eBwfRcuQk/Listeners

PATH=/Users/dcoudert/git-trac-command/bin:/usr/local/opt/gettext/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/Library/Apple/usr/bin

LaunchInstanceID=90C8C59C-1C78-4EF1-BCA9-31C985D6585E

PWD=/Users/dcoudert/sage

GRB_LICENSE_FILE=/Users/dcoudert/gurobi.lic

LANG=fr_FR.UTF-8

SAGE_ROOT=/Users/dcoudert/sage

XPC_FLAGS=0x0

GUROBI_HOME=/Library/gurobi811/mac64

XPC_SERVICE_NAME=0

HOME=/Users/dcoudert

SHLVL=1

LOGNAME=dcoudert

PKG_CONFIG_PATH=/usr/local/opt/zlib/lib/pkgconfig:/usr/local/opt/sqlite/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/openssl/lib/pkgconfig:/usr/local/opt/openblas/lib/pkgconfig:/usr/local/lib/pkgconfig:

ACLOCAL_PATH=/usr/local/opt/gettext/share/aclocal:

SECURITYSESSIONID=186a6

_=/usr/bin/env

[Matthias Köppe]

On Wednesday, September 9, 2020 at 2:49:19 AM UTC-7, david....@gmail.com wrote:

If I understand well, I’m facing the case (not completely sure): 

homebrew-macos-python3_xcode-gcc_spkg-{minimal,standard}: Various build errors (ignore for Sage 9.2)

That is: macOS 10.15.6 with clang version 11.0.3 (clang-1103.0.32.62) and all recommended packages installed with homebrew, and unable to compile beta12.

Actually your configuration is "homebrew-macos-standard" with probably some extra homebrew packages installed. 

(The configuration factor "gcc_spkg" refers to using gcc 9.2 from our SPKG instead of Xcode "gcc" (clang).)

My guess is that if you uninstall homebrew's ntl and flint packages and build from scratch (distclean), the build would go through.

https://trac.sagemath.org/ticket/27764 and tickets referenced within address the NTL / thread-local storage issues.

[david....@gmail.com]

I can try to install ntl and flint, but then I have to remove dependencies as well, right ?

sapristi:sage dcoudert$ brew uninstall ntl flint

Error: Refusing to uninstall /usr/local/Cellar/flint/2.6.3

because it is required by arb, which is currently installed.

You can override this and force removal with:

  brew uninstall --ignore-dependencies ntl flint

[Dima Pasechnik]

ok, you have a non-standard arb in your Homebrew install.

you need to reinstall it, or perhaps better just remove it.

you also have traces of gfortran 9 in LIBRARY_PATH - investigate and clean...

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[David Coudert]

The traces of fortran 9 (and actually gcc 9) are due to .homebrew-build-env. which contains: 

for l in "gcc@9/lib/gcc/9"; do
    if [ -d "$HOMEBREW/opt/$l" ]; then
        LIBRARY_PATH="$HOMEBREW/opt/$l:$LIBRARY_PATH"
    fi
done

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[Matthias Köppe]

On Wednesday, September 9, 2020 at 8:35:10 AM UTC-7, David Coudert wrote:

The traces of fortran 9 (and actually gcc 9) are due to .homebrew-build-env. which contains: 

for l in "gcc@9/lib/gcc/9"; do
    if [ -d "$HOMEBREW/opt/$l" ]; then
        LIBRARY_PATH="$HOMEBREW/opt/$l:$LIBRARY_PATH"
    fi
done

For that, see https://trac.sagemath.org/ticket/30536

 

Le 9 sept. 2020 à 17:01, Dima Pasechnik <dim...@gmail.com> a écrit :

ok, you have a non-standard arb in your Homebrew install.

you need to reinstall it, or perhaps better just remove it.

you also have traces of gfortran 9 in LIBRARY_PATH - investigate and clean...

On Wed, 9 Sep 2020, 15:57 david....@gmail.com, <david....@gmail.com> wrote:

I can try to install ntl and flint, but then I have to remove dependencies as well, right ?

sapristi:sage dcoudert$ brew uninstall ntl flint

Error: Refusing to uninstall /usr/local/Cellar/flint/2.6.3

because it is required by arb, which is currently installed.

You can override this and force removal with:

  brew uninstall --ignore-dependencies ntl flint

Le mercredi 9 septembre 2020 à 16:53:47 UTC+2, matthia...@gmail.com a écrit :

On Wednesday, September 9, 2020 at 2:49:19 AM UTC-7, david....@gmail.com wrote:

If I understand well, I’m facing the case (not completely sure): 

homebrew-macos-python3_xcode-gcc_spkg-{minimal,standard}: Various build errors (ignore for Sage 9.2)

That is: macOS 10.15.6 with clang version 11.0.3 (clang-1103.0.32.62) and all recommended packages installed with homebrew, and unable to compile beta12.

Actually your configuration is "homebrew-macos-standard" with probably some extra homebrew packages installed. 

(The configuration factor "gcc_spkg" refers to using gcc 9.2 from our SPKG instead of Xcode "gcc" (clang).)

My guess is that if you uninstall homebrew's ntl and flint packages and build from scratch (distclean), the build would go through.

https://trac.sagemath.org/ticket/27764 and tickets referenced within address the NTL / thread-local storage issues.

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[Dima Pasechnik]

by the way, I am not able to pick up Homebrew's python3.8 in the presence of python3.7, unless I modify python3's spkg-configure.m4 to exclude python3.7 and python3 from the list of Pythons it checks for.

(on linux this seems to work well, so perhaps it is a macOS-only bug)

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[Matthias Köppe]

On Wednesday, September 9, 2020 at 10:11:14 AM UTC-7, Dima Pasechnik wrote:

by the way, I am not able to pick up Homebrew's python3.8 in the presence of python3.7, unless I modify python3's spkg-configure.m4 to exclude python3.7 and python3 from the list of Pythons it checks for.

config.log?

 

[Justin C. Walker]

> On Sep 6, 2020, at 16:25 , Volker Braun <vbrau...@gmail.com> wrote:
>
> 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

I built 9.2.b12 from fresh clones of the tagged tree, on three macOS systems (10.13.6, 2019 iMac Pro, 18-core Xeon W), (10.14.6, 2017 MBP, 4-core Core i7), and (10.15.6, 2019 MBP, 8-core Core i9).

On the two MBP systems, the build completed without problems, and all tests (‘ptestlong’) passed.

On the 18-core iMac Pro, the build completed with no problems, but testing (‘ptestlong’) showed three failures. I reran these three and all passed. Then, I moved the “logs” directory out of the way and reran the build. This basically redid all the tests, with the same results. I did this three or four times, always with the same results. I have attached the “config.log” from one of these runs.

These are the failures:
sage -t --long --warn-long 91.6 --random-seed=0 src/sage/parallel/map_reduce.py # 18 doctests failed
sage -t --long --warn-long 91.6 --random-seed=0 src/sage/interfaces/singular.py # Killed due to segmentation fault
sage -t --long --warn-long 91.6 --random-seed=0 src/sage_setup/docbuild/utils.py # 1 doctest failed

On a hunch, based on the “too many open files” errors, I reran the whole thing, starting with the cloning. Normally on this system, I set “-j20”. In the past, there have been no problems of note. This time, I used “-j10”, and now, all tests pass.

I think this indicates that something has changed to affect either the number of open files involved (well, obviously) per process, or somehow, the number of processes active at any time is increasing.

One note: the singular failure seems to be different, but I am not familiar enough with that subsystem to know where to look. The log says that “^C” was pressed. I assume that is some part of the testing scheme, because no-one pressed that key (much less 3-4 times, just when the singular test was underway; and then it passed when fewer processes were involved).

Thoughts?

Justin

[Matthias Köppe]

On Tuesday, September 8, 2020 at 9:23:04 PM UTC-7, Matthias Köppe wrote:

conda-forge-macos-standard (https://github.com/sagemath/sage/runs/1078909711): 

  [sagelib-9.2.beta12]   /Users/runner/work/sage/sage/.tox/local-conda-forge-macos-standard/local/include/linbox/algorithms/det-rational.h:96:39: error: no viable overloaded '='

  [sagelib-9.2.beta12]                   void detMul (const Integer& m) {mul = m;} [...]

I have created https://trac.sagemath.org/ticket/30535 for this

Fixed, needs review

 

[Dima Pasechnik]

here it is. The account shell is zsh, but this most probably does not matter.

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[Matthias Köppe]

Is "python3.8" in PATH?

On Wednesday, September 9, 2020 at 12:44:50 PM UTC-7, Dima Pasechnik wrote:

here it is. The account shell is zsh, but this most probably does not matter.

On Wed, Sep 9, 2020 at 6:31 PM Matthias Köppe <matthia...@gmail.com> wrote:
>
> On Wednesday, September 9, 2020 at 10:11:14 AM UTC-7, Dima Pasechnik wrote:
>>
>> by the way, I am not able to pick up Homebrew's python3.8 in the presence of python3.7, unless I modify python3's spkg-configure.m4 to exclude python3.7 and python3 from the list of Pythons it checks for.
>>>
>>>
>
> config.log?
>
>
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[Dima Pasechnik]

On Wed, Sep 9, 2020 at 8:54 PM Matthias Köppe <matthia...@gmail.com> wrote:
>
> Is "python3.8" in PATH?
of course.

dima@oucl13243 sagetrac-mirror % python3
Python 3.7.8 (default, Jul 8 2020, 14:18:28)
[Clang 11.0.3 (clang-1103.0.32.62)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>

dima@oucl13243 sagetrac-mirror % python3.8
Python 3.8.5 (default, Jul 21 2020, 10:48:26)
[Clang 11.0.3 (clang-1103.0.32.62)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>

dima@oucl13243 sagetrac-mirror % python3.7
Python 3.7.8 (default, Jul 8 2020, 14:18:28)
[Clang 11.0.3 (clang-1103.0.32.62)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

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[Matthias Köppe]

Are you using a configure cache? Because according to your config.log, it's only checking 1 binary

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[Dima Pasechnik]

On Wed, Sep 9, 2020 at 9:04 PM Matthias Köppe <matthia...@gmail.com> wrote:
>
> Are you using a configure cache? Because according to your config.log, it's only checking 1 binary

I'm merely running

CC=clang CXX=clang++ ./configure --enable-download-from-upstream-url

after I reverted

--- a/build/pkgs/python3/spkg-configure.m4
+++ b/build/pkgs/python3/spkg-configure.m4
@@ -12,7 +12,7 @@ SAGE_SPKG_CONFIGURE([python3], [
         check_modules="sqlite3, ctypes, math, hashlib, crypt, readline, socket, zlib, distutils.core"
         AC_CACHE_CHECK([for python3 >= 3.6, < 3.9 with modules $check_modules], [ac_cv_path_PYTHON3], [
             AC_MSG_RESULT([])
-            AC_PATH_PROGS_FEATURE_CHECK([PYTHON3], [python3.8 python3.7 python3.6 python3], [
+            AC_PATH_PROGS_FEATURE_CHECK([PYTHON3], [python3.8], 
                 AC_MSG_CHECKING([... whether $ac_path_PYTHON3 is good])
                 python3_version=`"$ac_path_PYTHON3" --version 2>&1 \
                     | $SED -n -e 's/\([[0-9]]*\.[[0-9]]*\.[[0-9]]*\).*/\1/p'`

with which it duly picked up python3.8, I re-run ./bootstrap and

the above configure command, and then python3.7 gets picked up.

Perhaps it's a (mis)feature of AC_CACHE_CHECK?

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[Matthias Köppe]

Very strange, can you run it with ./configure CONFIG_SHELL="bash -x" and post the output?

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/a5b4735e-a729-4e7d-b421-9c95d320601eo%40googlegroups.com.

[Dima Pasechnik]

On Wed, Sep 9, 2020 at 9:31 PM Matthias Köppe <matthia...@gmail.com> wrote:

Very strange, can you run it with ./configure CONFIG_SHELL="bash -x" and post the output?

I think I know what's going on. 

The autoconf macro in question is looping over the entries in the PATH (and this is documented behaviour)

So the outer loop is

for as_dir in $PATH

now, the PATH is a bit funny in my case:

/usr/local/opt/gettext/bin:/usr/local/opt/gettext/bin:/usr/local/opt/python@3.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/Apple/usr/bin

for each $as_dir it loops over the list of Pythons we provide,

and the first match happens to be Python3.7, not Python3.8.

Indeed, to verify this,

I've added an echo for ac_path_PYTHON3 in the inner loop of ./configure and see

Checking whether SageMath should install SPKG python3...

checking whether any of sqlite libpng bzip2 xz libffi is installed as or will be installed as SPKG... no

checking for python3 >= 3.6, < 3.9 with modules sqlite3, ctypes, math, hashlib, crypt, readline, socket, zlib, distutils.core... 

ac_path_PYTHON3= /usr/local/opt/gettext/bin/python3.8

ac_path_PYTHON3= /usr/local/opt/gettext/bin/python3.7

ac_path_PYTHON3= /usr/local/opt/gettext/bin/python3.6

ac_path_PYTHON3= /usr/local/opt/gettext/bin/python3

ac_path_PYTHON3= /usr/local/opt/gettext/bin/python3.8

ac_path_PYTHON3= /usr/local/opt/gettext/bin/python3.7

ac_path_PYTHON3= /usr/local/opt/gettext/bin/python3.6

ac_path_PYTHON3= /usr/local/opt/gettext/bin/python3

ac_path_PYTHON3= /usr/local/opt/python@3.7/bin/python3.8

ac_path_PYTHON3= /usr/local/opt/python@3.7/bin/python3.7

checking ... whether /usr/local/opt/python@3.7/bin/python3.7 is good... yes

checking for python3 >= 3.6, < 3.9 with modules sqlite3, ctypes, math, hashlib, crypt, readline, socket, zlib, distutils.core... /usr/local/opt/python@3.7/bin/python3.7

configure: will use system package and not install SPKG python3

Indeed, intuitively, one would think that the outer loop should be over the programs in the list,

not the entries in the PATH, but, alas, it seems that all the autoconf macros dealing with finding 

executables loop over the PATH entries first.

 

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[Matthias Köppe]

On Wednesday, September 9, 2020 at 2:23:36 PM UTC-7, Dima Pasechnik wrote:

The autoconf macro in question is looping over the entries in the PATH (and this is documented behaviour)

So the outer loop is

for as_dir in $PATH

now, the PATH is a bit funny in my case:

/usr/local/opt/gettext/bin:/usr/local/opt/gettext/bin:/usr/local/opt/python@3.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/Apple/usr/bin

for each $as_dir it loops over the list of Pythons we provide,

and the first match happens to be Python3.7, not Python3.8.

OK that's good to know. So users just need to adjust the PATH. 

[Dima Pasechnik]

except that on macOS+Homebrew the latter wants the PATH like this:

% cat ~/.zshrc

export PATH="/usr/local/opt/python@3.7/bin:$PATH"

I am not sure whether putting /usr/local/bin first won't break Homebrew.

 

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[Matthias Köppe]

On Wednesday, September 9, 2020 at 3:08:31 PM UTC-7, Dima Pasechnik wrote:

except that on macOS+Homebrew the latter wants the PATH like this:

% cat ~/.zshrc

export PATH="/usr/local/opt/python@3.7/bin:$PATH"

I am not sure whether putting /usr/local/bin first won't break Homebrew.

Are you saying that a homebrew script put this in your .zshrc? 

[Dima Pasechnik]

I think so.
It surely wasn't me.

>
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[david....@gmail.com]

with  https://trac.sagemath.org/ticket/30536, I can compile and start sage, and all tests pass `make -j1 testlong`.

[Dima Pasechnik]

On Wed, Sep 9, 2020 at 11:23 PM Dima Pasechnik <dim...@gmail.com> wrote:
>
> On Wed, Sep 9, 2020 at 11:17 PM Matthias Köppe <matthia...@gmail.com> wrote:
> >
> > On Wednesday, September 9, 2020 at 3:08:31 PM UTC-7, Dima Pasechnik wrote:
> >>
> >>
> >> except that on macOS+Homebrew the latter wants the PATH like this:
> >>
> >> % cat ~/.zshrc
> >>
> >> export PATH="/usr/local/opt/python@3.7/bin:$PATH"
> >>
> >> I am not sure whether putting /usr/local/bin first won't break Homebrew.
> >
> >
> > Are you saying that a homebrew script put this in your .zshrc?
> I think so.
> It surely wasn't me.
>

anyhow, see #30546 for a fix, ensuring the sane order of pythons.

[Sébastien Labbé]

On Ubuntu 18.04, it picks up the python3.6 available on the machine:

## -------------------------------------------------------- ##
## Checking whether SageMath should install SPKG python3... ##
## -------------------------------------------------------- ##
configure:29604: checking whether any of sqlite libpng bzip2 xz libffi is installed as or will be installed as SPKG
configure:29613: result: no
configure:29623: checking for python3 >= 3.6, < 3.9 with modules sqlite3, ctypes, math, hashlib, crypt, readline, socket, zlib, distutils.core
configure:29629: result:
configure:29644: checking ... whether /usr/bin/python3.6 is good

...
configure:29837: result: yes
configure:29839: checking for python3 >= 3.6, < 3.9 with modules sqlite3, ctypes, math, hashlib, crypt, readline, socket, zlib, distutils.core
configure:29898: result: /usr/bin/python3.6
configure:29913: will use system package and not install SPKG python3

and ends up with an error while building the documentation right at the start:

[dochtml] Building reference manual, first pass.
[dochtml]
[dochtml] Error building the documentation.
[dochtml] Traceback (most recent call last):
[dochtml]   File "/usr/lib/python3.6/runpy.py", line 193, in _run_module_as_main
[dochtml]     "__main__", mod_spec)
[dochtml]   File "/usr/lib/python3.6/runpy.py", line 85, in _run_code
[dochtml]     exec(code, run_globals)
[dochtml]   File "/home/slabbe/GitBox/sage/local/lib/python3.6/site-packages/sage_setup/docbuild/__main__.py", line 2, in <module>
[dochtml]     main()
[dochtml]   File "/home/slabbe/GitBox/sage/local/lib/python3.6/site-packages/sage_setup/docbuild/__init__.py", line 1730, in main
[dochtml]     builder()
[dochtml]   File "/home/slabbe/GitBox/sage/local/lib/python3.6/site-packages/sage_setup/docbuild/__init__.py", line 344, in _wrapper
[dochtml]     getattr(get_builder(document), 'inventory')(*args, **kwds)
[dochtml]   File "/home/slabbe/GitBox/sage/local/lib/python3.6/site-packages/sage_setup/docbuild/__init__.py", line 568, in _wrapper
[dochtml]     self._build_bibliography(lang, format, *args, **kwds)
[dochtml]   File "/home/slabbe/GitBox/sage/local/lib/python3.6/site-packages/sage_setup/docbuild/__init__.py", line 545, in _build_bibliography
[dochtml]     build_many(build_ref_doc, references)
[dochtml]   File "/home/slabbe/GitBox/sage/local/lib/python3.6/site-packages/sage_setup/docbuild/__init__.py", line 296, in build_many
[dochtml]     _build_many(target, args, processes=NUM_THREADS)
[dochtml]   File "/home/slabbe/GitBox/sage/local/lib/python3.6/site-packages/sage_setup/docbuild/utils.py", line 289, in build_many
[dochtml]     raise worker_exc.original_exception
[dochtml] UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 2661: ordinal not in range(128)

[Dima Pasechnik]

On Thu, Sep 10, 2020 at 2:52 PM Sébastien Labbé <sla...@gmail.com> wrote:

On Ubuntu 18.04, it picks up the python3.6 available on the machine:

feel free to try #30546

you'd need to have autoconf etc installed on the box, so that you can update ./configure by running

./bootstrap

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[Matthias Köppe]

On Thursday, September 10, 2020 at 6:52:09 AM UTC-7, Sébastien Labbé wrote:

On Ubuntu 18.04, it picks up the python3.6 available on the machine:

## -------------------------------------------------------- ##
## Checking whether SageMath should install SPKG python3... ##
## -------------------------------------------------------- ##
configure:29604: checking whether any of sqlite libpng bzip2 xz libffi is installed as or will be installed as SPKG
configure:29613: result: no
configure:29623: checking for python3 >= 3.6, < 3.9 with modules sqlite3, ctypes, math, hashlib, crypt, readline, socket, zlib, distutils.core
configure:29629: result:
configure:29644: checking ... whether /usr/bin/python3.6 is good

Could you clarify if you expected it to use a different version of python?

[dochtml]   File "/home/slabbe/GitBox/sage/local/lib/python3.6/site-packages/sage_setup/docbuild/utils.py", line 289, in build_many

[dochtml]     raise worker_exc.original_exception
[dochtml] UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 2661: ordinal not in range(128)

Looks like more locale trouble - see https://trac.sagemath.org/ticket/30053

[Samuel Lelièvre]

Thanks for this new development release!

On a MacBook Air (early 2014) with
macOS 10.14.6 Mojave, with Homebrew
(but having removed Homebrew packages
gcc@9, python@3.7, arb, flint, gap, singular),
`make` succeeds but `make testlong` fails
unexpectedly still referring to python@3.7.

For example:

```
sage -t --long --warn-long 120.7 --random-seed=0 src/sage/misc/superseded.py
**********************************************************************
File "src/sage/misc/superseded.py", line 368, in
sage.misc.superseded.DeprecatedFunctionAlias.__name__
Failed example:
cython('\n'.join([
r"from sage.misc.superseded import deprecated_function_alias",
r"cdef class cython_cls(object):",
r" def new_cython_meth(self):",
r" return 1",
r" old_cython_meth = deprecated_function_alias(13109,
new_cython_meth)"
]))
Expected nothing
Got:
ld: warning: directory not found for option
'-L/usr/local/opt/python@3.7/lib'
**********************************************************************
1 item had failures:
1 of 10 in sage.misc.superseded.DeprecatedFunctionAlias.__name__
[59 tests, 1 failure, 3.46 s]
```

Logs:

https://www.math.u-psud.fr/~lelievre/sagelogs/
slel-2020-09-09-sage-9-2-b12-t-30536-mac.zip

[Matthias Köppe]

On Thursday, September 10, 2020 at 10:08:32 AM UTC-7, Samuel Lelievre wrote:

On a MacBook Air (early 2014) with
macOS 10.14.6 Mojave, with Homebrew
(but having removed Homebrew packages
gcc@9, python@3.7, arb, flint, gap, singular),
`make` succeeds but `make testlong` fails
unexpectedly still referring to python@3.7.

"make distclean" and rebuilding should fix this

[Samuel Lelievre]

I forgot to mention this was a fresh git clone.

I still tried your suggestion but testing failures

persist after "make distclean" and rebuilding.

[Markus Wageringel]

With a clean build on Ubuntu 20.04, ptestlong passes, but Jupyter does not start anymore due to an SSL problem, using Sage's Python 3. (The system Python 3.8 is not picked up because of missing dependencies sqlite and xz, but that is ok.)

    $ ./sage -n jupyter

    Please wait while the Sage Jupyter Notebook server starts...

    Traceback (most recent call last):

      File "/amd/compute/mwagerin/git/sage_compute/local/lib/python3.8/site-packages/sage/repl/ipython_kernel/install.py", line 307, in have_prerequisites

        from notebook.notebookapp import NotebookApp

      File "/amd/compute/mwagerin/git/sage_compute/local/lib/python3.8/site-packages/notebook/notebookapp.py", line 66, in <module>

        from tornado import httpserver

      File "/amd/compute/mwagerin/git/sage_compute/local/lib/python3.8/site-packages/tornado/httpserver.py", line 29, in <module>

        import ssl

      File "/amd/compute/mwagerin/git/sage_compute/local/lib/python3.8/ssl.py", line 98, in <module>

        import _ssl             # if we can't import it, let the error propagate

    ModuleNotFoundError: No module named '_ssl'

    The Jupyter notebook requires ssl, even if you do not use

    https. Install the openssl development packages in your system and

    then rebuild Python (sage -f python3).

Which packages need to be installed for this and why was this not a problem previously? OpenSSL is installed on the system:

    $ openssl version

    OpenSSL 1.1.1f  31 Mar 2020

On a different note, 9.2.beta11 has introduced crashes of the doctests in `src/sage/interfaces/singular.py` that were reproducible on about 20% of the test runs and have been observed by several other people as well. I have tracked that issue down to the Pexpect upgrade in #29240 via bisection. With 9.2.beta12 on the other hand, I cannot reproduce the problem anymore, possibly because of the Python upgrade. There are still reports about this with 9.2.beta12 though, so maybe this helps analyze the problem.

[Matthias Köppe]

On Friday, September 11, 2020 at 10:55:57 AM UTC-7, Markus Wageringel wrote:

9.2.beta11 has introduced crashes of the doctests in `src/sage/interfaces/singular.py` that were reproducible on about 20% of the test runs and have been observed by several other people as well. I have tracked that issue down to the Pexpect upgrade in #29240 via bisection. With 9.2.beta12 on the other hand, I cannot reproduce the problem anymore, possibly because of the Python upgrade. There are still reports about this with 9.2.beta12 though, so maybe this helps analyze the problem.

Is singular crashing in these tests or Sage? If it's singular, it would be helpful to enable logging in the Pexpect interface and then trying to reproduce the errors without Sage

[Matthias Köppe]

On Friday, September 11, 2020 at 10:55:57 AM UTC-7, Markus Wageringel wrote:

With a clean build on Ubuntu 20.04, ptestlong passes, but Jupyter does not start anymore due to an SSL problem, Which packages need to be installed for this and why was this not a problem previously? OpenSSL is installed on the system:

    $ openssl version

    OpenSSL 1.1.1f  31 Mar 2020

Is "libssl-dev" installed? (see build/pkgs/openssl/distros/debian.txt)

 

[Markus Wageringel]

> Am 11.09.2020 um 20:17 schrieb Matthias Köppe <matthia...@gmail.com>:
>
> Is "libssl-dev" installed? (see build/pkgs/openssl/distros/debian.txt)

It looks like it is not:

$ ldconfig -p | grep ssl
libxmlsec1-openssl.so.1 (libc6,x86-64) => /lib/x86_64-linux-gnu/libxmlsec1-openssl.so.1
libssl3.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libssl3.so
libssl.so.1.1 (libc6,x86-64) => /lib/x86_64-linux-gnu/libssl.so.1.1
libgnutls-openssl.so.27 (libc6,x86-64) => /lib/x86_64-linux-gnu/libgnutls-openssl.so.27

I do not have sudo rights to install it. Enabling the optional OpenSSL SPKG would fix this then, I assume.

[Matthias Köppe]

On Friday, September 11, 2020 at 11:34:15 AM UTC-7, Markus Wageringel wrote:

> Am 11.09.2020 um 20:17 schrieb Matthias Köppe <matthia...@gmail.com>:
>
> Is "libssl-dev" installed? (see build/pkgs/openssl/distros/debian.txt)

(This is the name of the Debian package with the header files.) Check for files in /usr/include/openssl

[Samuel Lelièvre]

2020-09-11 17:55 UTC, Markus Wageringel:

>
> With a clean build on Ubuntu 20.04, ptestlong passes, but Jupyter

> does not start anymore due to an SSL problem, using Sage's Python 3.
> (The system Python 3.8 is not picked up because of missing
> dependencies sqlite and xz, but that is ok.)
>
> $ ./sage -n jupyter
> Please wait while the Sage Jupyter Notebook server starts...
> Traceback (most recent call last):

> ...

> import _ssl # if we can't import it, let the error propagate
> ModuleNotFoundError: No module named '_ssl'
>
> The Jupyter notebook requires ssl, even if you do not use
> https. Install the openssl development packages in your system and
> then rebuild Python (sage -f python3).
>

> Which packages need to be installed for this and why was this not
> a problem previously? OpenSSL is installed on the system:
>
> $ openssl version
> OpenSSL 1.1.1f 31 Mar 2020

The build system apparently did not build Python's
`_ssl` module when it built Python. It is supposed to
always build it provided openssl is present, either from
the system or built as an spkg.

Or could it be that your system has OpenSSL but not
libssl-dev, as Matthias suggests?

2020-09-11 18:17 UTC, Matthias Köppe:

>
> Is "libssl-dev" installed?
> (see build/pkgs/openssl/distros/debian.txt)

On Debian or Debian-based system like Ubuntu, check whether
libssl-dev is installed with this command (sudo not needed):
```
$ dpkg-query --list libssl-dev
```

If indeed it was not installed, do this:
```
$ sudo apt install libssl-dev
$ ./sage -f python3
```

Oh, but you replied to Matthias now:

2020-09-11 18:34 UTC, Markus Wageringel

>
> It looks like it is not:

In the meantime I had opened a ticket:

- Build Python's ssl module
https://trac.sagemath.org/ticket/30556

in which I forgot about the libssl vs libssl-dev subtlety.

I'll change the ticket's goal to

- Warn when building Python without its SSL module

I know when there are errors, they are summarized
at the end of the build. Do we have a mechanism
to collect warnings and summarise them at the end
of the build?

It would be very useful when building on a system
without the appropriate ssl dependencies like yours
or most macOS systems to end the build with a word
such as

Sage was successfully built, and starts,
but be warned, it build its own Python
without the SSL module. To know more, visit
<some documentation or wiki page>

Would there be a way to make `sage -n jupyter` first check
for the ssl module, and if it is not found provide some
helpful error message with hints as to how to fix things?

If you get a chance to ask someone with sudo rights
on the machine you were using, have them install all
the pieces you were missing: xz, sqlite, libssl-dev,
for next time!

See at the end of the output of `./configure` for a list
of recommended packages to install system-wide.

In the meantime a workaround as you guessed is to build
Sage's openssl spkg and rebuild Sage's Python so it takes
advantage of it:
```
$ ./sage -i openssl
$ ./sage -f python3
```

This last command will also rebuild any packages
that depend on the `python3` spkg.

[Antonio Rojas]

This is the issue I mentioned in https://trac.sagemath.org/ticket/29240#comment:3

For some time I could reproduce it on sage-the-distro but not on my Arch package, then I could no longer reproduce it on sage-the-distro and suddenly started happening on the Arch package, triggered by the sympy 1.6.1 update (which shuffles some imports).

It seems that the singular instance is being unloaded from memory, which causes pexpect to crash. While trying to debug this, I found that removing almost *any* test block from singular.py will prevent it from crashing, which is certainly weird.

[Markus Wageringel]

> Am 11.09.2020 um 20:46 schrieb Samuel Lelièvre <samuel....@gmail.com>:
>
> On Debian or Debian-based system like Ubuntu, check whether
> libssl-dev is installed with this command (sudo not needed):
> ```
> $ dpkg-query --list libssl-dev
> ```

Thank you for the explanations. The command returns:

$ dpkg-query --list libssl-dev
dpkg-query: no packages found matching libssl-dev

Also, the directory Matthias mentioned `/usr/include/openssl` does not exist.

> It would be very useful when building on a system
> without the appropriate ssl dependencies like yours
> or most macOS systems to end the build with a word
> such as
>
> Sage was successfully built, and starts,
> but be warned, it build its own Python
> without the SSL module. To know more, visit
> <some documentation or wiki page>

I think it might be better to stop the build earlier (and maybe ask for confirmation) before proceeding to build Python, to avoid building Python and all its dependencies a second time after installing OpenSSL. That is, unless there is a reason to build Sage without OpenSSL.

[Matthias Köppe]

On Friday, September 11, 2020 at 12:06:51 PM UTC-7, Markus Wageringel wrote:

I think it might be better to stop the build earlier (and maybe ask for confirmation) before proceeding to build Python, to avoid building Python and all its dependencies a second time after installing OpenSSL. That is, unless there is a reason to build Sage without OpenSSL.

After the license change that will come with OpenSSL 3 (https://trac.sagemath.org/ticket/29555), we can make openssl a standard package. 

[Samuel Lelievre]

I'll reinstall gcc@9 and python@3.7 and  try again.

[Dima Pasechnik]

but why, install gcc (i.g. gcc@10), Sage now accepts it.

Probably you want to configure with CC=clang CXX=clang++

 You may also try installing python3.8 and use it with the experimental branch from https://trac.sagemath.org/ticket/30546 

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[Matthias Köppe]

On Friday, September 11, 2020 at 3:31:21 PM UTC-7, Dima Pasechnik wrote:

Probably you want to configure with CC=clang CXX=clang++

That's actually not necessary. homebrew does not provide unversioned gcc and g++ executables, so gcc ->  /usr/bin/gcc and g++ -> /usr/bin/g++

 

[Samuel Lelievre]

2020-09-11 22:31:21 UTC, Dima Pasechnik:
>
> On Fri, Sep 11, 2020 at 11:16 PM Samuel Lelievre:

>>
>> I'll reinstall gcc@9 and python@3.7 and  try again.
>
> but why, install gcc (i.g. gcc@10), Sage now accepts it.
> Probably you want to configure with CC=clang CXX=clang++
>
> You may also try installing python3.8 and use it
> with the experimental branch from
> https://trac.sagemath.org/ticket/30546

Can "git trac try" take several ticket numbers so as
to apply them both on top of the latest develop?
For instance will this work?

$ git trac try 30536 30546

Otherwise hopefully the next beta includes

at least 30536 which has positive review.

[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.beta6: OK

  - make ptestlong: all tests passed.

Eric.

[Sébastien Labbé]

Answering a question from few days ago:

On Thursday, September 10, 2020 at 5:13:00 PM UTC+2 matthia...@gmail.com wrote:

On Thursday, September 10, 2020 at 6:52:09 AM UTC-7, Sébastien Labbé wrote:

On Ubuntu 18.04, it picks up the python3.6 available on the machine:

## -------------------------------------------------------- ##
## Checking whether SageMath should install SPKG python3... ##
## -------------------------------------------------------- ##
configure:29604: checking whether any of sqlite libpng bzip2 xz libffi is installed as or will be installed as SPKG
configure:29613: result: no
configure:29623: checking for python3 >= 3.6, < 3.9 with modules sqlite3, ctypes, math, hashlib, crypt, readline, socket, zlib, distutils.core
configure:29629: result:
configure:29644: checking ... whether /usr/bin/python3.6 is good

Could you clarify if you expected it to use a different version of python?

Hitting tab on `python3` in the terminal gives:

$ python3[TAB]
python3            python3.6-config   python3.6m-config  python3m
python3.6          python3.6m         python3-config     python3m-config

so it seems python3.7 nor python3.8 are not available on the machine. So I was not expecting something different to happen.

 

[Emmanuel Charpentier]

Very similar (but not identical !) results on a slightly different machine :

On Debian testing running on core i7 + 16 GB RAM, upgrading 9.2.beta11 to 9.10.beta12 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

HTH,

​

Le lundi 7 septembre 2020 16:12:18 UTC+2, Emmanuel Charpentier a écrit :

On Debian testing running on core i5 + 8 GB RAM, upgrading 9.2.beta11 to 9.2.beta12 after make python3-cleanusing all system packages and running ptestlong gives 7 permanent failures :

File	Result	P/T
src/sage/schemes/hyperelliptic_curves/monsky_washnitzer.py	Killed due to abort	P
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/sage/rings/real_arb.pyx	2 doctests failed	P
src/sage/modules/free_module_morphism.py	3 doctests failed	P
src/doc/en/developer/coding_in_other.rst	1 doctest failed	P

These failures have been reported already for 2.9.beta11 on the same machine, except for the failure observed for coding_in_other.rst, which was transient in 2.9.beta11 and is now permanent.

Of note :

• ./configure failed to recognize the system’s Python packages ; notwithstanding this failure,
  • $SAGE_LOCAL/bin/python3.8 is a symlink to /usr/bin/python3.8
  • sage -standard | grep python reports python3 as
    (not_installed)
• gap-packages still no longer installs (complains about multiply-defined symbols).

HTH,

​

Le lundi 7 septembre 2020 01:25:39 UTC+2, Volker Braun 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 

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

5ec24db181 (tag: 9.2.beta12, trac/develop) Updated SageMath version to 9.2.beta12

5efa8df9cd Trac #30454: some details in doc of number fields

d1a1a28695 Trac #30443: Simplify setting and getting "edges" of edges, ridges, incidences in `CombinatorialPolyhedron`

f8c4e4b530 Trac #30409: Optional ideal parameter for normalize_coordinates

603aa8806e Trac #28722: update constants for S-unit solver

21f7af35b4 Trac #14735: Bug with Python int division in wigner.py

7d9921cca9 Trac #30490: Reduce doctesting time for polyhedra

11c8e5b6ff Trac #30487: GH Actions: Test also with Xcode 12 beta

80c4c5e916 Trac #30479: deprecate random_DAG

505f3f4065 Trac #30470: Make spanning_trees an iterator

80d9314aef Trac #30455: pep8 cleanup of the file e_one_star

d6b5a59b02 Trac #30452: "sage -startuptime" should accept file names too

9e5a3ba06e Trac #30449: Fix docbuild warning in combinat plus improve formatting

875d7180ca Trac #30442: Implement general table art for tableau-like objects

e8696d8001 Trac #30440: Pyramid for combinatorial polyhedron

dfa0d227a5 Trac #30410: Command "sage -tox"

b8421f50e2 Trac #30401: Unions of subsets of a fixed open set X are not known to be subsets of X

e0b21bfd1d Trac #30395: enhance fricas lists

50d0934dff Trac #30382: More voidlinux.txt

1185b94e8d Trac #30212: Fix tkz-graph and tkz-berge links: altermundus.com is gone

4974b90112 Trac #28982: Use CombinatorialPolyhedron to obtain faces lattice of polyhedra

dcf19afbfc Trac #27952: upgrade Normaliz to 3.8.8, PyNormaliz to 2.12, add script package libnauty

a5f5293ca6 Trac #30496: fix conversion of GAP univariate rat functions, which are polynomial with valuation>0

596988abf2 Trac #30489: Two fixes for test suite for products of polyhedra

b9c5e0bdbd Trac #30488: ci-cygwin: Remove sage_brial

b0465d76c9 Trac #30317: Update pip to 20.2.2, setuptools to 49.6.0

d96db5467d Trac #27754: Upgrade: Python 3.8.5

c353bce995 (tag: 9.2.beta11) Updated SageMath version to 9.2.beta11

[Eric Gourgoulhon]

On Ubuntu 20.04 running on Intel Core i7-8665U + 32 GB RAM:

- build (-j8) from a fresh git clone with a maximum of system packages (details below), including the system Python (3.8.2): OK

- all tests from ptestlong passed

Details of build:

As recommended in https://doc.sagemath.org/html/en/installation/source.html#prerequisites,  the following Ubuntu 20.04 packages were installed before the build:

sudo apt-get install bc binutils bzip2 ca-certificates cliquer curl eclib-tools fflas-ffpack flintqs g++ g++ gcc gcc gfan gfortran git glpk-utils gmp-ecm lcalc libatomic-ops-dev libboost-dev libbraiding-dev libbrial-dev libbrial-groebner-dev libbz2-dev libcdd-dev libcdd-tools libcliquer-dev libcurl4-openssl-dev libec-dev libecm-dev libffi-dev libflint-arb-dev libflint-dev libfreetype6-dev libgd-dev libgf2x-dev libgivaro-dev libglpk-dev libgmp-dev libgsl-dev libiml-dev liblfunction-dev liblrcalc-dev liblzma-dev libm4rie-dev libmpc-dev libmpfi-dev libmpfr-dev libncurses5-dev libntl-dev libopenblas-dev libpari-dev libpcre3-dev libplanarity-dev libppl-dev libpython3-dev libreadline-dev librw-dev libsqlite3-dev libsuitesparse-dev libsymmetrica2-dev libz-dev libzmq3-dev libzn-poly-dev m4 make nauty palp pari-doc pari-elldata pari-galdata pari-galpol pari-gp2c pari-seadata patch perl pkg-config planarity ppl-dev python3 python3 python3-distutils r-base-dev r-cran-lattice sqlite3 sympow tachyon tar xz-utils yasm

Then, after running

make configure

./configure

I've installed some supplementary packages as recommended in the outcome of configure:

sudo apt-get install coinor-cbc coinor-libcbc-dev libcdd-dev libcdd-tools cmake libisl-dev libnauty-dev ninja-build libxml-libxslt-perl libxml-writer-perl libxml2-dev libperl-dev libfile-slurp-perl libjson-perl libsvg-perl libterm-readkey-perl libterm-readline-gnu-perl libmongodb-perl libterm-readline-gnu-perl

I then ran

./config.status --recheck && ./config.status

which yielded the following recommendation:

configure: hint: installing the following system packages is recommended and may avoid building some of the above SPKGs from source:
configure:   $ sudo apt-get update
  $ sudo apt-get install libcdd-dev libcdd-tools libnauty-dev

However these packages are already installed in the system:

sudo apt-get install libcdd-dev libcdd-tools libnauty-dev
Lecture des listes de paquets... Fait
Construction de l'arbre des dépendances       
Lecture des informations d'état... Fait
Note : sélection de « libnauty2-dev » au lieu de « libnauty-dev »
libcdd-dev est déjà la version la plus récente (094j-2).
libcdd-tools est déjà la version la plus récente (094j-2).
libnauty2-dev est déjà la version la plus récente (2.6r10+ds-1ubuntu1).
Le paquet suivant a été installé automatiquement et n'est plus nécessaire :
  libfprint-2-tod1
Veuillez utiliser « sudo apt autoremove » pour le supprimer.
0 mis à jour, 0 nouvellement installés, 0 à enlever et 2 non mis à jour.

Finally, I ran

MAKE="make -j8" make

and the build proceeded smoothly.

Side note:  the launch of Sage in a terminal is very fast on this computer, less then 2 seconds. Maybe this is due to the use of the system Python?

Eric.

[Vincent Delecroix]

Le 16/09/2020 à 11:51, Eric Gourgoulhon a écrit :
> Side note: the launch of Sage in a terminal is very fast on this computer,
> less then 2 seconds. Maybe this is due to the use of the system Python?

On my computer, I have 3 sage with the following startup times
* conda (Sage 9.1, Python 3.7.8): around 1.3secs
* system (Sage 9.1, Python 3.8.5): around 1.3secs
* built from source (9.2.beta11, Python 3.7.3): around 1.5secs

[Samuel Lelievre]

2020-09-16 09:51:38 UTC, Eric Gourgoulhon:

>

> On Ubuntu 20.04 running on Intel Core i7-8665U + 32 GB RAM:

>

> - build (-j8) from a fresh git clone with a maximum of system

>   packages (details below), including the system Python (3.8.2): OK

> - all tests from ptestlong passed

>

> Details of build:

> As recommended in [...]

> the following Ubuntu 20.04 packages were installed before the build:

>

> sudo apt-get install [...]

>

> Then, after running

>

> make configure

> ./configure

>

> I've installed [...] as recommended in the outcome of configure:

>

> sudo apt-get install [...]

>

> I then ran

>

> ./config.status --recheck && ./config.status

>

> which yielded the following recommendation:

>

> configure: hint: installing the following system packages

> is recommended and may avoid building some of the above SPKGs

> from source:

> configure:   $ sudo apt-get update

>   $ sudo apt-get install libcdd-dev libcdd-tools libnauty-dev

>

> However these packages are already installed in the system:

Recommendations of packages to install can still be improved,

see the dedicated ticket:

  https://trac.sagemath.org/ticket/29586

but we need to balance the maintenance effort with the gains.

In this case, what you can conclude is:

- satisfactory versions of these packages (or possibly packages

  that depend on them) for that OS were not found

- on some version of that OS, satisfactory versions of these

  packages exist that would avoid having to build them

and what we should do about it is probably adapt the wording

to better convey that. For instance:

hint: installing the following system packages, if not already

present, is recommended and may avoid building some SPKGs from

source (though some may have to be built anyway):

[...]

[Eric Gourgoulhon]

I was speaking about a cold start, i.e. starting Sage for the first time after login to the computer.

For such starts, I was used to get about 10 or even 20 s, rather  than 1 s. For hot starts, it is indeed about 1 s.

Eric.

[Eric Gourgoulhon]

Le mercredi 16 septembre 2020 à 19:05:59 UTC+2, Samuel Lelievre a écrit :

Recommendations of packages to install can still be improved,

see the dedicated ticket:

  https://trac.sagemath.org/ticket/29586

but we need to balance the maintenance effort with the gains.

Indeed!

In this case, what you can conclude is:

- satisfactory versions of these packages (or possibly packages

  that depend on them) for that OS were not found

- on some version of that OS, satisfactory versions of these

  packages exist that would avoid having to build them

and what we should do about it is probably adapt the wording

to better convey that. For instance:

hint: installing the following system packages, if not already

present, is recommended and may avoid building some SPKGs from

source (though some may have to be built anyway):

+1

Eric.

[Kenji Iohara]

On my Mac OS 10.15.6 with XCode 12, it cannot compile Sage9.2.beta12.

 

[gf2x-1.3.0] Error configuring gf2x-1.3.0 See the file

[gf2x-1.3.0]     /Users/iohara/Desktop/sage-9.2.beta12/local/var/tmp/sage/build/gf2x-1.3.0/src/config.log

[gf2x-1.3.0] for details.

[gf2x-1.3.0] ********************************************************************************

[gf2x-1.3.0] 

[gf2x-1.3.0] real 0m11.879s

[gf2x-1.3.0] user 0m4.836s

[gf2x-1.3.0] sys 0m5.094s

[gf2x-1.3.0] ************************************************************************

[gf2x-1.3.0] Error installing package gf2x-1.3.0

[gf2x-1.3.0] ************************************************************************

[gf2x-1.3.0] Please email sage-devel (http://groups.google.com/group/sage-devel)

[gf2x-1.3.0] explaining the problem and including the log file

[gf2x-1.3.0]   /Users/iohara/Desktop/sage-9.2.beta12/logs/pkgs/gf2x-1.3.0.log

[gf2x-1.3.0] Describe your computer, operating system, etc.

[gf2x-1.3.0] If you want to try to fix the problem yourself, *don't* just cd to

[gf2x-1.3.0] /Users/iohara/Desktop/sage-9.2.beta12/local/var/tmp/sage/build/gf2x-1.3.0 and type 'make' or whatever is appropriate.

[gf2x-1.3.0] Instead, the following commands setup all environment variables

[gf2x-1.3.0] correctly and load a subshell for you to debug the error:

[gf2x-1.3.0]   (cd '/Users/iohara/Desktop/sage-9.2.beta12/local/var/tmp/sage/build/gf2x-1.3.0' && '/Users/iohara/Desktop/sage-9.2.beta12/sage' --buildsh)

[gf2x-1.3.0] When you are done debugging, you can type "exit" to leave the subshell.

[gf2x-1.3.0] ************************************************************************

make[4]: *** [gf2x-no-deps] Error 1

make[3]: *** [/Users/iohara/Desktop/sage-9.2.beta12/local/var/lib/sage/installed/gf2x-1.3.0] Error 2

make[2]: *** [all-start] Error 2

real 0m13.222s

user 0m5.417s

sys 0m5.707s

***************************************************************

Error building Sage.

[John H Palmieri]

With the newly released Xcode 12, if I run "make -k", I get failures building

ecl

ecm

gf2x

rubiks (which is about to be downgraded to optional, so I don't care)

scipy

symmetrica

The good news is that 141 other packages built successfully. See also the thread

https://groups.google.com/d/msg/sage-support/ZLgu-1pi6nc/LH2Mma_uAgAJ, which is addressing the same issues (but without concrete solutions).

[John H Palmieri]

See also https://trac.sagemath.org/ticket/30494

[Kenji Iohara]

Mac OS 10.15.6 with XCode 12, I cannot compile SAGE 9.2.Beta12.

If I run make -k, I get the failure building

gf2x

openblas

readline

ecm

symmetrica

rubiks

2020/09/17 19:54、John H Palmieri <jhpalm...@gmail.com>のメール:

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[Matthias Köppe]

On Wednesday, September 16, 2020 at 10:05:59 AM UTC-7 Samuel Lelievre wrote:

[...]  what we should do about it is probably adapt the wording

to better convey that. For instance:

hint: installing the following system packages, if not already

present, is recommended and may avoid building some SPKGs from

source (though some may have to be built anyway):

[...]

+1, ticket please

 

[John H Palmieri]

At https://trac.sagemath.org/ticket/30494 and the tickets it points to, people have made progress on many of these. Not openblas or readline yet, because those have suitable homebrew replacement packages. (There is a link to a ticket with an upgrade for readline which fixes the problem for me, but because of the homebrew situation, it is not as high priority as some of the other packages. I don't know if anyone has worked on openblas yet.)

Anyway, we have fixes for ecl, ecm, gf2c, scipy, and symmetrica. All but the one for symmetrica have been positively reviewed; the fix for symmetrica involves updating the package, so it needs checking on a range of platforms. It works for two of us with Xcode 12 on OS X.

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[Samuel Lelievre]

This is now:

- Sage Trac ticket 30624

  Improve configure's recommendation message

  https://trac.sagemath.org/ticket/30624

 

I don't have time to work on it now.

[Samuel Lelievre]

2020-09-21 09:23:54 UTC, Samuel Lelievre:

This is now:

- Sage Trac ticket 30624

  Improve configure's recommendation message

  https://trac.sagemath.org/ticket/30624

 

I don't have time to work on it now.

Update: I pushed a branch. Needs review.