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Sep 6, 2020, 7:25:39 PM9/6/20

to sage-release

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

Sep 7, 2020, 1:21:19 AM9/7/20

to sage-release

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:

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.

Sep 7, 2020, 5:09:29 AM9/7/20

to sage-r...@googlegroups.com

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:

Sep 7, 2020, 6:01:38 AM9/7/20

to sage-release

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.logMakefile: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.

Sep 7, 2020, 7:20:34 AM9/7/20

to sage-release

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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>

>

> 2020/09/07 7:21、Matthias Köppe <matthia...@gmail.com>のメール:

> --

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>

>

> --

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Otherwise it is not clear how to reproduce this, e.g. what Python is used.

> 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/558F391C-C79B-46BE-A579-0450178A7797%40gmail.com.

>

>

> 2020/09/07 7:21、Matthias Köppe <matthia...@gmail.com>のメール:

> 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/6563fac7-a1e5-4da3-862e-d1cc6631a3d0o%40googlegroups.com.

>

>

> --

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Sep 7, 2020, 7:43:22 AM9/7/20

to sage-release

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]

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]

Sep 7, 2020, 7:50:17 AM9/7/20

to sage-release

pynormaliz 2.12 isn't on the mirrors yet

(I can work around that)

Sep 7, 2020, 8:48:29 AM9/7/20

to sage-release

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 failedsage -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):

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

Sep 7, 2020, 10:12:18 AM9/7/20

to sage-release

On Debian testing running on core i5 + 8 GB RAM, upgrading `9.2.beta11 `

to `9.2.beta12`

after `make python3-clean`

using 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,

Sep 7, 2020, 11:55:07 AM9/7/20

to sage-release

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:

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

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

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

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:

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

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:

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:

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

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]

Sep 7, 2020, 3:04:58 PM9/7/20

to sage-release

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-{bullseye,sid}-minimal: Clean

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

linuxmint-{18,19,19.3}: 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.

gentoo-python3.7: Clean

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

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

[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

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

Sep 7, 2020, 3:13:07 PM9/7/20

to sage-release

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

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

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

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

Sep 7, 2020, 5:32:02 PM9/7/20

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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.

Sep 8, 2020, 3:22:09 AM9/8/20

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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.

Sep 8, 2020, 4:14:36 AM9/8/20

to sage-release

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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> <config.log>

>

>

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Sep 8, 2020, 4:26:09 AM9/8/20

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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.

Sep 8, 2020, 9:26:52 AM9/8/20

to sage-release

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.

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

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

Sep 8, 2020, 10:40:33 AM9/8/20

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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

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CAAWYfq2E9GnfDRYzWrLk2qhBUnKgFppkun4DZsXCaF%3Dxf%3Dfogw%40mail.gmail.com.

Sep 9, 2020, 12:23:04 AM9/9/20

to sage-release

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

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

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':

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)

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] ~~~ ^ ~

[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

Sep 9, 2020, 5:49:19 AM9/9/20

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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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Sep 9, 2020, 6:05:02 AM9/9/20

to sage-release

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
>

> 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.

>

Sep 9, 2020, 6:52:59 AM9/9/20

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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 9.2Is your xcode up to date?

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.

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.

Sep 9, 2020, 7:29:28 AM9/9/20

to sage-release

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.

$ source .homebrew-build-env

before builds, right?

Post the top-level config.log

Sep 9, 2020, 7:41:00 AM9/9/20

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> Le 9 sept. 2020 à 13:29, Dima Pasechnik <dim...@gmail.com> a écrit :

>

> you do

>

> $ source .homebrew-build-env

>

> before builds, right?

> Post the top-level config.log

Here it is

Sep 9, 2020, 9:40:17 AM9/9/20

to sage-release

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)

> > To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CAAWYfq31h8a5qgdyY%2BhzJeUuSdw%3DT__GTp5XWmV_QWXDDrwuUA%40mail.gmail.com.

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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Sep 9, 2020, 10:26:05 AM9/9/20

to sage-release

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

Sep 9, 2020, 10:53:47 AM9/9/20

to sage-release

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.

Sep 9, 2020, 10:57:19 AM9/9/20

to sage-release

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

Sep 9, 2020, 11:02:12 AM9/9/20

to sage-release

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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Sep 9, 2020, 11:35:10 AM9/9/20

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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

if [ -d "$HOMEBREW/opt/$l" ]; then

LIBRARY_PATH="$HOMEBREW/opt/$l:$LIBRARY_PATH"

fi

done

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Sep 9, 2020, 11:41:42 AM9/9/20

to sage-release

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

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...

I can try to install ntl and flint, but then I have to remove dependencies as well, right ?sapristi:sage dcoudert$ brew uninstall ntl flintError: Refusing to uninstall /usr/local/Cellar/flint/2.6.3because it is required by arb, which is currently installed.You can override this and force removal with:brew uninstall --ignore-dependencies ntl flintLe 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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Sep 9, 2020, 1:11:14 PM9/9/20

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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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Sep 9, 2020, 1:31:01 PM9/9/20

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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?

Sep 9, 2020, 3:32:18 PM9/9/20

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> 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

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

Sep 9, 2020, 3:39:38 PM9/9/20

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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

Sep 9, 2020, 3:44:50 PM9/9/20

to sage-release

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

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Sep 9, 2020, 3:54:16 PM9/9/20

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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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Sep 9, 2020, 3:58:26 PM9/9/20

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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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>

> 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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Sep 9, 2020, 4:04:14 PM9/9/20

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

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Sep 9, 2020, 4:17:04 PM9/9/20

to sage-release

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

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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Sep 9, 2020, 4:31:47 PM9/9/20

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

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Sep 9, 2020, 5:23:36 PM9/9/20

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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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Sep 9, 2020, 6:00:48 PM9/9/20

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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 isfor 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.

Sep 9, 2020, 6:08:31 PM9/9/20

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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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Sep 9, 2020, 6:17:16 PM9/9/20

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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?

Sep 9, 2020, 6:23:49 PM9/9/20