Doing make distclean and using system's python3.8 with ./configure --with-python=/usr/bin/python3.8 avoided my issue with compilation of python3.9.5.
On Ubuntu 18.04, make ptestall with following optional and external packages gives:
Using --optional=4ti2,build,ccache,cryptominisat,debian,dot2tex,e_antic,external,fricas,glucose,latte_int,lidia,normaliz,notedown,pandoc_attributes,pip,pycosat,pynormaliz,rst2ipynb,sage,sage_numerical_backends_coin,sage_spkg
----------------------------------------------------------------------
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 # 2 doctests 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/misc/package.py # 1 doctest failed
sage -t --long --random-seed=0 src/sage/modules/fg_pid/fgp_module.py # 2 doctests failed
sage -t --long --random-seed=0 src/sage/tests/cmdline.py # 1 doctest failed
----------------------------------------------------------------------
External software detected for doctesting: ffmpeg,graphviz,imagemagick,internet,latex,octave,pandoc
Rerunning failed tests, I get the same. Failures are copied below.
Follow up at
https://trac.sagemath.org/ticket/25536 for issues involving optional packages.
Running doctests with ID 2021-06-24-13-28-43-06b7e682.
Git branch: develop
Using --optional=4ti2,build,ccache,cryptominisat,debian,dot2tex,e_antic,external,fricas,glucose,latte_int,lidia,normaliz,notedown,pandoc_attributes,pip,pycosat,pynormaliz,rst2ipynb,sage,sage_numerical_backends_coin,sage_spkg
External software to be detected: cplex,ffmpeg,graphviz,gurobi,imagemagick,internet,latex,macaulay2,magma,maple,mathematica,matlab,octave,pandoc,rubiks,scilab
Doctesting entire Sage library.
Only doctesting files that failed last test.
Doctesting 7 files using 8 threads.
sage -t --long --random-seed=0 src/sage/modules/fg_pid/fgp_module.py
**********************************************************************
File "src/sage/modules/fg_pid/fgp_module.py", line 1274, in sage.modules.fg_pid.fgp_module.FGP_Module_class.coordinate_vector
Failed example:
Q.coordinate_vector(Q.0 - Q.1)
Expected:
(1, -1)
Got:
(1, 47)
**********************************************************************
File "src/sage/modules/fg_pid/fgp_module.py", line 1294, in sage.modules.fg_pid.fgp_module.FGP_Module_class.coordinate_vector
Failed example:
Q.coordinate_vector(x)
Expected:
(0, -1)
Got:
(0, 11)
**********************************************************************
1 item had failures:
2 of 23 in sage.modules.fg_pid.fgp_module.FGP_Module_class.coordinate_vector
0 tests not run because we ran out of time
[397 tests, 2 failures, 2.29 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
[339 tests, 1 failure, 1.57 s]
sage -t --long --random-seed=0 src/sage/graphs/graph.py
**********************************************************************
File "src/sage/graphs/graph.py", line 4236, 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 4631, 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 5841, 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
[1216 tests, 3 failures, 21.32 s]
sage -t --long --random-seed=0 src/sage/graphs/generic_graph.py
**********************************************************************
File "src/sage/graphs/generic_graph.py", line 8879, 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 9500, 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
[3535 tests, 2 failures, 37.33 s]
sage -t --long --random-seed=0 src/sage/tests/cmdline.py
**********************************************************************
File "src/sage/tests/cmdline.py", line 607, in sage.tests.cmdline.test_executable
Failed example:
err # optional - internet
Expected:
''
Got:
'/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/misc/package.py:115: UserWarning: failed to fetch the version of pkg=\'ore_algebra\' at
https://pypi.org/pypi/ore_algebra/json\n warnings.warn("failed to fetch the version of pkg={!r} at {}".format(pkg, url))\n'
**********************************************************************
1 item had failures:
1 of 257 in sage.tests.cmdline.test_executable
3 gdb tests not run
6 py2 tests not run
4 r tests not run
6 sagenb tests not run
0 tests not run because we ran out of time
[256 tests, 1 failure, 34.50 s]
sage -t --long --random-seed=0 src/sage/databases/oeis.py
**********************************************************************
File "src/sage/databases/oeis.py", line 1506, in sage.databases.oeis.OEISSequence.references
Failed example:
w.references() # optional -- internet
Expected:
0: A. H. Beiler, Recreations in the Theory of Numbers, Dover, NY, 1964, p. 52.
1: C. Clawson, Mathematical Mysteries, Plenum Press, 1996, p. 180.
2: R. Crandall and C. Pomerance, Prime Numbers: A Computational Perspective, Springer, NY, 2001; see p. 29.
3: G. H. Hardy and E. M. Wright, An Introduction to the Theory of Numbers, 5th ed., Oxford Univ. Press, 1979, th. 80.
...
Got:
0: N. G. W. H. Beeger, On the Congruence (p-1)! == -1 (mod p^2), Messenger of Mathematics, Vol. 49 (1920), pp. 177-178.
1: Albert H. Beiler, Recreations in the Theory of Numbers, Dover, NY, 1964, p. 52.
2: Calvin C. Clawson, Mathematical Mysteries, Plenum Press, 1996, p. 180.
3: Richard Crandall and Carl Pomerance, Prime Numbers: A Computational Perspective, Springer, NY, 2001; see p. 29.
4: G. H. Hardy and E. M. Wright, An Introduction to the Theory of Numbers, 5th ed., Oxford Univ. Press, 1979, th. 80.
5: Paulo Ribenboim, My Numbers, My Friends: Popular Lectures on Number Theory, Springer Science & Business Media, 2000, ISBN 0-387-98911-0.
6: Paulo Ribenboim, The Book of Prime Number Records. Springer-Verlag, NY, 2nd ed., 1989, p. 277.
7: N. J. A. Sloane and Simon Plouffe, The Encyclopedia of Integer Sequences, Academic Press, 1995 (includes this sequence).
8: Ilan Vardi, Computational Recreations in Mathematica. Addison-Wesley, Redwood City, CA, 1991, p. 73.
9: David Wells, The Penguin Dictionary of Curious and Interesting Numbers. Penguin Books, NY, 1986, 163.
**********************************************************************
File "src/sage/databases/oeis.py", line 1513, in sage.databases.oeis.OEISSequence.references
Failed example:
_[0] # optional -- internet
Expected:
'A. H. Beiler, Recreations in the Theory of Numbers, Dover, NY, 1964, p. 52.'
Got:
'N. G. W. H. Beeger, On the Congruence (p-1)! == -1 (mod p^2), Messenger of Mathematics, Vol. 49 (1920), pp. 177-178.'
**********************************************************************
1 item had failures:
2 of 6 in sage.databases.oeis.OEISSequence.references
5 webbrowser tests not run
0 tests not run because we ran out of time
[290 tests, 2 failures, 38.95 s]
sage -t --long --random-seed=0 src/sage/misc/package.py
**********************************************************************
File "src/sage/misc/package.py", line 101, in sage.misc.package.pip_remote_version
Failed example:
pip_remote_version(nap, pypi_url=pypi, ignore_URLError=False) # optional - internet
Expected:
Traceback (most recent call last):
...
HTTPError: HTTP Error 404: Not Found
Got:
<BLANKLINE>
Traceback (most recent call last):
File "/usr/lib/python3.8/urllib/request.py", line 1317, in do_open
h.request(req.get_method(), req.selector, req.data, headers,
File "/usr/lib/python3.8/http/client.py", line 1230, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.8/http/client.py", line 1276, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.8/http/client.py", line 1225, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.8/http/client.py", line 1004, in _send_output
self.send(msg)
File "/usr/lib/python3.8/http/client.py", line 944, in send
self.connect()
File "/usr/lib/python3.8/http/client.py", line 915, in connect
self.sock = self._create_connection(
File "/usr/lib/python3.8/socket.py", line 807, in create_connection
raise err
File "/usr/lib/python3.8/socket.py", line 796, in create_connection
sock.connect(sa)
TimeoutError: [Errno 110] Connection timed out
<BLANKLINE>
During handling of the above exception, another exception occurred:
<BLANKLINE>
Traceback (most recent call last):
File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/doctest/forker.py", line 714, 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 1133, in compile_and_execute
exec(compiled, globs)
File "<doctest sage.misc.package.pip_remote_version[4]>", line 1, in <module>
pip_remote_version(nap, pypi_url=pypi, ignore_URLError=False) # optional - internet
File "/home/slabbe/GitBox/sage/local/lib/python3.8/site-packages/sage/misc/package.py", line 109, in pip_remote_version
f = urlopen(url)
File "/usr/lib/python3.8/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/usr/lib/python3.8/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/usr/lib/python3.8/urllib/request.py", line 542, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
File "/usr/lib/python3.8/urllib/request.py", line 502, in _call_chain
result = func(*args)
File "/usr/lib/python3.8/urllib/request.py", line 1346, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/usr/lib/python3.8/urllib/request.py", line 1320, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [Errno 110] Connection timed out>
**********************************************************************
1 item had failures:
1 of 6 in sage.misc.package.pip_remote_version
2 beautifulsoup4 tests not run
1 not tested test not run
0 tests not run because we ran out of time
[57 tests, 1 failure, 278.08 s]