Also on Ubuntu 18.04 (without any optional packages apart ccache installed), I have the failing doctest with graph.py (two out of three runs) and consistently

$ ./sage -t --long --random-seed=0 src/sage/misc/package.py
Running doctests with ID 2021-05-27-16-31-10-59754af4.
Using --optional=build,ccache,debian,dochtml,pip,sage,sage_spkg
Doctesting 1 file.
sage -t --long --warn-long 42.6 --random-seed=0 src/sage/misc/package.py
**********************************************************************
File "src/sage/misc/package.py", line 359, in 
sage.misc.package.installed_packages
Failed example:
    installed_packages()['sage_conf']  # optional - build
Expected:
    'none'
Got:
    '9.4.beta0'
**********************************************************************


Am 27.05.21 um 14:44 schrieb Sébastien Labbé:
On Ubuntu 18.04, testing with various optional and external packages, I obtain:

----------------------------------------------------------------------
sage -t --long --warn-long 77.6 --random-seed=0 src/sage/databases/oeis.py  # 3 doctests failed sage -t --long --warn-long 77.6 --random-seed=0 src/sage/graphs/graph.py  # 1 doctest failed sage -t --long --warn-long 77.6 --random-seed=0 src/sage/symbolic/integration/external.py  # 1 doctest failed sage -t --long --warn-long 77.6 --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 test, the issue with graph.py does not show again:

----------------------------------------------------------------------
sage -t --long --warn-long 102.7 --random-seed=0 src/sage/databases/oeis.py  # 3 doctests failed sage -t --long --warn-long 102.7 --random-seed=0 src/sage/symbolic/integration/external.py  # 1 doctest failed sage -t --long --warn-long 102.7 --random-seed=0 src/sage/tests/cmdline.py  # 1 doctest failed
----------------------------------------------------------------------
External software detected for doctesting: internet,pandoc


The issue with graph.py is related to Gap, see below:


sage -t --long --warn-long 77.6 --random-seed=0 src/sage/graphs/graph.py
**********************************************************************
File "src/sage/graphs/graph.py", line 2713, in sage.graphs.graph.Graph.is_edge_transitive
Failed example:
     C.is_edge_transitive()
Exception raised:
     Traceback (most recent call last):
      File "/home/slabbe/GitBox/sage/local/lib/python3.9/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/python3.9/site-packages/sage/doctest/forker.py", line 1133, in compile_and_execute
         exec(compiled, globs)
      File "<doctest sage.graphs.graph.Graph.is_edge_transitive[3]>", line 1, in <module>
         C.is_edge_transitive()
      File "/home/slabbe/GitBox/sage/local/lib/python3.9/site-packages/sage/graphs/graph.py", line 2731, in is_edge_transitive
         return libgap(A).OrbitLength(e, libgap.OnSets) == self.size()
      File "sage/libs/gap/element.pyx", line 2677, in sage.libs.gap.element.GapElement_MethodProxy.__call__ (build/cythonized/sage/libs/gap/element.c:20776)         return GapElement_Function.__call__(self, * ([self.first_argument] + list(args)))       File "sage/libs/gap/element.pyx", line 2525, in sage.libs.gap.element.GapElement_Function.__call__ (build/cythonized/sage/libs/gap/element.c:19780)
         sig_on()
    sage.libs.gap.util.GAPError: Error, OnSets: <set> must be a set (not a immutable non-strictly-sorted plain list of cyclotomics)
**********************************************************************
1 item had failures:
    1 of   9 in sage.graphs.graph.Graph.is_edge_transitive
     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, 1 failure, 46.77 s]



The other failures are copied below (I am not able to see the problem with the first one):


sage -t --long --warn-long 102.7 --random-seed=0 src/sage/databases/oeis.py
**********************************************************************
File "src/sage/databases/oeis.py", line 48, in sage.databases.oeis
Failed example:
     c.examples()                                  # optional -- internet
Expected:
     0: Pi = 3.1415926535897932384...
     1:    = 3 + 1/(7 + 1/(15 + 1/(1 + 1/(292 + ...))))
     2:    = [a_0; a_1, a_2, a_3, ...] = [3; 7, 15, 1, 292, ...]
Got:
     0: Pi = 3.1415926535897932384...
     1:    = 3 + 1/(7 + 1/(15 + 1/(1 + 1/(292 + ...))))
     2:    = [a_0; a_1, a_2, a_3, ...] = [3; 7, 15, 1, 292, ...].
**********************************************************************
File "src/sage/databases/oeis.py", line 53, in sage.databases.oeis
Failed example:
     c.comments()                                  # optional -- internet
Expected:
    0: The first 5821569425 terms were computed by _Eric W. Weisstein_ on Sep 18 2011.     1: The first 10672905501 terms were computed by _Eric W. Weisstein_ on Jul 17 2013.     2: The first 15000000000 terms were computed by _Eric W. Weisstein_ on Jul 27 2013.
Got:
    0: The first 5821569425 terms were computed by _Eric W. Weisstein_ on Sep 18 2011.     1: The first 10672905501 terms were computed by _Eric W. Weisstein_ on Jul 17 2013.     2: The first 15000000000 terms were computed by _Eric W. Weisstein_ on Jul 27 2013.
     3: The first 30113021586 terms were computed by _Syed Fahad_ on Apr 27 
2021.
**********************************************************************
File "src/sage/databases/oeis.py", line 1706, in sage.databases.oeis.OEISSequence.examples
Failed example:
     c.examples()                          # optional -- internet
Expected:
     0: Pi = 3.1415926535897932384...
     1:    = 3 + 1/(7 + 1/(15 + 1/(1 + 1/(292 + ...))))
     2:    = [a_0; a_1, a_2, a_3, ...] = [3; 7, 15, 1, 292, ...]
Got:
     0: Pi = 3.1415926535897932384...
     1:    = 3 + 1/(7 + 1/(15 + 1/(1 + 1/(292 + ...))))
     2:    = [a_0; a_1, a_2, a_3, ...] = [3; 7, 15, 1, 292, ...].
**********************************************************************
2 items had failures:
    2 of  26 in sage.databases.oeis
    1 of   5 in sage.databases.oeis.OEISSequence.examples
     5 webbrowser tests not run
     0 tests not run because we ran out of time
     [290 tests, 3 failures, 40.15 s]
sage -t --long --warn-long 102.7 --random-seed=0 src/sage/graphs/graph.py
     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, 24.58 s]
sage -t --long --warn-long 102.7 --random-seed=0 src/sage/symbolic/integration/external.py
**********************************************************************
File "src/sage/symbolic/integration/external.py", line 152, in sage.symbolic.integration.external.request_wolfram_alpha
Failed example:
     [str(a) for a in sorted(page_data['queryresult'].keys())]  # optional 
internet
Expected:
     ['datatypes',
      'encryptedEvaluatedExpression',
      'encryptedParsedExpression',
      'error',
      'host',
      'id',
      'numpods',
      'parsetimedout',
      'parsetiming',
      'pods',
      'recalculate',
      'related',
      'server',
      'sponsorCategories',
      'success',
      'timedout',
      'timedoutpods',
      'timing',
      'version']
Got:
     ['datatypes',
      'encryptedEvaluatedExpression',
      'encryptedParsedExpression',
      'error',
      'host',
      'id',
      'inputstring',
      'numpods',
      'parsetimedout',
      'parsetiming',
      'pods',
      'recalculate',
      'related',
      'server',
      'sponsorCategories',
      'success',
      'timedout',
      'timedoutpods',
      'timing',
      'version']
**********************************************************************
1 item had failures:
    1 of   5 in sage.symbolic.integration.external.request_wolfram_alpha
     0 tests not run because we ran out of time
     [48 tests, 1 failure, 28.45 s]
sage -t --long --warn-long 102.7 --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/python3.9/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, 35.28 s]

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

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