Sage 9.0.beta7 released

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Volker Braun

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Nov 26, 2019, 7:28:33 PM11/26/19
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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 


d48a21c149 (tag: 9.0.beta7, trac/develop) Updated SageMath version to 9.0.beta7
22426a509b Trac #28797: 32-bit Python 3 failures in combinat
54072f6c3b Trac #28795: Python 3 overflow in IntegerModRing pow
7f2572fcdf Trac #28685: Upgrade from beautifulsoup to beautifulsoup4
c597ceea70 Trac #28737: remove deprecated stuff in old coercion model
a5c1185e7c Trac #28736: fix Texture for negative inputs
6c66325a63 Trac #28698: py3: HTML documentation for GlobalOptions does not show up correctly
aa0ac42b16 Trac #28675: Deprecate GraphicsArray import from sage.plot.graphics
5882b7f376 Trac #28564: Tensor Fields and Sections: Naming Consistencies
8f9b67d25c Trac #28304: add type information to _repr_ of Macaulay2 elements
e6e616380a Trac #28214: Compute and display graph of nth-preimage tree
a5bb40f91c Trac #27838: 5 internet doctests failing in findstat.py
6553536757 Trac #27790: compatibility with cplex 12.9
3c6a9108c1 Trac #23816: implement left action of matrices on scheme points
9c6f3dab7f Trac #28732: update sagetex to version 3.4
f856552b81 Trac #28748: Python 3 debug build fails to start
232ae1bddc (tag: 9.0.beta6) Updated SageMath version to 9.0.beta6

Emmanuel Charpentier

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Nov 27, 2019, 8:56:36 AM11/27/19
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Doubleplusungood...

On Deboan testing running on core i5 + 8 GB RAM, ptestalllong gets me (part of) the usual suspects (transient failures, plus 6 (six) permanent failures due to abort:

| File                                                     | Result              | P/T |
|----------------------------------------------------------+---------------------+-----|
| src/sage/crypto/mq/sr.py                                 | Killed due to abort | P   |
| src/sage/rings/polynomial/multi_polynomial_sequence.py   | Killed due to abort | P   |
| src/sage/combinat/posets/posets.py                       | 1 doctest failed    | T   |
| src/sage/plot/animate.py                                 | 7 doctests failed   | T   |
| src/sage/combinat/matrices/hadamard_matrix.py            | 2 doctests failed   | T   |
| src/sage/rings/polynomial/pbori.pyx                      | Killed due to abort | P   |
| src/sage/misc/latex.py                                   | 1 doctest failed    | T   |
| src/sage/coding/databases.py                             | 2 doctests failed   | T   |
| src/sage/misc/persist.pyx                                | 2 doctests failed   | T   |
| src/sage/repl/load.py                                    | 1 doctest failed    | T   |
| src/sage/graphs/graph_latex.py                           | 2 doctests failed   | T   |
| src/sage/rings/polynomial/polynomial_ring_constructor.py | Killed due to abort | P   |
| src/sage/sat/solvers/dimacs.py                           | Killed due to abort | P   |
| src/doc/en/reference/sat/index.rst                       | Killed due to abort | P   |
| src/sage/sat/boolean_polynomials.py                      | Killed due to abort | P   |
| src/sage/misc/remote_file.py                             | 2 doctests failed   | T   |
| src/sage/databases/findstat.py                           | 7 doctests failed   | T   |
| src/sage/interfaces/magma_free.py                        | 2 doctests failed   | T   |

Details : see the enclose checkerrs.txt

HTH,
checkerrs.txt

Emmanuel Charpentier

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Nov 27, 2019, 9:11:18 AM11/27/19
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Similar results on Debian testing running on core I7 + 16 GB RAM and a slightly different set of optional packages:

| File                                                     | Result                           | P/T |
|----------------------------------------------------------+----------------------------------+-----|
| src/sage/crypto/mq/sr.py                                 | Killed due to abort              | P   |
| src/sage/rings/polynomial/multi_polynomial_sequence.py   | Killed due to segmentation fault | P   |
| src/sage/combinat/posets/posets.py                       | 1 doctest failed                 | T   |
| src/sage/graphs/generators/smallgraphs.py                | 6 doctests failed                | T   |
| src/sage/plot/animate.py                                 | 7 doctests failed                | T   |
| src/sage/combinat/matrices/hadamard_matrix.py            | 2 doctests failed                | T   |
| src/sage/rings/polynomial/pbori.pyx                      | Killed due to abort              | P   |
| src/sage/coding/databases.py                             | 2 doctests failed                | T   |
| src/sage/misc/latex.py                                   | 1 doctest failed                 | T   |
| src/sage/misc/persist.pyx                                | 2 doctests failed                | T   |
| src/sage/tests/gap_packages.py                           | 1 doctest failed                 | P   |
| src/sage/symbolic/integration/external.py                | 1 doctest failed                 | T   |
| src/sage/repl/load.py                                    | 1 doctest failed                 | T   |
| src/sage/graphs/graph_latex.py                           | 2 doctests failed                | T   |
| src/sage/rings/polynomial/polynomial_ring_constructor.py | Killed due to abort              | P   |
| src/doc/en/reference/sat/index.rst                       | Killed due to abort              | P   |
| src/sage/sat/solvers/dimacs.py                           | Killed due to abort              | P   |
| src/sage/sat/boolean_polynomials.py                      | Killed due to abort              | P   |
| src/sage/misc/remote_file.py                             | 2 doctests failed                | T   |
| src/sage/databases/findstat.py                           | 29 doctests failed               | T   |
| src/sage/interfaces/magma_free.py                        | 2 doctests failed                | T   |

Details: see enclosed checkerrs2.txt

HTH,
checkerrs2.txt

Sébastien Labbé

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Nov 27, 2019, 10:08:06 AM11/27/19
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Using --optional=4ti2,cbc,ccache,cryptominisat,dot2tex,e_antic,external,glucose,latte_int,lidia,lrslib,memlimit,normaliz,notedown,openssl,pandoc_attributes,pycosat,pynormaliz,rst2ipynb,sage,sagenb

----------------------------------------------------------------------
sage -t --long src/doc/en/thematic_tutorials/linear_programming.rst  # 1 doctest failed
sage -t --long src/sage/coding/databases.py  # 2 doctests failed
sage -t --long src/sage/combinat/matrices/hadamard_matrix.py  # 2 doctests failed
sage -t --long src/sage/combinat/posets/posets.py  # 1 doctest failed
sage -t --long src/sage/databases/findstat.py  # 16 doctests failed
sage -t --long src/sage/geometry/polyhedron/base.py  # Killed due to abort
sage -t --long src/sage/graphs/generators/families.py  # 7 doctests failed
sage -t --long src/sage/graphs/generators/smallgraphs.py  # 2 doctests failed
sage -t --long src/sage/graphs/graph_latex.py  # 2 doctests failed
sage -t --long src/sage/misc/latex.py  # 1 doctest failed
sage -t --long src/sage/misc/persist.pyx  # 2 doctests failed
sage -t --long src/sage/misc/remote_file.py  # 2 doctests failed
sage -t --long src/sage/numerical/backends/gurobi_backend.pyx  # 17 doctests failed
sage -t --long src/sage/plot/animate.py  # 7 doctests failed
sage -t --long src/sage/repl/load.py  # 1 doctest failed
sage -t --long src/sage/sat/solvers/dimacs.py  # 7 doctests failed
sage -t --long src/sage/tests/cmdline.py  # 2 doctests failed
----------------------------------------------------------------------
External software detected for doctesting: cplex,ffmpeg,graphviz,gurobi,imagemagick,internet,latex,pandoc

Rerunning the failed test I get the same (except graphs/generators/families.py which disappeared):

----------------------------------------------------------------------
sage -t --long src/doc/en/thematic_tutorials/linear_programming.rst  # 1 doctest failed
sage -t --long src/sage/coding/databases.py  # 2 doctests failed
sage -t --long src/sage/combinat/matrices/hadamard_matrix.py  # 2 doctests failed
sage -t --long src/sage/combinat/posets/posets.py  # 1 doctest failed
sage -t --long src/sage/databases/findstat.py  # 18 doctests failed
sage -t --long src/sage/geometry/polyhedron/base.py  # Killed due to abort
sage -t --long src/sage/graphs/generators/smallgraphs.py  # 2 doctests failed
sage -t --long src/sage/graphs/graph_latex.py  # 2 doctests failed
sage -t --long src/sage/misc/latex.py  # 1 doctest failed
sage -t --long src/sage/misc/persist.pyx  # 2 doctests failed
sage -t --long src/sage/misc/remote_file.py  # 2 doctests failed
sage -t --long src/sage/numerical/backends/gurobi_backend.pyx  # 17 doctests failed
sage -t --long src/sage/plot/animate.py  # 7 doctests failed
sage -t --long src/sage/repl/load.py  # 1 doctest failed
sage -t --long src/sage/sat/solvers/dimacs.py  # 7 doctests failed
sage -t --long src/sage/tests/cmdline.py  # 2 doctests failed
----------------------------------------------------------------------
External software detected for doctesting: ffmpeg,graphviz,gurobi,imagemagick,internet,latex,pandoc

Many of the failures are already fixed (postive review tickets). Few other failures are waiting for work. Follow up at https://trac.sagemath.org/ticket/25536

Every other tests passed!

John Cremona

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Nov 27, 2019, 11:11:33 AM11/27/19
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I had this failure (I have gap_packages installed):

sage -t --long --warn-long 59.7 src/sage/tests/gap_packages.py
**********************************************************************
File "src/sage/tests/gap_packages.py", line 8, in sage.tests.gap_packages
Failed example:
    test_packages(pkgs, only_failures=True)    # optional - gap_packages
Expected:
      Status   Package   GAP Output
    +--------+---------+------------+
Got:
    #I  method installed for Matrix matches more than one declaration
      Status   Package   GAP Output
    +--------+---------+------------+
**********************************************************************
1 item had failures:
   1 of   5 in sage.tests.gap_packages
    [11 tests, 1 failure, 4.74 s]
----------------------------------------------------------------------
sage -t --long --warn-long 59.7 src/sage/tests/gap_packages.py  # 1 doctest failed




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John H Palmieri

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Nov 27, 2019, 12:01:55 PM11/27/19
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It's okay with Python 3, but I'm getting a failure on OS X when built with Python 2:


sage -t --long --warn-long 68.2 src/sage/libs/pynac/pynac.pyx
**********************************************************************
File "src/sage/libs/pynac/pynac.pyx", line 295, in sage.libs.pynac.pynac.subs_args_to_PyTuple
Failed example:
    tfunc(x).subs(x=1)   # py2
Expected:
    len(args): 3, types: [<class 'sage.symbolic.substitution_map.SubstitutionMap'>,
      <class 'int'>,       
      <class 'sage.symbolic.expression.Expression'>]
    x
Got:
    len(args): 3, types: [<type 'sage.symbolic.substitution_map.SubstitutionMap'>, <type 'int'>, <type 'sage.symbolic.expression.Expression'>]
    x

**********************************************************************
1 item had failures:
   1 of   5 in sage.libs.pynac.pynac.subs_args_to_PyTuple
    [332 tests, 1 failure, 4.15 s]
----------------------------------------------------------------------
sage -t --long --warn-long 68.2 src/sage/libs/pynac/pynac.pyx  # 1 doctest failed
----------------------------------------------------------------------

Dima Pasechnik

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Nov 27, 2019, 12:11:40 PM11/27/19
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IIRC this comes from Simon King's optional package.

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/CAD0p0K4hqxf-0rZT9DeL3ZhH8WLo0dsUesyKyQQadv5cREiTBg%40mail.gmail.com.

Emmanuel Charpentier

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Nov 27, 2019, 4:07:14 PM11/27/19
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I tried to recompile from scratch (i. e. make distclean ; make ; resinsttalling the same optional packages (+ python2) and R packages, then make ptestalllong). This time, I got five transient failures and three permanent failures, none of them due to a crash :

| File                                         | Result            | P/T |
|----------------------------------------------+-------------------+-----|
| src/sage/combinat/posets/posets.py           | 1 doctest failed  | T   |
| src/sage/plot/animate.py                     | 7 doctests failed | T   |
| src/sage/modular/ssmod/ssmod.py              | 2 doctests failed | T   |
| src/sage/numerical/backends/glpk_backend.pyx | 1 doctest failed  | P   |
| src/sage/tests/gap_packages.py               | 1 doctest failed  | P   |
| src/sage/libs/glpk/error.pyx                 | 1 doctest failed  | P   |
| src/sage/misc/latex.py                       | 1 doctest failed  | T   |
| src/sage/graphs/graph_latex.py               | 2 doctests failed | T   |

The temporary failures have been reported already (except possibly for ssmod). Details of the permanent failures :

  • glpk_backend.py:

Running doctests with ID 2019-11-27-21-45-09-4e9dc047.
Git branch: develop
Using --optional=build,dochtml,dot2tex,fricas,gap_packages,giacpy_sage,libsemigroups,memlimit,python2,sage,sagenb
Doctesting 1 file.
sage -t --long --warn-long 162.8 src/sage/numerical/backends/glpk_backend.pyx
**********************************************************************
File "src/sage/numerical/backends/glpk_backend.pyx", line 2287, in sage.numerical.backends.glpk_backend.GLPKBackend.print_ranges
Failed example:
    p.print_ranges()
Expected:
    glp_print_ranges: optimal basic solution required
    1
Got:
    1
**********************************************************************
1 item had failures:
   1 of  13 in sage.numerical.backends.glpk_backend.GLPKBackend.print_ranges
    [554 tests, 1 failure, 3.88 s]
----------------------------------------------------------------------
sage -t --long --warn-long 162.8 src/sage/numerical/backends/glpk_backend.pyx  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 4.0 seconds
    cpu time: 3.9 seconds
    cumulative wall time: 3.9 seconds

  • gap_packages:

Running doctests with ID 2019-11-27-21-45-16-07798fcc.
Git branch: develop
Using --optional=build,dochtml,dot2tex,fricas,gap_packages,giacpy_sage,libsemigroups,memlimit,python2,sage,sagenb
Doctesting 1 file.
sage -t --long --warn-long 162.8 src/sage/tests/gap_packages.py
**********************************************************************
File "src/sage/tests/gap_packages.py", line 8, in sage.tests.gap_packages
Failed example:
    test_packages(pkgs, only_failures=True)    # optional - gap_packages
Expected:
      Status   Package   GAP Output
    +--------+---------+------------+
Got:
    #I  method installed for Matrix matches more than one declaration
      Status   Package   GAP Output
    +--------+---------+------------+
**********************************************************************
1 item had failures:
   1 of   5 in sage.tests.gap_packages
    [11 tests, 1 failure, 3.82 s]
----------------------------------------------------------------------
sage -t --long --warn-long 162.8 src/sage/tests/gap_packages.py  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 3.9 seconds
    cpu time: 3.2 seconds
    cumulative wall time: 3.8 seconds

  • error.pyx:

Running doctests with ID 2019-11-27-21-45-23-f1e208db.
Git branch: develop
Using --optional=build,dochtml,dot2tex,fricas,gap_packages,giacpy_sage,libsemigroups,memlimit,python2,sage,sagenb
Doctesting 1 file.
sage -t --long --warn-long 162.8 src/sage/libs/glpk/error.pyx
**********************************************************************
File "src/sage/libs/glpk/error.pyx", line 100, in sage.libs.glpk.error.setup_glpk_error_handler
Failed example:
    res = p.solve()
Expected:
          0: obj = ...
Got:
    <BLANKLINE>
**********************************************************************
1 item had failures:
   1 of  11 in sage.libs.glpk.error.setup_glpk_error_handler
    [12 tests, 1 failure, 0.90 s]
----------------------------------------------------------------------
sage -t --long --warn-long 162.8 src/sage/libs/glpk/error.pyx  # 1 doctest failed
----------------------------------------------------------------------
Total time for all tests: 0.9 seconds
    cpu time: 0.5 seconds
    cumulative wall time: 0.9 seconds

The gap_packages failure is known already ; those pertinent to GLPK are new, AFAICT. They might be cosmetic.

HTH,

Emmanuel Charpentier

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Nov 27, 2019, 4:28:27 PM11/27/19
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THIS WAS A MISTAKE: those resuts are for 9.0.beta6, not beta7. Rebuilding beta7 and tests underway...

Sorry for the noise...

Dima Pasechnik

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Nov 27, 2019, 4:39:33 PM11/27/19
to sage-release
Since https://trac.sagemath.org/ticket/28459
Sage can use GLPK from the system, if it's version 4.63 or newer. Sage has 4.65.
The slight discrepancy in GLPK tests is due to this version
difference, and it's harmless.
(I set it to 4.63 to cover many more Linux distros)
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Dima Pasechnik

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Nov 27, 2019, 4:43:15 PM11/27/19
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there is also a small GLPK 4.65 discrepancy coming from a patch that
Sage applies,
but most distros don't.

Emmanuel Charpentier

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Nov 27, 2019, 7:12:24 PM11/27/19
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Thank you, Dima !

Upgrading my rebuilt 9.0beta6 to 9.0beta7 on my core i7/16 GB machine gives me 14 transient failures and the three permanent failures already knows (two GLPK-related and explained by Dima, one related to gap_packages, already known and explained). For completeness' sake:

| File                                          | Result             | P/T |
|-----------------------------------------------+--------------------+-----|
| src/sage/graphs/generators/smallgraphs.py     | 6 doctests failed  | T   |
| src/sage/combinat/matrices/hadamard_matrix.py | 2 doctests failed  | T   |
| src/sage/misc/package.py                      | 1 doctest failed   | T   |
| src/sage/symbolic/integration/external.py     | 1 doctest failed   | T   |
| src/sage/plot/animate.py                      | 7 doctests failed  | T   |
| src/sage/combinat/posets/posets.py            | 1 doctest failed   | T   |
| src/sage/coding/databases.py                  | 2 doctests failed  | T   |
| src/sage/misc/persist.pyx                     | 2 doctests failed  | T   |
| src/sage/numerical/backends/glpk_backend.pyx  | 1 doctest failed   | P   |
| src/sage/tests/gap_packages.py                | 1 doctest failed   | P   |
| src/sage/repl/load.py                         | 1 doctest failed   | T   |
| src/sage/misc/latex.py                        | 1 doctest failed   | T   |
| src/sage/libs/glpk/error.pyx                  | 1 doctest failed   | P   |
| src/sage/graphs/graph_latex.py                | 2 doctests failed  | T   |
| src/sage/combinat/designs/ext_rep.py          | 1 doctest failed   | T   |
| src/sage/misc/remote_file.py                  | 2 doctests failed  | T   |
| src/sage/databases/findstat.py                | 59 doctests failed | T   |

Details seemingly identical to what I reported before (available on demand).

HTH,
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Simon King

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Nov 28, 2019, 2:37:40 AM11/28/19
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Hi Dima,

which one? meataxe or p_group_cohomology? How would either of them
influence the gap packages? And is there a ticket for it?

Best regards,
Simon

Eric Gourgoulhon

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Nov 28, 2019, 4:41:15 AM11/28/19
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On Ubuntu 18.04 running on a bi-Xeon E5-2623 (8 cores) + 16 GB RAM computer:

  - incremental build (with -j16) from 9.0.beta6: OK
  - all tests from ptestlong passed

Eric.

Dima Pasechnik

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Nov 28, 2019, 12:11:53 PM11/28/19
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On Thu, Nov 28, 2019 at 7:37 AM Simon King <simon...@uni-jena.de> wrote:
>
> Hi Dima,
>
> which one? meataxe or p_group_cohomology? How would either of them
> influence the gap packages? And is there a ticket for it?

oops, I am sorry, memory failure :-)
It's https://github.com/gap-packages/Semigroups/issues/615
nothing to do with your package.

Best
Dima
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Emmanuel Charpentier

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Nov 28, 2019, 2:06:05 PM11/28/19
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After rebuilding from scratch, reinstalling packages (this time including gap_packages), ptestlong gives me :
  • no transient failure
  • the usual permanent failure on gap_packages
  • and a very strange, reproducible failure on rc/sage/graphs/strongly_regular_db.pyx.

Details on the latter :

charpent@p-202-021:/usr/local/sage-9$ sage -t --long --warn-long 53.5 src/sage/graphs/strongly_regular_db.pyx  # 4 doctests failed
Running doctests with ID 2019-11-28-19-21-27-1f4d95ea.
Git branch: develop
Using --optional=build,dochtml,dot2tex,fricas,gap_packages,giacpy_sage,libsemigroups,memlimit,python2,sage,sagenb
Doctesting 1 file.
sage -t --long --warn-long 53.5 src/sage/graphs/strongly_regular_db.pyx
**********************************************************************
File "src/sage/graphs/strongly_regular_db.pyx", line 2242, in sage.graphs.strongly_regular_db.SRG_280_135_70_60
Failed example:
    g=SRG_280_135_70_60()                  # long time # optional - gap_packages
Exception raised:
    Traceback (most recent call last):
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/gap.py", line 769, in _eval_line
        raise RuntimeError("%s produced error output\n%s\n   executing %s"%(self, error,line))
    RuntimeError: Gap produced error output
    Error, Record Element: <rec> must be a record (not a boolean or fail)

       executing \$sage1:=AtlasGenerators("J2",2).generators;;

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/expect.py", line 1471, in __init__
        self._name = parent._create(value, name=name)
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/interface.py", line 491, in _create
        self.set(name, value)
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/gap.py", line 1427, in set
        self._eval_line(cmd, allow_use_file=True)
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/gap.py", line 803, in _eval_line
        raise RuntimeError(exc)
    RuntimeError: Gap produced error output
    Error, Record Element: <rec> must be a record (not a boolean or fail)

       executing \$sage1:=AtlasGenerators("J2",2).generators;;

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 681, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1123, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.graphs.strongly_regular_db.SRG_280_135_70_60[1]>", line 1, in <module>
        g=SRG_280_135_70_60()                  # long time # optional - gap_packages
      File "sage/graphs/strongly_regular_db.pyx", line 2253, in sage.graphs.strongly_regular_db.SRG_280_135_70_60 (build/cythonized/sage/graphs/strongly_regular_db.c:34308)
        J2    = PermutationGroup(gap('AtlasGenerators("J2",2).generators'))
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/interface.py", line 288, in __call__
        return cls(self, x, name=name)
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/expect.py", line 1476, in __init__
        raise_(TypeError, TypeError(*x.args), sys.exc_info()[2])
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/six.py", line 692, in reraise
        raise value.with_traceback(tb)
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/expect.py", line 1471, in __init__
        self._name = parent._create(value, name=name)
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/interface.py", line 491, in _create
        self.set(name, value)
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/gap.py", line 1427, in set
        self._eval_line(cmd, allow_use_file=True)
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/gap.py", line 803, in _eval_line
        raise RuntimeError(exc)
    TypeError: Gap produced error output
    Error, Record Element: <rec> must be a record (not a boolean or fail)

       executing \$sage1:=AtlasGenerators("J2",2).generators;;
**********************************************************************
File "src/sage/graphs/strongly_regular_db.pyx", line 2243, in sage.graphs.strongly_regular_db.SRG_280_135_70_60
Failed example:
    g.is_strongly_regular(parameters=True) # long time # optional - gap_packages
Exception raised:
    Traceback (most recent call last):
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 681, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1123, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.graphs.strongly_regular_db.SRG_280_135_70_60[2]>", line 1, in <module>
        g.is_strongly_regular(parameters=True) # long time # optional - gap_packages
    NameError: name 'g' is not defined
**********************************************************************
File "src/sage/graphs/strongly_regular_db.pyx", line 2349, in sage.graphs.strongly_regular_db.SRG_416_100_36_20
Failed example:
    g = SRG_416_100_36_20()                # optional - gap_packages # long time
Exception raised:
    Traceback (most recent call last):
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 681, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1123, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.graphs.strongly_regular_db.SRG_416_100_36_20[1]>", line 1, in <module>
        g = SRG_416_100_36_20()                # optional - gap_packages # long time
      File "sage/graphs/strongly_regular_db.pyx", line 2359, in sage.graphs.strongly_regular_db.SRG_416_100_36_20 (build/cythonized/sage/graphs/strongly_regular_db.c:36484)
        h.add_edges(g.Orbit([1,5],libgap.OnSets))
      File "sage/libs/gap/element.pyx", line 2666, in sage.libs.gap.element.GapElement_MethodProxy.__call__ (build/cythonized/sage/libs/gap/element.c:20291)
        return GapElement_Function.__call__(self, * ([self.first_argument] + list(args)))
      File "sage/libs/gap/element.pyx", line 2514, in sage.libs.gap.element.GapElement_Function.__call__ (build/cythonized/sage/libs/gap/element.c:19304)
        sig_on()
    sage.libs.gap.util.GAPError: Error, no method found! Error, no 1st choice method found for `GeneratorsOfMagmaWithInverses' on 1 arguments
    The 1st argument is 'fail' which might point to an earlier problem
**********************************************************************
File "src/sage/graphs/strongly_regular_db.pyx", line 2350, in sage.graphs.strongly_regular_db.SRG_416_100_36_20
Failed example:
    g.is_strongly_regular(parameters=True) # optional - gap_packages # long time
Exception raised:
    Traceback (most recent call last):
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 681, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/local/sage-9/local/lib/python3.7/site-packages/sage/doctest/forker.py", line 1123, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.graphs.strongly_regular_db.SRG_416_100_36_20[2]>", line 1, in <module>
        g.is_strongly_regular(parameters=True) # optional - gap_packages # long time
    NameError: name 'g' is not defined
**********************************************************************
2 items had failures:
   2 of   4 in sage.graphs.strongly_regular_db.SRG_280_135_70_60
   2 of   4 in sage.graphs.strongly_regular_db.SRG_416_100_36_20
    [334 tests, 4 failures, 812.98 s]
----------------------------------------------------------------------
sage -t --long --warn-long 53.5 src/sage/graphs/strongly_regular_db.pyx  # 4 doctests failed
----------------------------------------------------------------------
Total time for all tests: 813.1 seconds
    cpu time: 27.9 seconds
    cumulative wall time: 813.0 seconds

The discrepancy between CPU time and elapsed time is puzzling. It s not an artifact : a system monitor confirmed that CPU activity was minimal during most of this test.

I have been unable to reproduce the problem on my other machine, running the same rebuilt 9.0.beta7, where this tests passes without any failure.

Cherry on the cake: I have been unable to run ptestalllong on this machine : this (reproducibly !) dies with a "too many open files" error (not captured in the log) about halfway, after a (failed) attempt to run sage -t --long src/sage/groups/perm_gps/permgroup_named.py, which passes normally on the other machine.

Last lines of the log:

Killing test src/sage/groups/perm_gps/permgroup_named.py
Killing test src/sage/combinat/designs/twographs.py
Killing test src/sage/databases/findstat.py
----------------------------------------------------------------------
sage -t --long src/sage/graphs/strongly_regular_db.pyx  # 5 doctests failed
sage -t --long src/sage/graphs/generators/smallgraphs.py  # 6 doctests failed
sage -t --long src/sage/plot/animate.py  # 7 doctests failed
sage -t --long src/sage/combinat/posets/posets.py  # 1 doctest failed
sage -t --long src/sage/combinat/matrices/hadamard_matrix.py  # 2 doctests failed
sage -t --long src/sage/misc/latex.py  # 1 doctest failed
sage -t --long src/sage/combinat/designs/ext_rep.py  # 2 doctests failed
sage -t --long src/sage/coding/databases.py  # 2 doctests failed
sage -t --long src/sage/misc/persist.pyx  # 2 doctests failed
sage -t --long src/sage/repl/load.py  # 1 doctest failed
Doctests interrupted: 1444/3793 files tested
----------------------------------------------------------------------


Any hint ?



Le mercredi 27 novembre 2019 14:56:36 UTC+1, Emmanuel Charpentier a écrit :

Dima Pasechnik

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Nov 28, 2019, 2:45:25 PM11/28/19
to sage-release
what does happen if you run

sage: from sage.graphs.strongly_regular_db import SRG_280_135_70_60
sage: SRG_280_135_70_60()

Does it print 

J_2 on cosets of 3.PGL(2,9): Graph on 280 vertices

?


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Dima Pasechnik

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Nov 28, 2019, 6:52:43 PM11/28/19
to sage-release
On Thu, Nov 28, 2019 at 7:45 PM Dima Pasechnik <dim...@gmail.com> wrote:
>
> what does happen if you run
>
> sage: from sage.graphs.strongly_regular_db import SRG_280_135_70_60
> sage: SRG_280_135_70_60()
>
> Does it print
>
> J_2 on cosets of 3.PGL(2,9): Graph on 280 vertices

here is a ticket that improves this function by switching from GAP to
libGAP interface,
please review
https://trac.sagemath.org/ticket/28818

Perhaps that was the general flakiness of pexpect that caused that failure.

Dima

Emmanuel Charpentier

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Nov 29, 2019, 5:17:37 AM11/29/19
to sage-release
Dear Dima,

You may have hit the nerve (see below):


Le vendredi 29 novembre 2019 00:52:43 UTC+1, Dima Pasechnik a écrit :
On Thu, Nov 28, 2019 at 7:45 PM Dima Pasechnik <dim...@gmail.com> wrote:
>
> what does happen if you run
>
> sage: from sage.graphs.strongly_regular_db import SRG_280_135_70_60
> sage: SRG_280_135_70_60()
>
> Does it print
>
> J_2 on cosets of 3.PGL(2,9): Graph on 280 vertices

  • On my core7/16 GB machine: yes (in about 1 second).
  • On my problematic machine (core i5, 8 GB): nope (and it takes an awful time (>5min) to fail...):

sage: from sage.graphs.strongly_regular_db import SRG_280_135_70_60
sage: SRG_280_135_70_60()
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/gap.py in _eval_line(self, line, allow_use_file, wait_for_prompt, restart_if_needed)
    768                 error = error.replace('\r','')
--> 769                 raise RuntimeError("%s produced error output\n%s\n   executing %s"%(self, error,line))
    770             if not len(normal):

RuntimeError: Gap produced error output
Error, Record Element: <rec> must be a record (not a boolean or fail)

   executing \$sage1:=AtlasGenerators("J2",2).generators;;

During handling of the above exception, another exception occurred:

RuntimeError                              Traceback (most recent call last)
/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/expect.py in __init__(self, parent, value, is_name, name)
   1470             try:
-> 1471                 self._name = parent._create(value, name=name)
   1472             # Convert ValueError and RuntimeError to TypeError for

/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/interface.py in _create(self, value, name)
    490         name = self._next_var_name() if name is None else name
--> 491         self.set(name, value)
    492         return name

/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/gap.py in set(self, var, value)
   1426         cmd = ('%s:=%s;;' % (var, value)).replace('\n','')
-> 1427         self._eval_line(cmd, allow_use_file=True)
   1428 

/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/gap.py in _eval_line(self, line, allow_use_file, wait_for_prompt, restart_if_needed)
    802             else:
--> 803                 raise RuntimeError(exc)
    804 

RuntimeError: Gap produced error output
Error, Record Element: <rec> must be a record (not a boolean or fail)

   executing \$sage1:=AtlasGenerators("J2",2).generators;;

During handling of the above exception, another exception occurred:

TypeError                                 Traceback (most recent call last)
<ipython-input-2-6f6fc5a36ce9> in <module>()
----> 1 SRG_280_135_70_60()

/usr/local/sage-9/local/lib/python3.7/site-packages/sage/graphs/strongly_regular_db.pyx in sage.graphs.strongly_regular_db.SRG_280_135_70_60 (build/cythonized/sage/graphs/strongly_regular_db.c:34308)()
   2251 
   2252     # A representation of J2 acting on a 3.PGL(2,9) it contains.
-> 2253     J2    = PermutationGroup(gap('AtlasGenerators("J2",2).generators'))
   2254     edges = J2.orbit((1,2),"OnSets")
   2255     g     = Graph()

/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/interface.py in __call__(self, x, name)
    286 
    287         if isinstance(x, string_types):
--> 288             return cls(self, x, name=name)
    289         try:
    290             # Special methods do not and should not have an option to

/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/expect.py in __init__(self, parent, value, is_name, name)
   1474             except (RuntimeError, ValueError) as x:
   1475                 self._session_number = -1
-> 1476                 raise_(TypeError, TypeError(*x.args), sys.exc_info()[2])
   1477             except BaseException:
   1478                 self._session_number = -1

/usr/local/sage-9/local/lib/python3.7/site-packages/six.py in reraise(tp, value, tb)
    690                 value = tp()
    691             if value.__traceback__ is not tb:
--> 692                 raise value.with_traceback(tb)
    693             raise value
    694         finally:

/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/expect.py in __init__(self, parent, value, is_name, name)
   1469         else:
   1470             try:
-> 1471                 self._name = parent._create(value, name=name)
   1472             # Convert ValueError and RuntimeError to TypeError for
   1473             # coercion to work properly.

/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/interface.py in _create(self, value, name)
    489     def _create(self, value, name=None):
    490         name = self._next_var_name() if name is None else name
--> 491         self.set(name, value)
    492         return name
    493 

/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/gap.py in set(self, var, value)
   1425         """
   1426         cmd = ('%s:=%s;;' % (var, value)).replace('\n','')
-> 1427         self._eval_line(cmd, allow_use_file=True)
   1428 
   1429     def get(self, var, use_file=False):

/usr/local/sage-9/local/lib/python3.7/site-packages/sage/interfaces/gap.py in _eval_line(self, line, allow_use_file, wait_for_prompt, restart_if_needed)
    801                     return ''
    802             else:
--> 803                 raise RuntimeError(exc)
    804 
    805         except KeyboardInterrupt:
>> To unsubscribe from this group and stop receiving emails from it, send an email to sage-r...@googlegroups.com.

Emmanuel Charpentier

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Nov 29, 2019, 5:19:41 AM11/29/19
to sage-release
I'll try that patch on my problematic machine and report (but that won't be fast...).


Le vendredi 29 novembre 2019 00:52:43 UTC+1, Dima Pasechnik a écrit :
>> To unsubscribe from this group and stop receiving emails from it, send an email to sage-r...@googlegroups.com.

Emmanuel Charpentier

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Nov 29, 2019, 6:35:55 AM11/29/19
to sage-release
Well... applying Trac#28818 didn't solve my problem. I cut'n'pasted the end of what is printed by make ptestalllong in the enclosed file end_of_ptestalllong.txt.

HTH...
end_of_ptestalllong.txt

Dima Pasechnik

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Nov 29, 2019, 6:43:55 AM11/29/19
to sage-release
on that machine, could you

./sage -f gap_packages

and try again? It seems that GAP's AtlasRep package is misbehaving for
you - it could be due to the fact that it needs internet
to pull data initially (and caches it): cf.

http://www.math.rwth-aachen.de/~Thomas.Breuer/atlasrep/
Note that the package archives do NOT contain the database part of the
package; the GAP interface accesses the data on demand via the
internet.
> 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/58a2ac85-5054-4748-afce-e53edc1376bb%40googlegroups.com.

Emmanuel Charpentier

unread,
Nov 29, 2019, 8:36:18 AM11/29/19
to sage-release


Le vendredi 29 novembre 2019 12:43:55 UTC+1, Dima Pasechnik a écrit :
on that machine, could you

./sage -f gap_packages

and try again?

Done. No relief :-(. Your test on SRG_280_135_70_60 just took about 5 minutes to fail (same messages as before, IIRC).
 
It seems that GAP's AtlasRep package is misbehaving for
you  - it could be due to the fact that it needs internet
to pull data initially (and caches it):

Aha ! My problematic machine is stuck behind our "public-corporate" firewall (i. e. a corporate firewall done wrong...). What can get used varies by protocol:
  • HTTP and HTTPS work, using specfic proxy addresses ;
  • I have to use passive FTP mode if I need FTP (more and more rare...) ;
  • SSH is open.
What does AtlasRep uses ?
 

Dima Pasechnik

unread,
Dec 1, 2019, 7:39:15 AM12/1/19
to sage-release
On Fri, Nov 29, 2019 at 1:36 PM Emmanuel Charpentier
<emanuel.c...@gmail.com> wrote:
>
>
>
> Le vendredi 29 novembre 2019 12:43:55 UTC+1, Dima Pasechnik a écrit :
>>
>> on that machine, could you
>>
>> ./sage -f gap_packages
>>
>> and try again?
>
>
> Done. No relief :-(. Your test on SRG_280_135_70_60 just took about 5 minutes to fail (same messages as before, IIRC).
>
>>
>> It seems that GAP's AtlasRep package is misbehaving for
>> you - it could be due to the fact that it needs internet
>> to pull data initially (and caches it):
>
>
> Aha ! My problematic machine is stuck behind our "public-corporate" firewall (i. e. a corporate firewall done wrong...). What can get used varies by protocol:
>
> HTTP and HTTPS work, using specfic proxy addresses ;
> I have to use passive FTP mode if I need FTP (more and more rare...) ;
> SSH is open.
>
> What does AtlasRep uses ?
>
it uses HTTP (either via wget, or using GAP package io)
it will be wget if io (from gap_packages) is not installed.

There are configuration parameters for AtlasRep and io packages
that govern how files are downloaded, but I don't know details, read on
http://www.math.rwth-aachen.de/~Thomas.Breuer/atlasrep/doc/chap0.html
http://gap-packages.github.io/io/doc/chap0.html

it might be easier to copy, from the non-firewalled machine on which
all these tests pass, the contents of
local/share/gap/pkg/atlasrep

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

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Dec 1, 2019, 7:36:46 PM12/1/19
to 'Justin C. Walker' via sage-release


> On Nov 26, 2019, at 16:28 , 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

Built from a fresh clone of the develop branch on two macOS systems: 10.13.6 (2017 iMac Pro, 18-core Xeon W); and 10.15.6 (2017 MBP, Quad Core i7). No problems with the builds, and all tests (‘ptestlong’) passed!

Justin

--
Justin C. Walker, Curmudgeon-At-Large
Institute for the Enhancement of the Director's Income
--------
Experience is what you get
when you don't get what you want.
--------



Emmanuel Charpentier

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Dec 2, 2019, 1:03:39 PM12/2/19
to sage-release
Followup (IMHO demonstrative) in this post related to 9.0.beta8.

HTH,
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