Sage 9.4.beta0 released

[Volker Braun]

As always, you can get the latest beta version from the "develop" git branch. Alternatively, the self-contained source tarball is at http://www.sagemath.org/download-latest.html 

6aa4ecee16 (tag: 9.4.beta0, trac/develop) Updated SageMath version to 9.4.beta0

9e7b0bd312 Trac #31567: tox.ini: Add local-macos-nohomebrew environments, deployment targets 10.14, 10.15, 11.1

16f52682ae Trac #31838: gfortran: Accept system gfortran 11

61b50f85a7 Trac #31581: Do not require base ring of quaternion algebra to be a field

068255ca05 Trac #31579: fix various lgtm suggestions

46ce983ad7 Trac #31575: Remove full boost package

5686795da4 Trac #31573: Improve the Weierstrass sigma function on the formal group of an elliptic curve

814efa4100 Trac #31571: Improve interface to plantri

cc3ff1c94b Trac #31570: iterator for maximal chains in poset

fdca3596a1 Trac #31562: Patch giac so that libintl from /usr/local does not leak in on macOS

fcc9af582f Trac #31561: some details in cluster_seed and fqsym

9b484245c0 Trac #31547: Creating finite field using strings for modulus does not cache

a80dc50086 Trac #31452: Problem with solution_dict in solve

9203633b9b Trac #31436: Provide alternate layout for the cube graph

9addf207d9 Trac #30211: Characteristic Classes: Sequences

0d8373f534 Trac #29936: Fix moebius_transform, midpoint and perpendicular_bisector

36a68a7a79 Trac #29527: GH Actions: Add docker-opensuse

75c60e17c5 Trac #28617: Comparison of Frobenius endomorphism is broken

cd34206193 Trac #27366: Polyhedron.affine_hull: more output options

08a5cf8f42 Trac #25122: Construct RationalPolyhedralFan from possibly overlapping cones

12831dd5b0 Trac #21295: recognizable series (a base for k-regular sequences)

78b00b0c86 Trac #31808: AA cannot convert real elements from a quadratic field

07db8a8b87 Trac #31545: deprecate or remove InfiniteAbstractCombinatorialClass

0df543c2a3 Trac #31542: Fix edge multiplicity in multidigraph plot with color_by_label

a6c66a1d24 Trac #31540: Implement the alternating central extension of the q-Onsager algebra

87d5c86cd2 Trac #31532: GH Actions: Restore test for optional/experimental packages on macOS platforms

aa2223a86e Trac #31517: Make Sage output MathJax3 compatible htmls

e07c1ef197 Trac #31516: Update arb to 2.19.0

7af69c5116 Trac #31514: number_field_elements_from_algebraics with complex embeddings

f2c8b34947 Trac #31499: Check OpenMP at configuration

ba189b2319 Trac #31469: Galois groups for finite fields

701d36be1e Trac #31427: Improve .dockerignore

3d738182cd Trac #31384: cython_aliases: Do not fail if one of the listed libraries is not known to pkgconfig

21274d870a Trac #31345: Improve Selmer Group method for number fields

1da81a0ac8 Trac #31307: interactive_simplex_method: Add static methods "random_element" to LPDictionary, InteractiveLPProblemStandardForm

9665ac4990 Trac #31179: Add package ipympl - Makes interactive features of matplotlib available also in JupyterLab

6d05b6bf8c Trac #31108: Relaxed p-adics

08eadb587f Trac #31103: sage.numerical.backends: Replace use of TestSuite by pytest

a2ca61b1ac Trac #30861: Add more homebrew system package information, including packages without spkg-configure.m4

3859440591 Trac #30551: Drop Python 3.6 support

dce94e3121 Trac #30311: Immutability of Scalar Fields II

eed9fe4be8 Trac #30213: tox.ini: Add scientificlinux

8cab4cd2e2 Trac #29972: Make stats doctests ready for random seeds

05c2ecadc5 Trac #29703: Upgrade gcc to 10.3 (latest 10.x)

7ee6218134 Trac #29013: Add configure option --with-sage-venv=SAGE_VENV to create venv there instead of in SAGE_LOCAL

89134ebdbc Trac #29009: Error using mpmath (python 3 version)

b15fe7517b Trac #27957: AG codes and decoders

b47d2ad084 Trac #26161: Refine polynomial quotient rings to the finite subcategory on initialization

5919b40d0a Trac #23940: implement proper black-box discrete logarithm for AdditiveAbelianGroupWrapper

7f610a53c0 Trac #21295: recognizable series (a base for k-regular sequences)

9bdf65da5d Trac #20165: Speedup CrystalOfLSPaths

d2a0b73c1d Trac #18863: Subgroup doesn't work with number field unit group

c8258dbf7e Trac #18272: unset MACOSX_DEPLOYMENT_TARGET, rather than sometimes setting a bogus value

2a3f0073b9 Trac #15216: Parking functions reject their offspring

337d941a2f Trac #13111: variable camera position, light, etc. for tachyon ray tracer

9a0dfef090 Trac #10928: Test that getitem of numpy matrix using Sage integers works

2cf65a584d Trac #31556: Update libgd to 2.3.2

bab8d46b84 Trac #31069: Upgrade: Flint 2.7.1

1c01281a1e Trac #30913: sagelib: Generate pyproject.toml and setup.cfg [install_requires], requirements.txt, Pipfile, and src/Pipfile

c21d3c6a1c Trac #31756: regression: conversion of Mathematica's Sqrt to Sage fails

d6c5cd9be7 (tag: 9.3, trac/master) Updated SageMath version to 9.3

[Kwankyu Lee]

Thanks for the beta release.

It seems unusual that the tickets included in the release are not yet closed in Trac.

[Sébastien Labbé]

Thank you for the release.

I observe that #21295 was merged twice:

12831dd5b0 Trac #21295: recognizable series (a base for k-regular sequences)

7f610a53c0 Trac #21295: recognizable series (a base for k-regular sequences)

It is the first time that I see such a thing.

Sébastien

[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

[Sébastien Labbé]

I have python3.6 and python3.8 installed on my system:

$ python3
Python 3.6.9 (default, Jan 26 2021, 15:33:00)
[GCC 8.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>>

$ python3.8
Python 3.8.0 (default, Feb 25 2021, 22:10:10)
[GCC 8.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import sqlite3, ctypes, math, hashlib, crypt, readline, socket, zlib, distutils.core

>>>

My python3.8 has the above librairies available. But, it seems that my python3.8 is not picked up by the configure script:

## -------------------------------------------------------- ##
## Checking whether SageMath should install SPKG python3... ##
## -------------------------------------------------------- ##
configure:31962: checking whether any of bzip2 xz libffi is installed as or will be installed as SPKG
configure:31971: result: no
configure:31975: checking for python3 >= 3.7.0, < 3.10.0 with modules sqlite3, ctypes, math, hashlib, crypt, readline, socket, zlib, distutils.core
configure:32642: result:
configure:32666: checking ... whether /usr/bin/python3 is good
configure:33250: result: no, Python 3.6.9 is too old
configure:33288: result:
configure:33292: to try to use a different system python, use ./configure --with-python=/path/to/python
configure:33316: no suitable system package found for SPKG python3

Do you know why is my system python3.8 not picked up during installation?

Sébastien

On Wednesday, May 26, 2021 at 11:13:19 PM UTC+2 Volker Braun wrote:

[Samuel Lelièvre]

2021-05-27 12:44 UTC, Sébastien Labbé:

>
> On Ubuntu 18.04, testing with various optional
> and external packages, I obtain:
>

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

Probably the "period" / "full stop" at the very end.

> ... 292, ...]
> ... 292, ...].

[Sébastien Labbé]

Probably the "period" / "full stop" at the very end.

> ... 292, ...]
> ... 292, ...].

Goodeye, goodeye!

Needs review at:

https://trac.sagemath.org/ticket/31865

https://trac.sagemath.org/ticket/31866

Also the random failure with graph.py was noticed by Volker already:

https://trac.sagemath.org/ticket/31848

[Clemens Heuberger]

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:

[Dima Pasechnik]

On Thu, 27 May 2021, 15:34 Clemens Heuberger, <clemens....@aau.at> wrote:

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'

this is fixed in a ticket I reviewed today.

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[Matthias Köppe]

On Thursday, May 27, 2021 at 5:55:39 AM UTC-7 Sébastien Labbé wrote:

I have python3.6 and python3.8 installed on my system:

[...]

My python3.8 has the above librairies available. But, it seems that my python3.8 is not picked up by the configure script:

See https://wiki.sagemath.org/ReleaseTours/sage-9.2#Selecting_a_system_Python_to_use_for_Sage.27s_venv 

[Justin C. Walker]

> On May 26, 2021, at 14:13, 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 tree on macOS 10.15.7 (8-core Core i9 2019 MBP). No problems during build.

Two test failures (‘ptestlong’). Both have been reported earlier:

sage -t --long --warn-long 82.1 --random-seed=0 src/sage/graphs/graph.py # 1 doctest failed
sage -t --long --warn-long 82.1 --random-seed=0 src/sage/misc/package.py # 1 doctest failed

At the end, the following was printed:
Pytest is not installed, skip checking tests that rely on it.

Have not heard of this. Should it be/have been installed?

Thanks!

Justin

[Volker Braun]

The "sage.libs.gap.util.GAPError: Error, OnSets: <set> must be a set (not a immutable non-strictly-sorted plain list of cyclotomics)" is a known random failure, its pretty easy to repro by running the test in a loop. I made https://trac.sagemath.org/ticket/31848 for it.

[Matthias Köppe]

On Thursday, May 27, 2021 at 12:11:11 PM UTC-7 jus...@mac.com wrote:

> On May 26, 2021, at 14:13, 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 tree on macOS 10.15.7 (8-core Core i9 2019 MBP). No problems during build.

[...] At the end, the following was printed:

Pytest is not installed, skip checking tests that rely on it.

Have not heard of this. Should it be/have been installed?

This was introduced in https://trac.sagemath.org/ticket/31103

 

[Matthias Köppe]

On Wednesday, May 26, 2021 at 2:13:19 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 

6aa4ecee16 (tag: 9.4.beta0, trac/develop) Updated SageMath version to 9.4.beta0

Thanks, Volker, for preparing the new beta. When you have a moment, could you react to the discussion regarding the 9.4 release cycle over in sage-devel?

All: Here are some comments:

> 16f52682ae Trac #31838: gfortran: Accept system gfortran 11

> 05c2ecadc5 Trac #29703: Upgrade gcc to 10.3 (latest 10.x)

As a result of these tickets, on macOS with homebrew, it should no longer be necessary to pin gcc to version 10 now. Likely a "make distclean" to trigger a full rebuild will be necessary after switching to the latest toolchain.

> 3859440591 Trac #30551: Drop Python 3.6 support

Unfortunately, this ticket contained a bad change to sage-bootstrap-python.

If you are on a system with python 3.6, you might need to merge https://trac.sagemath.org/ticket/31860, which reverts this change.

[Justin C. Walker]

Thanks, Matthias,

> On May 27, 2021, at 13:53, Matthias Köppe <matthia...@gmail.com> wrote:
>
> On Thursday, May 27, 2021 at 12:11:11 PM UTC-7 jus...@mac.com wrote:
>
> > On May 26, 2021, at 14:13, 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 tree on macOS 10.15.7 (8-core Core i9 2019 MBP). No problems during build.
>
> [...]

> > Have not heard of this. Should it be/have been installed?


> This was introduced in https://trac.sagemath.org/ticket/31103

Excuse the lame questions, but should PyTest have been downloaded/installed when I installed 9.4-b0? I see references to it, when I search the tree. Should this have been run?

Justin

[Matthias Köppe]

On Thursday, May 27, 2021 at 3:21:35 PM UTC-7 jus...@mac.com wrote:

> On May 27, 2021, at 13:53, Matthias Köppe <matthia...@gmail.com> wrote:
> This was introduced in https://trac.sagemath.org/ticket/31103

should PyTest have been downloaded/installed when I installed 9.4-b0? I see references to it, when I search the tree. Should this have been run?

No, it is only an optional package at this time. In https://trac.sagemath.org/ticket/31110, I propose to make it a standard package.

[Volker Braun]

On Thursday, May 27, 2021 at 11:46:37 PM UTC+2 matthia...@gmail.com wrote:

Thanks, Volker, for preparing the new beta. When you have a moment, could you react to the discussion regarding the 9.4 release cycle over in sage-devel?

Sounds good to me! Shorter release cycles are always better...

 

[Kenji Iohara]

On my Mac OS 11.3, it compiled without problem. For ptestlong, it failed : 

2021年5月28日(金) 0:47 Volker Braun <vbrau...@gmail.com>:

On Thursday, May 27, 2021 at 11:46:37 PM UTC+2 matthia...@gmail.com wrote:

Thanks, Volker, for preparing the new beta. When you have a moment, could you react to the discussion regarding the 9.4 release cycle over in sage-devel?

Sounds good to me! Shorter release cycles are always better...

 

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[Kwankyu Lee]

With this release, the command

    sage -docbuild all pdf

stops with the failure below. How about others?

Building it/a_tour_of_sage.

[a_tour_of] building [latex]: all documents

[a_tour_of] Merging environment/index files...

[a_tour_of] ... done (0 todos, 1 index, 0 citations, 0 modules)

...

(/usr/local/texlive/2021/texmf-dist/tex/latex/hyperref/nameref.sty

(/usr/local/texlive/2021/texmf-dist/tex/latex/refcount/refcount.sty)

(/usr/local/texlive/2021/texmf-dist/tex/generic/gettitlestring/gettitlestring.s

ty)) (/usr/local/texlive/2021/texmf-dist/tex/latex/psnfss/t1phv.fd)

! Package inputenc Error: Unicode character リ (U+30EA)

(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.

Type  H <return>  for immediate help.

 ...                                              

                                                  

l.304 \sphinxmaketitle

                      

? 

! Emergency stop.

 ...                                              

                                                  

l.304 \sphinxmaketitle

                      

!  ==> Fatal error occurred, no output PDF file produced!

Transcript written on a_tour_of_sage.log.

Latexmk: Examining 'a_tour_of_sage.log'

=== TeX engine is 'pdfTeX'

Latexmk: Index file 'a_tour_of_sage.idx' was written

Latexmk: Summary of warnings from last run of *latex:

  =====Latex reported missing or unavailable character(s).

=====See log file for details.

Latexmk: Errors, so I did not complete making targets

...

[Emmanuel Charpentier]

FWIWn on Debian testing running on core i7 + 16 GB RAM, after upgrading from 9.3 to 9.4.beta0, ptestlong gives me the same results (one transient timeout and two gap-related permanent failures) as before, plus one more transient failure on src/sage/graphs/graph.py :

sage -t --long --warn-long 228.8 --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 "/usr/local/sage-9/local/lib/python3.9/site-packages/sage/doctest/forker.py", line 714, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/local/sage-9/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 "/usr/local/sage-9/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:20775)
        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:19779)
        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
    [1216 tests, 1 failure, 75.95 s]

However, this is transient :

harpent@zen-book-flip:/usr/local/sage-9$ sage -t --long --warn-long 228.8 --random-seed=0 src/sage/graphs/graph.py  # 1 doctest failed
Running doctests with ID 2021-05-28-13-24-34-ceab9ba0.
Git branch: develop
Using --optional=build,debian,dochtml,dot2tex,fricas,gap_jupyter,gap_packages,kenzo,libsemigroups,pip,pysingular,saclib,sage,sage_spkg,singular_jupyter
Doctesting 1 file.
sage -t --long --warn-long 228.8 --random-seed=0 src/sage/graphs/graph.py
    [1216 tests, 16.62 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 16.8 seconds
    cpu time: 15.2 seconds
    cumulative wall time: 16.6 seconds
Pytest is not installed, skip checking tests that rely on it.

This error being transient is more cause for questions than for reassurance, IMHO…

HTH,

​

[Samuel Lelièvre]

2021-05-27 14:43 UTC, Dima Pasechnik:

>
> On Thu, 27 May 2021, 15:34 Clemens Heuberger, <clemens....@aau.at> wrote:
>>
>> 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'
>
> this is fixed in a ticket I reviewed today.

For reference:

- Sage Trac ticket 31825: Failure when testing sage_conf version
https://trac.sagemath.org/ticket/31825

[Paul Masson]

I haven't built Sage in some time, so perhaps something has changed recently of which I am unaware. After "make distclean" and "configure", my build on MacOS 10.15.7 is stopping at symmetrica. Here is the log:

Attempting to download package symmetrica-3.0.1.tar.xz from mirrors

http://files.sagemath.org/spkg/upstream/symmetrica/symmetrica-3.0.1.tar.xz

[......................................................................]

symmetrica-3.0.1

====================================================

Setting up build directory for symmetrica-3.0.1

Error: Unknown file type: /Users/Masson/Downloads/GitHub/sage/upstream/symmetrica-3.0.1.tar.xz

Finished extraction

/Users/Masson/Downloads/GitHub/sage/build/bin/sage-spkg: line 488: cd: src: No such file or directory

No patch files found in ../patches

Error: There is no spkg-install script, no setup.py, and no configure

script, so I do not know how to install /Users/Masson/Downloads/GitHub/sage/upstream/symmetrica-3.0.1.tar.xz.

Not making any sense to me, since all the files are there.

On Wednesday, May 26, 2021 at 2:13:19 PM UTC-7 Volker Braun wrote:

[Volker Braun]

Seems like extracting the xz achive fails

[Paul Masson]

Installed xz using Homebrew. Appears to have done the trick. Thanks Volker.

[Samuel Lelièvre]

Paul Masson:

>
> Installed xz using Homebrew. Appears to have done the trick. Thanks Volker.

https://trac.sagemath.org/ticket/31915

[Paul Masson]

Now having a problem with the documentation. The first run stopped at this point:

[sage_docbuild-9.4.beta0] Installing collected packages: sage-docbuild

[sage_docbuild-9.4.beta0] 

[sage_docbuild-9.4.beta0] Successfully installed sage-docbuild-9.4b0

[sage_docbuild-9.4.beta0] Removed build tracker: '/private/var/folders/np/_r579ck92g1f9x1tzcvdhy5m0000gn/T/pip-req-tracker-l7mxw1p6'

touch "/Users/Masson/Downloads/GitHub/sage/local/var/lib/sage/installed/sage_docbuild-9.4.beta0"

Tried terminating the process and rerunning, but still hangs at this line. Tried "chmod 755" on the file and still hangs at this line. Any ideas anyone?

On Saturday, June 5, 2021 at 6:29:51 AM UTC-7 Volker Braun wrote:

[Dima Pasechnik]

typically these hangs mean something stale in ~/.sage/

try moving it away and re-run make.

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[Paul Masson]

Removed that directory under my user name and build still hangs at that line. Do I need to start from the beginning after removing the directory?

[Dima Pasechnik]

On Sat, 5 Jun 2021, 21:51 Paul Masson, <paulm...@comcast.net> wrote:

Removed that directory under my user name and build still hangs at that line. Do I need to start from the beginning after removing the directory?

hmm, no. I see these hangs happen now and then.

I don't know how to debug this on macOS.

To view this discussion on the web visit https://groups.google.com/d/msgid/sage-release/2fec7e97-9fa4-4a15-95ce-00a67eec75d6n%40googlegroups.com.

[Justin C. Walker]

> On May 26, 2021, at 14:13, 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 tree on macOS 10.13.6 (2017 iMac Pro, Xeon W). No problems during build.

Two test failures (‘ptestlong’):

sage -t --long --warn-long 72.7 --random-seed=0 src/sage/geometry/polyhedron/base.py # 1 doctest failed
sage -t --long --warn-long 72.7 --random-seed=0 src/sage/misc/package.py # 1 doctest failed

First failure:
File "src/sage/geometry/polyhedron/base.py", line 6523, in sage.geometry.polyhedron.base.Polyhedron_base.face_lattice
Failed example:
n == get_memory_usage()
Expected:
True
Got:
False

Second failure known and fixed.

Thanks!

Justin