Sage 9.6.rc3 released

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Volker Braun

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Apr 30, 2022, 5:47:14 AMApr 30
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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

eb1a786c04 (tag: 9.6.rc3, trac/develop) Updated SageMath version to 9.6.rc3
8e8d7b448d Trac #33655: Website/wiki/documentation: Streamline entry points for installation and development, update conda instructions for Sage 9.6
8def33a9c7 Trac #33325: First display of an object is slow
bc44ac8bd2 Trac #33587: 'MAKE="make V=0" make' and 'V=0 ./sage -b' are broken
316f3f9649 Trac #33750: Update gcc/gfortran to 11.x - to fix build on macOS 12.3.1
67c34fee1d (tag: 9.6.rc2) Updated SageMath version to 9.6.rc2

Kenji Iohara

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May 1, 2022, 1:51:49 PMMay 1
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Thanks Volker  for this version. 

 On my Mac OS 12.3.1,IntelCore i5  with Homebrew, I could compile Sage 9.6.rc2, but not Sage 9.6.rc3.
Here is the error what I have:

* package:         gmpy2-2.1.1
  last build time: May 1 00:26
  log file:        /Users/iohara/Desktop/sage-9.6.rc3/logs/pkgs/gmpy2-2.1.1.log

* package:         cysignals-1.11.2
  last build time: May 1 00:27
  log file:        /Users/iohara/Desktop/sage-9.6.rc3/logs/pkgs/cysignals-1.11.2.log

* package:         matplotlib-3.5.1
  last build time: May 1 18:50
  log file:        /Users/iohara/Desktop/sage-9.6.rc3/logs/pkgs/matplotlib-3.5.1.log


cysignals-1.11.2.log
gmpy2-2.1.1.log
matplotlib-3.5.1.log

Matthias Köppe

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May 1, 2022, 2:06:48 PMMay 1
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config.log please; did you run ". ./.homebrew-build-env"?

Kenji Iohara

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May 1, 2022, 2:08:59 PMMay 1
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I think so... 

2022年5月1日(日) 20:06 Matthias Köppe <matthia...@gmail.com>:
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config.log

Matthias Köppe

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May 1, 2022, 2:15:41 PMMay 1
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If the terminal is still open, you can check by typing "echo $CPATH"

Matthias Köppe

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May 1, 2022, 3:04:41 PMMay 1
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On Saturday, April 30, 2022 at 2:47:14 AM 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

eb1a786c04 (tag: 9.6.rc3, trac/develop) Updated SageMath version to 9.6.rc3

Thanks, Volker, for preparing this rc. Tests for Linux ran at https://github.com/sagemath/sage/actions/runs/2248155397:

ubuntu-{trusty, ..., jammy}, debian-{stretch, ..., sid}, linuxmint-{17,...,20.3}: Clean
- except for familiar sporadic failures related to pexpect
- except for ubuntu-jammy-standard (https://github.com/sagemath/sage/runs/6236167662) and debian-sid-standard: error exit caused by Giac's signal handling, but this can be worked around by using our giac spkg now that https://trac.sagemath.org/ticket/33706 is merged, so this should not hold up the release.
- except for ubuntu-jammy-standard: src/sage/numerical/backends/logging_backend.py # Killed due to abort
- except for debian-bullseye-standard (https://github.com/sagemath/sage/runs/6236168030): Severe numerical trouble (seen before)

fedora-{26,...36}, centos-{7,stream-8}: Clean
- except for fedora-28-standard (https://github.com/sagemath/sage/runs/6236169025): src/sage/rings/polynomial/groebner_fan.py # 3 doctests failed
- except for fedora-32-standard (https://github.com/sagemath/sage/runs/6236169358): src/sage/geometry/cone.py # Timed out, src/sage/schemes/toric/sheaf/klyachko.py # 1 doctest failed
- except for fedora-33-minimal (https://github.com/sagemath/sage/runs/6236169387): src/sage/homology/tests.py: Expected: Chain complex with at most ... nonzero terms over Integer Ring Got:  Trivial chain complex over Integer Ring
- except for fedora-34-standard (https://github.com/sagemath/sage/runs/6236169544): src/sage/libs/giac/__init__.py: Aborted
- except for centos-7-standard (https://github.com/sagemath/sage/runs/6236169862): src/sage/numerical/linear_tensor_element.pyx: Aborted

gentoo: Clean
- except for (https://github.com/sagemath/sage/runs/6236170009): src/sage/interfaces/giac.py

sage -t --random-seed=118900258066036661703918984796240637250 src/sage/interfaces/singular.py  # 5 doctests failed
sage -t --random-seed=118900258066036661703918984796240637250 src/sage/libs/singular/function.pyx  # 1 doctest failed
sage -t --random-seed=118900258066036661703918984796240637250 src/sage/libs/singular/singular.pyx  # 1 doctest failed
sage -t --random-seed=118900258066036661703918984796240637250 src/sage/numerical/backends/logging_backend.py  # Killed due to abort
sage -t --random-seed=118900258066036661703918984796240637250 src/sage/plot/plot3d/tachyon.py  # 2 doctests failed

opensuse-{15.3, tumbleweed}: Clean, except for failures because tachyon is too new (https://trac.sagemath.org/ticket/23712)

slackware-14.2: Clean except for (https://github.com/sagemath/sage/runs/6236170632) src/sage/numerical/linear_tensor_element.pyx: Aborted
 
conda-forge-standard: Clean



 

François Bissey

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May 1, 2022, 3:41:18 PMMay 1
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That is https://github.com/cschwan/sage-on-gentoo/issues/682

> On 2/05/2022, at 07:04, Matthias Köppe <matthia...@gmail.com> wrote:
>
> gentoo: Clean
> - except for (https://github.com/sagemath/sage/runs/6236170009): src/sage/interfaces/giac.py
>

It means something went wrong when giac was updated on the system in the past and the documentation is not pointed to the right place.

Nothing to do with sage itself.

François

G. M.-S.

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May 1, 2022, 3:43:16 PMMay 1
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Thanks, Volker.

Nothing new on Apple Silicon Macs with Homebrew up to date (make, make pytest, make ptestlong).

Guillermo

Kenji Iohara

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May 1, 2022, 4:57:22 PMMay 1
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Thanks Matthias. After (re)running ../homebrew-nuid-env, it compiled !

01/05/2022 20:15、Matthias Köppe <matthia...@gmail.com>のメール:

Nasser M. Abbasi

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May 1, 2022, 7:21:22 PMMay 1
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I get the following error compiling on Ubuntu 20.04 under WSL-2 linux subsystem. Under windows 10.

I used the same steps I did for rc0 and rc1, rc2 But now with rc3 I get this error

=========================================
[sagemath_doc_html-none] [plot3d ] from matplotlib import _qhull
[sagemath_doc_html-none] [plot3d ] ImportError: /home/me/TMP/sage-9.6.rc3/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/matplotlib/_qhull.cpython-310-x86_64-linux-gnu.so: undefined symbol: _Z15qh_memfreeshortP3qhTPiS1_
[sagemath_doc_html-none] [plot3d ] The inventory files are in local/share/doc/sage/inventory/en/reference/plot3d.
[sagemath_doc_html-none] Error building the documentation.
[sagemath_doc_html-none] Traceback (most recent call last):
[sagemath_doc_html-none] File "/usr/lib/python3.10/runpy.py", line 196, in _run_module_as_main
[sagemath_doc_html-none] return _run_code(code, main_globals, None,
[sagemath_doc_html-none] File "/usr/lib/python3.10/runpy.py", line 86, in _run_code
[sagemath_doc_html-none] exec(code, run_globals)
[sagemath_doc_html-none] File "/home/me/TMP/sage-9.6.rc3/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/sage_docbuild/__main__.py", line 2, in <module>
[sagemath_doc_html-none] main()
[sagemath_doc_html-none] File "/home/me/TMP/sage-9.6.rc3/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/sage_docbuild/__init__.py", line 1762, in main
[sagemath_doc_html-none] builder()
[sagemath_doc_html-none] File "/home/me/TMP/sage-9.6.rc3/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/sage_docbuild/__init__.py", line 801, in _wrapper
[sagemath_doc_html-none] getattr(DocBuilder, build_type)(self, *args, **kwds)
[sagemath_doc_html-none] File "/home/me/TMP/sage-9.6.rc3/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/sage_docbuild/__init__.py", line 145, in f
[sagemath_doc_html-none] runsphinx()
[sagemath_doc_html-none] File "/home/me/TMP/sage-9.6.rc3/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/sage_docbuild/sphinxbuild.py", line 326, in runsphinx
[sagemath_doc_html-none] sys.stderr.raise_errors()
[sagemath_doc_html-none] File "/home/me/TMP/sage-9.6.rc3/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/sage_docbuild/sphinxbuild.py", line 262, in raise_errors
[sagemath_doc_html-none] raise OSError(self._error)
[sagemath_doc_html-none] OSError: /home/me/TMP/sage-9.6.rc3/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/sage/plot/plot3d/list_plot3d.py:docstring of sage.plot.plot3d.list_plot3d.list_plot3d_tuples:63: WARNING: Exception occurred in plotting list_plot3d-18
[sagemath_doc_html-none]
[sagemath_doc_html-none] Note: incremental documentation builds sometimes cause spurious
[sagemath_doc_html-none] error messages. To be certain that these are real errors, run
[sagemath_doc_html-none] "make doc-clean doc-uninstall" first and try again.
[sagemath_doc_html-none] make[6]: *** [Makefile:20: doc-inventory--reference-plot3d] Error 1
[sagemath_doc_html-none] make[5]: *** [Makefile:37: doc-inventory-reference] Error 2
make[4]: *** [Makefile:2936: sagemath_doc_html-SAGE_DOCS-no-deps] Error 2
make[3]: *** [Makefile:2936: /home/me/TMP/sage-9.6.rc3/local/var/lib/sage/installed/sagemath_doc_html-none] Error 2
make[2]: *** [Makefile:2497: all-start] Error 2
make[2]: Leaving directory '/home/me/TMP/sage-9.6.rc3/build/make'

real 100m59.136s
user 101m12.626s
sys 7m46.868s
====================================

I made sure to do all the sudo apt commands needed before doing make. I did  

./configure
sudo apt etc... as instructed by messages from the above
make

>uname -a
Linux DESKTOP-6879BT0 5.10.102.1-microsoft-standard-WSL2 #1 SMP Wed Mar 2 00:30:59 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

The following is a link to top level log file

ls -l *.log
-rw-r--r-- 1 me me 340308 May  1 16:08 config.log

Matthias Köppe

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May 1, 2022, 10:54:15 PMMay 1
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From config.log:
PATH: /home/me/TMP/sage-9.6.rc2/local/bin

Don't try to build Sage when the PATH includes an earlier installation of Sage. 

Emmanuel Charpentier

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May 2, 2022, 6:59:00 AMMay 2
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FWIW, upgrading 9.6.rc1 to rc3 on Debian testing running on core i5 + 8 GB RAM and running ptestlong gets the transient failure (already reported) :

sage -t --long --warn-long 63.6 --random-seed=328597402089894452158952134173781439187 src/sage/schemes/cyclic_covers/cycliccover_finite_field.py  # 1 doctest failed

HTH,

Nasser M. Abbasi

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May 2, 2022, 8:40:15 AMMay 2
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Thanks. I redid the build. It now worked. 
Changed $SAGE_ROOT in my .bashrc to point to rc3 _BEFORE_ starting anything (even though rc is not yet build).  Then redid everything from scratch.
It was not clear if one should change $SAGE_ROOT to the new root before or after the build is done.


And this is the config.log after doing the recheck command


This is all on 

>cat /etc/os-release
NAME="Ubuntu"
VERSION="20.04.4 LTS (Focal Fossa)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 20.04.4 LTS"

Dima Pasechnik

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May 2, 2022, 8:57:29 AMMay 2
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On Mon, 2 May 2022, 13:40 'Nasser M. Abbasi' via sage-release, <sage-r...@googlegroups.com> wrote:
Thanks. I redid the build. It now worked. 
Changed $SAGE_ROOT in my .bashrc to point to rc3 _BEFORE_ starting anything (even though rc is not yet build).  Then redid everything from scratch.
It was not clear if one should change $SAGE_ROOT to the new root before or after the build is done.

There is no need to set SAGE_ROOT for building, at all.


Sébastien Labbé

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May 2, 2022, 11:52:55 AMMay 2
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Thanks for the release. On Ubuntu 18.04, with some optional and external packages installed, I get:

----------------------------------------------------------------------
sage -t --long --random-seed=10041023278531363329797553849793068311 src/sage/combinat/designs/incidence_structures.py  # 1 doctest failed
sage -t --long --random-seed=10041023278531363329797553849793068311 src/sage/databases/oeis.py  # 1 doctest failed
sage -t --long --random-seed=10041023278531363329797553849793068311 src/sage/graphs/generic_graph.py  # 2 doctests failed
sage -t --long --random-seed=10041023278531363329797553849793068311 src/sage/graphs/graph.py  # 3 doctests failed
sage -t --long --random-seed=10041023278531363329797553849793068311 src/sage/tests/cmdline.py  # 1 doctest failed
----------------------------------------------------------------------
Features detected for doctesting: dvipng,ffmpeg,gfan,graphviz,imagemagick,internet,latex,latex_package_tkz_graph,lualatex,nauty,octave,palp,pandoc,pdf2svg,pdflatex,pdftocairo,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.plot,sage.rings.number_field,sage.rings.padics,sage.rings.real_double,sage.symbolic,sagemath_doc_html,sphinx,xelatex

Rerunning failed tests, I get the same list. A new failures is in oeis.py (copied below) but it is not harmful.

Other failures are known from a long time and no solution will be out before the release of 9.6, see https://trac.sagemath.org/ticket/25536


sage -t --long --random-seed=145140706964628952529635198083628764457 src/sage/databases/oeis.py
**********************************************************************
File "src/sage/databases/oeis.py", line 129, in sage.databases.oeis
Failed example:
    [i for i in b.comments() if 'prime' in i][-1]     # optional -- internet
Expected:
    'Number n is prime if mod(a(n)-2,n) = 0...'
Got:
    'Number n is prime if (a(n)-2) mod n = 0. - _Dmitry Kruchinin_, Feb 14 2012 - Incorrect; see 2007 comment by David W. Wilson above. - _Jeppe Stig Nielsen_, Apr 22 2022'
**********************************************************************
1 item had failures:
   1 of  26 in sage.databases.oeis
    5 webbrowser tests not run
    0 tests not run because we ran out of time
    [289 tests, 1 failure, 33.81 s]



Matthias Köppe

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May 2, 2022, 2:38:12 PMMay 2
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On Sunday, May 1, 2022 at 12:04:41 PM UTC-7 Matthias Köppe wrote:
On Saturday, April 30, 2022 at 2:47:14 AM 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

eb1a786c04 (tag: 9.6.rc3, trac/develop) Updated SageMath version to 9.6.rc3

Thanks, Volker, for preparing this rc. 


The build succeeded. "make ptest" (https://github.com/sagemath/sagetrac-mirror/runs/6256042215) shows various segfaults, likely related to GAP, that may be new.

This should not hold up the release. 
Users/Developers who like to continue using the Cygwin port are asked to step up to investigating and fixing these bugs on Cygwin.
Otherwise, it is unlikely that we'll be able to continue offering the Cygwin port.
In the updated installation manual for Sage 9.6, we have already deemphasized Cygwin in favor of using WSL on Windows.


sage -t --random-seed=50463910914964877037575760797017411618 src/doc/de/tutorial/tour_groups.rst
    Killed due to segmentation fault
**********************************************************************
Tests run before process (pid=35829) failed:
[...]
sage: MS = MatrixSpace(GF(7), 2) ## line 50 ##
sage: gens = [MS([[1,0],[-1,1]]),MS([[1,1],[0,1]])] ## line 51 ##
sage: G = MatrixGroup(gens) ## line 52 ##
sage: G.conjugacy_classes_representatives() ## line 53 ##

age -t --random-seed=50463910914964877037575760797017411618 src/doc/en/thematic_tutorials/explicit_methods_in_number_theory/nf_galois_groups.rst
    Killed due to segmentation fault
**********************************************************************
Tests run before process (pid=37406) failed:
sage: K.<alpha> = NumberField(x^6 + 40*x^3 + 1372) ## line 16 ##
sage: G = K.galois_group() ## line 17 ##
sage: G ## line 18 ##
Galois group 6T2 ([3]2) with order 6 of x^6 + 40*x^3 + 1372
sage: G.order() ## line 28 ##
6
sage: G.gens() ## line 30 ##
[(1,2)(3,4)(5,6), (1,4,6)(2,5,3)]
sage: f = G.1; f(alpha) ## line 32 ##
1/36*alpha^4 + 1/18*alpha
sage: P = K.primes_above(2)[0] ## line 41 ##
sage: G.inertia_group(P) ## line 42 ##
Subgroup generated by [(1,4,6)(2,5,3)] of (Galois group 6T2 ([3]2) with order 6 of x^6 + 40*x^3 + 1372)
sage: sorted([G.artin_symbol(Q) for Q in K.primes_above(5)])  # random order, see Trac #18308 ## line 44 ##

sage -t --random-seed=50463910914964877037575760797017411618 src/doc/en/thematic_tutorials/group_theory.rst
    Killed due to segmentation fault

sage -t --random-seed=50463910914964877037575760797017411618 src/doc/en/thematic_tutorials/lie/branching_rules.rst
    Killed due to segmentation fault
**********************************************************************
Tests run before process (pid=37552) failed:
sage: b=branching_rule("A3","C2",rule="symmetric"); b ## line 53 ##
symmetric branching rule A3 => C2
sage: A3=WeylCharacterRing("A3",style="coroots") ## line 65 ##


Also the docbuild failed with:
  [sagemath_doc_html-none]   OSError: /cygdrive/d/a/sagetrac-mirror/sagetrac-mirror/src/doc/en/reference/index.rst:34: WARNING: unknown document: categories/index
 

 

tsc...@ucdavis.edu

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May 5, 2022, 9:25:54 PMMay 5
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On Ubuntu with a bunch of optional packages installed, I am getting the following failures due to pynormaliz:

Using --optional=bliss,coxeter3,database_knotinfo,debian,dot2tex,e_antic,fricas,gap_packages,kenzo,libsemigroups,lidia,meataxe,normaliz,pip,pynormaliz,sage,sage_spkg,sirocco,tides
Features to be detected: 4ti2,benzene,bliss,buckygen,conway_polynomials,csdp,database_cremona_ellcurve,database_cremona_mini_ellcurve,database_jones_numfield,database_knotinfo,dvipng,gfan,graphviz,imagemagick,jupymake,kenzo,latte_int,lrslib,mcqd,meataxe,nauty,palp,pandoc,pdf2svg,pdftocairo,plantri,polytopes_db,polytopes_db_4d,pynormaliz,python_igraph,rubiks,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.plot,sage.rings.number_field,sage.rings.padics,sage.rings.real_double,sage.symbolic,sage_numerical_backends_coin,sagemath_doc_html,sphinx,tdlib

sage -t --warn-long 40.4 --random-seed=39360907713219164614940484824980321981 src/sage/geometry/polyhedron/base_QQ.py  # 8 doctests failed
sage -t --warn-long 40.4 --random-seed=39360907713219164614940484824980321981 src/sage/geometry/polyhedron/backend_normaliz.py  # 7 doctests failed

It seems like all failures are due to a change in a permutation group.

Best,
Travis

Matthias Köppe

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May 5, 2022, 9:33:21 PMMay 5
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On Thursday, May 5, 2022 at 6:25:54 PM UTC-7 tsc...@ucdavis.edu wrote:
On Ubuntu with a bunch of optional packages installed, I am getting the following failures due to pynormaliz:

Using --optional=bliss,coxeter3,database_knotinfo,debian,dot2tex,e_antic,fricas,gap_packages,kenzo,libsemigroups,lidia,meataxe,normaliz,pip,pynormaliz,sage,sage_spkg,sirocco,tides
Features to be detected: 4ti2,benzene,bliss,buckygen,conway_polynomials,csdp,database_cremona_ellcurve,database_cremona_mini_ellcurve,database_jones_numfield,database_knotinfo,dvipng,gfan,graphviz,imagemagick,jupymake,kenzo,latte_int,lrslib,mcqd,meataxe,nauty,palp,pandoc,pdf2svg,pdftocairo,plantri,polytopes_db,polytopes_db_4d,pynormaliz,python_igraph,rubiks,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.plot,sage.rings.number_field,sage.rings.padics,sage.rings.real_double,sage.symbolic,sage_numerical_backends_coin,sagemath_doc_html,sphinx,tdlib

sage -t --warn-long 40.4 --random-seed=39360907713219164614940484824980321981 src/sage/geometry/polyhedron/base_QQ.py  # 8 doctests failed
sage -t --warn-long 40.4 --random-seed=39360907713219164614940484824980321981 src/sage/geometry/polyhedron/backend_normaliz.py  # 7 doctests failed

It seems like all failures are due to a change in a permutation group.

I've seen these failures too on one machine. I think some of the doctests introduced in https://trac.sagemath.org/ticket/27637 need to be made more robust.



 

Matthias Köppe

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May 7, 2022, 2:37:18 PMMay 7
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Can we get a release out soon please?


On Saturday, April 30, 2022 at 2:47:14 AM UTC-7 Volker Braun wrote:
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