Sage 9.5.rc3 released

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Volker Braun

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Jan 18, 2022, 7:05:13 PMJan 18
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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

8ea92d580a (tag: 9.5.rc3, trac/develop) Updated SageMath version to 9.5.rc3
ad7e1731c0 Trac #33200: trying to fix .zenodo.json
809b80c433 Trac #33195: iml: Refresh build scripts with current autotools
290af2b0c4 Trac #33191: tachyon, primecountpy, libhomfly, m4ri: Fix build errors on Apple Silicon with homebrew
8e3116e243 Trac #33081: Segmentation fault with integers using musl libc 1.2.2
33d12f2b66 Trac #32288: add CITATION.cff file for GitHub / zenodo integration and citation support
8a05f2e79d Trac #29285: Unbreak the build when pyenv is present
f9b2db94f6 (tag: 9.5.rc2) Updated SageMath version to 9.5.rc2

Kenji Iohara

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Jan 19, 2022, 5:55:29 PMJan 19
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Thanks Volker for this version.

On my Mac OS 12.1, with IntelCore i5, and with Python 3.10.1,
it compiled from the first built.  

19/01/2022 1:05、Volker Braun <vbrau...@gmail.com>のメール:

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Matthias Köppe

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Jan 20, 2022, 6:44:26 PMJan 20
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On Tuesday, January 18, 2022 at 4:05:13 PM UTC-8 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

8ea92d580a (tag: 9.5.rc3, trac/develop) Updated SageMath version to 9.5.rc3

LGTM
 

G. M.-S.

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Jan 20, 2022, 7:50:29 PMJan 20
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About building on an M1 Mac with macOS 12.1.

1)
After ./configuremake fails to install

* package:         tachyon-0.98.9.p7
* package:         libhomfly-1.02r6
* package:         m4ri-20200115
* package:         openblas-0.3.18

No logs attached (already known).

2)
After ./configure --with-system-openblasmake fails to install

* package:         openblas-0.3.18

* package:         singular-4.2.1p3

Logs attached.

Guillermo

--
config.log
install.log
openblas-0.3.18.log.zip
singular-4.2.1p3.log.zip

Matthias Köppe

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Jan 20, 2022, 8:26:32 PMJan 20
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I thought we had solved the problems on M1 already in https://trac.sagemath.org/ticket/30592?

G. M.-S.

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Jan 20, 2022, 8:44:36 PMJan 20
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I just got access to an M1 Mac with macOS 12.1 (Monterey), so I tried 9.5.rc3 with the results given below.

I can confirm that on an M1 Mac with macOS 11.6.2 (Big Sur), after ./configure --with-system-openblasmake succeeds for 9.5.rc3.

Sorry.

Guillermo

Matthias Köppe

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Jan 20, 2022, 9:51:38 PMJan 20
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Might be worth checking if on this machine there is some stuff in /usr/local ...

G. M.-S.

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Jan 20, 2022, 10:25:01 PMJan 20
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You were right:  I had /usr/local/lib -> /opt/homebrew/lib (because I tried to brew install apaffenholz/polymake/polymake, which fails in Monterey).  After erasing it, ./configure --with-system-openblas followed by make succeeds for 9.5.rc3 on an M1 Mac with macOS 12.1.

Thanks again and sorry for the noise…

Guillermo

Matthias Köppe

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Jan 20, 2022, 10:36:22 PMJan 20
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Thanks for testing! Glad it works now.

G. M.-S.

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Jan 20, 2022, 11:03:10 PMJan 20
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Here are the results of make ptestlong for an M1 Mac with macOS 12.1.

----------------------------------------------------------------------

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/misc/sagedoc.py  # 2 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/tests/cmdline.py  # 4 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/misc/sageinspect.py  # 35 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/graphs/connectivity.pyx  # 2 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/structure/element.pyx  # 43 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/misc/cachefunc.pyx  # 54 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/repl/ipython_extension.py  # 2 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/misc/cython.py  # 20 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/parallel/decorate.py  # 2 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/env.py  # 1 doctest failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/features/__init__.py  # 2 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/graphs/graph_decompositions/fast_digraph.pyx  # 5 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/rings/complex_arb.pyx  # 2 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/misc/superseded.py  # 6 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/cpython/cython_metaclass.pyx  # 4 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/rings/polynomial/ore_polynomial_element.pyx  # 6 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/ext/memory_allocator.pxd  # 6 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/ext/memory_allocator.pyx  # 9 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/structure/factory.pyx  # 8 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/rings/tate_algebra_ideal.pyx  # 6 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/arith/long.pxd  # 14 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/cpython/getattr.pyx  # 4 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/misc/lazy_attribute.pyx  # 3 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/docs/instancedoc.pyx  # 4 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/misc/inherit_comparison.pyx  # 5 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/misc/session.pyx  # 2 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/rings/integer_fake.pxd  # 1 doctest failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/misc/nested_class.pyx  # 6 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/repl/load.py  # 2 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/symbolic/pynac.pxi  # 1 doctest failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/cpython/wrapperdescr.pxd  # 6 doctests failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/cpython/string.pyx  # 1 doctest failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/functions/error.py  # 1 doctest failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/matrix/matrix_gf2e_dense.pyx  # 1 doctest failed

sage -t --long --random-seed=197037298609633803429304901817476325006 src/sage/rings/real_arb.pyx  # 5 doctests failed

----------------------------------------------------------------------

Total time for all tests: 784.5 seconds

    cpu time: 5621.8 seconds

    cumulative wall time: 6022.8 seconds

Features detected for doctesting: dvipng,ffmpeg,graphviz,imagemagick,pandoc,pdf2svg,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.plot,sage.rings.number_field,sage.rings.real_double,sage.symbolic,sagemath_doc_html,sphinx

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

make: *** [ptestlong] Error 1


Guillermo
config_Monterey.log
install_Monterey.log
ptestlong_Monterey.log

G. M.-S.

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Jan 20, 2022, 11:05:44 PMJan 20
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The message
Screenshot 2022-01-21 at 04.53.33.png

appeared a number of times.  I ignored it.

G. M.-S.

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Jan 20, 2022, 11:21:08 PMJan 20
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And here the results of make ptestlong for an M1 Mac with macOS 11.6.2.

----------------------------------------------------------------------

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/misc/sagedoc.py  # 2 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/tests/cmdline.py  # 4 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/misc/sageinspect.py  # 35 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/graphs/connectivity.pyx  # 2 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/misc/cachefunc.pyx  # 54 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/repl/ipython_extension.py  # 2 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/env.py  # 1 doctest failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/misc/cython.py  # 20 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/graphs/graph_decompositions/fast_digraph.pyx  # 5 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/parallel/decorate.py  # 2 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/features/__init__.py  # 2 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/cpython/cython_metaclass.pyx  # 4 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/misc/superseded.py  # 6 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/rings/polynomial/ore_polynomial_element.pyx  # 6 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/rings/tate_algebra_ideal.pyx  # 6 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/misc/lazy_attribute.pyx  # 3 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/rings/complex_arb.pyx  # 2 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/symbolic/pynac.pxi  # 1 doctest failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/misc/inherit_comparison.pyx  # 5 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/structure/factory.pyx  # 8 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/cpython/wrapperdescr.pxd  # 6 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/ext/memory_allocator.pxd  # 6 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/ext/memory_allocator.pyx  # 9 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/misc/session.pyx  # 2 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/cpython/getattr.pyx  # 4 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/arith/long.pxd  # 14 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/misc/nested_class.pyx  # 6 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/repl/load.py  # 2 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/docs/instancedoc.pyx  # 4 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/rings/integer_fake.pxd  # 1 doctest failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/cpython/string.pyx  # 1 doctest failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/functions/error.py  # 1 doctest failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/rings/real_arb.pyx  # 5 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/structure/element.pyx  # 43 doctests failed

sage -t --long --random-seed=96683426040789602717194775641076435201 src/sage/matrix/matrix_gf2e_dense.pyx  # 1 doctest failed

----------------------------------------------------------------------

Total time for all tests: 1221.0 seconds

    cpu time: 7833.2 seconds

    cumulative wall time: 9451.2 seconds

Features detected for doctesting: dvipng,ffmpeg,graphviz,imagemagick,pandoc,pdf2svg,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.plot,sage.rings.number_field,sage.rings.real_double,sage.symbolic,sagemath_doc_html,sphinx

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

make: *** [ptestlong] Error 1


(No messages "Python quit unexpectedly.")

On Fri, 21 Jan 2022 at 05:02, G. M.-S. <list...@gmail.com> wrote:
config_BigSur.log
install_BigSur.log
ptestlong_BigSur.log

Sébastien Labbé

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Jan 21, 2022, 11:20:09 AMJan 21
to sage-release
Thanks Volker for the release. My first try at building with configuration

  $ ./configure --enable-experimental-packages --enable-download-from-upstream-url --enable-ccache --enable-dot2tex --enable-rst2ipynb --enable-openssl --enable-cbc --enable-cryptominisat --enable-pycosat --enable-glucose --enable-sage_numerical_backends_coin --enable-pynormaliz --enable-latte_int --enable-awali --enable-fricas

finishes soon enough with:

[cryptominisat-5.6.8] installing. Log file: /home/slabbe/GitBox/sage/logs/pkgs/cryptominisat-5.6.8.log
  [cryptominisat-5.6.8] error installing, exit status 1. End of log file:
  [cryptominisat-5.6.8]         _Distribution.__init__(
  [cryptominisat-5.6.8]       File "/home/slabbe/GitBox/sage/local/lib/python3.9/distutils/dist.py", line
  [cryptominisat-5.6.8]         self.finalize_options()
  [cryptominisat-5.6.8]       File "/home/slabbe/GitBox/sage/local/lib/python3.9/site-packages/setuptools
  [cryptominisat-5.6.8]         for ep in sorted(loaded, key=by_order):
  [cryptominisat-5.6.8]       File "/home/slabbe/GitBox/sage/local/lib/python3.9/site-packages/setuptools
  [cryptominisat-5.6.8]         loaded = map(lambda e: e.load(), filtered)
  [cryptominisat-5.6.8]       File "/home/slabbe/GitBox/sage/local/lib/python3.9/site-packages/pkg_resour
  [cryptominisat-5.6.8]         self.require(*args, **kwargs)
  [cryptominisat-5.6.8]       File "/home/slabbe/GitBox/sage/local/lib/python3.9/site-packages/pkg_resour
  [cryptominisat-5.6.8]         items = working_set.resolve(reqs, env, installer, extras=self.extras)
  [cryptominisat-5.6.8]       File "/home/slabbe/GitBox/sage/local/lib/python3.9/site-packages/pkg_resour
  [cryptominisat-5.6.8]         raise DistributionNotFound(req, requirers)
  [cryptominisat-5.6.8]     pkg_resources.DistributionNotFound: The 'packaging>=20.0' distribution was no
  [cryptominisat-5.6.8]     Preparing metadata (setup.py): finished with status 'error'
  [cryptominisat-5.6.8]   WARNING: Discarding file:///home/slabbe/GitBox/sage/local/var/tmp/sage/build/cr
the logs for full command output.
  [cryptominisat-5.6.8]   ERROR: Command errored out with exit status 1: python setup.py egg_info Check t
  [cryptominisat-5.6.8]   *******************************************************************************
  [cryptominisat-5.6.8]   Error building a wheel for cryptominisat-5.6.8
  [cryptominisat-5.6.8]   *******************************************************************************
  [cryptominisat-5.6.8]
  [cryptominisat-5.6.8]   real  0m8.220s
  [cryptominisat-5.6.8]   user  0m6.452s
  [cryptominisat-5.6.8]   sys   0m1.650s
  [cryptominisat-5.6.8]   ************************************************************************
  [cryptominisat-5.6.8]   Error installing package cryptominisat-5.6.8
  [cryptominisat-5.6.8]   ************************************************************************
  [cryptominisat-5.6.8] Full log file: /home/slabbe/GitBox/sage/logs/pkgs/cryptominisat-5.6.8.log


The relevent part of  logs/pkgs/cryptominisat-5.6.8.log is copied below




Installing cryptominisat-5.6.8
Processing /home/slabbe/GitBox/sage/local/var/tmp/sage/build/cryptominisat-5.6.8/src/pycryptosat
  Preparing metadata (setup.py): started
  Running command python setup.py egg_info
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "/home/slabbe/GitBox/sage/local/var/tmp/sage/build/cryptominisat-5.6.8/src/pycryptosat/setup.py", line 134, in <module>
      setup(
    File "/home/slabbe/GitBox/sage/local/lib/python3.9/distutils/core.py", line 108, in setup
      _setup_distribution = dist = klass(attrs)
    File "/home/slabbe/GitBox/sage/local/lib/python3.9/site-packages/setuptools/dist.py", line 453, in __init__
      _Distribution.__init__(
    File "/home/slabbe/GitBox/sage/local/lib/python3.9/distutils/dist.py", line 292, in __init__
      self.finalize_options()
    File "/home/slabbe/GitBox/sage/local/lib/python3.9/site-packages/setuptools/dist.py", line 830, in finalize_options
      for ep in sorted(loaded, key=by_order):
    File "/home/slabbe/GitBox/sage/local/lib/python3.9/site-packages/setuptools/dist.py", line 829, in <lambda>
      loaded = map(lambda e: e.load(), filtered)
    File "/home/slabbe/GitBox/sage/local/lib/python3.9/site-packages/pkg_resources/__init__.py", line 2463, in load
      self.require(*args, **kwargs)
    File "/home/slabbe/GitBox/sage/local/lib/python3.9/site-packages/pkg_resources/__init__.py", line 2486, in require
      items = working_set.resolve(reqs, env, installer, extras=self.extras)
    File "/home/slabbe/GitBox/sage/local/lib/python3.9/site-packages/pkg_resources/__init__.py", line 777, in resolve
      raise DistributionNotFound(req, requirers)
  pkg_resources.DistributionNotFound: The 'packaging>=20.0' distribution was not found and is required by the application
  Preparing metadata (setup.py): finished with status 'error'
WARNING: Discarding file:///home/slabbe/GitBox/sage/local/var/tmp/sage/build/cryptominisat-5.6.8/src/pycryptosat. Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
********************************************************************************
Error building a wheel for cryptominisat-5.6.8
********************************************************************************

Sébastien Labbé

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Jan 21, 2022, 11:47:54 AMJan 21
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Dear Volker,
I have a question for you. As I understood the past years, I was feeling the following principles about which tickets are getting merged into sage:
- in beta and in rc0: any ticket with positive review since at least one or two days and since the last 2-3 weeks.
- in early release candidates like rc1, rc2 : any ticket of type "defect" (so no new features added, only trying to fix bugs important or not important)
- in late release candidates like rc3, rc4, rc5, etc. : only critical tickets solving important bugs and allowing to make sure sagemath still work on every supported platform

This time for the 9.5 cycle, I have the feeling that the early release candidates was short if not existent, leaving a bunch of positive reviewed ticket fixing bugs (important or not), but still making the 9.5 version not as optimal as it could be.

For reference, here is a list of remaining tickets for milestone 9.5 including more than a dozen of positive reviewed tickets fixing a defect which did not made it yet into 9.5:

Please don't interpret this badly as I respect very much the time you put on merging everything and on the release management. And I want you to be happy to continue your very good work on this important part of the development of sage. But I would be curious to have your vision on my interpretation of these "three phases".

Sincerely,

Sébastien Labbé

Matthias Köppe

unread,
Jan 21, 2022, 1:48:41 PMJan 21
to sage-release
Thanks for testing. Looking at ptestlong_Monterey.log, I see:

1) failures from run-time use of compilers like this:   
  RuntimeError: Command "gcc -bundle -undefined dynamic_lookup -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -L/Users/admin/SageMath/Git/sage/local/lib -Wl,-rpath,/Users/admin/SageMath/Git/sage/local/lib /Users/admin/.sage/temp/MBP16GMS/16939/spyx/_Users_admin__sage_temp_MBP16GMS_16939_tmp_6gfq9l9q_pyx/build/temp.macosx-12-arm64-3.9/Users/admin/.sage/temp/MBP16GMS/16939/spyx/_Users_admin__sage_temp_MBP16GMS_16939_tmp_6gfq9l9q_pyx/_Users_admin__sage_temp_MBP16GMS_16939_tmp_6gfq9l9q_pyx_0.o -L/Users/admin/SageMath/Git/sage/local/lib -L/opt/homebrew/Cellar/openblas/0.3.19/lib -L///opt/homebrew/opt/ntl/lib -lmpfr -lgmp -lgmpxx -lpari -lm -lec -lgsl -lopenblas -lntl -o /Users/admin/.sage/temp/MBP16GMS/16939/spyx/_Users_admin__sage_temp_MBP16GMS_16939_tmp_6gfq9l9q_pyx/_Users_admin__sage_temp_MBP16GMS_16939_tmp_6gfq9l9q_pyx_0.cpython-39-darwin.so" failed with exit status 1
    ld: library not found for -lmpfr

This is tracked in https://trac.sagemath.org/ticket/31348 and can likely be worked around by using ". .homebrew-build-env " before running the tests.

2) some numerical tolerances, including

sage -t --long --random-seed=56125665350235692256846696198278705067 src/sage/functions/error.py
**********************************************************************
File "src/sage/functions/error.py", line 270, in sage.functions.error.Function_erf._evalf_
Failed example:
    RealBallField(128)(erf(5))
Expected:
    [0.99999999999846254020557196514981165651 +/- 7.33e-39]
Got:
    [0.99999999999846254020557196514981165651 +/- 6.25e-39]
**********************************************************************

Samuel Lelièvre

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Jan 21, 2022, 2:43:00 PMJan 21
to sage-release
2022-01-21 16:20 UTC, Sébastien Labbé:
>
> Thanks Volker for the release. My first try at building with configuration.
>
> The relevant part of logs/pkgs/cryptominisat-5.6.8.log is copied below.

Might be solved by:

- Sage Trac ticket #33183:
Better fix installation of cryptominisat and pycryptosat
https://trac.sagemath.org/ticket/33183

G. M.-S.

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Jan 21, 2022, 2:43:57 PMJan 21
to sage-r...@googlegroups.com

Thanks Matthias.

I was sure I had done it, but once again, you are right.  After source .homebrew-build-envmake ptestlong gives on an M1 Mac with macOS 12.1 only the following:

----------------------------------------------------------------------

sage -t --long --random-seed=123615508850610353335041616442807883363 src/sage/rings/complex_arb.pyx  # 2 doctests failed

sage -t --long --random-seed=123615508850610353335041616442807883363 src/sage/functions/error.py  # 1 doctest failed

sage -t --long --random-seed=123615508850610353335041616442807883363 src/sage/matrix/matrix_gf2e_dense.pyx  # 1 doctest failed

sage -t --long --random-seed=123615508850610353335041616442807883363 src/sage/rings/real_arb.pyx  # 5 doctests failed

----------------------------------------------------------------------

Total time for all tests: 793.9 seconds

    cpu time: 5622.8 seconds

    cumulative wall time: 6043.3 seconds

Features detected for doctesting: dvipng,ffmpeg,graphviz,imagemagick,pandoc,pdf2svg,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.plot,sage.rings.number_field,sage.rings.real_double,sage.symbolic,sagemath_doc_html,sphinx

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

make: *** [ptestlong] Error 1


All of them come as you say from numerical tolerances, except perhaps this one?

**********************************************************************

File "src/sage/matrix/matrix_gf2e_dense.pyx", line 524, in sage.matrix.matrix_gf2e_dense.Matrix_gf2e_dense._multiply_karatsuba

Failed example:

    A._multiply_karatsuba(B) == A._multiply_classical(B)

Expected:

    True

Got:

    False

**********************************************************************


Guillermo
ptestlong.log

Matthias Köppe

unread,
Jan 21, 2022, 2:46:22 PMJan 21
to sage-release
The failure in src/sage/matrix/matrix_gf2e_dense.pyx probably deserves a ticket for further investigation

G. M.-S.

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Jan 21, 2022, 3:21:43 PMJan 21
to sage-r...@googlegroups.com

Done.

G. M.-S.

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Jan 21, 2022, 4:07:32 PMJan 21
to sage-r...@googlegroups.com

Update:  After source .homebrew-build-envmake ptestlong gives on an M1 Mac with macOS 11.6.2 only the following:

----------------------------------------------------------------------

sage -t --long --random-seed=86576699284060881752818494907984839405 src/sage/rings/complex_arb.pyx  # 2 doctests failed

sage -t --long --random-seed=86576699284060881752818494907984839405 src/sage/functions/error.py  # 1 doctest failed

sage -t --long --random-seed=86576699284060881752818494907984839405 src/sage/matrix/matrix_gf2e_dense.pyx  # 1 doctest failed

sage -t --long --random-seed=86576699284060881752818494907984839405 src/sage/rings/real_arb.pyx  # 5 doctests failed

----------------------------------------------------------------------

Total time for all tests: 1205.9 seconds

    cpu time: 7828.7 seconds

    cumulative wall time: 9285.1 seconds

Features detected for doctesting: dvipng,ffmpeg,graphviz,imagemagick,pandoc,pdf2svg,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.plot,sage.rings.number_field,sage.rings.real_double,sage.symbolic,sagemath_doc_html,sphinx

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

make: *** [ptestlong] Error 1


All of them come from numerical tolerances, except this one:

**********************************************************************

File "src/sage/matrix/matrix_gf2e_dense.pyx", line 524, in sage.matrix.matrix_gf2e_dense.Matrix_gf2e_dense._multiply_karatsuba

Failed example:

    A._multiply_karatsuba(B) == A._multiply_classical(B)

Expected:

    True

Got:

    False

**********************************************************************

Matthias Köppe

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Jan 21, 2022, 6:14:07 PMJan 21
to sage-release
Thanks for opening the ticket https://trac.sagemath.org/ticket/33212 for this failure

Samuel Lelièvre

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Jan 22, 2022, 8:05:04 AMJan 22
to sage-release
2022-01-19 00:05 UTC, Volker Braun on sage-release:
>
> 8ea92d580a (tag: 9.5.rc3, trac/develop) Updated SageMath version to 9.5.rc3

Thanks Volker!

On Cygwin: failed to build sagemath_doc_html.

On Debian: failed to build sagemath_doc_html.
See the ticket 0 patchbot report for pascaline at
https://patchbot.sagemath.org/ticket/0/

Volker Braun

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Jan 22, 2022, 12:57:03 PMJan 22
to sage-release
On Friday, January 21, 2022 at 5:47:54 PM UTC+1 Sébastien Labbé wrote:
I have a question for you. As I understood the past years, I was feeling the following principles about which tickets are getting merged into sage:
- in beta and in rc0: any ticket with positive review since at least one or two days and since the last 2-3 weeks.

Frankly, the quality of positively reviewed tickets has taken a nosedive recently. Its a regular occurrence now that positively reviewed tickets do not build and / or do not pass tests. If you want speedy merges then you can't use me as a CI and throw untested crap at me to see if it works.

I'm actively looking at ways to improve this, and the solution will be either social (certain authors/reviewers will automatically be at the end of the queue) or automatic ticket rejections (which have a pretty high chance of false negatives, in particular since incremental builds are currently flakey).
 
- in early release candidates like rc1, rc2 : any ticket of type "defect" (so no new features added, only trying to fix bugs important or not important)
- in late release candidates like rc3, rc4, rc5, etc. : only critical tickets solving important bugs and allowing to make sure sagemath still work on every supported platform

I don't think we should have two different phases; Its usually pretty clear when we are close to the end of the release cycle (and I do announce it on sage-devel). Of course if anyone wants to volunteer to release a "Sage-LTS" (long term support) with more bugfixes I certainly wont' be in your way.


Matthias Köppe

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Jan 22, 2022, 1:08:43 PMJan 22
to sage-release
On Saturday, January 22, 2022 at 9:57:03 AM UTC-8 Volker Braun wrote:
I don't think we should have two different phases; Its usually pretty clear when we are close to the end of the release cycle (and I do announce it on sage-devel). 

Volker, your only message regarding release management of the 9.5 cycle was in the 9.5.beta8 announcement: 
"We should probably make a release some time soon... if you have anything that you want to get into 9.5 then get it polished now ;)" (https://groups.google.com/g/sage-release/c/vo_m79EHAVc/m/mMlNPz5sBAAJ)

You forgot to explain to developers that you do not merge anything that is not marked as a "blocker".


 

Matthias Köppe

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Jan 22, 2022, 1:55:03 PMJan 22
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On Saturday, January 22, 2022 at 9:57:03 AM UTC-8 Volker Braun wrote:
I'm actively looking at ways to improve this, and the solution will be [...] automatic ticket rejections

Wait... are you telling us that the process that is setting tickets back from "positive review" to "needs work" with 0 details is _not_ a script currently?


Volker Braun

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Jan 22, 2022, 6:55:25 PMJan 22
to sage-release
No, I'm not running a private CI service for the Sage project. I'm relying on you all to only positively review tickets that actually work. 

In the rare cases where somebody is inexperienced or there is some unexpected interaction between tickets I typically lend a hand and provide some hints on the ticket. But for those that should know better I'm not doing that any more since I feel like that gives the wrong incentive (= instead of testing it myself I'll just let Volker run the tests and then report back any errors)

Dima Pasechnik

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Jan 22, 2022, 7:33:36 PMJan 22
to sage-release
On Sat, Jan 22, 2022 at 11:55 PM Volker Braun <vbrau...@gmail.com> wrote:
>
> No, I'm not running a private CI service for the Sage project. I'm relying on you all to only positively review tickets that actually work.
>
> In the rare cases where somebody is inexperienced or there is some unexpected interaction between tickets I typically lend a hand and provide some hints on the ticket. But for those that should know better I'm not doing that any more since I feel like that gives the wrong incentive (= instead of testing it myself I'll just let Volker run the tests and then report back any errors)

That's fair enough, but you could have mentioned this as a part of
your workflow earlier.

On the other hand, it's not unusual (at least with tickets related to
the build system) that you present
us with a hard puzzle to crack - and sometimes it's you assuming that
you can just update a build,
rather than build from scratch. Perhaps such tickets deserve a special
flag/keyword/tag.

Dima


>
> On Saturday, January 22, 2022 at 7:55:03 PM UTC+1 matthia...@gmail.com wrote:
>>
>> On Saturday, January 22, 2022 at 9:57:03 AM UTC-8 Volker Braun wrote:
>>>
>>> I'm actively looking at ways to improve this, and the solution will be [...] automatic ticket rejections
>>
>>
>> Wait... are you telling us that the process that is setting tickets back from "positive review" to "needs work" with 0 details is _not_ a script currently?
>>
>>
> --
> You received this message because you are subscribed to the Google Groups "sage-release" group.
> 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/1004b687-e8af-4fa6-b9fa-f5d49e7b9e7en%40googlegroups.com.

Matthias Köppe

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Jan 22, 2022, 8:04:02 PMJan 22
to sage-release
I'd say replacing this with a mild-mannered script that does the said "automatic ticket rejections" would be an improvement for the project.
Key ingredients:
- Respect the ticket milestone.
- Post the build logs when it fails.
If you need help implementing this script, let me know.

Volker Braun

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Jan 23, 2022, 6:19:21 AMJan 23
to sage-release
On Sunday, January 23, 2022 at 2:04:02 AM UTC+1 matthia...@gmail.com wrote:
I'd say replacing this with a mild-mannered script that does the said "automatic ticket rejections" would be an improvement for the project.

I'm sorry, but which part of "not running a private CI service for the Sage project" is unclear to you?

We definitely should have better CI, but I can't provide that in addition to the integration work that happens after tickets pass their tests (i.e. after they should have been set to positive review). 

Matthias Köppe

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Jan 23, 2022, 12:28:02 PMJan 23
to sage-release
Thanks for the clarification. I was only referring to the 2nd of the two solutions that you brought up in your previous message. 
"I'm actively looking at ways to improve this, and the solution will be either social (certain authors/reviewers will automatically be at the end of the queue) or automatic ticket rejections (which have a pretty high chance of false negatives, in particular since incremental builds are currently flakey)."

Samuel Lelievre

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Jan 23, 2022, 12:57:38 PMJan 23
to sage-release
2022-01-22 13:05:04 UTC, Samuel Lelievre on sage-release:

On Cygwin: failed to build sagemath_doc_html.

On Debian: failed to build sagemath_doc_html.
See the ticket 0 patchbot report for pascaline at
https://patchbot.sagemath.org/ticket/0/

On Debian (but not on Cygwin), running `make distclean`
and then `make` again allowed `sagemath_doc_html`
to build and the whole build to complete.

Tests then timed out in two files:

- `src/sage/features/interfaces.py`
- `src/sage/coding/linear_code.py`

and failed in one file

- `src/sage/game_theory/parser.py`

The test failures in that file are due to lrslib doctests,
fixed in #33101 which already has positive review.
Not sure about the timeouts, maybe they also have
to do with feature detection.

See the second pascaline report at


(for as long as that page is about Sage 9.5.rc3 ---
not sure how to refer to that report longer term).

Samuel Lelievre

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Jan 23, 2022, 6:27:11 PMJan 23
to sage-release
2022-01-19 00:05:13 UTC, Volker Braun on sage-release:

>
> 8ea92d580a (tag: 9.5.rc3, trac/develop) Updated SageMath version to 9.5.rc3

On Ubuntu 21.10, the build succeeded but 5 doctests
failed in `src/sage/modules/free_module_integer.py`.

I don't know whether that failure is already tracked.
Can anybody point to an existing ticket? Otherwise
I can open one.  Details below.   --Samuel

-----

Failure summary:
```
$ make -s V=0 testlong
...
----------------------------------------------------------------------
sage -t --long --warn-long 127.1 --random-seed=243861417107614574365038834487998971463 src/sage/modules/free_module_integer.py  # 5 doctests failed
----------------------------------------------------------------------
Total time for all tests: 11153.8 seconds
    cpu time: 9705.7 seconds
    cumulative wall time: 10720.0 seconds
Features detected for doctesting: 4ti2,dvipng,ffmpeg,graphviz,imagemagick,lrslib,pandoc,pdf2svg,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.plot,sage.rings.number_field,sage.rings.real_double,sage.symbolic,sagemath_doc_html,sphinx

Pytest is not installed, skip checking tests that rely on it.
make: *** [Makefile:242: testlong] Error 1
```

The failure persists when testing that file again.

```
$ SEED=243861417107614574365038834487998971463
$ alias sagetest="./sage -t --long --warn-long 128 --random-seed=$SEED"
$ sagetest src/sage/modules/free_module_integer.py  # 5 doctests failed
Running doctests with ID 2022-01-23-22-42-46-e3b619c7.
Git branch: develop
Using --optional=build,debian,pip,sage,sage_spkg
Features to be detected: 4ti2,benzene,bliss,buckygen,conway_polynomials,csdp,database_cremona_ellcurve,database_cremona_mini_ellcurve,database_jones_numfield,database_knotinfo,dvipng,ffmpeg,graphviz,imagemagick,jupymake,kenzo,latte_int,lrslib,mcqd,meataxe,pandoc,pdf2svg,plantri,pynormaliz,rubiks,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.plot,sage.rings.number_field,sage.rings.real_double,sage.symbolic,sage_numerical_backends_coin,sagemath_doc_html,sphinx,tdlib
Doctesting 1 file.
sage -t --long --warn-long 128.0 --random-seed=243861417107614574365038834487998971463 src/sage/modules/free_module_integer.py
**********************************************************************
File "src/sage/modules/free_module_integer.py", line 213, in sage.modules.free_module_integer.FreeModule_submodule_with_basis_integer
Failed example:
    L.shortest_vector()
Exception raised:

    Traceback (most recent call last):
      File "sage/misc/cachefunc.pyx", line 1943, in sage.misc.cachefunc.CachedMethodCaller.__call__ (build/cythonized/sage/misc/cachefunc.c:10347)
        return cache[k]
    KeyError: ((True, 'fplll'), ())

    During handling of the above exception, another exception occurred:


    Traceback (most recent call last):
      File "/opt/s/sage-9-5-c3-fresh-clone/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/doctest/forker.py", line 694, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/opt/s/sage-9-5-c3-fresh-clone/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/doctest/forker.py", line 1088, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.modules.free_module_integer.FreeModule_submodule_with_basis_integer[2]>", line 1, in <module>
        L.shortest_vector()
      File "sage/misc/cachefunc.pyx", line 1948, in sage.misc.cachefunc.CachedMethodCaller.__call__ (build/cythonized/sage/misc/cachefunc.c:10483)
        w = self._instance_call(*args, **kwds)
      File "sage/misc/cachefunc.pyx", line 1824, in sage.misc.cachefunc.CachedMethodCaller._instance_call (build/cythonized/sage/misc/cachefunc.c:9949)
        return self.f(self._instance, *args, **kwds)
      File "/opt/s/sage-9-5-c3-fresh-clone/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/modules/free_module_integer.py", line 591, in shortest_vector
        w = vector(ZZ, SVP.shortest_vector(L, *args, **kwds))
      File "src/fpylll/fplll/svpcvp.pyx", line 77, in fpylll.fplll.svpcvp.shortest_vector
      File "src/fpylll/fplll/bkz_param.pyx", line 269, in fpylll.fplll.bkz_param.load_strategies_json
    RuntimeError: Aborted
**********************************************************************
File "src/sage/modules/free_module_integer.py", line 563, in sage.modules.free_module_integer.FreeModule_submodule_with_basis_integer.shortest_vector
Failed example:
    L.shortest_vector().norm().n()
Exception raised:

    Traceback (most recent call last):
      File "sage/misc/cachefunc.pyx", line 1943, in sage.misc.cachefunc.CachedMethodCaller.__call__ (build/cythonized/sage/misc/cachefunc.c:10347)
        return cache[k]
    KeyError: ((True, 'fplll'), ())

    During handling of the above exception, another exception occurred:


    Traceback (most recent call last):
      File "/opt/s/sage-9-5-c3-fresh-clone/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/doctest/forker.py", line 694, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/opt/s/sage-9-5-c3-fresh-clone/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/doctest/forker.py", line 1088, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.modules.free_module_integer.FreeModule_submodule_with_basis_integer.shortest_vector[4]>", line 1, in <module>
        L.shortest_vector().norm().n()
      File "sage/misc/cachefunc.pyx", line 1948, in sage.misc.cachefunc.CachedMethodCaller.__call__ (build/cythonized/sage/misc/cachefunc.c:10483)
        w = self._instance_call(*args, **kwds)
      File "sage/misc/cachefunc.pyx", line 1824, in sage.misc.cachefunc.CachedMethodCaller._instance_call (build/cythonized/sage/misc/cachefunc.c:9949)
        return self.f(self._instance, *args, **kwds)
      File "/opt/s/sage-9-5-c3-fresh-clone/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/modules/free_module_integer.py", line 591, in shortest_vector
        w = vector(ZZ, SVP.shortest_vector(L, *args, **kwds))
      File "src/fpylll/fplll/svpcvp.pyx", line 77, in fpylll.fplll.svpcvp.shortest_vector
      File "src/fpylll/fplll/bkz_param.pyx", line 269, in fpylll.fplll.bkz_param.load_strategies_json
    RuntimeError: Aborted
**********************************************************************
File "src/sage/modules/free_module_integer.py", line 618, in sage.modules.free_module_integer.FreeModule_submodule_with_basis_integer.update_reduced_basis
Failed example:
    v = L.shortest_vector(update_reduced_basis=False)
Exception raised:

    Traceback (most recent call last):
      File "sage/misc/cachefunc.pyx", line 1943, in sage.misc.cachefunc.CachedMethodCaller.__call__ (build/cythonized/sage/misc/cachefunc.c:10347)
        return cache[k]
    KeyError: ((False, 'fplll'), ())

    During handling of the above exception, another exception occurred:


    Traceback (most recent call last):
      File "/opt/s/sage-9-5-c3-fresh-clone/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/doctest/forker.py", line 694, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/opt/s/sage-9-5-c3-fresh-clone/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/doctest/forker.py", line 1088, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.modules.free_module_integer.FreeModule_submodule_with_basis_integer.update_reduced_basis[4]>", line 1, in <module>
        v = L.shortest_vector(update_reduced_basis=False)
      File "sage/misc/cachefunc.pyx", line 1948, in sage.misc.cachefunc.CachedMethodCaller.__call__ (build/cythonized/sage/misc/cachefunc.c:10483)
        w = self._instance_call(*args, **kwds)
      File "sage/misc/cachefunc.pyx", line 1824, in sage.misc.cachefunc.CachedMethodCaller._instance_call (build/cythonized/sage/misc/cachefunc.c:9949)
        return self.f(self._instance, *args, **kwds)
      File "/opt/s/sage-9-5-c3-fresh-clone/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/modules/free_module_integer.py", line 591, in shortest_vector
        w = vector(ZZ, SVP.shortest_vector(L, *args, **kwds))
      File "src/fpylll/fplll/svpcvp.pyx", line 77, in fpylll.fplll.svpcvp.shortest_vector
      File "src/fpylll/fplll/bkz_param.pyx", line 269, in fpylll.fplll.bkz_param.load_strategies_json
    RuntimeError: Aborted
**********************************************************************
File "src/sage/modules/free_module_integer.py", line 619, in sage.modules.free_module_integer.FreeModule_submodule_with_basis_integer.update_reduced_basis
Failed example:
    L.update_reduced_basis(v)
Exception raised:

    Traceback (most recent call last):
      File "/opt/s/sage-9-5-c3-fresh-clone/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/doctest/forker.py", line 694, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/opt/s/sage-9-5-c3-fresh-clone/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/doctest/forker.py", line 1088, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.modules.free_module_integer.FreeModule_submodule_with_basis_integer.update_reduced_basis[5]>", line 1, in <module>
        L.update_reduced_basis(v)
    NameError: name 'v' is not defined
**********************************************************************
File "src/sage/modules/free_module_integer.py", line 620, in sage.modules.free_module_integer.FreeModule_submodule_with_basis_integer.update_reduced_basis
Failed example:
    bool(L.reduced_basis[0].norm() < B[0].norm())

Expected:
    True
Got:
    False
**********************************************************************
3 items had failures:
   1 of   4 in sage.modules.free_module_integer.FreeModule_submodule_with_basis_integer
   1 of  11 in sage.modules.free_module_integer.FreeModule_submodule_with_basis_integer.shortest_vector
   3 of   8 in sage.modules.free_module_integer.FreeModule_submodule_with_basis_integer.update_reduced_basis
    [109 tests, 5 failures, 18.48 s]
----------------------------------------------------------------------
sage -t --long --warn-long 128.0 --random-seed=243861417107614574365038834487998971463 src/sage/modules/free_module_integer.py  # 5 doctests failed
----------------------------------------------------------------------
Total time for all tests: 18.6 seconds
    cpu time: 18.5 seconds
    cumulative wall time: 18.5 seconds
Features detected for doctesting:
Pytest is not installed, skip checking tests that rely on it.
$
```

Matthias Köppe

unread,
Jan 23, 2022, 6:58:35 PMJan 23
to sage-release
Made one for you, first for the case of merge conflicts: https://github.com/sagemath/git-trac-command/pull/57

Samuel Lelievre

unread,
Jan 30, 2022, 8:25:56 AMJan 30
to sage-release
Fixing links in my previous post, thanks Frédéric's tip at

2022-01-23 à 17:57:38 UTC, Samuel Lelièvre a écrit :
2022-01-22 13:05:04 UTC, Samuel Lelièvre on sage-release:

On Cygwin: failed to build sagemath_doc_html.

On Debian: failed to build sagemath_doc_html.
See the ticket 0 patchbot report for pascaline at
https://patchbot.sagemath.org/ticket/0/

 That's the earlier of two pascaline reports at

 
On Debian (but not on Cygwin), running `make distclean`
and then `make` again allowed `sagemath_doc_html`
to build and the whole build to complete.

Tests then timed out in two files:

- `src/sage/features/interfaces.py`
- `src/sage/coding/linear_code.py`

and failed in one file

- `src/sage/game_theory/parser.py`

The test failures in that file are due to lrslib doctests,
fixed in #33101 which already has positive review.
Not sure about the timeouts, maybe they also have
to do with feature detection.

See the second pascaline report at

That's the latest of two pascaline reports at


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