Your message dated Sun, 25 Dec 2022 01:49:46 +0000
with message-id <e1p9g94-00fi2q...@fasolo.debian.org>
and subject line Bug#1024859: fixed in cctbx 2022.9+ds2+~3.11.2+ds1-5
has caused the Debian Bug report #1024859,
regarding cctbx: (autopkgtest) needs update for python3.11: initialization of
scitbx_linalg_ext raised unreported exception
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1024859: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1024859
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: cctbx
Version: 2022.9+ds2+~3.11.2+ds1-4
Severity: serious
Tags: sid bookworm
User: debian...@lists.debian.org
Usertags: needs-update
User: debian-pyt...@lists.debian.org
Usertags: python3.11
Control: affects -1 src:python3-defaults
Dear maintainer(s),
We are in the transition of adding python3.11 as a supported Python
version [0]. With a recent upload of python3-defaults the autopkgtest of
cctbx fails in testing when that autopkgtest is run with the binary
packages of python3-defaults from unstable. It passes when run with only
packages from testing. In tabular form:
pass fail
python3-defaults from testing 3.10.6-3
cctbx from testing 2022.9+ds2+~3.11.2+ds1-4
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration of python3-defaults
to testing [1]. https://docs.python.org/3/whatsnew/3.11.html lists
what's new in Python3.11, it may help to identify what needs to be updated.
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[0] https://bugs.debian.org/1021984
[1] https://qa.debian.org/excuses.php?package=python3-defaults
https://ci.debian.net/data/autopkgtest/testing/amd64/c/cctbx/28708326/log.gz
Testing cctbx with python3.11:
Discovering pytest tests for smtbx:
refinement/constraints/tests/test_disorder.py: 1
refinement/constraints/tests/test_occupancies.py: 1
refinement/constraints/tests/test_rigid.py: 9
refinement/constraints/tests/test_same_group.py: 2
==================================== ERRORS
====================================
_______ ERROR collecting refinement/constraints/tests/test_direction.py
________
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1206: in _gcd_import
???
<frozen importlib._bootstrap>:1178: in _find_and_load
???
<frozen importlib._bootstrap>:1128: in _find_and_load_unlocked
???
<frozen importlib._bootstrap>:241: in _call_with_frames_removed
???
<frozen importlib._bootstrap>:1206: in _gcd_import
???
<frozen importlib._bootstrap>:1178: in _find_and_load
???
<frozen importlib._bootstrap>:1128: in _find_and_load_unlocked
???
<frozen importlib._bootstrap>:241: in _call_with_frames_removed
???
<frozen importlib._bootstrap>:1206: in _gcd_import
???
<frozen importlib._bootstrap>:1178: in _find_and_load
???
<frozen importlib._bootstrap>:1128: in _find_and_load_unlocked
???
<frozen importlib._bootstrap>:241: in _call_with_frames_removed
???
<frozen importlib._bootstrap>:1206: in _gcd_import
???
<frozen importlib._bootstrap>:1178: in _find_and_load
???
<frozen importlib._bootstrap>:1149: in _find_and_load_unlocked
???
<frozen importlib._bootstrap>:690: in _load_unlocked
???
<frozen importlib._bootstrap_external>:940: in exec_module
???
<frozen importlib._bootstrap>:241: in _call_with_frames_removed
???
/usr/lib/python3/dist-packages/smtbx/refinement/__init__.py:2: in <module>
from cctbx import xray
/usr/lib/python3/dist-packages/cctbx/xray/__init__.py:4: in <module>
from cctbx.xray.scatterer import *
/usr/lib/python3/dist-packages/cctbx/xray/scatterer.py:3: in <module>
import cctbx.eltbx.xray_scattering
/usr/lib/python3/dist-packages/cctbx/eltbx/xray_scattering/__init__.py:2:
in <module>
import scitbx.math.gaussian # base class for gaussian
/usr/lib/python3/dist-packages/scitbx/math/__init__.py:8: in <module>
import scitbx.linalg.eigensystem
/usr/lib/python3/dist-packages/scitbx/linalg/__init__.py:2: in <module>
from scitbx.linalg.ext import *
/usr/lib/python3/dist-packages/scitbx/linalg/ext.py:3: in <module>
bp.import_ext("scitbx_linalg_ext")
/usr/lib/python3/dist-packages/boost_adaptbx/boost/python.py:22: in
import_ext
try: mod = __import__(name)
E SystemError: initialization of scitbx_linalg_ext raised unreported
exception
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: cctbx
Source-Version: 2022.9+ds2+~3.11.2+ds1-5
Done: Stefano Rivera <stefa...@debian.org>
We believe that the bug you reported is fixed in the latest version of
cctbx, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1024...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Stefano Rivera <stefa...@debian.org> (supplier of updated cctbx package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sat, 24 Dec 2022 21:14:52 -0400
Source: cctbx
Architecture: source
Version: 2022.9+ds2+~3.11.2+ds1-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers
<debian-science-maintain...@lists.alioth.debian.org>
Changed-By: Stefano Rivera <stefa...@debian.org>
Closes: 1024859
Changes:
cctbx (2022.9+ds2+~3.11.2+ds1-5) unstable; urgency=medium
.
* Team upload.
.
[ Picca Frédéric-Emmanuel ]
* d/control: added B-D python3-pymol
.
[ Stefano Rivera ]
* Patch: setuptools > 60 support (avoid pip breaking setuptools distutils
magic). (Closes: #1024859)
* Patch: Use the python3 binary when calling pip.
* Depend on python3-h5py in the 2nd autopkgtest.
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