Your message dated Fri, 02 Dec 2022 12:06:58 +0000
with message-id <[email protected]>
and subject line Bug#1025116: fixed in python-pybedtools 0.9.0-3
has caused the Debian Bug report #1025116,
regarding python-pybedtools: (autopkgtest) needs update for python3.11: No
module named 'pysam.libchtslib'
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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--
1025116: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1025116
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: python-pybedtools
Version: 0.9.0-2
Severity: serious
Tags: sid bookworm
User: [email protected]
Usertags: needs-update
User: [email protected]
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
python-pybedtools 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
python-pybedtools from testing 0.9.0-2
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/p/python-pybedtools/28750381/log.gz
Testing with python3.11:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/lib/python3/dist-packages/pybedtools/__init__.py", line
16, in <module>
from . import contrib
File "/usr/lib/python3/dist-packages/pybedtools/contrib/__init__.py",
line 3, in <module>
from . import venn_maker
File
"/usr/lib/python3/dist-packages/pybedtools/contrib/venn_maker.py", line
11, in <module>
from pybedtools import helpers
File "/usr/lib/python3/dist-packages/pybedtools/helpers.py", line 12,
in <module>
import pysam
File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 5, in
<module>
from pysam.libchtslib import *
ModuleNotFoundError: No module named 'pysam.libchtslib'
autopkgtest [23:15:21]: test autodep8-python3
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: python-pybedtools
Source-Version: 0.9.0-3
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
python-pybedtools, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <[email protected]> (supplier of updated python-pybedtools
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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Fri, 02 Dec 2022 12:19:36 +0100
Source: python-pybedtools
Architecture: source
Version: 0.9.0-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1025116
Changes:
python-pybedtools (0.9.0-3) unstable; urgency=medium
.
* Team Upload.
* d/watch: repair watch file from github changes.
* d/control: stick to python3.10. (Closes: #1025116)
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python-pybedtools_0.9.0-3.dsc
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