Your message dated Tue, 10 Jan 2023 21:35:19 +0000
with message-id <e1pfmh9-002r4j...@fasolo.debian.org>
and subject line Bug#1028354: fixed in apbs 3.4.1-5
has caused the Debian Bug report #1028354,
regarding apbs fails with python3.11: "invalid mode rU"
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.
(NB: If you are a system administrator and have no idea what this
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misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1028354: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1028354
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: apbs
Version: 3.4.1-4
Severity: grave
Tags: patch
Justification: renders package unusable
User: ubuntu-de...@lists.ubuntu.com
Usertags: origin-ubuntu lunar ubuntu-patch
apbs fails its autopkgtests with python3.11, revealing a bug in the
software, because it uses a mode flag to open() which has been deprecated
since python 3 and is now obsolete in python 3.11:
[...]
--------------------------------------------------------------------------------
Testing input file apbs-mol-parallel.in
Splitting the input file into 4 separate files using the inputgen utility
Test failed: invalid mode: 'rU'
Elapsed time: 0.000597 seconds
--------------------------------------------------------------------------------
[...]
(https://autopkgtest.ubuntu.com/results/autopkgtest-lunar/lunar/amd64/a/apbs/20221229_092334_1918a@/log.gz)
This is not an autopkgtest regression in Debian because the autopkgtest
itself is also buggy, using bash-specific shell syntax in a file with no
interpreter line that as a result fails under /bin/sh. (I'm not sure why it
gets farther on Ubuntu's autopkgtest infrastructure.) However, despite not
being detected as an autopkgtest regression, it shows a significant code
defect when run under python3.11 and should be fixed.
Please see the attached patch.
Thanks for considering,
--
Steve Langasek Give me a lever long enough and a Free OS
Debian Developer to set it on, and I can move the world.
Ubuntu Developer https://www.debian.org/
slanga...@ubuntu.com vor...@debian.org
diff -Nru apbs-3.4.1/debian/patches/open-U-obsolete.patch
apbs-3.4.1/debian/patches/open-U-obsolete.patch
--- apbs-3.4.1/debian/patches/open-U-obsolete.patch 1969-12-31
16:00:00.000000000 -0800
+++ apbs-3.4.1/debian/patches/open-U-obsolete.patch 2023-01-09
13:27:36.000000000 -0800
@@ -0,0 +1,21 @@
+Description: Drop obsolete "U" mode passed to open()
+ The "U" mode has been deprecated in python since python3 and has had no
+ effect. In python 3.11, it is now disallowed. Drop this mode flag that
+ causes runtime failures.
+Author: Steve Langasek <steve.langa...@ubuntu.com>
+Last-Update: 2023-01-09
+Forwarded: no
+
+Index: apbs-3.4.1/tools/manip/inputgen.py
+===================================================================
+--- apbs-3.4.1.orig/tools/manip/inputgen.py
++++ apbs-3.4.1/tools/manip/inputgen.py
+@@ -311,7 +311,7 @@
+ file (string)
+ """
+ nproc = 0
+- file = open(filename, "rU")
++ file = open(filename, "r")
+ text = ""
+ while 1:
+ line = file.readline()
diff -Nru apbs-3.4.1/debian/patches/series apbs-3.4.1/debian/patches/series
--- apbs-3.4.1/debian/patches/series 2022-06-04 00:58:09.000000000 -0700
+++ apbs-3.4.1/debian/patches/series 2023-01-09 13:26:06.000000000 -0800
@@ -5,3 +5,4 @@
python3.patch
cmake.patch
docs.patch
+open-U-obsolete.patch
--- End Message ---
--- Begin Message ---
Source: apbs
Source-Version: 3.4.1-5
Done: Michael Banck <mba...@debian.org>
We believe that the bug you reported is fixed in the latest version of
apbs, 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 1028...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Michael Banck <mba...@debian.org> (supplier of updated apbs 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: SHA256
Format: 1.8
Date: Tue, 10 Jan 2023 21:56:38 +0100
Source: apbs
Architecture: source
Version: 3.4.1-5
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org>
Changed-By: Michael Banck <mba...@debian.org>
Closes: 1028354
Changes:
apbs (3.4.1-5) unstable; urgency=medium
.
* Team upload.
* Add patch to drop obsolete "U" mode passed to open(), which causes runtime
errors with python 3.11, by Steve Langasek. Closes: #1028354.
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