Your message dated Wed, 11 Jan 2023 10:34:31 +0000
with message-id <e1pfyrd-005chf...@fasolo.debian.org>
and subject line Bug#1028449: fixed in changeo 1.3.0-1
has caused the Debian Bug report #1028449,
regarding changeo 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
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1028449: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1028449
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: changeo
Version: 1.2.0-1
Severity: grave
Tags: patch
Justification: renders package unusable
User: ubuntu-de...@lists.ubuntu.com
Usertags: origin-ubuntu lunar ubuntu-patch
Dear maintainers,
changeo 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:
[...]
Traceback (most recent call last):
File "/usr/bin/CreateGermlines.py", line 354, in <module>
createGermlines(**args_dict)
File "/usr/bin/CreateGermlines.py", line 94, in createGermlines
reference_dict = readGermlines(references)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/changeo/IO.py", line 2201, in
readGermlines
with open(file_name, 'rU') as file_handle:
^^^^^^^^^^^^^^^^^^^^^
ValueError: invalid mode: 'rU'
[...]
(https://ci.debian.net/data/autopkgtest/testing/amd64/c/changeo/30225356/log.gz)
I'm assuming this is fairly core functionality in the package so have marked
the bug grave. If it's not, then the autopkgtest regression is still
serious.
I've applied the attached trivial patch in Ubuntu to fix the regression
there.
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 changeo-1.2.0/debian/patches/open-U-obsolete.patch
changeo-1.2.0/debian/patches/open-U-obsolete.patch
--- changeo-1.2.0/debian/patches/open-U-obsolete.patch 1969-12-31
16:00:00.000000000 -0800
+++ changeo-1.2.0/debian/patches/open-U-obsolete.patch 2023-01-10
21:53:30.000000000 -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: 2023-01-10
+Forwarded: no
+
+Index: changeo-1.2.0/changeo/IO.py
+===================================================================
+--- changeo-1.2.0.orig/changeo/IO.py
++++ changeo-1.2.0/changeo/IO.py
+@@ -2198,7 +2198,7 @@
+ repo_dict = {}
+ duplicates = []
+ for file_name in repo_files:
+- with open(file_name, 'rU') as file_handle:
++ with open(file_name, 'r') as file_handle:
+ germlines = SeqIO.parse(file_handle, 'fasta')
+ for g in germlines:
+ germ_key = getAllele(g.description, 'first') if not asis else
g.id
diff -Nru changeo-1.2.0/debian/patches/series
changeo-1.2.0/debian/patches/series
--- changeo-1.2.0/debian/patches/series 1969-12-31 16:00:00.000000000 -0800
+++ changeo-1.2.0/debian/patches/series 2023-01-10 21:52:41.000000000 -0800
@@ -0,0 +1 @@
+open-U-obsolete.patch
--- End Message ---
--- Begin Message ---
Source: changeo
Source-Version: 1.3.0-1
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
changeo, 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.
Andreas Tille <ti...@debian.org> (supplier of updated changeo 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: Wed, 11 Jan 2023 11:01:43 +0100
Source: changeo
Architecture: source
Version: 1.3.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 1028449
Changes:
changeo (1.3.0-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
Closes: #1028449
* Standards-Version: 4.6.2 (routine-update)
* Fix cut-n-pasto in autopkgtest
* Refresh checksums in autopkgtest to match output of new version
Checksums-Sha1:
c7ae2c68e6e796328f48119d36bd722f8af985c7 2315 changeo_1.3.0-1.dsc
ccb0dda221c2d753b0b79a5bd57b53ee86f7c12e 514141
changeo_1.3.0.orig-debian-tests-data.tar.gz
0515fd1ce642820f26adf4c400c911f1222e5a90 151532 changeo_1.3.0.orig.tar.gz
cca614e6b03a970b3f901e4578792bd6b9e9df23 14168 changeo_1.3.0-1.debian.tar.xz
1a3c078f8cd006322477c554d8c9f4de11c43295 6824 changeo_1.3.0-1_amd64.buildinfo
Checksums-Sha256:
846dda30768a36db2152ac29f46c57fdee9fc25e8ef2663c072f848fbe292ed1 2315
changeo_1.3.0-1.dsc
71083354ae0f3bc015f95c1c404fdba4c29f7a934d57b6e206f7c23d01888074 514141
changeo_1.3.0.orig-debian-tests-data.tar.gz
febec2503086b4d76a177d60f9bcb742645d24417750e976409790e9b68288ad 151532
changeo_1.3.0.orig.tar.gz
2023a45ed3667f13913cf3d4a19aee5045d45ab2cfa33da1bb748983ef43fce6 14168
changeo_1.3.0-1.debian.tar.xz
90424e96199d1669a3977d10cf882c6f4233011817ae7d64a60295b9763add9d 6824
changeo_1.3.0-1_amd64.buildinfo
Files:
b1918620d44950d68d2ef20ebbb939e6 2315 science optional changeo_1.3.0-1.dsc
d43661a4b5ba2823f87f98cef12fbe5c 514141 science optional
changeo_1.3.0.orig-debian-tests-data.tar.gz
8d2d964d79803f3dcbbc506a9d0ccca6 151532 science optional
changeo_1.3.0.orig.tar.gz
eb3803fb9efd39f1b488c51aba29bb02 14168 science optional
changeo_1.3.0-1.debian.tar.xz
0cb3abc1566e35559ef089f54a6c3e5a 6824 science optional
changeo_1.3.0-1_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----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=Np22
-----END PGP SIGNATURE-----
--- End Message ---
