Your message dated Wed, 09 Sep 2026 12:19:23 +0000
with message-id <[email protected]>
and subject line Bug#1146889: fixed in python-skbio 0.7.3-2
has caused the Debian Bug report #1146889,
regarding python-skbio: FTBFS against python 3.15rc2
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 [email protected]
immediately.)
--
1146889: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1146889
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:python-skbio
Version: 0.7.3-1
User: [email protected]
Usertags: python3.15
Tags: patch, ftbfs, forky, sid
Severity: important
Hi!
While rebuilding the python related packages against the Python 3.15rc2
version we found that python-skbio fails to build from source [1].
The error is:
super(CompressedMixin, self).__init__(*args, **kwargs)
E io.UnsupportedOperation: File or stream is not readable.
It seems that its open in write only instead of read only as the test
expects, I've created a patch that sets the explicit mode and solves the
problem.
I applied the fix in the sandbox [2] to be able to build the packages
that depend on python-skbio, please consider applying the patch to
support the upcoming 3.15 version.
Setting the severity to important for now. Once Python 3.15 is released,
it will be added to python3-defaults and this bug will become release
critical.
Happy hacking,
[1]: https://debusine.debian.net/debian/r-python-python3.15/artifact/4462291/
[2]: https://debusine.debian.net/debian/r-python-python3.15/
--
"Can you imagine what I would do if I could do all I can?" -- Sun Tzu
Saludos /\/\ /\ >< `/
Description: Explicitly specify mode="rb" in GzipCompressor.get_reader
GzipFile without explicit mode defaults to fileobj.mode (e.g. 'w+b' for
temporary files), causing it to open for writing instead of reading.
Forwarded: not-needed
--- a/skbio/io/_iosources.py
+++ b/skbio/io/_iosources.py
@@ -215,7 +215,7 @@ class GzipCompressor(Compressor):
return self.file.peek(2)[:2] == b"\x1f\x8b"
def get_reader(self):
- return gzip.GzipFile(fileobj=self.file)
+ return gzip.GzipFile(fileobj=self.file, mode="rb")
def get_writer(self):
return gzip.GzipFile(
--- End Message ---
--- Begin Message ---
Source: python-skbio
Source-Version: 0.7.3-2
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
python-skbio, 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.
Andreas Tille <[email protected]> (supplier of updated python-skbio 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: Wed, 09 Sep 2026 13:52:58 +0200
Source: python-skbio
Architecture: source
Version: 0.7.3-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1146889
Changes:
python-skbio (0.7.3-2) unstable; urgency=medium
.
[ Maximiliano Curia ]
* Explicitly specify mode="rb" in GzipCompressor.get_reader
Closes: #1146889
.
[ Andreas Tille ]
* Simplify d/salsa-ci.yml
Checksums-Sha1:
c83cd39c2e84fb0cf10dee35cdbc6cd9918f1e14 3167 python-skbio_0.7.3-2.dsc
55778f12dbd0f9dc23d13912ce5ce154df25589e 17112
python-skbio_0.7.3-2.debian.tar.xz
6f34786b326e8ab041badb059203bb9afd5aee53 13530
python-skbio_0.7.3-2_amd64.buildinfo
Checksums-Sha256:
c9efe99ccd07e8ccfda3f62a546f46897516481b328de4778610ba08effc1999 3167
python-skbio_0.7.3-2.dsc
acb817286040cadcf37a0e6ce44cd83ffba98a8e03caaa37ec57121c122de567 17112
python-skbio_0.7.3-2.debian.tar.xz
ec3f48164aeda4e0b69345c739193833c1ac8ed041f55591a484d410ccc1624c 13530
python-skbio_0.7.3-2_amd64.buildinfo
Files:
538dc3c2e5004c1efc608da6eba50b14 3167 python optional python-skbio_0.7.3-2.dsc
86e8b38e14070ad512fd522130dfe902 17112 python optional
python-skbio_0.7.3-2.debian.tar.xz
e1dee47961e95ccfad0b41025ca2658e 13530 python optional
python-skbio_0.7.3-2_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----
iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmqhS1ARHHRpbGxlQGRl
Ymlhbi5vcmcACgkQV4oElNHGRtGONBAAmecKU7RGq+HI680cyxWqkR/bXm7Spdfl
sNuDqc8h2R3iTPQELQbs4AiuRdCq4n80H6Bpy1m3X7EUSgb+ZIiblDm2HZor2YFt
VNQV+buvwk9SkxwtRItm7JQZ51eUYvl1HP37zhjPak8hLOgUK6VTJYgmyAHEw4BV
DCC5xqc0iobzGCrqs9sNONQnllsUOTpdJdTVIlEbEmKFqSJrJvoZ3g7EzEgOg7ks
w/LNoHRHyVPURd52A+hkuwImtCigvl0u2ER6blZkNCKUN0x3/w9tVug9MXQaiVj/
xtLOekN88ymt2vw1vjMr3S2CcuQGpg/1ztned1fptXOtv0hBCHygQjkzfATBkCcN
TOxeiSP8265IZhz4ssI7pFkeIEfV9CVWIf+V2FsdckUpav5K04P4uNbX0B51YcXB
YrMAv5KPafXmtQ77AIyQJFPGNoW68/miwbOtR6re2Acn4hfskqca5oqYwqY51suD
pczVIkHKkbXewVWT8cQrynPBnn3F3xZTm6MvQ13o45ScerkVUpshVGgS0OuQXwzc
MMgBmIPlLXrZ/huVoMD8swn4ixGs2E6G5u6xt0Sj/H3whok4ysWIT7qtuHalksZw
P8fCXoVe/jbPmIb4/zdBi9GTqjErAZSi+a0rKR8QjggHfSwNPqtKJSkSRAePr9c/
G7k54SrjA6g=
=q/7K
-----END PGP SIGNATURE-----
pgpnutgsa6M0n.pgp
Description: PGP signature
--- End Message ---
