Debian Bug report logs - #975511
segfaults on s390x

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Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Christian Ehrhardt <christian.ehrhardt@canonical.com>

To: Debian Bug Tracking System <submit@bugs.debian.org>

Subject: segfaults on s390x

Date: Mon, 23 Nov 2020 07:42:48 +0100

Package: clustalo
Version: 1.2.4-6

Hi,
as initially found and discussed on Launchpad/Ubuntu [1] there is a
segfault of clustalo on s390x.
So far it didn't hit you on your s390x builds [2] but it seems pretty
reliable for us already and on a rebuild in Debian unstable I've hit
it as well. It is triggered by the new self-test after build in
1.2.4-6.

The underlying root cause was identified in [3] which I also reported
to upstream and the Debian Med Team as mail. We now have three
options:

- wait for upstreams stance on the suggested change
- switch optimization to -O0 on s390x which avoids the issue for now
- apply the suggested patch without upstream commenting on it

This is up to you to decide what you prefer and I last week already
opened an MR for it [4].

[1]: https://bugs.launchpad.net/ubuntu/+source/clustalo/+bug/1903817
[2]: https://buildd.debian.org/status/architecture.php?a=s390x&suite=sid
[3]: https://bugs.launchpad.net/ubuntu/+source/clustalo/+bug/1903817/comments/15
[4]: https://salsa.debian.org/med-team/clustalo/-/merge_requests/1

-- 
Christian Ehrhardt
Staff Engineer, Ubuntu Server
Canonical Ltd

Message #10 received at 975511-close@bugs.debian.org (full text, mbox, reply):

From: Debian FTP Masters <ftpmaster@ftp-master.debian.org>

To: 975511-close@bugs.debian.org

Subject: Bug#975511: fixed in clustalo 1.2.4-7

Date: Mon, 23 Nov 2020 08:44:25 +0000

Source: clustalo
Source-Version: 1.2.4-7
Done: crusoe@debian.org (Michael R. Crusoe)

We believe that the bug you reported is fixed in the latest version of
clustalo, 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 975511@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Michael R. Crusoe <crusoe@debian.org> (supplier of updated clustalo 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 ftpmaster@ftp-master.debian.org)


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Hash: SHA512

Format: 1.8
Date: Mon, 23 Nov 2020 09:14:51 +0100
Source: clustalo
Architecture: source
Version: 1.2.4-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Michael R. Crusoe <crusoe@debian.org>
Closes: 975511
Changes:
 clustalo (1.2.4-7) unstable; urgency=medium
 .
   * Team upload.
   * debian/rules: fix segfaults on s390x by compiling with -O0, courtesy
     Christian Ehrhardt <christian.ehrhardt@canonical.com>. Closes: #975511
   * Standards-Version: 4.5.1 (routine-update)
   * debhelper-compat 13 (routine-update)
   * debian/control: mark libclustalo-doc as Multi-Arch: foreign, thanks to the
     Multiarch hinter
   * debian/docs: use installed path for README to appease dh-missing
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Checksums-Sha256:
 234f0b4323ad2ba2ade3386aea5476b0f84fdbf020e942d83fa525c6a957c6b5 2153 clustalo_1.2.4-7.dsc
 26f02f64ebb9d9bd0bb9c66a2e3a425f5daf24108d85c5b82787cf9acd70d275 10908 clustalo_1.2.4-7.debian.tar.xz
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Files:
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 c4f56d9ef571cba29fc40742e39d1451 10908 science optional clustalo_1.2.4-7.debian.tar.xz
 8320bbd101c211811b023f896c372418 8643 science optional clustalo_1.2.4-7_source.buildinfo

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