[Debian-med-packaging] [Advent bug squashing] Bug#997884: marked as done (libgclib breaks cdbfasta autopkgtest: ABI breakage?)

Thu Dec 2 19:01:01 GMT 2021

Does this one count for December 2nd?  :)

----- Forwarded message from Debian Bug Tracking System <owner at bugs.debian.org> -----

Date: Thu, 02 Dec 2021 18:03:03 +0000
From: Debian Bug Tracking System <owner at bugs.debian.org>
To: Étienne Mollier <emollier at debian.org>
Subject: Bug#997884: marked as done (libgclib breaks cdbfasta autopkgtest: ABI breakage?)
X-Mailer: MIME-tools 5.509 (Entity 5.509)

Your message dated Thu, 02 Dec 2021 18:00:10 +0000
with message-id <E1msqNO-000GLN-DD at fasolo.debian.org>
and subject line Bug#997884: fixed in libgclib 0.12.7+ds-3~0exp0
has caused the Debian Bug report #997884,
regarding libgclib breaks cdbfasta autopkgtest: ABI breakage?
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 owner at bugs.debian.org
immediately.)

-- 
997884: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=997884
Debian Bug Tracking System
Contact owner at bugs.debian.org with problems

Date: Tue, 26 Oct 2021 16:58:28 +0200
From: Paul Gevers <elbrus at debian.org>
To: submit at bugs.debian.org
Subject: libgclib breaks cdbfasta autopkgtest: ABI breakage?
User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101
 Thunderbird/78.14.0

Source: libgclib
Control: found -1 libgclib/0.12.7+ds-2
Severity: serious
Tags: sid bookworm
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: breaks
Control: affects -1 src:cdbfasta

Dear maintainer(s),

With a recent upload of libgclib the autopkgtest of cdbfasta fails in
testing when that autopkgtest is run with the binary packages of
libgclib from unstable. It passes when run with only packages from
testing. In tabular form:

                       pass            fail
libgclib               from testing    0.12.7+ds-2
cdbfasta               from testing    1.00+git20181005.014498c+dfsg-2
all others             from testing    from testing

I copied some of the output at the bottom of this report. Looking at the
message and the changelog, it seems that symbols were changed, but this
one was apparently used by cdbfasta. I think this points at an ABI
breakage and the SONAME of libgclib must be bumped and a transition must
be followed through. (I could be wrong).

Currently this regression is blocking the migration of libgclib to
testing [1]. Can you please investigate the situation?

More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[1] https://qa.debian.org/excuses.php?package=libgclib

https://ci.debian.net/data/autopkgtest/testing/amd64/c/cdbfasta/16212088/log.gz

+ cdbfasta ebola.fasta
cdbfasta: symbol lookup error: cdbfasta: undefined symbol: _Z8GReallocPPvm
autopkgtest [22:12:39]: test run-unit-tests

Date: Thu, 02 Dec 2021 18:00:10 +0000
From: Debian FTP Masters <ftpmaster at ftp-master.debian.org>
To: 997884-close at bugs.debian.org
Subject: Bug#997884: fixed in libgclib 0.12.7+ds-3~0exp0

Source: libgclib
Source-Version: 0.12.7+ds-3~0exp0
Done: Étienne Mollier <emollier at debian.org>

We believe that the bug you reported is fixed in the latest version of
libgclib, 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 997884 at bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Étienne Mollier <emollier at debian.org> (supplier of updated libgclib 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 at ftp-master.debian.org)

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Wed, 27 Oct 2021 20:30:06 +0200
Binary: libgclib-dev libgclib3 libgclib3-dbgsym
Source: libgclib
Architecture: amd64 source
Version: 0.12.7+ds-3~0exp0
Distribution: experimental
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier at debian.org>
Closes: 997884
Description: 
 libgclib-dev - header files for Genome Code Lib (GCLib)
 libgclib3  - C++ library to handle biological short sequence data
Changes:
 libgclib (0.12.7+ds-3~0exp0) experimental; urgency=medium
 .
   * Team upload.
   * Bump libgclib soname (Closes: #997884)
   * d/copyright: add khashl.hh, wyhash.h and xxhash.h
Checksums-Sha1: 
 dff51f30add69b58a63ad1b0075988c514965634 130708 libgclib-dev_0.12.7+ds-3~0exp0_amd64.deb
 915e15c41c320028a55f8165eac95c5e1b3cbcf4 604396 libgclib3-dbgsym_0.12.7+ds-3~0exp0_amd64.deb
 10004500405f9d7ad6b39693b30b7319c7a43712 150368 libgclib3_0.12.7+ds-3~0exp0_amd64.deb
 c3faab3483ad9b5b6083e029d6e922a086976496 6678 libgclib_0.12.7+ds-3~0exp0_amd64.buildinfo
 a59951b2dd06e58a970cf3cdb98a29e9a46ba023 2197 libgclib_0.12.7+ds-3~0exp0.dsc
 a6e27b4efa7fc8fa6d8832a73bdabc3872422c78 14816 libgclib_0.12.7+ds-3~0exp0.debian.tar.xz
Checksums-Sha256: 
 32a5dfdedc2af4079dc5c2abbc673791422731e502220a8a8c446e134770a18c 130708 libgclib-dev_0.12.7+ds-3~0exp0_amd64.deb
 7191d70965d9c30bec0cfdd4f06178aee5bc8d4207dde2ba4cd1b0489057aac7 604396 libgclib3-dbgsym_0.12.7+ds-3~0exp0_amd64.deb
 1692bbbad8232489384e2d58faac2ac4481c61ab89535945fd73caea699b09fc 150368 libgclib3_0.12.7+ds-3~0exp0_amd64.deb
 d780272765bc5683a8018972e513e01bc583d8e8dd0aa0abe85395a201c60f3a 6678 libgclib_0.12.7+ds-3~0exp0_amd64.buildinfo
 0ef180cd07dcadfa2117819d058f98e5c872adfaef857f9008907eadac20d7f5 2197 libgclib_0.12.7+ds-3~0exp0.dsc
 654aafe158d13b0e5bc91ae531ff9d224108664072cef7433cce6cf64513f44d 14816 libgclib_0.12.7+ds-3~0exp0.debian.tar.xz
Files: 
 df7ec62beec61dd42c028b81d30ab9cf 130708 libdevel optional libgclib-dev_0.12.7+ds-3~0exp0_amd64.deb
 8791e8d09f15658e645df0afa2e909ef 604396 debug optional libgclib3-dbgsym_0.12.7+ds-3~0exp0_amd64.deb
 cfcc5cb0ddebe8f5fd29835bc9459f1a 150368 libs optional libgclib3_0.12.7+ds-3~0exp0_amd64.deb
 fec0c8aa1f4da96a8c17d775d6922f62 6678 science optional libgclib_0.12.7+ds-3~0exp0_amd64.buildinfo
 1fb722885d9edb47146bb5e743b164fc 2197 science optional libgclib_0.12.7+ds-3~0exp0.dsc
 31d5c01788864ddded9976f4461b5f70 14816 science optional libgclib_0.12.7+ds-3~0exp0.debian.tar.xz

-----BEGIN PGP SIGNATURE-----
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=CH//
-----END PGP SIGNATURE-----

----- End forwarded message -----

-- 
Étienne Mollier <emollier at emlwks999.eu>
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/3, please excuse my verbosity.
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 833 bytes
Desc: not available
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20211202/f5a4683d/attachment.sig>