Source: r-bioc-rhtslib
Version: 2.4.1+dfsg-1
Severity: serious
User: debian-arm@lists.debian.org
Usertags: time-t

Hi Andreas,

Analysis of the archive for the 64-bit time_t transition[0][1] identifies r-bioc-rhtslib as an affected package, on the basis that it depends on some library whose ABI is sensitive to time_t, which requires
reverse-dependencies to be built with LFS support enabled, and
r-bioc-rhtslib's own ABI is sensitive to LFS support.

However, r-bioc-rhtslib's shlibs file declares a dependency on a library package name that contains no ABI information:

$ cat DEBIAN/shlibs
libhts 3 r-bioc-rhtslib (>= 2.4.1+dfsg)
$

It is not obvious that we should rename the package to 'r-bioc-rhtslibt64'
as part of this transition. Looking at the archive, there are packages
built from the separate r-bioc-rsamtools and r-bioc-variantannotation source packages that depend on this library.

Since there is no self-evident thing to do with the library package name
here, we will not be handling this package as part of the mass NMUs.
Instead I am filing a serious bug because partial upgrades from bookworm to trixie on 32-bit architectures will result in ABI skew and may result in
broken behavior.

Thanks,
--
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/ slangasek@ubuntu.com vorlon@debian.org

[0] https://wiki.debian.org/ReleaseGoals/64bit-time
[1] https://lists.debian.org/debian-devel/2024/01/msg00041.html

-----BEGIN PGP SIGNATURE-----

iQIzBAABCgAdFiEErEg/aN5yj0PyIC/KVo0w8yGyEz0FAmXBdJoACgkQVo0w8yGy Ez2ZnxAAmqRnpO9oawkU1/5novi9IJABjFI0e3kVsxtHdn/azmx/2NEMi8KY/O0A jOx6Mxh50QLsYB/9uspmxxGhFDSWUQ2GPckrSpFb2IRu3J+ulTCFqRlH0OhNzexo s/TL9qUkBdXxxJr6Vsi8mZckJj4m96QfU5Gr7yQ1AMlRwd2a4Ypnmh5xRl1yh96A hRJGfNR67dM88wn/8xEVOILdSa6nVzWTqBLY6nJnhT0qYbXbQA39o5XFrQpzdwEV ozQzzYsLwkE70Reft2rW7Y65qWOeULxEaF6ZkHELcZtSP3/JDM0+OMsN1BKcFKrm R5OGL4B0kywj/oKW6I9w1M5I+V0eXisEgJggM7PbVmGJRPUmgovHyDj9eQYq2kQN 5E7i53fE7F+lTAzw8OZJy9aIGzXLbVz6HxUgm1dzWO98VJ9+N/CguflO8VUrE4k+ inOhHZO4p+QcqaoWtRcClhqEkJ8Nm3qI

This is a multi-part message in MIME format...

Your message dated Wed, 07 Feb 2024 07:23:43 +0000
with message-id <E1rXcHX-001o1v-TF@fasolo.debian.org>
and subject line Bug#1063275: fixed in r-bioc-rhtslib 2.4.1+dfsg-2
has caused the Debian Bug report #1063275,
regarding r-bioc-rhtslib: identified for time_t transition but no ABI in shlibs 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@bugs.debian.org
immediately.)


--
1063275: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1063275
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems

Received: (at submit) by bugs.debian.org; 5 Feb 2024 23:52:02 +0000 X-Spam-Checker-Version: SpamAssassin 3.4.6-bugs.debian.org_2005_01_02
(2021-04-09) on buxtehude.debian.org
X-Spam-Level:
X-Spam-Status: No, score=-111.5 required=4.0 tests=BAYES_00,DKIMWL_WL_HIGH,
DKIM_SIGNED,DKIM_VALID,DKIM_VALID_AU,DKIM_VALID_EF,FROMDEVELOPER,
PGPSIGNATURE,SPF_HELO_NONE,SPF_NONE,T_SCC_BODY_TEXT_LINE,
USER_IN_DKIM_WELCOMELIST,USER_IN_DKIM_WHITELIST autolearn=ham
autolearn_force=no version=3.4.6-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 9; hammy, 150; neutral, 87; spammy, 0.
spammytokens: hammytokens:0.000-+--bookworm, 0.000-+--trixie,
0.000-+--langasek, 0.000-+--Langasek, 0.000-+--H*ct:application Return-path: <vorlon@debian.org>
Received: from becquer.dodds.net ([2001:470:e980::2]:43477)
by buxtehude.debian.org with esmtps (TLS1.3:E