Your message dated Thu, 29 Feb 2024 16:01:04 +0000
with message-id <e1rfiqg-00btqo...@fasolo.debian.org>
and subject line Bug#1062316: fixed in libgkarrays 2.1.0+dfsg-4.2
has caused the Debian Bug report #1062316,
regarding libgkarrays: NMU diff for 64-bit time_t transition
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.
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--
1062316: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1062316
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: libgkarrays
Version: 2.1.0+dfsg-4
Severity: serious
Tags: patch pending
Justification: library ABI skew on upgrade
User: debian-...@lists.debian.org
Usertags: time-t
Dear maintainer,
As part of the 64-bit time_t transition required to support 32-bit
architectures in 2038 and beyond
(https://wiki.debian.org/ReleaseGoals/64bit-time), we have identified
libgkarrays as a source package shipping runtime libraries whose ABI
either is affected by the change in size of time_t, or could not be
analyzed via abi-compliance-checker (and therefore to be on the safe
side we assume is affected).
To ensure that inconsistent combinations of libraries with their
reverse-dependencies are never installed together, it is necessary to
have a library transition, which is most easily done by renaming the
runtime library package.
Since turning on 64-bit time_t is being handled centrally through a change
to the default dpkg-buildflags (https://bugs.debian.org/1037136), it is
important that libraries affected by this ABI change all be uploaded close
together in time. Therefore I have prepared a 0-day NMU for libgkarrays
which will initially be uploaded to experimental if possible, then to
unstable after packages have cleared binary NEW.
Please find the patch for this NMU attached.
If you have any concerns about this patch, please reach out ASAP. Although
this package will be uploaded to experimental immediately, there will be a
period of several days before we begin uploads to unstable; so if information
becomes available that your package should not be included in the transition,
there is time for us to amend the planned uploads.
-- System Information:
Debian Release: trixie/sid
APT prefers unstable
APT policy: (500, 'unstable'), (500, 'testing'), (1, 'experimental')
Architecture: amd64 (x86_64)
Kernel: Linux 6.5.0-14-generic (SMP w/12 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE
Locale: LANG=C, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
diff -Nru libgkarrays-2.1.0+dfsg/debian/changelog
libgkarrays-2.1.0+dfsg/debian/changelog
--- libgkarrays-2.1.0+dfsg/debian/changelog 2020-11-19 09:41:29.000000000
+0000
+++ libgkarrays-2.1.0+dfsg/debian/changelog 2024-02-01 01:32:52.000000000
+0000
@@ -1,3 +1,11 @@
+libgkarrays (2.1.0+dfsg-4.1) experimental; urgency=medium
+
+ * Non-maintainer upload.
+ * Rename libraries for 64-bit time_t transition.
+ * Bump build-dependency on d-shlibs for --t64 support.
+
+ -- Steve Langasek <vor...@debian.org> Thu, 01 Feb 2024 01:32:52 +0000
+
libgkarrays (2.1.0+dfsg-4) unstable; urgency=medium
* Fix installation of shared library
diff -Nru libgkarrays-2.1.0+dfsg/debian/control
libgkarrays-2.1.0+dfsg/debian/control
--- libgkarrays-2.1.0+dfsg/debian/control 2020-11-19 09:41:29.000000000
+0000
+++ libgkarrays-2.1.0+dfsg/debian/control 2024-02-01 01:32:52.000000000
+0000
@@ -4,7 +4,7 @@
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
- d-shlibs,
+ d-shlibs (>= 0.106),
zlib1g-dev
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/libgkarrays
@@ -12,7 +12,10 @@
Homepage: http://crac.gforge.inria.fr/gkarrays/
Rules-Requires-Root: no
-Package: libgkarrays1
+Package: libgkarrays1t64
+Provides: ${t64:Provides}
+Replaces: libgkarrays1
+Conflicts: libgkarrays1 (<< ${source:Version})
Architecture: any
Section: libs
Depends: ${shlibs:Depends},
@@ -34,7 +37,7 @@
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends},
- libgkarrays1 (= ${binary:Version})
+ libgkarrays1t64 (= ${binary:Version})
Description: library to query large collection of NGS sequences (development)
Gk-arrays are provided as a simple-to-use C++ library dedicated to
queries on large collection of sequences as produced by high-throughput
diff -Nru libgkarrays-2.1.0+dfsg/debian/libgkarrays1t64.lintian-overrides
libgkarrays-2.1.0+dfsg/debian/libgkarrays1t64.lintian-overrides
--- libgkarrays-2.1.0+dfsg/debian/libgkarrays1t64.lintian-overrides
1970-01-01 00:00:00.000000000 +0000
+++ libgkarrays-2.1.0+dfsg/debian/libgkarrays1t64.lintian-overrides
2024-02-01 01:32:52.000000000 +0000
@@ -0,0 +1 @@
+libgkarrays1t64: package-name-doesnt-match-sonames libgkarrays1
diff -Nru libgkarrays-2.1.0+dfsg/debian/rules
libgkarrays-2.1.0+dfsg/debian/rules
--- libgkarrays-2.1.0+dfsg/debian/rules 2020-11-19 09:41:29.000000000 +0000
+++ libgkarrays-2.1.0+dfsg/debian/rules 2024-02-01 01:32:52.000000000 +0000
@@ -12,6 +12,7 @@
override_dh_install:
dh_install
d-shlibmove --commit \
+ --t64 \
--multiarch \
--devunversioned \
--exclude-la \
@@ -20,7 +21,7 @@
--movedev
debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig
usr/lib/$(DEB_HOST_MULTIARCH) \
debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)/libGkArrays.so
# now move libProgressBar manually
- dh_install -p libgkarrays1
usr/lib/$(DEB_HOST_MULTIARCH)/libProgressBar.so.0*
usr/lib/$(DEB_HOST_MULTIARCH)
+ dh_install -p libgkarrays1t64
usr/lib/$(DEB_HOST_MULTIARCH)/libProgressBar.so.0*
usr/lib/$(DEB_HOST_MULTIARCH)
chmod -x debian/*/usr/lib/$(DEB_HOST_MULTIARCH)/libProgressBar.so.0.*
dh_install -p libgkarrays-dev
usr/lib/$(DEB_HOST_MULTIARCH)/libProgressBar.so
usr/lib/$(DEB_HOST_MULTIARCH)
dh_install -p libgkarrays-dev
usr/lib/$(DEB_HOST_MULTIARCH)/libProgressBar.a
usr/lib/$(DEB_HOST_MULTIARCH)
--- End Message ---
--- Begin Message ---
Source: libgkarrays
Source-Version: 2.1.0+dfsg-4.2
Done: Benjamin Drung <bdr...@debian.org>
We believe that the bug you reported is fixed in the latest version of
libgkarrays, 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 1062...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Benjamin Drung <bdr...@debian.org> (supplier of updated libgkarrays 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, 28 Feb 2024 18:55:49 +0000
Source: libgkarrays
Built-For-Profiles: noudeb
Architecture: source
Version: 2.1.0+dfsg-4.2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Benjamin Drung <bdr...@debian.org>
Closes: 1062316
Changes:
libgkarrays (2.1.0+dfsg-4.2) unstable; urgency=medium
.
* Non-maintainer upload.
* Rename libraries for 64-bit time_t transition. Closes: #1062316
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