[Debian-med-packaging] Bug#1062316: libgkarrays: NMU diff for 64-bit time_t transition

[Steve Langasek]

Source: libgkarrays
Version: 2.1.0+dfsg-4
Severity: serious
Tags: patch pending
Justification: library ABI skew on upgrade
User: debian-arm at 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)
-------------- next part --------------
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 <vorlon at 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)