[Debian-med-packaging] Bug#1062229: libbigwig: NMU diff for 64-bit time_t transition
Steve Langasek
vorlon at debian.org
Wed Jan 31 19:51:40 GMT 2024
Source: libbigwig
Version: 0.4.7+dfsg-3
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
libbigwig 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 libbigwig
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 libbigwig-0.4.7+dfsg/debian/changelog libbigwig-0.4.7+dfsg/debian/changelog
--- libbigwig-0.4.7+dfsg/debian/changelog 2022-09-10 07:33:51.000000000 +0000
+++ libbigwig-0.4.7+dfsg/debian/changelog 2024-01-31 19:51:21.000000000 +0000
@@ -1,3 +1,10 @@
+libbigwig (0.4.7+dfsg-3.1) experimental; urgency=medium
+
+ * Non-maintainer upload.
+ * Rename libraries for 64-bit time_t transition.
+
+ -- Steve Langasek <vorlon at debian.org> Wed, 31 Jan 2024 19:51:21 +0000
+
libbigwig (0.4.7+dfsg-3) unstable; urgency=medium
* Team upload.
diff -Nru libbigwig-0.4.7+dfsg/debian/control libbigwig-0.4.7+dfsg/debian/control
--- libbigwig-0.4.7+dfsg/debian/control 2022-08-29 16:56:21.000000000 +0000
+++ libbigwig-0.4.7+dfsg/debian/control 2024-01-31 19:51:21.000000000 +0000
@@ -14,7 +14,10 @@
Homepage: https://github.com/dpryan79/libBigWig/
Rules-Requires-Root: no
-Package: libbigwig0
+Package: libbigwig0t64
+Provides: ${t64:Provides}
+Replaces: libbigwig0
+Breaks: libbigwig0 (<< ${source:Version})
Architecture: any
Section: libs
Multi-Arch: same
@@ -31,7 +34,7 @@
Architecture: any
Multi-Arch: same
Section: libdevel
-Depends: libbigwig0 (= ${binary:Version}),
+Depends: libbigwig0t64 (= ${binary:Version}),
${misc:Depends}
Description: C library for handling bigWig files - header files
This package provides the files needed to develop with the libBigWig
diff -Nru libbigwig-0.4.7+dfsg/debian/libbigwig0.symbols libbigwig-0.4.7+dfsg/debian/libbigwig0.symbols
--- libbigwig-0.4.7+dfsg/debian/libbigwig0.symbols 2022-08-29 16:52:07.000000000 +0000
+++ libbigwig-0.4.7+dfsg/debian/libbigwig0.symbols 1970-01-01 00:00:00.000000000 +0000
@@ -1,66 +0,0 @@
-libBigWig.so.0 libbigwig0 #MINVER#
- GLOBAL_DEFAULTBUFFERSIZE at Base 0.4.6
- addIntervalValue at Base 0.4.6
- bbDestroyOverlappingEntries at Base 0.4.6
- bbGetOverlappingEntries at Base 0.4.6
- bbGetOverlappingEntriesCore at Base 0.4.6
- bbGetSQL at Base 0.4.6
- bbIsBigBed at Base 0.4.6
- bbOpen at Base 0.4.6
- bbOverlappingEntriesIterator at Base 0.4.6
- bwAddIntervalSpanSteps at Base 0.4.6
- bwAddIntervalSpans at Base 0.4.6
- bwAddIntervals at Base 0.4.6
- bwAppendIntervalSpanSteps at Base 0.4.6
- bwAppendIntervalSpans at Base 0.4.6
- bwAppendIntervals at Base 0.4.6
- bwCleanup at Base 0.4.6
- bwClose at Base 0.4.6
- bwCreateChromList at Base 0.4.6
- bwCreateHdr at Base 0.4.6
- bwDestroyIndex at Base 0.4.6
- bwDestroyIndexNode at Base 0.4.6
- bwDestroyOverlappingIntervals at Base 0.4.6
- bwFillBuffer at Base 0.4.6
- bwFillDataHdr at Base 0.4.6
- bwFinalize at Base 0.4.6
- bwGetOverlappingIntervals at Base 0.4.6
- bwGetOverlappingIntervalsCore at Base 0.4.6
- bwGetTid at Base 0.4.6
- bwGetValues at Base 0.4.6
- bwInit at Base 0.4.6
- bwIsBigWig at Base 0.4.6
- bwIteratorDestroy at Base 0.4.6
- bwIteratorNext at Base 0.4.6
- bwOpen at Base 0.4.6
- bwOverlappingIntervalsIterator at Base 0.4.6
- bwRead at Base 0.4.6
- bwReadIndex at Base 0.4.6
- bwSetPos at Base 0.4.6
- bwStats at Base 0.4.6
- bwStatsFromFull at Base 0.4.6
- bwStrdup at Base 0.4.7
- bwTell at Base 0.4.6
- bwWriteHdr at Base 0.4.6
- constructZoomLevels at Base 0.4.6
- destroyBWOverlapBlock at Base 0.4.6
- destroyVals_t at Base 0.4.6
- getContentLength at Base 0.4.6
- getScalar at Base 0.4.6
- makeZoomLevels at Base 0.4.6
- nextPos at Base 0.4.6
- overlapsInterval at Base 0.4.6
- updateInterval at Base 0.4.6
- urlClose at Base 0.4.6
- urlFetchData at Base 0.4.6
- urlOpen at Base 0.4.6
- urlRead at Base 0.4.6
- urlSeek at Base 0.4.6
- url_fread at Base 0.4.6
- walkRTreeNodes at Base 0.4.6
- writeIndex at Base 0.4.6
- writeIndexOffsets at Base 0.4.6
- writeIndexTree at Base 0.4.6
- writeIndexTreeNode at Base 0.4.6
- writeSummary at Base 0.4.6
- writeZoomLevels at Base 0.4.6
diff -Nru libbigwig-0.4.7+dfsg/debian/libbigwig0t64.lintian-overrides libbigwig-0.4.7+dfsg/debian/libbigwig0t64.lintian-overrides
--- libbigwig-0.4.7+dfsg/debian/libbigwig0t64.lintian-overrides 1970-01-01 00:00:00.000000000 +0000
+++ libbigwig-0.4.7+dfsg/debian/libbigwig0t64.lintian-overrides 2024-01-31 19:51:21.000000000 +0000
@@ -0,0 +1 @@
+libbigwig0t64: package-name-doesnt-match-sonames libbigwig0
diff -Nru libbigwig-0.4.7+dfsg/debian/libbigwig0t64.symbols libbigwig-0.4.7+dfsg/debian/libbigwig0t64.symbols
--- libbigwig-0.4.7+dfsg/debian/libbigwig0t64.symbols 1970-01-01 00:00:00.000000000 +0000
+++ libbigwig-0.4.7+dfsg/debian/libbigwig0t64.symbols 2024-01-31 19:51:21.000000000 +0000
@@ -0,0 +1,66 @@
+libBigWig.so.0 libbigwig0t64 #MINVER#
+ GLOBAL_DEFAULTBUFFERSIZE at Base 0.4.6
+ addIntervalValue at Base 0.4.6
+ bbDestroyOverlappingEntries at Base 0.4.6
+ bbGetOverlappingEntries at Base 0.4.6
+ bbGetOverlappingEntriesCore at Base 0.4.6
+ bbGetSQL at Base 0.4.6
+ bbIsBigBed at Base 0.4.6
+ bbOpen at Base 0.4.6
+ bbOverlappingEntriesIterator at Base 0.4.6
+ bwAddIntervalSpanSteps at Base 0.4.6
+ bwAddIntervalSpans at Base 0.4.6
+ bwAddIntervals at Base 0.4.6
+ bwAppendIntervalSpanSteps at Base 0.4.6
+ bwAppendIntervalSpans at Base 0.4.6
+ bwAppendIntervals at Base 0.4.6
+ bwCleanup at Base 0.4.6
+ bwClose at Base 0.4.6
+ bwCreateChromList at Base 0.4.6
+ bwCreateHdr at Base 0.4.6
+ bwDestroyIndex at Base 0.4.6
+ bwDestroyIndexNode at Base 0.4.6
+ bwDestroyOverlappingIntervals at Base 0.4.6
+ bwFillBuffer at Base 0.4.6
+ bwFillDataHdr at Base 0.4.6
+ bwFinalize at Base 0.4.6
+ bwGetOverlappingIntervals at Base 0.4.6
+ bwGetOverlappingIntervalsCore at Base 0.4.6
+ bwGetTid at Base 0.4.6
+ bwGetValues at Base 0.4.6
+ bwInit at Base 0.4.6
+ bwIsBigWig at Base 0.4.6
+ bwIteratorDestroy at Base 0.4.6
+ bwIteratorNext at Base 0.4.6
+ bwOpen at Base 0.4.6
+ bwOverlappingIntervalsIterator at Base 0.4.6
+ bwRead at Base 0.4.6
+ bwReadIndex at Base 0.4.6
+ bwSetPos at Base 0.4.6
+ bwStats at Base 0.4.6
+ bwStatsFromFull at Base 0.4.6
+ bwStrdup at Base 0.4.7
+ bwTell at Base 0.4.6
+ bwWriteHdr at Base 0.4.6
+ constructZoomLevels at Base 0.4.6
+ destroyBWOverlapBlock at Base 0.4.6
+ destroyVals_t at Base 0.4.6
+ getContentLength at Base 0.4.6
+ getScalar at Base 0.4.6
+ makeZoomLevels at Base 0.4.6
+ nextPos at Base 0.4.6
+ overlapsInterval at Base 0.4.6
+ updateInterval at Base 0.4.6
+ urlClose at Base 0.4.6
+ urlFetchData at Base 0.4.6
+ urlOpen at Base 0.4.6
+ urlRead at Base 0.4.6
+ urlSeek at Base 0.4.6
+ url_fread at Base 0.4.6
+ walkRTreeNodes at Base 0.4.6
+ writeIndex at Base 0.4.6
+ writeIndexOffsets at Base 0.4.6
+ writeIndexTree at Base 0.4.6
+ writeIndexTreeNode at Base 0.4.6
+ writeSummary at Base 0.4.6
+ writeZoomLevels at Base 0.4.6
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