Your message dated Thu, 29 Feb 2024 10:05:13 +0000
with message-id <[email protected]>
and subject line Bug#1062229: fixed in libbigwig 0.4.7+dfsg-3.1
has caused the Debian Bug report #1062229,
regarding libbigwig: 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.
(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 [email protected]
immediately.)
--
1062229: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1062229
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: libbigwig
Version: 0.4.7+dfsg-3
Severity: serious
Tags: patch pending
Justification: library ABI skew on upgrade
User: [email protected]
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)
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 <[email protected]> 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@Base 0.4.6
- addIntervalValue@Base 0.4.6
- bbDestroyOverlappingEntries@Base 0.4.6
- bbGetOverlappingEntries@Base 0.4.6
- bbGetOverlappingEntriesCore@Base 0.4.6
- bbGetSQL@Base 0.4.6
- bbIsBigBed@Base 0.4.6
- bbOpen@Base 0.4.6
- bbOverlappingEntriesIterator@Base 0.4.6
- bwAddIntervalSpanSteps@Base 0.4.6
- bwAddIntervalSpans@Base 0.4.6
- bwAddIntervals@Base 0.4.6
- bwAppendIntervalSpanSteps@Base 0.4.6
- bwAppendIntervalSpans@Base 0.4.6
- bwAppendIntervals@Base 0.4.6
- bwCleanup@Base 0.4.6
- bwClose@Base 0.4.6
- bwCreateChromList@Base 0.4.6
- bwCreateHdr@Base 0.4.6
- bwDestroyIndex@Base 0.4.6
- bwDestroyIndexNode@Base 0.4.6
- bwDestroyOverlappingIntervals@Base 0.4.6
- bwFillBuffer@Base 0.4.6
- bwFillDataHdr@Base 0.4.6
- bwFinalize@Base 0.4.6
- bwGetOverlappingIntervals@Base 0.4.6
- bwGetOverlappingIntervalsCore@Base 0.4.6
- bwGetTid@Base 0.4.6
- bwGetValues@Base 0.4.6
- bwInit@Base 0.4.6
- bwIsBigWig@Base 0.4.6
- bwIteratorDestroy@Base 0.4.6
- bwIteratorNext@Base 0.4.6
- bwOpen@Base 0.4.6
- bwOverlappingIntervalsIterator@Base 0.4.6
- bwRead@Base 0.4.6
- bwReadIndex@Base 0.4.6
- bwSetPos@Base 0.4.6
- bwStats@Base 0.4.6
- bwStatsFromFull@Base 0.4.6
- bwStrdup@Base 0.4.7
- bwTell@Base 0.4.6
- bwWriteHdr@Base 0.4.6
- constructZoomLevels@Base 0.4.6
- destroyBWOverlapBlock@Base 0.4.6
- destroyVals_t@Base 0.4.6
- getContentLength@Base 0.4.6
- getScalar@Base 0.4.6
- makeZoomLevels@Base 0.4.6
- nextPos@Base 0.4.6
- overlapsInterval@Base 0.4.6
- updateInterval@Base 0.4.6
- urlClose@Base 0.4.6
- urlFetchData@Base 0.4.6
- urlOpen@Base 0.4.6
- urlRead@Base 0.4.6
- urlSeek@Base 0.4.6
- url_fread@Base 0.4.6
- walkRTreeNodes@Base 0.4.6
- writeIndex@Base 0.4.6
- writeIndexOffsets@Base 0.4.6
- writeIndexTree@Base 0.4.6
- writeIndexTreeNode@Base 0.4.6
- writeSummary@Base 0.4.6
- writeZoomLevels@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@Base 0.4.6
+ addIntervalValue@Base 0.4.6
+ bbDestroyOverlappingEntries@Base 0.4.6
+ bbGetOverlappingEntries@Base 0.4.6
+ bbGetOverlappingEntriesCore@Base 0.4.6
+ bbGetSQL@Base 0.4.6
+ bbIsBigBed@Base 0.4.6
+ bbOpen@Base 0.4.6
+ bbOverlappingEntriesIterator@Base 0.4.6
+ bwAddIntervalSpanSteps@Base 0.4.6
+ bwAddIntervalSpans@Base 0.4.6
+ bwAddIntervals@Base 0.4.6
+ bwAppendIntervalSpanSteps@Base 0.4.6
+ bwAppendIntervalSpans@Base 0.4.6
+ bwAppendIntervals@Base 0.4.6
+ bwCleanup@Base 0.4.6
+ bwClose@Base 0.4.6
+ bwCreateChromList@Base 0.4.6
+ bwCreateHdr@Base 0.4.6
+ bwDestroyIndex@Base 0.4.6
+ bwDestroyIndexNode@Base 0.4.6
+ bwDestroyOverlappingIntervals@Base 0.4.6
+ bwFillBuffer@Base 0.4.6
+ bwFillDataHdr@Base 0.4.6
+ bwFinalize@Base 0.4.6
+ bwGetOverlappingIntervals@Base 0.4.6
+ bwGetOverlappingIntervalsCore@Base 0.4.6
+ bwGetTid@Base 0.4.6
+ bwGetValues@Base 0.4.6
+ bwInit@Base 0.4.6
+ bwIsBigWig@Base 0.4.6
+ bwIteratorDestroy@Base 0.4.6
+ bwIteratorNext@Base 0.4.6
+ bwOpen@Base 0.4.6
+ bwOverlappingIntervalsIterator@Base 0.4.6
+ bwRead@Base 0.4.6
+ bwReadIndex@Base 0.4.6
+ bwSetPos@Base 0.4.6
+ bwStats@Base 0.4.6
+ bwStatsFromFull@Base 0.4.6
+ bwStrdup@Base 0.4.7
+ bwTell@Base 0.4.6
+ bwWriteHdr@Base 0.4.6
+ constructZoomLevels@Base 0.4.6
+ destroyBWOverlapBlock@Base 0.4.6
+ destroyVals_t@Base 0.4.6
+ getContentLength@Base 0.4.6
+ getScalar@Base 0.4.6
+ makeZoomLevels@Base 0.4.6
+ nextPos@Base 0.4.6
+ overlapsInterval@Base 0.4.6
+ updateInterval@Base 0.4.6
+ urlClose@Base 0.4.6
+ urlFetchData@Base 0.4.6
+ urlOpen@Base 0.4.6
+ urlRead@Base 0.4.6
+ urlSeek@Base 0.4.6
+ url_fread@Base 0.4.6
+ walkRTreeNodes@Base 0.4.6
+ writeIndex@Base 0.4.6
+ writeIndexOffsets@Base 0.4.6
+ writeIndexTree@Base 0.4.6
+ writeIndexTreeNode@Base 0.4.6
+ writeSummary@Base 0.4.6
+ writeZoomLevels@Base 0.4.6
--- End Message ---
--- Begin Message ---
Source: libbigwig
Source-Version: 0.4.7+dfsg-3.1
Done: Lukas Märdian <[email protected]>
We believe that the bug you reported is fixed in the latest version of
libbigwig, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Lukas Märdian <[email protected]> (supplier of updated libbigwig 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Thu, 29 Feb 2024 08:50:16 +0000
Source: libbigwig
Architecture: source
Version: 0.4.7+dfsg-3.1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Lukas Märdian <[email protected]>
Closes: 1062229
Changes:
libbigwig (0.4.7+dfsg-3.1) unstable; urgency=medium
.
* Non-maintainer upload.
* Rename libraries for 64-bit time_t transition. Closes: #1062229
Checksums-Sha1:
f461facf18c97c0fb9a1bd9eacdbbea39a0e6da3 2318 libbigwig_0.4.7+dfsg-3.1.dsc
fe5a015fa0f98eb60fb83c3dc7f81004782d958a 5212
libbigwig_0.4.7+dfsg-3.1.debian.tar.xz
d8fb854f75b08b9df14792535ef7b3c3288d1827 7200
libbigwig_0.4.7+dfsg-3.1_source.buildinfo
Checksums-Sha256:
523654121728fe41e4c6ad82c3fce98767c2749f4ca7c7673e8fea6358e7c6a4 2318
libbigwig_0.4.7+dfsg-3.1.dsc
831334b1f3448eeadb5b4d024f56d879a64caee5dc90a7ee57474dfda54c0237 5212
libbigwig_0.4.7+dfsg-3.1.debian.tar.xz
13dda848af07a7f9df4db2ab1cd29f9438e91f187aad3979716811d576322ad4 7200
libbigwig_0.4.7+dfsg-3.1_source.buildinfo
Files:
642f33a5b72a287687668d4c4a9d05da 2318 science optional
libbigwig_0.4.7+dfsg-3.1.dsc
2b9048ad4d92c019b2e86c9a6c0c45d9 5212 science optional
libbigwig_0.4.7+dfsg-3.1.debian.tar.xz
3d0e398decb58300b1fe6c0d04d2c517 7200 science optional
libbigwig_0.4.7+dfsg-3.1_source.buildinfo
-----BEGIN PGP SIGNATURE-----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=DMbH
-----END PGP SIGNATURE-----
pgpNW1NxFi2vR.pgp
Description: PGP signature
--- End Message ---
