Your message dated Tue, 28 May 2024 05:19:53 +0000
with message-id <e1sbpfz-009khd...@fasolo.debian.org>
and subject line Bug#1064311: fixed in rdkit 202309.3-4
has caused the Debian Bug report #1064311,
regarding rdkit: 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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--
1064311: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1064311
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: rdkit
Version: 202309.3-2
Severity: important
Tags: patch pending sid trixie
User: debian-...@lists.debian.org
Usertags: time-t
NOTICE: these changes must not be uploaded to unstable yet!
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
rdkit 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 rdkit
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')
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 rdkit-202309.3/debian/changelog rdkit-202309.3/debian/changelog
--- rdkit-202309.3/debian/changelog 2024-01-17 13:03:19.000000000 +0000
+++ rdkit-202309.3/debian/changelog 2024-02-19 20:49:34.000000000 +0000
@@ -1,3 +1,10 @@
+rdkit (202309.3-2.1) experimental; urgency=medium
+
+ * Non-maintainer upload.
+ * Rename libraries for 64-bit time_t transition.
+
+ -- Steve Langasek <vor...@debian.org> Mon, 19 Feb 2024 20:49:34 +0000
+
rdkit (202309.3-2) unstable; urgency=medium
* Team upload.
diff -Nru rdkit-202309.3/debian/control rdkit-202309.3/debian/control
--- rdkit-202309.3/debian/control 2024-01-17 13:03:19.000000000 +0000
+++ rdkit-202309.3/debian/control 2024-02-19 20:49:33.000000000 +0000
@@ -102,7 +102,10 @@
.
This package contains data files.
-Package: librdkit1
+Package: librdkit1t64
+Provides: ${t64:Provides}
+Replaces: librdkit1
+Breaks: librdkit1 (<< ${source:Version})
Section: libs
Architecture: any
Depends: ${misc:Depends}, ${shlibs:Depends}
@@ -137,7 +140,7 @@
Package: librdkit-dev
Section: libdevel
Architecture: any
-Depends: librdkit1 (= ${binary:Version}), ${misc:Depends}, ${shlibs:Depends}
+Depends: librdkit1t64 (= ${binary:Version}), ${misc:Depends}, ${shlibs:Depends}
Description: Collection of cheminformatics and machine-learning software
(development files)
RDKit is a Python/C++ based cheminformatics and machine-learning software
environment. Features Include:
diff -Nru rdkit-202309.3/debian/control.in rdkit-202309.3/debian/control.in
--- rdkit-202309.3/debian/control.in 2023-09-20 14:24:08.000000000 +0000
+++ rdkit-202309.3/debian/control.in 2024-02-19 20:49:33.000000000 +0000
@@ -102,7 +102,10 @@
.
This package contains data files.
-Package: librdkit1
+Package: librdkit1t64
+Provides: ${t64:Provides}
+Replaces: librdkit1
+Breaks: librdkit1 (<< ${source:Version})
Section: libs
Architecture: any
Depends: ${misc:Depends}, ${shlibs:Depends}
@@ -137,7 +140,7 @@
Package: librdkit-dev
Section: libdevel
Architecture: any
-Depends: librdkit1 (= ${binary:Version}), ${misc:Depends}, ${shlibs:Depends}
+Depends: librdkit1t64 (= ${binary:Version}), ${misc:Depends}, ${shlibs:Depends}
Description: Collection of cheminformatics and machine-learning software
(development files)
RDKit is a Python/C++ based cheminformatics and machine-learning software
environment. Features Include:
diff -Nru rdkit-202309.3/debian/librdkit1.install
rdkit-202309.3/debian/librdkit1.install
--- rdkit-202309.3/debian/librdkit1.install 2023-09-20 14:24:08.000000000
+0000
+++ rdkit-202309.3/debian/librdkit1.install 1970-01-01 00:00:00.000000000
+0000
@@ -1 +0,0 @@
-usr/lib/lib*.so.*
diff -Nru rdkit-202309.3/debian/librdkit1.lintian-overrides
rdkit-202309.3/debian/librdkit1.lintian-overrides
--- rdkit-202309.3/debian/librdkit1.lintian-overrides 2023-09-20
14:24:08.000000000 +0000
+++ rdkit-202309.3/debian/librdkit1.lintian-overrides 1970-01-01
00:00:00.000000000 +0000
@@ -1,7 +0,0 @@
-# the library package contains several libraries by intention
-librdkit1: package-name-doesnt-match-sonames
-# seem to be false positives - #896012 against lintian possibly related
-librdkit1: library-not-linked-against-libc [usr/lib/libRDKitCatalogs.so.*]
-librdkit1: library-not-linked-against-libc [usr/lib/libRDKitOptimizer.so.*]
-# CONECT is used in the PDB file format
-librdkit1: spelling-error-in-binary CONECT CONNECT [*]
\ No newline at end of file
diff -Nru rdkit-202309.3/debian/librdkit1t64.install
rdkit-202309.3/debian/librdkit1t64.install
--- rdkit-202309.3/debian/librdkit1t64.install 1970-01-01 00:00:00.000000000
+0000
+++ rdkit-202309.3/debian/librdkit1t64.install 2023-09-20 14:24:08.000000000
+0000
@@ -0,0 +1 @@
+usr/lib/lib*.so.*
diff -Nru rdkit-202309.3/debian/librdkit1t64.lintian-overrides
rdkit-202309.3/debian/librdkit1t64.lintian-overrides
--- rdkit-202309.3/debian/librdkit1t64.lintian-overrides 1970-01-01
00:00:00.000000000 +0000
+++ rdkit-202309.3/debian/librdkit1t64.lintian-overrides 2024-02-19
20:49:34.000000000 +0000
@@ -0,0 +1,7 @@
+# the library package contains several libraries by intention
+librdkit1t64: package-name-doesnt-match-sonames
+# seem to be false positives - #896012 against lintian possibly related
+librdkit1t64: library-not-linked-against-libc [usr/lib/libRDKitCatalogs.so.*]
+librdkit1t64: library-not-linked-against-libc [usr/lib/libRDKitOptimizer.so.*]
+# CONECT is used in the PDB file format
+librdkit1t64: spelling-error-in-binary CONECT CONNECT [*]librdkit1t64:
package-name-doesnt-match-sonames librdkit1
--- End Message ---
--- Begin Message ---
Source: rdkit
Source-Version: 202309.3-4
Done: Andrius Merkys <mer...@debian.org>
We believe that the bug you reported is fixed in the latest version of
rdkit, 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 1064...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andrius Merkys <mer...@debian.org> (supplier of updated rdkit 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: Tue, 28 May 2024 00:55:45 -0400
Source: rdkit
Architecture: source
Version: 202309.3-4
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org>
Changed-By: Andrius Merkys <mer...@debian.org>
Closes: 1064311
Changes:
rdkit (202309.3-4) unstable; urgency=medium
.
* Team upload.
* Upload to unstable for 64-bit time_t transition (Closes: #1064311)
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