Your message dated Tue, 08 Sep 2026 10:19:10 +0000
with message-id <[email protected]>
and subject line Bug#1146843: fixed in rdkit 202603.4-2
has caused the Debian Bug report #1146843,
regarding rdkit: FTBFS with new eigen3 and also fails in arm64
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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--
1146843: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1146843
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:rdkit
Version: 202603.4-1
User: [email protected]
Usertags: python3.15
Tags: patch, ftbfs, forky, sid
Severity: serious
Hi!
While rebuilding the python related packages against the Python 3.15rc1
version we found that rdkit fails to build from source [1], now because
it fails to detect a newer eigen3.
Upstream commit d8ce92b61ce356bc2764e13f0d4b9a5df48094c5 [2] improved
handling of finding eigen and solves the problem.
After applying this fix, I found that it also fails on arm64
architecture [3], due to a different reason.
This one can be fixed with upstream commit
fab08afd7000ac6000358a7c79e95cc1940e1c39 [4] test: increase
DistGeomHelpers compareConfs tolerance to 0.1
Please consider applying these patches as well as the one reported on
#1146588, to get rdkit to build successfully.
Happy hacking,
[1]: https://debusine.debian.net/debian/r-python-python3.15/artifact/4631477/
[2]:
https://github.com/rdkit/rdkit/commit/d8ce92b61ce356bc2764e13f0d4b9a5df48094c5
[3]: https://debusine.debian.net/debian/r-python-python3.15/artifact/4632989/
[4]:
https://github.com/rdkit/rdkit/commit/fab08afd7000ac6000358a7c79e95cc1940e1c39
--
"Can you imagine what I would do if I could do all I can?" -- Sun Tzu
Saludos /\/\ /\ >< `/
From: Greg Landrum <[email protected]>
Date: Wed, 2 Sep 2026 18:10:13 +0200
Subject: improved handling of finding eigen (#9543)
Origin: upstream, https://github.com/rdkit/rdkit/commit/d8ce92b61ce356bc2764e13f0d4b9a5df48094c5
* improved handling of finding eigen
Fixes #8896
---
CMakeLists.txt | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -407,9 +407,9 @@ else(RDK_BUILD_PYTHON_WRAPPERS)
find_package(Boost ${RDK_BOOST_VERSION} REQUIRED CONFIG)
endif(RDK_BUILD_PYTHON_WRAPPERS)
-find_package(Eigen3)
+find_package(Eigen3 NO_MODULE)
if(RDK_BUILD_DESCRIPTORS3D)
- if(NOT EIGEN3_FOUND)
+ if(NOT TARGET Eigen3::Eigen)
add_subdirectory(External/Eigen)
endif()
target_compile_definitions(rdkit_base INTERFACE "-DRDK_BUILD_DESCRIPTORS3D")
From: younes ouzza <[email protected]>
Date: Wed, 22 Jul 2026 11:16:03 +0100
Subject: test: increase DistGeomHelpers compareConfs tolerance to 0.1 (#9413)
Origin: upstream, https://github.com/rdkit/rdkit/commit/fab08afd7000ac6000358a7c79e95cc1940e1c39
This prevents false test failures on systems using -march=native,
where compiler optimizations cause tiny, harmless math differences.
(See issue #[9406])
---
Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
--- a/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp
+++ b/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp
@@ -135,7 +135,7 @@ void compareConfs(const RWMol *m, const
RDGeom::Point3D pt1i = conf1.getAtomPos(i);
RDGeom::Point3D pt2i = conf2.getAtomPos(i);
- CHECK((pt1i - pt2i).length() < 0.05);
+ CHECK((pt1i - pt2i).length() < 0.1);
}
}
} // namespace
--- End Message ---
--- Begin Message ---
Source: rdkit
Source-Version: 202603.4-2
Done: Andrius Merkys <[email protected]>
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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andrius Merkys <[email protected]> (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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 08 Sep 2026 05:59:04 -0400
Source: rdkit
Architecture: source
Version: 202603.4-2
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Andrius Merkys <[email protected]>
Closes: 1136322 1146843
Changes:
rdkit (202603.4-2) unstable; urgency=medium
.
* Backport modified upstream commit to fix FTBFS with eigen3 >= 5.0.0
(Closes: #1136322)
* Backport upstream commit increasing test tolerance to fix test failure on
arm64 (Closes: #1146843)
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