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
