[RDKit] update to 2025.09.3

[se-schmitt]

No description provided.

[fingolfin]

macOS jobs fail:

[17:47:26] In file included from /workspace/srcdir/rdkit/Code/DataStructs/RealValueVect.cpp:11:
[17:47:26] /workspace/srcdir/rdkit/Code/DataStructs/RealValueVect.h:96:23: error: implicit instantiation of undefined template 'std::vector<double>'
[17:47:26]    96 |   std::vector<double> d_data;
[17:47:26]       |                       ^
[17:47:26] /opt/x86_64-apple-darwin14/x86_64-apple-darwin14/sys-root/usr/include/c++/v1/iosfwd:217:28: note: template is declared here
[17:47:26]   217 | class _LIBCPP_TEMPLATE_VIS vector;
[17:47:26]       |                            ^
[17:47:26] 1 error generated.

And for w64-mingw32 (i.e., Windows) it failed as it did not found a suitable version of boost_jll?

[fingolfin]

The build error looks as if the rdkit is missing an #include <vector> in one or multiple files. (It is possible this works in GCC's C++ lib because of indirect includes).

You could try patching rdkit/Code/DataStructs/RealValueVect.h to insert that, and see if it helps (at least to progress beyond compiling rdkit/Code/DataStructs/RealValueVect.cpp)