Quick update in case others run into my segmentation fault problem: I figured out that my problem had to do with how python libraries are compiled in conda. As far as I understand it, conda compiles static python libraries, and the dynamic library that I was using does not necessarily reference the python that my conda environment provided. Long story short, if I add the following line to my CMakeLists.txt and do not try to link the conda python library with target_link_libraries, my problem goes away:
set_target_properties(rdkit_extension PROPERTIES LINK_FLAGS "-undefined dynamic_lookup") Also, thanks for the namespace tip! This helped me solve another issue I ran into after the segmentation fault issue where the original RDKit ReactionRunner functions were being used still even though my new ones were defined (and I thought I was importing them in my python code). I guess the old ones were overwriting my new ones, since they were in the same namespace. - Kovas On 5/31/18, 10:50 AM, "Paul Emsley" <[email protected]> wrote: On 31/05/2018 02:00, Kovas Palunas wrote: > If anyone has an idea for what is going wrong with my setup, or can point me to general tutorials for how to > get something like this working, I’m a little stuck at the moment. > When you make you copy of ReactionRunner.cpp/.h change them so that they use your namespace rather than RDKit:: Paul. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
