build RDKit package from scratch

first download up-to-date package from its Git repository: https://github.com/rdkit/rdkit, either zip file or git-repo.

cd RDKIT_ROOT
mkdir build
cd build
cmake ..
make
make install
  

for my system, it has two problems occurred, when makeing..

failed on shared library

  Linking CXX shared library ../../lib/libRDBoost.so
/usr/bin/ld: /home/xiang/Applications/pyenv/versions/3.8.3/lib/libpython3.8.a(obmalloc.o):
relocation R_X86_64_PC32 against symbol `stderr@@GLIBC_2.2.5' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status
make[2]: *** [Code/RDBoost/CMakeFiles/RDBoost.dir/build.make:91: lib/libRDBoost.so.1.2016.09.1.dev1] Error 1
make[1]: *** [CMakeFiles/Makefile2:2323: Code/RDBoost/CMakeFiles/RDBoost.dir/all] Error 2
make: *** [Makefile:163: all] Error 2
  

after Googling awhile, I found the solution from this question:

https://stackoverflow.com/questions/42582712/relocation-r-x86-64-32s-against-py-notimplementedstruct-can-not-be-used-when

which is due to libpython3.8.a installed by pyenv(see above the python path) not a --enable-shared object.

I solved this problem by using the system wide python.

failed on #include <boost/python/numeric.hpp>

  Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o
/home/xiang/Applications/rdkit-master/Code/DataStructs/Wrap/DataStructs.cpp:18:10: fatal error: boost/python/numeric.hpp: No such file or directory
   18 | #include <boost/python/numeric.hpp>
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make:63: Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:2518: Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/all] Error 2
make: *** [Makefile:163: all] Error 2
  

this problem is due to the removing of head files of numeric.hpp of boost since version 1.65(maybe), thus to solve this problem, either:

install version libboost-dev==1.58 (for Ubuntu system, for any other OS, please find the corresponding correct package name)
inside the source codes, modify the header file to numpy.hpp

instead of all those things, I proposed a simplest solution: by creating a symbolic link: please refer to this link: https://github.com/BerkeleyAutomation/meshpy/issues/7

interestingly, I happen to find a issue report for RDKit at https://github.com/rdkit/rdkit/issues/1581, is this problem really fixed??

remember, today's date is Feb 22, 2022, and their discussions were on early 2018.

Important Notes!!

in its official document, it provides an alternative way to specify which python executable to use, however it does not work as it expects: https://www.rdkit.org/docs/Install.html#specifying-an-alternate-python-installation

cmake -D PYTHON_LIBRARY=/usr/lib/python3.6/config/libpython3.6.a -D PYTHON_INCLUDE_DIR=/usr/include/python3.6/ -D PYTHON_EXECUTABLE=/usr/bin/python3 ..
  

The reason is that it is using a static python configuration object (generally, any compiled object ends with a .a), thus to properly fix it, one should change this object to the shared object, e.g., .so file.

cmake -D PYTHON_LIBRARY=/usr/lib/python3.6/config/libpython3.6.so -D PYTHON_INCLUDE_DIR=/usr/include/python3.6/ -D PYTHON_EXECUTABLE=/usr/bin/python3 ..
  

see the change: libpython3.6.a to libpython3.6.so.