Dear all: I searched the mailing list here and came up with a very similar issue: https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg08044.html However, this helped me only so much. I am trying to compile rdkit from source and I followed the steps outlined in the manual: bash Anaconda3-5.2.0-x86_64.sh conda install -y cmake cairo pillow eigen pkg-config conda install -y boost-cpp boost py-boost conda install -y gxx_linux-64 git clone https://github.com/rdkit/rdkit.git cd rdkit mkdir build && cd build cmake -DPy_ENABLE_SHARED=1 \ -DRDK_INSTALL_INTREE=ON \ -DRDK_INSTALL_STATIC_LIBS=OFF \ -DRDK_BUILD_CPP_TESTS=ON \ -DPYTHON_NUMPY_INCLUDE_PATH="$(python -c 'import numpy ; print(numpy.get_include())')" \ -DBOOST_ROOT="$CONDA_PREFIX" \ .. This process stops with the following error message for the RingDecomposerLib: -- The C compiler identification is GNU 7.3.0 -- The CXX compiler identification is GNU 7.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /home/xyz/anaconda3/envs/comp_rdkit/bin/x86_64-conda_cos6-linux-gnu-cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /home/xyz/anaconda3/envs/comp_rdkit/bin/x86_64-conda_cos6-linux-gnu-c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Found Catch2: /home/xyz/software/rdkit_09012020/External/catch/catch CATCH: /home/xyz/software/rdkit_09012020/External/catch/catch -- Found PythonInterp: /home/xyz/anaconda3/envs/comp_rdkit/bin/python (found version "3.6.12") -- Found PythonLibs: /home/xyz/anaconda3/envs/comp_rdkit/lib/ libpython3.6m.so (found version "3.6.12") PYTHON Py_ENABLE_SHARED: 0 PYTHON USING LINK LINE: -pthread -shared -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,-rpath,/home/xyz/anaconda3/envs/comp_rdkit/lib -L/home/xyz/anaconda3/envs/comp_rdkit/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,-rpath,/home/mmetz/anaconda3/envs/comp_rdkit/lib -L/home/mmetz/anaconda3/envs/comp_rdkit/lib -- Found Eigen3: /home/xyz/anaconda3/envs/comp_rdkit/include/eigen3 (Required is at least version "2.91.0") -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found Boost: /home/xyz/anaconda3/envs/comp_rdkit/lib/cmake/Boost-1.73.0/BoostConfig.cmake (found suitable version "1.73.0", minimum required is "1.67.0") found components: serialization == Using strict rotor definition -- Found Boost: /home/xyz/anaconda3/envs/comp_rdkit/lib/cmake/Boost-1.73.0/BoostConfig.cmake (found suitable version "1.73.0", minimum required is "1.67.0") found components: system iostreams -- maeparser include dir set as '/usr/local/include' -- maeparser libraries set as '/usr/local/lib64/libmaeparser.so' -- Found maeparser: /usr/local/include -- coordgen include dir set as /usr/local/include -- coordgen libraries set as '/usr/local/lib64/libcoordgen.so' -- Found coordgen: /usr/local/include Downloading https://github.com/rareylab/RingDecomposerLib/archive/v1.1.3_rdkit.tar.gz... % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:05:00 --:--:-- 0 curl: (28) Operation timed out after 300137 milliseconds with 0 out of 0 bytes received CMake Error at Code/cmake/Modules/RDKitUtils.cmake:213 (MESSAGE): The md5 checksum for
/home/xyz/software/rdkit_09012020/External/RingFamilies/RingDecomposerLib-v1.1.3_rdkit.tar.gz is incorrect; expected: e9a0bcdda8b921a35e812b9888a9a874, found: d41d8cd98f00b204e9800998ecf8427e Call Stack (most recent call first): External/RingFamilies/CMakeLists.txt:12 (downloadAndCheckMD5) -- Configuring incomplete, errors occurred! See also "/home/xyz/software/rdkit_09012020/build/CMakeFiles/CMakeOutput.log". See also "/home/xyz/software/rdkit_09012020/build/CMakeFiles/CMakeError.log". So it seems the Checksum is causing issues. At first I had Checksum issues with the Catch2, maeparser and coordgen too. Following Dan Nealschneider's comment I downloaded the tar.gz files and installed them. That worked nicely. Some of the libraries are installed under /usr/local, which is at this point fine. I also downloaded the RingDecomposerLib and installed it locally but cmake does not seem to pick up the necessary files. I also tried to make some minor changes to the CMakeList.txt file. But not with much luck. Does anybody know how I can tell cmake where the RingDecomposerLib files are? Thank you very much in advance, Markus
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