Hi Joerg, in order to run the tests and use the local rdkit installation, I think you'll also need to set the LD_LIBRARY_PATH environment variable to include $RDBASE/lib and the PYTHONPATH environment variable to include $RDBASE:
export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH export PYTHONPATH=$RDBASE:$PYTHONPATH (there might be additional issues, but those two env variables are a likely cause for the failing tests). An easier way to get the latest RDKit release (including the python bindings, but not the Java wrappers) is provided by the conda packages that are available from the rdkit channel on https://anaconda.org. With a conda-based environment the whole installation process could reduce to a single command e.g.: $ conda create -c rdkit -n my_rdkit_env rdkit HTH, Riccardo On Sat, Sep 5, 2015 at 4:08 PM, Jörg Kurt Wegner <[email protected]> wrote: > Hi all, I am trying to get RDKit to work from a source install on RHEL6. > I already disabled Java (due to errors), but would like to get Python to > work, though neither a Python import, nor ctest seem to work. > So, Python-RDKit was not correctly installed. Here the toolchain I use, > any idea why this is not working? > > ## dependencies > #Boost version: 1.55.0 > #SWIG: /usr/local/bin/swig (found version "3.0.7") > > cd /tmp > wget > http://sourceforge.net/projects/rdkit/files/rdkit/Q1_2015/RDKit_2015_03_1.tgz > tar xzvf RDKit_2015_03_1.tgz > export RDBASE=/tmp/rdkit-Release_2015_03_1 > cd $RDBASE > mkdir build > cd build > wget -nv -O junit.jar > http://search.maven.org/remotecontent?filepath=junit/junit/4.12/junit-4.12.jar > mkdir ../External/java_lib > mv junit.jar ../External/java_lib/ > export DEPENDENCY_BOOST=boost_1_55_0 > export BOOST_ROOT=/usr/local/src/$DEPENDENCY_BOOST > export BOOST_INCLUDEDIR=/usr/local/include > export BOOST_LIBRARYDIR=/usr/local/lib > export PYTHONBASE=/usr/local/lib/python2.7 > export > PYTHON_NUMPY_INCLUDE_PATH=/usr/local/lib/python2.7/site-packages/numpy/core/include > export PYTHONPATH=$PYTHONBASE/site-packages:$PYTHONPATH > cmake -D Boost_NO_SYSTEM_PATHS=ON -D RDK_BUILD_SWIG_WRAPPERS=ON -D > RDK_BUILD_SWIG_JAVA_WRAPPER=OFF -D > PYTHON_LIBRARY=$PYTHONBASE/config/libpython2.7.a -D > PYTHON_INCLUDE_DIR=$PYTHONBASE -D > PYTHON_EXECUTABLE=/usr/local/bin/python2.7 .. > #cmake -D Boost_NO_SYSTEM_PATHS=ON -D RDK_BUILD_SWIG_WRAPPERS=ON -D > PYTHON_LIBRARY=/usr/local/lib/python2.7/config/libpython2.7.a -D > PYTHON_INCLUDE_DIR=/usr/local/include/python2.7/ -D > PYTHON_EXECUTABLE=/usr/local/bin/python2.7 .. > make -j8 > make install > ctest > > Start 1: testDict > 1/90 Test #1: testDict ......................... Passed 0.03 sec > Start 2: testDataStructs > 2/90 Test #2: testDataStructs .................. Passed 0.01 sec > Start 3: pyBV > 3/90 Test #3: pyBV .............................***Failed 0.02 sec > Start 4: pyDiscreteValueVect > 4/90 Test #4: pyDiscreteValueVect ..............***Failed 0.03 sec > Start 5: pySparseIntVect > 5/90 Test #5: pySparseIntVect ..................***Failed 0.03 sec > > > /.Joerg > > > > -- > Google+ <https://plus.google.com/116731043002877336055/posts>, LinkedIn > <http://linkedin.com/in/joergkurtwegner>, Twitter > <http://twitter.com/joergkurtwegner>, FaceBook > <http://www.facebook.com/joergkurtwegner> > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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