Hi Jörg,
if you install the "classical" way, you could also put an "rdkit.conf"
into "/etc/ld.so.conf.d/" containing the following:
/your/path/to/RDKit/lib
and run "sudo ldconfig" after "make install" and before "ctest" to
update the library paths. Also, in the past I had problems with the
package from Sourceforge. Try cloning the GitHub version (git clone
https://github.com/rdkit/rdkit.git) instead.
Kind regards,
Axel
On 05.09.2015 17:26, Riccardo Vianello wrote:
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] <mailto:[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
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