I just tried to install on a fresh OSX, I had installed Anaconda before RDKit, then tried to brew RDKit. I got the following errors during the brew
For Bash, put something like this in your $HOME/.bashrc export RDBASE=/usr/local/share/RDKit export PYTHONPATH=$PYTHONPATH:/usr/local/lib/python2.7 :: Anaconda 1.7.0 (x86_64)/site-packages Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/SimDivFilters/rdSimDivPickers.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/rdBase.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/Numerics/rdAlignment.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/ML/InfoTheory/rdInfoTheory.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/ML/InfoTheory/cEntropy.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/ML/FeatureSelect/rdFeatSelect.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/ML/Data/cQuantize.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/ML/Cluster/Clustering.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/Geometry/rdGeometry.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/ForceField/rdForceField.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/DistanceGeometry/DistGeom.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/DataStructs/cDataStructs.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/DataManip/Metric/rdMetricMatrixCalc.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/Chem/rdSLNParse.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/Chem/rdShapeHelpers.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/Chem/rdPartialCharges.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/Chem/rdMolTransforms.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/Chem/rdmolops.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/Chem/rdmolfiles.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/Chem/rdMolDescriptors.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/Chem/rdMolChemicalFeatures.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/Chem/rdMolCatalog.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/Chem/rdMolAlign.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/Chem/rdfragcatalog.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/Chem/rdForceFieldHelpers.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/Chem/rdDistGeom.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/Chem/rdDepictor.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/Chem/rdChemReactions.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/Chem/rdChemicalFeatures.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/python2.7/site-packages/rdkit/Chem/rdchem.so Warning: Could not fix libpython2.7.dylib in /usr/local/Cellar/rdkit/2013.06.1/lib/libRDBoost.2013.06.1.dylib Then when I tried to create a mol in python I got Python 2.7.5 |Anaconda 1.7.0 (x86_64)| (default, Jun 28 2013, 22:20:13) [GCC 4.0.1 (Apple Inc. build 5493)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> from rdkit import Chem Fatal Python error: PyThreadState_Get: no current thread Abort trap: 6 Then I removed Anaconda and tried again and had no problems at all. Best, Nick Nicholas C. Firth | PhD Student | Cancer Therapeutics The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey | SM2 5NG T 020 8722 4033 | E nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter @ICRnews ________________________________________ From: Greg Landrum [greg.land...@gmail.com] Sent: 27 September 2013 15:09 To: Zachary Charlop-Powers Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Anaconda Biuild on MacOSX On Fri, Sep 27, 2013 at 4:03 PM, Zachary Charlop-Powers <zchar...@mail.rockefeller.edu<mailto:zchar...@mail.rockefeller.edu>> wrote: Hi Greg, Thanks for spotting that typo. When I update the paths as you suggest the import error changes. It looks like that was the problem for loading the RDKit python libraries. The new Import error, however, suggests that now there is a problem loading tlibboost_python.dylib. I don't see this in the ~/anaconda/include/boost folder nor in ~/ rdkit/lib. One of the steps in the wiki page had you copy that file from the boost build directory to ~/anaconda/lib. It's this step: cp stage/lib/*.so ~/anaconda/lib Are there boost libs in that directory? -greg The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. 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