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.
Here is the changed configuration with the fixed typo:
export RDBASE=/Users/zachpowers/rdkit/
export DYLD_LIBRARY_PATH=$RDBASE/lib
export PYTHONPATH=$PYTHONPATH:$RDBASE
here is the previous error message:
ImportError:
dlopen(/Users/zachpowers/anaconda/python.app/Contents/lib/python2.7/site-packages/rdkit/rdBase.so,
2): Library not loaded: libRDGeneral.1.dylib
Here is the new Import error that is related to the boost libraries:
In [16]: from rdkit import Chem
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-16-17d7acb427ab> in <module>()
----> 1 from rdkit import Chem
/Users/zachpowers/rdkit/rdkit/Chem/__init__.py in <module>()
16
17 """
---> 18 from rdkit import rdBase
19 from rdkit import RDConfig
20
ImportError: dlopen(/Users/zachpowers/rdkit/rdkit/rdBase.so, 2): Library not
loaded: libboost_python.dylib
Referenced from: /Users/zachpowers/rdkit/rdkit/rdBase.so
Reason: image not found
In [17]:
Thanks,
zach cp
On Sep 27, 2013, at 9:17 AM, Greg Landrum
<greg.land...@gmail.com<mailto:greg.land...@gmail.com>>
wrote:
Hi Zach,
On Thu, Sep 26, 2013 at 4:02 PM, Zachary Charlop-Powers
<zchar...@mail.rockefeller.edu<mailto:zchar...@mail.rockefeller.edu>> wrote:
After following the directions on the AnacondaBuild webpage I configure my
.zshrc as follows (rdkit root is my homedirectory/rdkit ):
export PATH=/usr/local/bin:$PATH
export RDBase=/Users/zachpowers/rdkit/
export DYLD_LIBRARY_PATH=$RDBASE/lib
export PYTHONPATH=$PYTHONPATH:$RDBASE
export PATH=~/anaconda/bin:$PATH
When I try to load RDKit I encounter an error:
In [1]: from rdkit import Chem
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-17d7acb427ab> in <module>()
----> 1 from rdkit import Chem
/Users/zachpowers/anaconda/python.app/Contents/lib/python2.7/site-packages/rdkit/Chem/__init__.py
in <module>()
16
17 """
---> 18 from rdkit import rdBase
19 from rdkit import RDConfig
20
ImportError:
dlopen(/Users/zachpowers/anaconda/python.app/Contents/lib/python2.7/site-packages/rdkit/rdBase.so,
2): Library not loaded: libRDGeneral.1.dylib
Referenced from:
/Users/zachpowers/anaconda/python.app/Contents/lib/python2.7/site-packages/rdkit/rdBase.so
Reason: image not found
I have tried changing the DYLD_Library and PYTHONPATH directories to include
the folders with libRDGeneral.1.dylib but am still running into trouble.
I was not able to reproduce this particular problem, but I had other problems
making the RDKit build work with anaconda on my Mac. I am still trying to get
to the bottom of those.
Looking a second time, there is a typo in the above. You have:
export RDBase=/Users/zachpowers/rdkit/
export DYLD_LIBRARY_PATH=$RDBASE/lib
export PYTHONPATH=$PYTHONPATH:$RDBASE
but I think you should have:
export RDBASE=/Users/zachpowers/rdkit/
export DYLD_LIBRARY_PATH=$RDBASE/lib
export PYTHONPATH=$PYTHONPATH:$RDBASE
Can you please give that a try and see if it helps?
-greg
Zach Charlop-Powers
Post-Doctoral Fellow
Laboratory of Genetically Encoded Small Molecules
Rockefeller University
zchar...@rockefeller.edu<mailto:zchar...@rockefeller.edu>
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