Hi,
On Sat, Feb 2, 2013 at 4:00 PM, hatmatrix <[email protected]> wrote:
> Hi, I'm trying to install RDKit for access from Python.
>
> I'm using Enthought Python Distribution (academic) on Mac OS X 10.7 (located
> in /Library/Frameworks/EPD64.framework). I've installed boost through
> MacPorts in /opt/local.
>
> export RDBASE=~/src/rdkit
> export DYLD_LIBRARY_PATH=$RDBASE/lib:/opt/local
> export PYTHONPATH=$PYTHONPATH:$RDBASE
> cd $RDBASE
> mkdir build && cd build
> cmake -D
> PYTHON_LIBRARY=/Library/Frameworks/EPD64.framework/Versions/Current/lib/python2.7/config/libpython2.7.a
> \
> -D
> PYTHON_INCLUDE_DIR=/Library/Frameworks/EPD64.framework/Versions/Current/include/python2.7/
> \
> -D
> PYTHON_EXECUTABLE=/Library/Frameworks/EPD64.framework/Versions/Current/bin/python
> ..
> make
> sudo make install
so far, so good.
> cd ..
> python setup.py build
> sudo python setup.py install
These shouldn't be necessary. In fact, I should probably get rid of
that setup.py script entirely.
The usual approach, as described in the INSTALL documents and on the
wiki is to set PYTHONPATH to include $RDBASE.
> ('python' is linked to the Enthought Python executable so I am sure it's not
> a conflict there).
>
> In any case, I get the error:
>
>>>> from rdkit import Chem
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File
> "/Library/Frameworks/EPD64.framework/Versions/Current/lib/python2.7/site-packages/rdkit/Chem/__init__.py",
> line 18, in <module>
> from rdkit import rdBase
> ImportError:
> dlopen(/Library/Frameworks/EPD64.framework/Versions/Current/lib/python2.7/site-packages/rdkit/rdBase.so,
> 2): Library not loaded: libRDGeneral.1.dylib
> Referenced from:
> /Library/Frameworks/EPD64.framework/Versions/Current/lib/python2.7/site-packages/rdkit/rdBase.so
> Reason: image not found
please try removing the directory
/Library/Frameworks/EPD64.framework/Versions/Current/lib/python2.7/site-packages/rdkit,
setting the PYTHONPATH as described above, making sure
DYLD_LIBRARY_PATH includes $RDBASE/lib and then try again.
-greg
>
> But the image does exist:
>
> $ ls -lah
> /Library/Frameworks/EPD64.framework/Versions/Current/lib/python2.7/site-packages/rdkit/*.so
>
> shows
>
> -rwxr-xr-x 1 root wheel 1.7M Feb 2 15:41
> /Library/Frameworks/EPD64.framework/Versions/Current/lib/python2.7/site-packages/rdkit/rdBase.so*
>
> And
>
> $ find $RDBASE -iname "libRDGeneral.1.dylib"
>
> shows that it exists in $RDBASE/lib/
>
> /Users/hatmatrix/src/rdkit/build/lib/libRDGeneral.1.dylib
> /Users/hatmatrix/src/rdkit/lib/libRDGeneral.1.dylib
>
> There was a similar error message reported on this thread:
> http://www.mail-archive.com/[email protected]/msg01873.html
> with a solution that the RDKit lib/ directory needed to be defined in
> DY_LIBRARY_PATH.
>
> so I've added this statement
> export DY_LIBRARY_PATH=$RDBASE/lib
>
> which does not work; I wasn't sure if this environment variable needed to be
> set before installation along with RDBASE, DYLD_LIBRARY_PATH, and
> PYTHONPATH, so I deleted the build/ directory and rebuilt it after setting
> this variable. However, I still get the same error.
>
> I would appreciate any further advice.
>
> Many thanks.
>
> hm
>
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