Hi guys,
I am currently trying to create a conda recipe for RDKit to streamline the
installation process (by simply doing "conda install rdkit" in the future).
Before that I successfully (I think so at least) created a recipe to build
boost, which is required for RDKit. The build.sh script used by conda looks
like this:
mkdir build
cd build
cmake
\
-DRDK_INSTALL_INTREE=OFF
\
-DCMAKE_INSTALL_PREFIX=$PREFIX
\
-DBOOST_ROOT=$PREFIX
\
-DPYTHON_LIBRARY=$PREFIX/lib/python${PY_VER}/config/libpython${PY_VER}.a \
-DPYTHON_INCLUDE_DIR=$PREFIX/include/python${PY_VER}
\
-DPYTHON_NUMPY_INCLUDE_PATH=$SP_DIR/numpy/core/include
\
..
make -j4
make install
which builds and installs RDKit successfully in the anaconda environment.
However, using it fails with the following 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/adrian/Software/anaconda/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/adrian/Software/anaconda/lib/python2.7/site-packages/rdkit/rdBase.so,
2): Library not loaded: @loader_path/../../../libRDBoost.1.dylib
Referenced from:
/Users/adrian/Software/anaconda/lib/python2.7/site-packages/rdkit/rdBase.so
Reason: no suitable image found. Did find:
/Users/adrian/Software/anaconda/lib/python2.7/site-packages/rdkit/../../../libRDBoost.1.dylib:
truncated mach-o error: segment __LINKEDIT extends to 2245228 which is past
end of file 2245227
/Users/adrian/Software/anaconda/lib/python2.7/site-packages/rdkit/../../../libRDBoost.1.dylib:
truncated mach-o error: segment __LINKEDIT extends to 2245228 which is past
end of file 2245227
The rdBase library is linked to
$ otool -L
/Users/adrian/Software/anaconda/lib/python2.7/site-packages/rdkit/rdBase.so
/Users/adrian/Software/anaconda/lib/python2.7/site-packages/rdkit/rdBase.so:
@loader_path/../../../libRDGeneral.1.dylib (compatibility version 1.0.0,
current version 2013.9.1)
@loader_path/../../../libRDBoost.1.dylib (compatibility version 1.0.0,
current version 2013.9.1)
@loader_path/../../../libboost_python.dylib (compatibility version 0.0.0,
current version 0.0.0)
/usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version
60.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
1197.1.1)
/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version
2577.0.0)
Maybe somebody who has experience with building RDKit packages knows what
the problem might be. As you can see this is on Mac OS X.
Cheers
Adrian
------------------------------------------------------------------------------
Android is increasing in popularity, but the open development platform that
developers love is also attractive to malware creators. Download this white
paper to learn more about secure code signing practices that can help keep
Android apps secure.
http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
