Dear Benjamin,
On Sun, Oct 4, 2009 at 6:09 PM, Benjamin Esham <[email protected]> wrote: > Greg Landrum wrote: > > at that point, you should be able to start Python and do: > > from rdkit import RDConfig > > from rdkit import rdBase > > from rdkit import Chem > > These test, in order, $PYTHONPATH, $DYLD_LIBRARY_PATH, your general > configuration. If all three imports work, you should be able to use > the RDKit. > > Hi Greg, > Thanks a lot for these binaries! Unfortunately the second and third tests > fail, and the culprit seems to be the boost libraries. The first import > command works fine, but the second gives >>>> from rdkit import rdBase > Fatal Python error: Interpreter not initialized (version mismatch?) > Abort > and if I relaunch python and try just the third line, I get the same error. > From what I can find online ([1], [2], [3]), this error is probably being > caused by a mismatch between the versions of boost and python used to build > the binaries and the versions of boost and python I have installed. I use > fink to install packages like that, so I tried three different boost > packages (labeled for python 2.5, python 2.6, and the system-installed > python) and running the python interpreter as version 2.5 or 2.6, but I got > the same error every time. I've used the system python to build and run everything: ~ > type python python is hashed (/usr/bin/python) ~ > python Python 2.5.1 (r251:54863, Feb 6 2009, 19:02:12) [GCC 4.0.1 (Apple Inc. build 5465)] on darwin Type "help", "copyright", "credits" or "license" for more information. I included the required boost shared libraries in the binary distribution, so if you have $RDBASE/bin at the front of your DYLD_LIBRARY_PATH the libs I provided ought to be picked up and things "ought to" work. > > I'm guessing that this isn't a problem with RDKit per se, but merely an > annoyance with boost. Unfortunately, I think the upshot is probably that > it's not really feasible to distribute "binaries" of RDKit like I asked for, > since boost seems really sensitive to configuration changes. My hope was to avoid this by including the boost libraries in the binary distribution. > On a completely different note, are there prebuilt packages of RDKit for any > Linux distributions? I'd be willing to install e.g. Ubuntu on a virtual > machine or thumbdrive if it meant that I could set this all up without > worrying about version mismatches or compiling anything. > Thanks for all of the help! I have done binaries in the past and can do them again, but if you don't mind playing along, I'd like to try iterating on the mac binary a bit. Thanks. -greg
