Hi Greg,
Cheers for the reply. You were right, the problem was the version of boost.
I imagine this is a common problem if you use a Homebrew version of Python.
(Homebrew even gives you a warning that this may be the case at the end of its
install)
The quickest fix I found is to run these commands
$ brew rm boost
$ brew install --with-icu --build-from-source boost
Thanks a lot,
J.
On 1 Mar 2014, at 01:24, Greg Landrum
<greg.land...@gmail.com<mailto:greg.land...@gmail.com>> wrote:
Hi,
On Fri, Feb 28, 2014 at 4:44 PM, Joshua Meyers
<joshua.mey...@icr.ac.uk<mailto:joshua.mey...@icr.ac.uk>> wrote:
Hi,
I have been trying to use rdkit in python but cannot seem to get it to import
properly
RDKit works fine through C++, I have compiled and can run programs but it will
not import as a python module
from rdkit import Chem
Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6
I am using Mac OS X 10.8.5 and have home-brewed version of rdkit
I have two versions of Python installed (the Mac default, and a newer version
in /usr/local/bin/python which I believe is the problem but I can't seem to fix
it through altering the $PATH variable in the terminal
This is almost always caused by using a different version of python/boost than
the one you used to build the RDKit, so I guess it is the second installation
that's causing the problem.
Based on the log file, it looks like you actually did use the system python in
that session, could it be that /usr/local/bin/python was used by homebrew to
build the rdkit?
If you try explicitly running /usr/local/bin/python, can you import the rdkit
from there?
-greg
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