Hi Greg, Many thanks. I’ll take a look.
Huw > On 20 Nov 2015, at 16:02, Greg Landrum <greg.land...@gmail.com> wrote: > > Hi Huw, > > This is not directly responsive to your question, but if you're working with > anaconda, it is probably easier to just build and install the RDKit using the > conda-rdkit recipes here: > https://github.com/rdkit/conda-rdkit <https://github.com/rdkit/conda-rdkit> > The development branch there pulls from master. > > -greg > > > On Fri, Nov 20, 2015 at 4:26 PM, Huw Jones <huwdjo...@hotmail.com > <mailto:huwdjo...@hotmail.com>> wrote: > Hi there, > > I’ve been building the Python RDKit modules direct from the GitHub repository > recently on an Ubuntu 14.04 LTS VM (i.e. git clone > https://github.com/rdkit/rdkit.git <https://github.com/rdkit/rdkit.git>). > > I use the following aptitude packages for the build process: > > flex 2.5.35-10.1ubuntu2 > bison 2:3.0.2.dfsg-2 > build-essential 11.6ubuntu6 > cmake 2.8.12.2-0ubuntu3 > libboost-dev 1.54.0.1ubuntu1 > libboost-regex-dev 1.54.0.1ubuntu1 > python-dev 2.7.5-5ubuntu3 > libboost-python-dev 1.54.0.1ubuntu1 > python-numpy 1:1.8.2-0ubuntu0.1 > > The build process is as follows: > > git clone https://github.com/rdkit/rdkit.git > <https://github.com/rdkit/rdkit.git> rdkit-latest > source /opt/virtualenv/current/bin/activate > export RDBASE=/path/to/rdkit-latest > cd rdkit-latest > mkdir build > cd build > cmake .. > make -j 2 > make install > cd .. > cp -r rdkit /opt/virtualenv/current/lib/python2.7/site-packages > mkdir /opt/virtualenv/current/lib/python2.7/lib-rdkit > cp lib/* /opt/virtualenv/current/lib/python2.7/lib-rdkit > > I have recently been experiencing this error: > > Python 2.7.10 (default, Nov 20 2015, 07:14:39) > [GCC 4.8.4] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > >>> from rdkit import rdBase > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > ImportError: /opt/virtualenv/current/lib/python2.7/lib-rdkit/libRDBoost.so.1: > undefined symbol: _ZN5boost6python23throw_error_already_setEv > > It looks like this error starts appearing from this commit onwards: > > https://github.com/rdkit/rdkit/commit/9965702691b039c936c3fcca579fbd9ded8f5331 > > <https://github.com/rdkit/rdkit/commit/9965702691b039c936c3fcca579fbd9ded8f5331> > > Any ideas? > > Many thanks as ever. > > Huw Jones > > ------------------------------------------------------------------------------ > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > <mailto:Rdkit-discuss@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > <https://lists.sourceforge.net/lists/listinfo/rdkit-discuss> > >
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