I've hit the same issue. Any thoughts on what the underlying issue is
(without reverting to using anaconda)?
An example that illustrates this is here:
https://github.com/InformaticsMatters/rdkit
Tim
On 20/11/2015 16:02, Greg Landrum 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
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).
*I use the following aptitude packages for the build process:*
flex2.5.35-10.1ubuntu2
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 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
Any ideas?
Many thanks as ever.
Huw Jones
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