Brian: thanks, adding libboost-system-dev libboost-thread-dev and
libboost-serialization-dev solves the problem.
Greg: confirmed, flex and bison are not needed.
Many thanks.
Tim
On 17/04/2016 15:28, Greg Landrum wrote:
On Sun, Apr 17, 2016 at 2:43 PM, Brian Kelley <fustiga...@gmail.com
<mailto:fustiga...@gmail.com>> wrote:
Now that we made thread safe the default, you also need
boost-system ( and boost-serialization for FilterCatalog
serialization)
|Here is the apt get we use to configure docker files.|
|apt install -y wget flex bison build-essential python-numpy cmake
python-dev sqlite3 libsqlite3-dev libboost-dev libboost-system-dev
libboost-thread-dev libboost-serialization-dev libboost-python-dev
libboost-regex-dev; |
Flex and bison don't need to be on this list.
It looks like I should add a PR to detect this at build time?
We should probably add the explicit boost-system dependency to the
appropriate CMakeLists.txt. It's technically not required for some
older boost versions (I want to say pre 1.51, but that may not be
correct), but it's not a heavy dependency. Serialization is a (very)
nice to have, so don't think it should show up as an actual
requirement in the CMakeLists.txt (i.e. I think the status quo is fine).
-greg
I admit to being confused why this builds but doesn't run...
See here for more details:
https://github.com/rdkit/rdkit/issues/762
----
Brian Kelley
On Apr 17, 2016, at 8:28 AM, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
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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