No, afraid that doesn't seem to help.
The boost libs seem to be in /usr/lib/x86_64-linux-gnu but adding that
directory to LD_LIBRARY_PATH doesn't fix the problem.
In fact, for the plain rdkit image it works fine with just $RDBASE being
on LD_LIBRARY_PATH.
Tim
On 18/04/2016 19:43, Paolo Tosco wrote:
Dear Tim,
did you check that the Boost libraries you linked the RDKit against
are in the postgres user LD_LIBRARY_PATH? You might need to login as
root, then su postgres, and echo "export
LD_LIBRARY_PATH=</path/to/Boost/libs>" > ~/.bashrc. Then, as root,
restart the postgres service. That fixed the problem for me.
Kind regards,
p.
On 18/04/2016 09:18, Tim Dudgeon wrote:
I spoke too soon!
I'm still having problem with postgres cartridge.
psql -c 'create extension rdkit' rdkitdb
ERROR: could not load library
"/usr/lib/postgresql/9.4/lib/rdkit.so":
/usr/lib/postgresql/9.4/lib/rdkit.so: undefined symbol:
_ZTIN5boost6detail16thread_data_baseE
Is something else needed for cartridge?
The docker image is here:
https://github.com/InformaticsMatters/rdkit_cartridge/blob/master/Dockerfile
which is based on rdkit build that now works OK based on the earlier
discussions in this thread.
Tim
On 17/04/2016 13:43, Brian Kelley 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; |
It looks like I should add a PR to detect this at build time?
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> 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>
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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