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 <[email protected]> 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 <[email protected]> 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:
>>>
>>> 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 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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>>> Rdkit-discuss mailing list
>>> [email protected]
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>>
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