On Sun, Apr 17, 2016 at 2:43 PM, Brian Kelley <[email protected]> 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 <[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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>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
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