Hi Gonzalo,
These failures look like this:
2/198 Test #2: pyCoordGen .............................***Failed
0.04 sec
Traceback (most recent call last):
File "/home/gonzalo/rdkit/External/CoordGen/Wrap/testCoordGen.py", line
13, in <module>
from rdkit.Chem import rdCoordGen, rdMolAlign
ModuleNotFoundError: No module named 'rdkit'
That's an indication that you don't have your PYTHONPATH set correctly. It
should include the $RDBASE directory (make sure that RDBASE is also set
correctly).
The documentation doesn't include this... we'll fix that.
-greg
On Mon, Oct 18, 2021 at 4:53 PM Gonzalo Colmenarejo <
colmenarejo.gonz...@gmail.com> wrote:
> Hi Greg et al.,
>
> Please find attached the results of ctest --output-on-failure and cmake. I
> followed the instructions in https://www.rdkit.org/docs/Install.html,
> section "How to install from source with Conda/Linux x86_64: Python 3
> environment".
>
> Thanks a lot
>
> Gonzalo
>
> On Sat, Oct 9, 2021 at 3:55 PM Greg Landrum <greg.land...@gmail.com>
> wrote:
>
>> Hi Gonzalo,
>>
>> The message you show below is just a warning, not an actual error.
>> Do you get actual compilation errors? If so please share them.
>>
>> Try running the tests with:
>> ctest --output-on-failure
>> and sharing the error messages you see.
>>
>> Best,
>> -greg
>>
>>
>> On Fri, Oct 8, 2021 at 1:49 PM Gonzalo Colmenarejo <
>> colmenarejo.gonz...@gmail.com> wrote:
>>
>>> Hi,
>>> I'm having issues trying to build RDKt from source with Conda using the
>>> recipe in the RDKit web page. The build is apparently complete but the
>>> ctest only achieves 35% of passed tests. I'm using an Ubuntu 20
>>> workstation.
>>>
>>> I first generate a Conda environment with all the required stuff:
>>>
>>> conda create --name rdksc python==3.8.1 cmake cairo pillow eigen
>>> pkg-config boost boost-cpp py-boost gxx_linux-64 numpy
>>>
>>> After cloning the git repository then I run cmake (following the
>>> instructions):
>>>
>>> cmake -DPy_ENABLE_SHARED=1 -DRDK_INSTALL_INTREE=ON
>>> -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_CPP_TESTS=ON
>>> -DPYTHON_NUMPY_INCLUDE_PATH="$(python -c 'import numpy ;
>>> print(numpy.get_include())')" -DBOOST_ROOT="$CONDA_PREFIX" ..
>>>
>>> Finally I run make and make install, and the build is complete but with
>>> a series of messages. The ctest gives only a 35% of test passed.
>>>
>>> The messages I get in compilation are like these:
>>>
>>> In file included from
>>> /home/gonzalo/anaconda3/envs/rdksc/include/boost/bind.hpp:30,
>>> from
>>> /home/gonzalo/anaconda3/envs/rdksc/include/boost/python/exception_translator.hpp:10,
>>> from
>>> /home/gonzalo/anaconda3/envs/rdksc/include/boost/python.hpp:28,
>>> from /home/gonzalo/rdkit/Code/RDBoost/python.h:3,
>>> from
>>> /home/gonzalo/rdkit/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp:12:
>>> /home/gonzalo/anaconda3/envs/rdksc/include/boost/bind.hpp:36:1: note:
>>> #pragma message: The practice of declaring the Bind placeholders (_1, _2,
>>> ...) in the global namespace is deprecated. Please use
>>> <boost/bind/bind.hpp> + using namespace boost::placeholders, or define
>>> BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.
>>> 36 | BOOST_PRAGMA_MESSAGE(
>>> | ^~~~~~~~~~~~~~~~~~~~
>>>
>>> I'd really acknowledge any help in getting this fixed and why is this
>>> message showing up.
>>>
>>> Thanks a lot in advance
>>>
>>> Gonzalo
>>>
>>> _______________________________________________
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>
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