Thanks Greg. What then should I use as $RDBASE? The path for the rdkit directory created after the git clone?
Thanks a lot Gonzalo On Tue, Oct 19, 2021 at 6:53 AM Greg Landrum <greg.land...@gmail.com> wrote: > 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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