Excellent, I'm glad everything worked. I'll make a note that we need to update those instructions to make this easier.
-greg On Fri, Oct 22, 2021 at 9:51 AM Gonzalo Colmenarejo < colmenarejo.gonz...@gmail.com> wrote: > Hi Greg et al, > > I finally passed all the test after defining export > LD_LIBRARY_PATH=$RDBASE/lib (this fixed all the tests but > pythonTestDirChem; in turn, this was fixed by installing pandas). > > Thanks for all your help > > Gonzalo > > On Thu, Oct 21, 2021 at 5:28 PM Gonzalo Colmenarejo < > colmenarejo.gonz...@gmail.com> wrote: > >> Hi Greg, >> >> after setting RDBASE and PYTHONPATH I get a much reduced set of errors >> with ctest, but still some test fail. In all the cases, the output on >> failure is like this: >> >> Traceback (most recent call last): >> File "/home/gonzalo/rdkit/Code/GraphMol/Depictor/Wrap/testDepictor.py", >> line 12, in <module> >> from rdkit import Chem >> File "/home/gonzalo/rdkit/rdkit/__init__.py", line 2, in <module> >> from . import rdBase >> ImportError: /home/gonzalo/rdkit/rdkit/rdBase.so: undefined symbol: >> _ZN5RDLog9BlockLogsC1Ev >> >> And if I run ldd rdkit/rdBase.so I get: >> >> linux-vdso.so.1 (0x00007ffc4f922000) >> libgtk3-nocsd.so.0 => /usr/lib/x86_64-linux-gnu/libgtk3-nocsd.so.0 >> (0x00007f1c495a8000) >> libRDKitRDBoost.so.1 => >> /home/gonzalo/rdkit/build/lib/libRDKitRDBoost.so.1 (0x00007f1c4959c000) >> libRDKitRDGeneral.so.1 => >> /home/gonzalo/rdkit/build/lib/libRDKitRDGeneral.so.1 (0x00007f1c4957a000) >> libboost_python38.so.1.73.0 => >> /home/gonzalo/anaconda3/envs/rdksc/lib/libboost_python38.so.1.73.0 >> (0x00007f1c4953c000) >> libstdc++.so.6 => /home/gonzalo/anaconda3/envs/rdksc/lib/libstdc++.so.6 >> (0x00007f1c49391000) >> libgcc_s.so.1 => /home/gonzalo/anaconda3/envs/rdksc/lib/libgcc_s.so.1 >> (0x00007f1c4937a000) >> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f1c49188000) >> libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f1c49182000) >> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 >> (0x00007f1c4915f000) >> /lib64/ld-linux-x86-64.so.2 (0x00007f1c498af000) >> librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f1c49154000) >> libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f1c4914f000) >> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f1c48ffe000) >> >> Do you know how can this be fixed? >> >> Thanks a lot >> >> Gonzalo >> >> On Tue, Oct 19, 2021 at 9:42 AM Gonzalo Colmenarejo < >> colmenarejo.gonz...@gmail.com> wrote: >> >>> 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 >>>>>>> >>>>>>
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
