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 >>>>>> >>>>>
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