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 <
[email protected]> 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 <[email protected]>
> 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 $RDBASE directory (make sure that RDBASE is also set
>> correctly).
>>
>> The documentation doesn't include this... we'll fix that.
>>
>> -greg
>>
>>
>>
>> On Mon, Oct 18, 2021 at 4:53 PM Gonzalo Colmenarejo <
>> [email protected]> wrote:
>>
>>> Hi Greg et al.,
>>>
>>> Please find attached the results of ctest --output-on-failure and cmake.
>>> I followed the instructions in https://www.rdkit.org/docs/Install.html,
>>> section "How to install from source with Conda/Linux x86_64: Python 3
>>> environment".
>>>
>>> Thanks a lot
>>>
>>> Gonzalo
>>>
>>> On Sat, Oct 9, 2021 at 3:55 PM Greg Landrum <[email protected]>
>>> wrote:
>>>
>>>> Hi Gonzalo,
>>>>
>>>> The message you show below is just a warning, not an actual error.
>>>> Do you get actual compilation errors? If so please share them.
>>>>
>>>> Try running the tests with:
>>>> ctest --output-on-failure
>>>> and sharing the error messages you see.
>>>>
>>>> Best,
>>>> -greg
>>>>
>>>>
>>>> On Fri, Oct 8, 2021 at 1:49 PM Gonzalo Colmenarejo <
>>>> [email protected]> wrote:
>>>>
>>>>> Hi,
>>>>> I'm having issues trying to build RDKt from source with Conda using
>>>>> the recipe in the RDKit web page. The build is apparently complete but the
>>>>> ctest only achieves 35% of passed tests. I'm using an Ubuntu 20
>>>>> workstation.
>>>>>
>>>>> I first generate a Conda environment with all the required stuff:
>>>>>
>>>>> conda create --name rdksc python==3.8.1 cmake cairo pillow eigen
>>>>> pkg-config boost boost-cpp py-boost gxx_linux-64 numpy
>>>>>
>>>>> After cloning the git repository then I run cmake (following the
>>>>> instructions):
>>>>>
>>>>> cmake -DPy_ENABLE_SHARED=1 -DRDK_INSTALL_INTREE=ON
>>>>> -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_CPP_TESTS=ON
>>>>> -DPYTHON_NUMPY_INCLUDE_PATH="$(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
>>>>> [email protected]
>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>
>>>>
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