Hi Greg,
Thanks for quick reply. I corrected paths in my cmake invocation (they
where wrong) and it compiled without problems. But now after running tests
I have:
RDBASE=$PWD PYTHONPATH=$PWD LD_LIBRARY_PATH=$PWD/lib python
70% tests passed, 23 tests failed out of 76
The following tests FAILED:
11 - pyAlignment (Failed)
15 - pyDistGeom (Failed)
25 - pyDepictor (Failed)
35 - pyChemReactions (Failed)
40 - pyFragCatalog (Failed)
42 - pyMolDescriptors (Failed)
44 - pyPartialCharges (Failed)
46 - pyMolTransforms (Failed)
48 - pyForceFieldHelpers (Failed)
50 - pyDistGeom (Failed)
52 - pyMolAlign (Failed)
54 - pyChemicalFeatures (Failed)
56 - pyShapeHelpers (Failed)
58 - pyMolCatalog (Failed)
60 - pySLNParse (Failed)
61 - pyGraphMolWrap (Failed)
62 - pyTestConformerWrap (Failed)
65 - pyMatCalc (Failed)
67 - pyRanker (Failed)
69 - pyFeatures (Failed)
70 - pythonTestDbCLI (Failed)
71 - pythonTestDirML (Failed)
76 - pythonTestDirChem (Failed)
Errors while running CTest
Any clues?
On Mon, Jul 22, 2013 at 10:49 AM, Greg Landrum <[email protected]>wrote:
> Hi Michal,
>
>
> On Mon, Jul 22, 2013 at 4:58 AM, Michał Nowotka <[email protected]> wrote:
>
>> Hi,
>>
>> I'm trying to compile rdkit on RHEL. I started with running cmake using
>> following command:
>>
>> cmake
>> -DPYTHON_INCLUDE_PATH=/nfs/web-hx/chembl/utils/python-2.7.5/include/
>> -DPYTHON_LIBRARY=/nfs/web-hx/chembl/utils/python-2.7.5/lib/
>> -DPYTHON_NUMPY_INCLUDE_PATH=/net/isilonP/public/rw/homes/cbl_adm/.virtualenvs/chembl_webservices/lib/python2.7/site-packages/numpy/
>>
>> So, as you see my python installation is not in default place. This
>> command passed without problems.
>>
>> Now I have problems with make, it seems it has problems with finding
>> python headers:
>>
>> /usr/include/boost/python/detail/wrap_python.hpp:50:23: error:
>> pyconfig.h: No such file or directory
>> /usr/include/boost/python/detail/wrap_python.hpp:75:24: error:
>> patchlevel.h: No such file or directory
>> /usr/include/boost/python/detail/wrap_python.hpp:78:2: error: #error
>> Python 2.2 or higher is required for this version of Boost.Python.
>> /usr/include/boost/python/detail/wrap_python.hpp:142:21: error: Python.h:
>> No such file or directory
>>
>> I guess I'm missing some parameter but I don't know which. Can you help
>> me?
>>
>
> This is the command I execute on an RHEL 5 machine where I regularly build
> the RDKit:
> cmake -D PYTHON_INCLUDE_DIR=/usr/prog/python/2.6.6_gnu/include/python2.6
> -D
> PYTHON_LIBRARY=/usr/prog/python/2.6.6_gnu/lib/python2.6/config/libpython2.6.a
> ..
>
> I run this from a shell where the bin directory containing python is early
> in my PATH, so that just typing "python" at the prompt invokes the correct
> version.
>
> I believe that the PYTHON_NUMPY_INCLUDE_PATH bit should not be necessary
> if you follow the above steps.
>
> Note: it looks like you are doing this where at least part of your python
> environment is using virtualenv (the numpy bit for sure); this is something
> I have not tried.
>
> -greg
>
>
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