You built against python3.4, but it looks like you are running python2.7
-greg
On Mon, Oct 3, 2016 at 5:39 PM, Philip Adler <[email protected]> wrote:
> Greg,
>
> The output of the commands is as follows:
>
> Segmentation fault (core dumped)
>
> and
>
> linux-vdso.so.1 => (0x00007fff3d6be000)
> libRDGeneral.so.1 => /usr/lib/libRDGeneral.so.1 (0x00007f03d51df000)
> libRDBoost.so.1 => /usr/lib/libRDBoost.so.1 (0x00007f03d4fdc000)
> libpython3.4m.so.1.0 => /usr/lib/x86_64-linux-gnu/libpython3.4m.so.1.0
> (0x00007f03d49a7000)
> libboost_python-py34.so.1.54.0 =>
> /usr/lib/x86_64-linux-gnu/libboost_python-py34.so.1.54.0
> (0x00007f03d475b000)
> libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
> (0x00007f03d4457000)
> libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
> (0x00007f03d4241000)
> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f03d3e7c000)
> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f03d3b76000)
> libpython2.7.so.1.0 => /usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0
> (0x00007f03d3612000)
> libboost_python-py27.so.1.54.0 =>
> /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.54.0
> (0x00007f03d33c5000)
> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
> (0x00007f03d31a7000)
> libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1
> (0x00007f03d2f7d000)
> libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f03d2d64000)
> libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f03d2b60000)
> libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1
> (0x00007f03d295d000)
> /lib64/ld-linux-x86-64.so.2 (0x00007f03d56fc000)
>
> Thanks,
>
> Phil
>
>
> On Mon, Oct 3, 2016 at 11:34 AM, Greg Landrum <[email protected]>
> wrote:
>
>> Hi Phil,
>>
>> I can't think of any particular reason that Ubuntu 14.04 should be a
>> problem, so this should be solvable.
>>
>> This kind of thing (every python test failing) is typically a problem
>> with either the python version or the boost libraries.
>>
>> The first check is to see what error message you get when you do:
>> python -c 'from rdkit import rdBase'
>>
>> That will hopefully point to a particular library that is the problem.
>> Another useful diagnosis command is:
>> ldd $RDBASE/rdkit/rdBase.so
>>
>> That will show which dynamic libraries are being pulled in.
>>
>> -greg
>>
>>
>> On Mon, Oct 3, 2016 at 5:05 PM, Philip Adler <[email protected]>
>> wrote:
>>
>>> Dear All,
>>>
>>> I am trying to compile rdkit to run with Python3.4 on Ubuntu 14.04 as
>>> per the instructions at http://www.rdkit.org/docs/Install.html For
>>> reasons which I don't really want to get into we would prefer to avoid
>>> anaconda for the time being.
>>>
>>> That being said, when I try to test the build, I get a number of errors
>>> and failed tests (the build does not work when called from Python, which is
>>> unsurprising).
>>>
>>> For reference, the cmake command I issued was:
>>>
>>> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -D PYTHON_LIBRARY=/usr/lib/python
>>> 3.4/config-3.4m-x86_64-linux-gnu/libpython3.4.so -D
>>> PYTHON_INCLUDE_DIR=/usr/include/python3.4/ -D
>>> PYTHON_EXECUTABLE=/usr/bin/python3.4 -DBOOST_ROOT=/usr/lib/x86_64-linux-gnu/
>>> ..
>>>
>>> The tests which fail are as follows:
>>>
>>> The following tests FAILED:
>>> 5 - pyBV (SEGFAULT)
>>> 6 - pyDiscreteValueVect (SEGFAULT)
>>> 7 - pySparseIntVect (SEGFAULT)
>>> 8 - pyFPB (SEGFAULT)
>>> 11 - testPyGeometry (SEGFAULT)
>>> 14 - pyAlignment (Failed)
>>> 18 - pyForceFieldConstraints (SEGFAULT)
>>> 20 - pyDistGeom (Failed)
>>> 33 - pyDepictor (SEGFAULT)
>>> 45 - pyChemReactions (SEGFAULT)
>>> 50 - pyFilterCatalog (SEGFAULT)
>>> 52 - pyFragCatalog (SEGFAULT)
>>> 54 - pyMolDescriptors (SEGFAULT)
>>> 57 - pyPartialCharges (SEGFAULT)
>>> 59 - pyMolTransforms (SEGFAULT)
>>> 63 - pyForceFieldHelpers (SEGFAULT)
>>> 65 - pyDistGeom (SEGFAULT)
>>> 67 - pyMolAlign (SEGFAULT)
>>> 69 - pyChemicalFeatures (SEGFAULT)
>>> 71 - pyShapeHelpers (SEGFAULT)
>>> 73 - pyMolCatalog (SEGFAULT)
>>> 75 - pyMolDraw2D (SEGFAULT)
>>> 77 - pyFMCS (SEGFAULT)
>>> 80 - pyMolHash (SEGFAULT)
>>> 82 - pyMMPA (SEGFAULT)
>>> 84 - pyReducedGraphs (SEGFAULT)
>>> 86 - pySLNParse (SEGFAULT)
>>> 87 - pyGraphMolWrap (SEGFAULT)
>>> 88 - pyTestConformerWrap (SEGFAULT)
>>> 89 - pyTestThreads (SEGFAULT)
>>> 92 - pyMatCalc (SEGFAULT)
>>> 93 - pySimDivPickers (SEGFAULT)
>>> 94 - pyRanker (Failed)
>>> 96 - pyFeatures (SEGFAULT)
>>> 97 - pythonTestDbCLI (Failed)
>>> 98 - pythonTestDirML (Failed)
>>> 99 - pythonTestDirDataStructs (Failed)
>>> 101 - pythonTestDirSimDivFilters (Failed)
>>> 102 - pythonTestDirVLib (Failed)
>>> 103 - pythonTestDirChem (SEGFAULT)
>>>
>>> I must confess I'm a little out of my depth right now, so I don't even
>>> know where to begin debugging this. Any advice would be greatly appreciated,
>>>
>>> Best,
>>>
>>> Phil
>>>
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>>>
>>
>
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