Python2.7 is the default install for Ubuntu 14.04, but I ran the first
command using python3.4
On Mon, Oct 3, 2016 at 11:43 AM, Greg Landrum <[email protected]>
wrote:
> 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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