Paolo,
Thankyou for this advice, but it does not seem to have resolved the issue.
Best,
Phil
On Mon, Oct 3, 2016 at 12:00 PM, Paolo Tosco <[email protected]> wrote:
> Hi Philip,
>
> in the shell where you are building the RDKit, I suggest that you do the
> following:
> - first, create in your $HOME/bin directory (or another directory which in
> your PATH environment variable stands before /usr/bin) a "python" symlink
> which points to /usr/bin/python3.
> - check that issuing
> python -V
> returns 3.4.
> - cmake && make the RDKit
> - see if that helped removing the dependency from Python 2.7. I wonder if
> CMake at some point invokes Python and mixes things up in spite of your
> PYTHON_LIBRARY and PYTHON_INCLUDE_DIR definitions.
>
> HTH, cheers
> p.
>
>
> On 10/03/16 16:45, Philip Adler wrote:
>
> 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]>
>> [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]>
>>> [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]>
>>>> [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>
>>>>> 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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