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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