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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