Hi! Greg, thanks a lot for your message! First of all I have to apologize for the subject of my email, I am actually building under Red Hat, not CentOS (...the upgrade from CentOS to RedHat being the whole reason for this exercise).
To get cmake to ignore the systems boost.python and use my own version, I've installed cmake-2.8.9 and used that to build rdkit, giving the -D Boost_NO_SYSTEM_PATHS=ON parameter. The output from $ cmake [found the right boost version, found python libs /my/path/libpython2.6.so.1.0, found python interpreter /my/path/python, found boost libraries regex + python], $ make and $ make install looked fine but then for $ ctest I get SEGFAULTS for some of the python functions (see pasted at the bottom). Has anyone had similar problems? I found a previous thread http://www.mail-archive.com/[email protected]/msg02505.html. However, I think that my boost.python was built against the correct python version, at least it says so in the project.config.jam... Any advice would be welcome thanks a lot for the support! f The following tests FAILED: 11 - pyAlignment (SEGFAULT) 15 - pyDistGeom (SEGFAULT) 25 - pyDepictor (SEGFAULT) 35 - pyChemReactions (SEGFAULT) 40 - pyFragCatalog (SEGFAULT) 42 - pyMolDescriptors (SEGFAULT) 44 - pyPartialCharges (SEGFAULT) 46 - pyMolTransforms (SEGFAULT) 48 - pyForceFieldHelpers (SEGFAULT) 50 - pyDistGeom (SEGFAULT) 52 - pyMolAlign (SEGFAULT) 54 - pyChemicalFeatures (SEGFAULT) 56 - pyShapeHelpers (SEGFAULT) 58 - pyMolCatalog (SEGFAULT) 60 - pySLNParse (SEGFAULT) 61 - pyGraphMolWrap (SEGFAULT) 62 - pyTestConformerWrap (SEGFAULT) 65 - pyMatCalc (SEGFAULT) 67 - pyRanker (SEGFAULT) 69 - pyFeatures (SEGFAULT) 70 - pythonTestDbCLI (Failed) 71 - pythonTestDirML (Failed) 76 - pythonTestDirChem (Failed) On 28/08/2012 14:25, Greg Landrum wrote: > Hi Felix, > > On Tue, Aug 28, 2012 at 3:20 PM, Felix Krüger > <[email protected]> wrote: > >> If I try to import from rdkit in an interactive python session I get: >> >> from rdkit import Chem >> >> ImportError: /usr/lib64/libboost_python-mt.so.5: undefined symbol: >> PyUnicodeUCS4_FromEncodedObject >> > > Did you install your own version of boost.python? If so, it looks like > it is not being found. There's some specific help on how to ignore the > system boost libraries here: > http://code.google.com/p/rdkit/wiki/BuildingWithCmake > in the "frequently encountered problems" section. > > -greg > -- Felix twitter: @MoSander skype: mo_sander ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
