On Fri, Jun 22, 2012 at 5:46 PM, Leonardo Trabuco <[email protected]> wrote: > > Thanks for following up. Below is the output you asked for. Looks like an > import error in the boost library. Any ideas?
Based on what I've been able to find on the 'net, the error is typical for a version mismatch between the python you're using and the one that boost was linked against. You can check this with ldd; % ldd /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/boost/lib/libboost_python.so.1.49.0 If it is using the wrong version of python, I'm afraid you'll have to re-build boost. There's documentation here that describes how to ensure the correct python version is being used: http://www.boost.org/doc/libs/1_49_0/libs/python/doc/building.html#python-configuration-parameters An aside: my successful (and easy) build of the RDKit on CenOS 5.7 used a self-installed version of python 2.7. It's documented here: http://code.google.com/p/rdkit/wiki/BuildingOnCentOS57 -greg > > UpdateCTestConfiguration from > :/net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/DartConfiguration.tcl > Start processing tests > UpdateCTestConfiguration from > :/net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/DartConfiguration.tcl > Test project > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build > Constructing a list of tests > Done constructing a list of tests > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/RDGeneral > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/DataStructs > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/DataStructs/Wrap > 3/ 76 Testing pyBV > Test command: /usr/bin/python2.6 > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/Code/DataStructs/Wrap/testBV.py > Test timeout computed to be: 9.99988e+06 > Traceback (most recent call last): > File > "/net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/Code/DataStructs/Wrap/testBV.py", > line 1, in <module> > from rdkit import DataStructs > File > "/net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/rdkit/DataStructs/__init__.py", > line 11, in <module> > from rdkit import rdBase > ImportError: > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/boost/lib/libboost_python.so.1.49.0: > undefined symbol: Py_InitModule4 > -- Process completed > ***Failed > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Geometry > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Geometry/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Numerics > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Numerics/Alignment > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Numerics/Alignment/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Numerics/Optimizer > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/ForceField > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/DistGeom > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/DistGeom/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Depictor > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Depictor/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/SmilesParse > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/FileParsers > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Substruct > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/ChemReactions > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/ChemReactions/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/ChemTransforms > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Subgraphs > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/FragCatalog > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/FragCatalog/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Descriptors > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Descriptors/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Fingerprints > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/PartialCharges/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/MolTransforms > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/MolTransforms/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/ForceFieldHelpers > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/ForceFieldHelpers/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/DistGeomHelpers > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/DistGeomHelpers/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/MolAlign > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/MolAlign/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/MolChemicalFeatures > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/MolChemicalFeatures/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/ShapeHelpers > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/ShapeHelpers/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/MolCatalog > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/MolCatalog/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/SLNParse > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/SLNParse/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Query > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/DataManip/MetricMatrixCalc > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/DataManip/MetricMatrixCalc/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/ML/FeatureSelect/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/ML/InfoTheory/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/ChemicalFeatures > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/ChemicalFeatures/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Projects > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/rdkit > > 0% tests passed, 1 tests failed out of 1 > 3 - pyBV (Failed) > > > > On Fri, Jun 22, 2012 at 4:53 PM, Greg Landrum <[email protected]> > wrote: >> >> Hi Leo, >> >> >> On Fri, Jun 22, 2012 at 4:45 PM, Leonardo Trabuco <[email protected]> >> wrote: >> > >> > I'm trying to build RDKit_2012_03_1 on a machine running CentOS 5.8. >> > After >> > finally getting the build to complete, almost all Python-related tests >> > fail. >> >> <snip> >> >> > >> > Finally: >> > $ cd $RDBASE >> > $ mkdir build >> > $ cd build >> > $ cmake -DBOOST_ROOT=$installbase/boost -D >> > PYTHON_EXECUTABLE=/usr/bin/python2.6 .. >> > $ make >> > $ make install >> > $ ctest >> > >> > All python-related tests fail (py*, except for the last ones: >> > pythonTest*). Any suggestions for what to try are highly appreciated! >> >> can you please run: >> ctest -V -R pyBV >> and send the output? >> >> Thanks, >> -greg > > > > > -- > Leonardo Trabuco, Postdoctoral fellow (Russell group) > CellNetworks, University of Heidelberg, Germany > http://www.russelllab.org/people/leo/ ------------------------------------------------------------------------------ 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
