Hi Greg,
Thanks for following up. Below is the output you asked for. Looks like an
import error in the boost library. Any ideas?
Thanks again,
Leo
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
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/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
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/net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Numerics/Optimizer
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/net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/DistGeom
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/net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/DistGeom/Wrap
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/net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol
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/net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/FileParsers
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/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
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/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
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/net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/PartialCharges/Wrap
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/net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/MolTransforms
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/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
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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
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/net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/ChemicalFeatures
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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/
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