Hi
I got past that error by symlinking the numpy headers to the place in the
cmake include path in specified
in Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/flags.make
cd /Library/Frameworks/Python.framework/Headers
sudo ln -s
/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/core/include/numpy
.
Thanks
Hari
On Fri, Jan 14, 2011 at 6:13 AM, hari jayaram <[email protected]> wrote:
> Hi
>
> I am trying to build rdkit on my Core duo OSX laptop running Snow Leopard.
>
> I got boost and the newest numpy installed following the instructions
> posted here <http://code.google.com/p/rdkit/wiki/BuildingWithCmake>(
> http://code.google.com/p/rdkit/wiki/BuildingWithCmake)
>
> However the compile of rdAlignment.cpp.o fails because the
> numpy/arrayobject.h is not in the include path.
>
> I can see this file at several locations including
>
>
> /System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h
>
>
> Just wondering how to make cmake aware of that location ?
> Sorry this is strictly not an rdkit issue.
>
> The detailed error msg is posted below
>
> Thanks in advance
>
> Hari
>
>
> [ 13%] Building CXX object
> Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:14:31:
> error: numpy/arrayobject.h: No such file or directory
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp: In
> function ‘void
> RDNumeric::Alignments::GetPointsFromPythonSequence(boost::python::api::object&,
> RDGeom::Point3DConstPtrVect&)’:
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:31:
> error: ‘PyArray_Check’ was not declared in this scope
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:33:
> error: ‘PyArrayObject’ was not declared in this scope
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:33:
> error: ‘ptsMat’ was not declared in this scope
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:33:
> error: expected type-specifier before ‘PyArrayObject’
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:33:
> error: expected `>' before ‘PyArrayObject’
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:33:
> error: expected `(' before ‘PyArrayObject’
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:33:
> error: expected primary-expression before ‘>’ token
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:33:
> error: expected `)' before ‘;’ token
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp: In
> function ‘PyObject*
> RDNumeric::Alignments::AlignPointPairs(boost::python::api::object,
> boost::python::api::object, boost::python::api::object, bool, unsigned
> int)’:
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:103:
> error: ‘PyArray_Check’ was not declared in this scope
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:104:
> error: ‘PyArrayObject’ was not declared in this scope
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:104:
> error: ‘wtsMat’ was not declared in this scope
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:104:
> error: expected type-specifier before ‘PyArrayObject’
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:104:
> error: expected `>' before ‘PyArrayObject’
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:104:
> error: expected `(' before ‘PyArrayObject’
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:104:
> error: expected primary-expression before ‘>’ token
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:104:
> error: expected `)' before ‘;’ token
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:130:
> error: ‘npy_intp’ was not declared in this scope
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:130:
> error: expected `;' before ‘dims’
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:131:
> error: ‘dims’ was not declared in this scope
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:133:
> error: ‘PyArrayObject’ was not declared in this scope
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:133:
> error: ‘res’ was not declared in this scope
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:133:
> error: expected primary-expression before ‘)’ token
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:133:
> error: expected `;' before ‘PyArray_SimpleNew’
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:154:
> error: ‘PyArray_Return’ was not declared in this scope
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp: In
> function ‘void init_module_rdAlignment()’:
> /Users/hari/rdkit/trunk/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:162:
> error: ‘import_array’ was not declared in this scope
> make[2]: ***
> [Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o]
> Error 1
> make[1]: *** [Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/all]
> Error 2
>
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