we're going to solve this numpy problem using the age-old hack of having a Jamroot.in; this older version should still work if the python wrappers are not desired

Code/CompleteJamroot.py

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+import os,sys
+try:
+    import numpy
+except ImportError:
+    print >>sys.stderr,"ERROR: numpy module not found.\nThe RDKit python wrappers will not build correctly, but the rest of the code should be fine."
+    sys.exit(0)
+
+incDir = os.path.join(os.path.split(numpy.__file__)[0],'core','include')
+inD = file('Jamroot.in','r').read()
+print >>file('Jamroot','w+'),inD.replace('NUMPY_INCLUDE_DIR',incDir)
+    

Code/Jamroot.in

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+import os ;
+local BOOSTHOME = [ os.environ BOOSTHOME ] ;
+local RDBASE = [ os.environ RDBASE ] ;
+
+# make sure all executables end in .exe:
+import type : change-generated-target-suffix ;
+type.change-generated-target-suffix EXE : <target-os>linux : exe ;
+type.change-generated-target-suffix EXE : <target-os>darwin : exe ;
+
+# Specify the path to the Boost project.
+use-project boost 
+  : $(BOOSTHOME) ;
+use-project RDKit_Externals 
+  : $(RDBASE)/External  ;
+
+
+project RDKit
+	: requirements <include>.  <threading>multi
+          <include>$(BOOSTHOME)
+          <include>$(RDBASE)/External/Lapack++/include
+          <include>$(RDBASE)/External/vflib-2.0/include
+          <toolset>gcc:<cflags>-Wno-unused-function
+          <toolset>darwin:<cflags>-Wno-unused-function
+          <toolset>gcc:<cflags>-fno-strict-aliasing
+          <toolset>msvc:<define>WIN32
+          <include>NUMPY_INCLUDE_DIR
+	  <address-model>64:<cflags>-fPIC
+          # <define>RDK_USELAPACKPP #<- uncomment this to use lapack++
+          <target-os>windows:<define>BOOST_NUMERIC_BINDINGS_USE_CLAPACK
+          <toolset>msvc:<define>_CRT_SECURE_NO_DEPRECATE
+        : default-build release ;
+
+
+alias all-libraries : Catalogs DistGeom ForceField DataManip/MetricMatrixCalc DataStructs Geometry Query RDBoost RDGeneral Numerics  SimDivPickers ChemicalFeatures GraphMol
+;
+
+
+alias all-wrappers : RDBoost/Wrap 
+  DataStructs/Wrap
+  Geometry/Wrap
+  ML/Cluster/Murtagh ML/InfoTheory/Wrap ML/Data ML/FeatureSelect/Wrap
+  DataManip/MetricMatrixCalc/Wrap
+  SimDivPickers/Wrap
+  ForceField/Wrap 
+  DistGeom/Wrap
+  Numerics/Alignment/Wrap 
+  ChemicalFeatures/Wrap
+  GraphMol//all-wrappers
+ ;
+
+
+alias nonmol-libraries : Catalogs DistGeom ForceField DataManip/MetricMatrixCalc DataStructs Geometry Query RDBoost RDGeneral Numerics  SimDivPickers ChemicalFeatures 
+;
+
+alias nonmol-wrappers : RDBoost/Wrap 
+  DataStructs/Wrap
+  Geometry/Wrap
+  ML/Cluster/Murtagh ML/InfoTheory/Wrap ML/Data ML/FeatureSelect/Wrap
+  DataManip/MetricMatrixCalc/Wrap
+  SimDivPickers/Wrap
+  ForceField/Wrap 
+  DistGeom/Wrap
+  Numerics/Alignment/Wrap 
+  ChemicalFeatures/Wrap
+ ;
+
+
+
+lib lapack
+  :
+  : <name>lapack
+  <target-os>windows:<file>$(RDBASE)/External/Lapack/win32/LAPACK.lib
+  :
+  ;
+lib blas
+  :
+  : <name>blas
+  <target-os>windows:<file>$(RDBASE)/External/Lapack/win32/BLAS.lib
+  :
+  ;
+# if you want to use Lapack++, use this version:
+#alias lapacklibs : /RDKit_Externals//Lapack++ lapack blas ;
+alias lapacklibs : lapack blas ;
+alias vflib : /RDKit_Externals//vflib ;
+