[Biopython-dev] Work towards getting KDTree compiling

[Jeffrey Chang]

On Apr 19, 2004, at 7:56 AM, Brad Chapman wrote:

> So, I checked in a modified setup.py that compiles KDTree by default
> and sets the language to c++:


> I hope maybe this will fix the problem on non-gcc systems and get
> KDTree compiled by default.
>
> I was wondering if people on potential problem systems (Solaris,
> Windows, Mac OSX) would mind testing this out to see if it compiles
> happily. If so, I'll leave it in for the next release -- otherwise,
> we'll have to keep working.

It built successfully for me, on Mac OS X 10.3.3.  The native compiler 
for Macs is gcc, so it also worked before the modification.  The 
modification did, however, change the compiler for the module from gcc 
to c++.  However, this is fine, because c++ is symlinked (by default?  
I didn't do it) to g++.

Relevant build output is attached.

Jeff



building 'Bio.KDTree._CKDTree' extension
creating build/temp.darwin-7.3.0-Power_Macintosh-2.3/Bio/KDTree
gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp 
-mno-fused-madd -DNDEBUG -g -O3 -Wall -Wstrict-prototypes 
-I/opt/local/include/python2.3 -c Bio/KDTree/KDTree.C -o 
build/temp.darwin-7.3.0-Power_Macintosh-2.3/Bio/KDTree/KDTree.o
Bio/KDTree/KDTree.C: In member function `void
    KDTree::neighbor_simple_search(float)':
Bio/KDTree/KDTree.C:914: warning: comparison between signed and unsigned
    integer expressions
Bio/KDTree/KDTree.C:923: warning: comparison between signed and unsigned
    integer expressions
gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp 
-mno-fused-madd -DNDEBUG -g -O3 -Wall -Wstrict-prototypes 
-I/opt/local/include/python2.3 -c Bio/KDTree/KDTree.swig.C -o 
build/temp.darwin-7.3.0-Power_Macintosh-2.3/Bio/KDTree/KDTree.swig.o
c++ -L/opt/local/lib -bundle -bundle_loader /opt/local/bin/python2.3 
build/temp.darwin-7.3.0-Power_Macintosh-2.3/Bio/KDTree/KDTree.o 
build/temp.darwin-7.3.0-Power_Macintosh-2.3/Bio/KDTree/KDTree.swig.o 
-lstdc++ -o 
build/lib.darwin-7.3.0-Power_Macintosh-2.3/Bio/KDTree/_CKDTree.so