[Biopython] Biopython and Snow Leopard

[Peter]

On Wed, Sep 9, 2009 at 4:46 PM, Kelly F Oakeson<kelly.oakeson at utah.edu> wrote:
> Peter,
> I installed the 10.4 SDK and tried the install again. It still failed,
> here is the output:
>
> $ sudo python setup.py install
> Password:
> running install
>
> Numerical Python (NumPy) is not installed.
>
> This package is required for many Biopython features.  Please install
> it before you install Biopython. You can install Biopython anyway, but
> anything dependent on NumPy will not work. If you do this, and later
> install NumPy, you should then re-install Biopython.
>
> You can find NumPy at http://numpy.scipy.org
>
> Do you want to continue this installation? (y/N)  Y

As an aside, from following the NumPy mailing list, it can be installed
on Snow Leopard but there were some similar glitches and I don't
know how easy it is.

> running build
> running build_py
> running build_ext
> building 'Bio.clistfns' extension
> gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -
> fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd -
> fno-common -dynamic -DNDEBUG -g -O3 -I/Library/Frameworks/
> Python.framework/Versions/2.5/include/python2.5 -c Bio/
> clistfnsmodule.c -o build/temp.macosx-10.3-x86_64-2.5/Bio/
> clistfnsmodule.o
> cc1: error: unrecognized command line option "-Wno-long-double"
> cc1: error: unrecognized command line option "-Wno-long-double"
> lipo: can't figure out the architecture type of: /var/tmp//cc6kttGl.out
> error: command 'gcc' failed with exit status 1
>
> $ arch
> i386
>
> I do have the 64 bit kernel enabled, could that be causing the issue?

Maybe - it looks like gcc has been called with "-arch ppc -arch i386",
which should probably be "-arch x86_64" (or left as the default?) as
you are running in full 64 bit mode (and you must have an Intel CPU,
not a PowerPC). Try:

gcc -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -
fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd -
fno-common -dynamic -DNDEBUG -g -O3 -I/Library/Frameworks/
Python.framework/Versions/2.5/include/python2.5 -c Bio/
clistfnsmodule.c -o build/temp.macosx-10.3-x86_64-2.5/Bio/
clistfnsmodule.o

[all as one line] and see what gcc says then.

Peter