[Biopython] Biopython and Snow Leopard

[Kelly F Oakeson]

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
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?




Kelly Oakeson
kelly.oakeson at utah.edu




On Sep 9, 2009, at 7:57 AM, Peter wrote:

> Hi Kelly,
>
> From some Google searching this is a general Python issue. This blog
> post looked helpful,
>
> http://mtrichardson.com/2009/09/fixing-jinja2-and-pycrypto-and-probably-others-on-snow-leopard/
>
> It suggests the simplest solution is you should install the optional
> 10.4 SDK on the system, which Snow Leopard does not install by default
> – it’s an optional install in the developer tools installer.
>
> This fits with the error message you had,
>
>> Compiling with an SDK that doesn't seem to exist: /Developer/SDKs/
>> MacOSX10.4u.sdk
>> Please check your Xcode installation
>
> Can you give that a go please?
>
> Peter