[Biopython] Biopython and Snow Leopard

[Kelly F Oakeson]

Peter,
It looks like I may have solved it! Taking the advice from the post on http://mtrichardson.com/2009/09/fixing-jinja2-and-pycrypto-and-probably-others-on-snow-leopard/ 
  I changed the makefile in /Library/Frameworks/Python.framework/ 
Versions/2.6/lib/python2.6/config/Makefile replacing all of the  
occurrences of 10.4u with 10.6.
I then ran
$python setup.py build
$python setup.py test
$sudo python setup.py install

Everything worked just fine without any gcc errors. This worked on  
both my MacBook pro and MacPro both running the 64 bit kernel.

Thanks for all of the help.



On Sep 9, 2009, at 10:05 AM, Peter wrote:

> 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