[Biopython-dev] Problem on Mac OS X since update Xcode 5.1

[Peter Cock]

On Mon, Apr 14, 2014 at 6:32 PM, Lenna Peterson <arklenna at gmail.com> wrote:
> On Apr 14, 2014 7:36 AM, "Peter Cock" <p.j.a.cock at googlemail.com> wrote:
>>
>> I just retested with XCode 5.1.1 (released last week and updated
>> via the App Store), and the problem persists.
>>
>> $ cc -v
>> Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
>> Target: x86_64-apple-darwin13.1.0
>> Thread model: posix
>>
>> $ which python-config
>> /Library/Frameworks/Python.framework/Versions/Current/bin/python-config
>>
>> $ python-config --cflags
>> -I/Library/Frameworks/Python.framework/Versions/2.5/include/python2.5
>> -I/Library/Frameworks/Python.framework/Versions/2.5/include/python2.5
>> -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.e. Apple's current Python still says to use C compliler options which
>> Apple's current clang compiler rejects :(
>
> But Python is distributed with the OS, not XCode. I'm still hoping the next
> update to Mavericks will fix it.

Still broken :(

>> The good news is the environment variable trick still works.
>>
>> It appears Apple are not going to fix this, so perhaps we do need
>> to add a hack to our setup.py file?
>
> I suppose modifying env variables is easier when it doesn't need to be cross
> platform!

Since we want this to work "out of the box" for Biopython 1.64 which
will probably be released this week, I have checked in a hack which
ought not to do anything on other platforms.

https://github.com/biopython/biopython/commit/2ceecabc3e559c35377b697aef69aef4f0341c55

This closes the issue reported on GitHub:

https://github.com/biopython/biopython/issues/324
https://github.com/biopython/biopython/issues/325

Regards,

Peter