[Biopython] Biopython and Snow Leopard

[Peter]

On Wed, Sep 9, 2009 at 2:05 PM, Kelly F Oakeson<kelly.oakeson at utah.edu> wrote:
> Thanks Peter,
> I gave it a shot and it won't install for me. Here are my results:
>
> $ python --version
> Python 2.5.4
>
> $ gcc -v
> Using built-in specs.
> Target: i686-apple-darwin10
> Configured with: /var/tmp/gcc/gcc-5646~6/src/configure
> --disable-checking --enable-werror --prefix=/usr --mandir=/share/man
> --enable-languages=c,objc,c++,obj-c++
> --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/
> --with-slibdir=/usr/lib --build=i686-apple-darwin10
> --with-gxx-include-dir=/include/c++/4.2.1
> --program-prefix=i686-apple-darwin10-
> --host=x86_64-apple-darwin10 --target=i686-apple-darwin10

Did the last few lines get lost in the cut and paste?

> $python setup.py install
> running build
> running build_py
> creating build/lib.macosx-10.3-x86_64-2.5
> creating build/lib.macosx-10.3-x86_64-2.5/Bio
> copying Bio/__init__.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
...
> .
> copying Bio/PopGen/SimCoal/data/ssm_2d.par -> build/lib.macosx-10.3-
> x86_64-2.5/Bio/PopGen/SimCoal/data
> running build_ext
> building 'Bio.clistfns' extension
> creating build/temp.macosx-10.3-x86_64-2.5
> creating build/temp.macosx-10.3-x86_64-2.5/Bio
> Compiling with an SDK that doesn't seem to exist: /Developer/SDKs/
> MacOSX10.4u.sdk
> Please check your Xcode installation
> 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//ccQJ2KcH.out
> error: command 'gcc' failed with exit status 1

OK, as I feared, the C code isn't compiling. Have you got XCode
installed? Which version? The message "Please check your Xcode
installation" is troubling.

Could you also double check the gcc version (see above).

Was this a clean Snow Leopard install, or an update?

Thanks,

Peter