[Biopython] Biopython and Snow Leopard

[Kelly F Oakeson]

On Sep 9, 2009, at 7:20 AM, Peter wrote:

> 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?
Here is how it looks exactly on my screen:
$ 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
Thread model: posix
gcc version 4.2.1 (Apple Inc. build 5646)

>
>> $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
I installed XCode from the snow leopard install DVD, It is Version 3.2  
(1610). It was an update on a MacPro that hadn't had Biopython  
installed before. I installed Python 2.5.4 and then tried to install  
Biopython.

I also updated to Python 2.6 on a MacbookPro, also running 10.6 and  
that seemed to have broken my previous Biopython install.

Thanks for the help,