[Biopython] Biopython and Snow Leopard

[Kelly F Oakeson]

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

$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/distance.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/DocSQL.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/EZRetrieve.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/File.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/FilteredReader.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/HotRand.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/Index.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/kNN.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/listfns.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/LogisticRegression.py -> build/lib.macosx-10.3-x86_64-2.5/ 
Bio
copying Bio/MarkovModel.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/mathfns.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/MaxEntropy.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/NaiveBayes.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/NetCatch.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/pairwise2.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/ParserSupport.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/PropertyManager.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/PubMed.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/Search.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/Seq.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/SeqFeature.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/SeqRecord.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/stringfns.py -> build/lib.macosx-10.3-x86_64-2.5/Bio
copying Bio/Transcribe.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


On Sep 9, 2009, at 3:13 AM, Peter wrote:

> On Wed, Sep 9, 2009 at 4:22 AM, Kelly F  
> Oakeson<kelly.oakeson at utah.edu> wrote:
>> Hello list,
>> I am wondering of Biopython is compatible with Mac OS 10.6?
>
> In theory yes, but I don't know if anyone has tested it yet.
> Apple have updated the compiler (gcc), and probably the
> system Python since Mac OS 10.5 Leopard.
>
> On Leopard:
>
> $ python --version
> Python 2.5.2
>
> $ gcc -v
> Using built-in specs.
> Target: i686-apple-darwin9
> Configured with: /var/tmp/gcc/gcc-5465~16/src/configure
> --disable-checking -enable-werror --prefix=/usr --mandir=/share/man
> --enable-languages=c,objc,c++,obj-c++
> --program-transform-name=/^[cg][^.-]*$/s/$/-4.0/
> --with-gxx-include-dir=/include/c++/4.0.0 --with-slibdir=/usr/lib
> --build=i686-apple-darwin9 --with-arch=apple --with-tune=generic
> --host=i686-apple-darwin9 --target=i686-apple-darwin9
> Thread model: posix
> gcc version 4.0.1 (Apple Inc. build 5465)
>
> So, try it and see? If you run into problems compiling, or running
> the unit tests please let us know. Also in case it matters, was
> this an update or a clean install of Snow Leopard?
>
> Peter