[Biopython] question on installation of BioPython on Mac OS 10.7

Iddo Friedberg idoerg at gmail.com
Mon Feb 27 21:27:31 UTC 2012


Seems like there is a NumPy for Python 2.7 on Mac:


In any case, you should not skip the NumPy installation. Even if for teh
combination of your OS and Python version there is only NumPy for Python
2.6, you should install that. There is very little difference between
Python 2.6 and 2.7, and NumPy should not break (and, in any case, seems
like your desired version is in the link above).



On Mon, Feb 27, 2012 at 4:00 PM, Daria Fedyukina <fedyukina at gmail.com>wrote:

> Hello,
> I am trying to install BioPython 1.58. My BioPython and python are both in
> the Applications folder.
> My configuration is:
> OS: Mac OS 10.7.3
> Python: 2.7.2
> Apple Xcode is installed.
> NumPy is not installed (could not install for 2.7, only available for 2.6;
> decided to skip)
> When I try to install it, I go to X11 -> go inside biopython-1.58 older ->
> type "python setup.py build" -> choose to proceed without NumPy -> get an
> error.
> Here how it looks:
> bash-3.2$ cd biopython-1.58
> bash-3.2$ ls
> Bio             DEPRECATED      MANIFEST.in     README          build
> BioSQL          Doc             NEWS            Scripts         do2to3.py
> CONTRIB         LICENSE         PKG-INFO        Tests           setup.py
> bash-3.2$ python setup.py build
> running build
> running build_py
> 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
> running build_ext
> building 'Bio.cpairwise2' extension
> gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -isysroot
> /Developer/SDKs/MaSX10.6.sdk -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3
> -IBio -I/Library/Fraworks/Python.framework/Versions/2.7/include/python2.7
> -c Bio/cpairwise2module.-o
> build/temp.macosx-10.6-intel-2.7/Bio/cpairwise2module.o
> In file included from
> /Library/Frameworks/Python.framework/Versions/2.7/includpython2.7/unicodeobject.h:4,
>                 from
> /Library/Frameworks/Python.framework/Versions/2.7/includpython2.7/Python.h:85,
>                 from Bio/cpairwise2module.c:12:
> /Developer/SDKs/MacOSX10.6.sdk/usr/include/stdarg.h:4:25: error: stdarg.h:
> No ch file or directory
> In file included from
> /Library/Frameworks/Python.framework/Versions/2.7/includpython2.7/unicodeobject.h:4,
>                 from
> /Library/Frameworks/Python.framework/Versions/2.7/includpython2.7/Python.h:85,
>                 from Bio/cpairwise2module.c:12:
> /Developer/SDKs/MacOSX10.6.sdk/usr/include/stdarg.h:4:25: error: stdarg.h:
> No ch file or directory
> lipo: can't figure out the architecture type of:
> /var/folders/nt/1ppm7j953zv2qylmtwydqm0000gn/T//ccODIZmY.out
> error: command 'gcc-4.2' failed with exit status 1
> bash-3.2$
> I googled this error, it turned out that gcc-4.2 needs to be installed. I
> did. Then, the situation is exactly the same when I repeat biopython
> installation.
> Does anyone know what could've happened? My only suspicion now is that
> Lion is messing stuff up. Looks like Snow Leopard works better.
> Thank you very much for any help or advice!
> -Daria
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Iddo Friedberg

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