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