Weird Problem Installing Biopython on OS X Mavericks

Question

[jxiang15]

Hello, I'm trying to install Biopython on my Mavericks laptop. When I run "python setup.py build" I get the following error:

running build
running build_py
running build_ext
building 'Bio.cpairwise2' extension
/ A p p l i c a t i o n s / X c o d e . a p p / C o n t e n t s / D e v e l o p e r / T o o l c h a i n s / X c o d e D e f a u l t . x c t o o l c h a i n / u s r / b i n / c l a n g - D N D E B U G - g - f w r a p v - O s - W a l l - W s t r i c t - p r o t o t y p e s - Q u n u s e d - a r g u m e n t s - Q u n u s e d - a r g u m e n t s - a r c h x 8 6 _ 6 4 - a r c h i 3 8 6 - p i p e -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c Bio/cpairwise2module.c -o build/temp.macosx-10.9-intel-2.7/Bio/cpairwise2module.o
unable to execute /: Permission denied
error: command '/' failed with exit status 1

It seems like for some reason the script is inserting a bunch of spaces between characters, and thus the resulting command cannot be executed properly. Any insight on how to fix this?

Thanks!

[Peter]

That is very strange. Have you had similar problems installing any other Python modules? Have you been able to use the C compiler from Xcode to compile other code?

Answer 1

[Haluk]

Try the following steps:

cd /tmp
git clone https://github.com/pypa/virtualenv.git
cd virtualenv
python virtualenv.py ~/pythonenv
source ~/pythonenv/bin/activate
pip install biopython

Answer 2

[Renesh]

Use MacPort

sudo port install py27-biopython

Source: Problems Installing Biopython On Mac