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Weird Problem Installing Biopython on OS X Mavericks

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!

biopython python mavericks mac

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?

2 answers

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

Use MacPort

sudo port install py27-biopython

Source: Problems Installing Biopython On Mac

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