Weird Problem Installing Biopython on OS X Mavericks
Entering edit mode
7.1 years ago
jxiang15 ▴ 20

Hello, I'm trying to install Biopython on my Mavericks laptop. When I run "python 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?


biopython python mavericks mac • 2.2k views
Entering edit mode

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?

Entering edit mode
7.1 years ago
Haluk ▴ 190

Try the following steps:

cd /tmp
git clone
cd virtualenv
python ~/pythonenv
source ~/pythonenv/bin/activate
pip install biopython
Entering edit mode
7.1 years ago
Renesh ★ 2.0k

Use MacPort

sudo port install py27-biopython

Source: Problems Installing Biopython On Mac


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