Question: Weird Problem Installing Biopython on OS X Mavericks
0
gravatar for jxiang15
5.6 years ago by
jxiang1510
United States
jxiang1510 wrote:

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!

mavericks biopython python mac • 1.8k views
ADD COMMENTlink modified 5.6 years ago by Renesh1.8k • written 5.6 years ago by jxiang1510

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?

ADD REPLYlink written 5.6 years ago by Peter5.8k
0
gravatar for Haluk
5.6 years ago by
Haluk170
Lincoln, Nebraska
Haluk170 wrote:

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
ADD COMMENTlink written 5.6 years ago by Haluk170
0
gravatar for Renesh
5.6 years ago by
Renesh1.8k
United States
Renesh1.8k wrote:

Use MacPort

sudo port install py27-biopython

 

Source:Problems Installing Biopython On Mac

ADD COMMENTlink written 5.6 years ago by Renesh1.8k
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