Installing SciPy on Mac OS Lion in Virtualenv

Question

I am trying to install scipy in my vertualenv on mac.

Python using in virtualenv:

(Django)miki725mac:Django miki725$ python
Python 2.7.2 (default, Aug  3 2011, 00:58:00) 
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> 

I tries installing scipy by doing this which fails:

$ svn co http://svn.scipy.org/svn/scipy/trunk scipy
$ python setup.py build
$ python setup.py install

Then I tried:

$ pip install scipy

Also as per the suggestion I tried:

$ pip install -e git://github.com/scipy/scipy@effa6f68f8ada57b7986#egg=scipy-dev

Logs

Here are the complete logs for all the insallation steps: (they were too long for stackoverflow)

python setup.py build

http://www.diglo.com/download/3dfc7a1af18617d7ee49faa8bea3464703ea

python setup.py install

http://www.diglo.com/download/ab13985c76ad709b25464fa1254daa4b03ea

pip install scipy

http://www.diglo.com/download/9e808fe5b57b6b01a8265d4b01958da703ea (pastebin: http://paste.pocoo.org/show/454004/ )

pip install -e git://github.com/scipy/scipy@effa6f68f8ada57b7986#egg=scipy-dev

http://www.diglo.com/download/085f7bd08e7cb86823718b94641ecacd03ea

Please help. I am new at all this. Thank you in advance.

Answer 1

Personally, I found the easiest and reliable way to install scipy/numpy on Mac OS Lion was through the scipy superpack shell-script on github . As Steve Jobs says - it just works. Nothing more to do.

Steps to install scipy in a virtual env:

• Download the scipy superpack install script
• Open the install script and change PYTHON=/usr/bin/python to PYTHON=`which python`
• Activate virtual env, and inside your virtual env, run the install script
• Bingo! that's all you need to do

Answer 2

Up until August 2011 Scipy was broken on Mac OS X Lion. Fixed in this commit: https://github.com/scipy/scipy/commit/effa6f68f8ada57b79864852b609ff06d2527306

It looks like this change has not yet been merged to SVN trunk. Try github instead:

pip install -e git://github.com/scipy/scipy@effa6f68f8ada57b7986#egg=scipy-dev

That's worked for me on two installs of Lion. However if it doesn't I've heard using GCC-4.0 (instead of the current default: GCC-4.2) also solves the issue (haven't verified it though):

1. Install macports
2. sudo port install gcc40
3. Create a symlink from gcc-4.0 to gcc
4. Recommended: after scipy is installed, change the symlink to point back to the xcode version of gcc-4.2

Steps 1 & 2 are only needed if you don't already have gcc-4.0.

Answer 3

I ran into similar problem recently. After following the office doc for installing scipy on Lion to no avail, I found the following resources that helped me fix it:

1. Installing Python, virtualenv, NumPy, SciPy, matplotlib and IPython on Lion (didn't really work for me but I imagine it works for most people)

2. Install Python, NumPy, SciPy, and matplotlib on Mac OS X (this one works for me too, just remember to install gfortran with homebrew first, and then use pip install scipy to build and install scipy . Though I suspect it might not always work).

3. Scipy Superpack (this one is the easiest and fastest since it simply installs compiled binaries for Lion)

Answer 4

What about going with the official instructions ?

It seems you are using the default Python installation, which is not recommended...