Numpy Installation on Mac 10.8.2

Question

I am running python 2.6 on MacOS 10.8.2, and trying to install Numpy to use NLTK. I have looked at several approaches highlighted below, but am yet to have any luck installing the package.

1. I have installed xcode as per this suggestion, but this has not resolved anything.

2. I tried building directly, using

   python setup.py build --fcompiler=gnu95
   

   that returns the following message

   RuntimeError: Broken toolchain: cannot link a simple C program
   

3. Direct installation, I downloaded the dmg file from here. When extracting the file directly, numpy complains that it requires Python 2.6 or higher to be installed, so this fails too.

   I read somewhere that MacOS comes with the Apple version of Python, and that I want to avoid using this; I have installed Eclipse & PyDev, and believe I am not using the Apple version, but is there a way to confirm that this is true and that numpy is being installed on the 'proper' version of Python?

4. When I try and run

   sudo easy_install numpy

   I get the below output. Initially I thought it had something to do with a C/Fortran compiler not being found, but I installed gfortran when I built it directly, so perhaps the issue is something else ... I am not able to diagnose the issue looking at the rest of the message though.

Is anyone able to point me to something definitive that would help me install numpy after all this? What - if anything - is wrong with what I have tried so far?

Thank you humbly, in advance!

Searching for numpy
Reading http://pypi.python.org/simple/numpy/
Reading http://numpy.scipy.org
Reading http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=175103
Reading http://numeric.scipy.org
Best match: numpy 1.6.2
Downloading http://pypi.python.org/packages/source/n/numpy/numpy-1.6.2.zip#md5=7e13c931985f90efcfa0408f845d6fee
Processing numpy-1.6.2.zip
Running numpy-1.6.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-6DObmd/numpy-1.6.2/egg-dist-tmp-KMbGBl
Running from numpy source directory.non-existing path in '/private/tmp/easy_install-6DObmd/numpy-1.6.2/numpy/distutils': 'site.cfg'
/bin/sh: svnversion: command not found
/bin/sh: svnversion: command not found
Could not locate executable f95
Could not locate executable f90
Could not locate executable f77
Could not locate executable xlf90
Could not locate executable xlf
Could not locate executable ifort
Could not locate executable ifc
Could not locate executable g77
Found executable /usr/local/bin/gfortran
sh: /usr/bin/gcc-4.2: No such file or directory
sh: /usr/bin/gcc-4.2: No such file or directory
Traceback (most recent call last):
  File "/opt/local/bin/easy_install", line 8, in <module>
    load_entry_point('setuptools==0.6c11', 'console_scripts', 'easy_install')()
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg/setuptools/command/easy_install.py", line 1712, in main
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg/setuptools/command/easy_install.py", line 1700, in with_ei_usage
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg/setuptools/command/easy_install.py", line 1716, in <lambda>
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/core.py", line 152, in setup
    dist.run_commands()
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 987, in run_commands
    self.run_command(cmd)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 1007, in run_command
    cmd_obj.run()
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg/setuptools/command/easy_install.py", line 211, in run
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg/setuptools/command/easy_install.py", line 446, in easy_install
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg/setuptools/command/easy_install.py", line 476, in install_item
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg/setuptools/command/easy_install.py", line 655, in install_eggs
 File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg/setuptools/command/easy_install.py", line 930, in build_and_install
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg/setuptools/command/easy_install.py", line 919, in run_setup
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg/setuptools/sandbox.py", line 62, in run_setup
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg/setuptools/sandbox.py", line 105, in run
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg/setuptools/sandbox.py", line 64, in <lambda>
  File "setup.py", line 214, in <module>
  File "setup.py", line 207, in setup_package
  File "/tmp/easy_install-GH52RV/numpy-1.6.2/numpy/distutils/core.py", line 186, in setup
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/core.py", line 152, in setup
    dist.run_commands()
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 987, in run_commands
    self.run_command(cmd)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 1007, in run_command
    cmd_obj.run()
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg/setuptools/command/bdist_egg.py", line 167, in run
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/cmd.py", line 333, in run_command
    self.distribution.run_command(command)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 1007, in run_command
    cmd_obj.run()
  File "/tmp/easy_install-GH52RV/numpy-1.6.2/numpy/distutils/command/egg_info.py", line 8, in run
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/cmd.py", line 333, in run_command
    self.distribution.run_command(command)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 1007, in run_command
    cmd_obj.run()
  File "/tmp/easy_install-GH52RV/numpy-1.6.2/numpy/distutils/command/build_src.py", line 152, in run
  File "/tmp/easy_install-GH52RV/numpy-1.6.2/numpy/distutils/command/build_src.py", line 163, in build_sources
  File "/tmp/easy_install-GH52RV/numpy-1.6.2/numpy/distutils/command/build_src.py", line 298, in build_library_sources
  File "/tmp/easy_install-GH52RV/numpy-1.6.2/numpy/distutils/command/build_src.py", line 385, in generate_sources
  File "/private/tmp/easy_install-GH52RV/numpy-1.6.2/numpy/core/setup.py", line 696, in get_mathlib_info
RuntimeError: Broken toolchain: cannot link a simple C program
/tmp/easy_install-GH52RV/numpy-1.6.2/numpy/distutils/misc_util.py:252: RuntimeWarning: Parent module 'numpy.distutils' not found while handling absolute import
Error in atexit._run_exitfuncs:
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/atexit.py", line 24, in _run_exitfuncs
    func(*targs, **kargs)
  File "/tmp/easy_install-GH52RV/numpy-1.6.2/numpy/distutils/misc_util.py", line 252, in clean_up_temporary_directory
ImportError: No module named numpy.distutils
Error in sys.exitfunc:
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/atexit.py", line 24, in _run_exitfuncs
    func(*targs, **kargs)
  File "/tmp/easy_install-GH52RV/numpy-1.6.2/numpy/distutils/misc_util.py", line 252, in clean_up_temporary_directory
ImportError: No module named numpy.distutils

Answer 1

This is how I fixed this problem:

export CC=gcc
export CXX=g++
export FFLAGS=ff2c

Based on the information I found under the 10.7 installation instructions here: http://www.scipy.org/Installing_SciPy/Mac_OS_X

Answer 2

There was a comment here saying that the Apple version of python 2.7 comes with numpy so you shouldn't have to install it at all.

Try running

>>> /usr/bin/python2.7
Python 2.7.2 (default, Jun 20 2012, 16:23:33) 
[GCC 4.2.1 Compatible Apple Clang 4.0 (tags/Apple/clang-418.0.60)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy

Should work without a problem. Now you just need to configure the system Python 2.7 to be the default one, and install NLTK for that.

I also found a solution to why gcc fails even after installing xcode. You need to install the command line tools separately. Have a look at this post.

Answer 3

Spicy Superpack installs the latest 64 bit scientific software packages for Mac 10.8.2 and other Intel Mac versions:

Numpy (1.8) and Scipy (0.12) Matplotlib (1.3) iPython (0.14) Pandas (0.10) Statsmodels (0.5.0) Scikit-Learn 0.14 PyMC (2.2)

Spicy Superpack for Mac