error installing numpy on Mac OS X 10.6

Question

I am having lots of trouble installing numpy on Mac OS X 10.6. When I try to install it from source, I get the following error:

customize NAGFCompiler
Could not locate executable f95
customize AbsoftFCompiler
Could not locate executable f90
Could not locate executable f77
customize IBMFCompiler
Could not locate executable xlf90
Could not locate executable xlf
customize IntelFCompiler
Could not locate executable ifort
Could not locate executable ifc
customize GnuFCompiler
Could not locate executable g77
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
/Users/Software/numpy/numpy/distutils/fcompiler/gnu.py:126: UserWarning: Env. variable MACOSX_DEPLOYMENT_TARGET set to 10.3
  warnings.warn(s)
customize Gnu95FCompiler
customize Gnu95FCompiler using config
C compiler: gcc-4.0 -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c'
gcc-4.0: _configtest.c
gcc-4.0 _configtest.o -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
C compiler: gcc-4.0 -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c'
gcc-4.0: _configtest.c
_configtest.c:1: warning: conflicting types for built-in function ‘exp’
_configtest.c:1: warning: conflicting types for built-in function ‘exp’
gcc-4.0 _configtest.o -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
building extension "numpy.core._sort" sources
Generating build/src.macosx-10.3-fat-2.6/numpy/core/include/numpy/config.h
C compiler: gcc-4.0 -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c'
gcc-4.0: _configtest.c
In file included from /Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/unicodeobject.h:4,
                 from /Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/Python.h:85,
                 from _configtest.c:1:
/Developer/SDKs/MacOSX10.4u.sdk/usr/include/stdarg.h:4:25: error: stdarg.h: No such file or directory
In file included from /Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/unicodeobject.h:4,
                 from /Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/Python.h:85,
                 from _configtest.c:1:
/Developer/SDKs/MacOSX10.4u.sdk/usr/include/stdarg.h:4:25: error: stdarg.h: No such file or directory
lipo: can't figure out the architecture type of: /var/tmp//ccRwrtCy.out
In file included from /Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/unicodeobject.h:4,
                 from /Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/Python.h:85,
                 from _configtest.c:1:
/Developer/SDKs/MacOSX10.4u.sdk/usr/include/stdarg.h:4:25: error: stdarg.h: No such file or directory
In file included from /Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/unicodeobject.h:4,
                 from /Library/Frameworks/Python.framework/Versions/2.6/include/python2.6/Python.h:85,
                 from _configtest.c:1:
/Developer/SDKs/MacOSX10.4u.sdk/usr/include/stdarg.h:4:25: error: stdarg.h: No such file or directory
lipo: can't figure out the architecture type of: /var/tmp//ccRwrtCy.out
failure.
removing: _configtest.c _configtest.o
Traceback (most recent call last):
  File "setup.py", line 210, in <module>
    setup_package()
  File "setup.py", line 203, in setup_package
    configuration=configuration )
  File "/Users/Software/numpy/numpy/distutils/core.py", line 186, in setup
    return old_setup(**new_attr)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/core.py", line 152, in setup
    dist.run_commands()
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 975, in run_commands
    self.run_command(cmd)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 995, in run_command
    cmd_obj.run()
  File "/Users/Software/numpy/numpy/distutils/command/install.py", line 55, in run
    r = old_install.run(self)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/command/install.py", line 577, in run
    self.run_command('build')
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/cmd.py", line 333, in run_command
    self.distribution.run_command(command)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 995, in run_command
    cmd_obj.run()
  File "/Users/Software/numpy/numpy/distutils/command/build.py", line 37, in run
    old_build.run(self)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/command/build.py", line 134, in run
    self.run_command(cmd_name)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/cmd.py", line 333, in run_command
    self.distribution.run_command(command)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 995, in run_command
    cmd_obj.run()
  File "/Users/Software/numpy/numpy/distutils/command/build_src.py", line 152, in run
    self.build_sources()
  File "/Users/Software/numpy/numpy/distutils/command/build_src.py", line 169, in build_sources
    self.build_extension_sources(ext)
  File "/Users/Software/numpy/numpy/distutils/command/build_src.py", line 328, in build_extension_sources
    sources = self.generate_sources(sources, ext)
  File "/Users/Software/numpy/numpy/distutils/command/build_src.py", line 385, in generate_sources
    source = func(extension, build_dir)
  File "numpy/core/setup.py", line 395, in generate_config_h
    moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
  File "numpy/core/setup.py", line 41, in check_types
    out = check_types(*a, **kw)
  File "numpy/core/setup.py", line 260, in check_types
    "Cannot compile 'Python.h'. Perhaps you need to "\
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.

I already installed Xcode since I have gcc (version i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1) so it seems unlikely that these header files don't exist. Any idea what might be happening?

thanks.

Answer 1

I installed the EPD packaged python with all the scientific packages on OS X 10.6 based on these two pages: http://cse.ucdavis.edu/~chaos/courses/nlp/Software/PythonOSXInstall.html http://www.soton.ac.uk/~fangohr/computing/pythonsoft.html

Hopefully it is useful.

Answer 2

There is a version (albeit a little bit outdated) of numpy already included on Mac OS X 10.6 in the default Python 2.6 installation. However, if you want a newer version of numpy or would like numpy+scipy, then I suggest you read my installation instructions: Python2.6+NumPy+SciPy+MatPlotLib on Mac OS X 10.6.

Edit
As to the error messages that you are getting.... note that it says "10.4"; numpy has the Mac OS X 10.4 SDK hard-coded into it for some reason, so if you have not installed the 10.4 SDK (which is optional and not installed by default), then you will get these errors. If you reinstall Xcode, and select the Mac OS X 10.4 SDK, so that it is installed, then that should fix the issues that you are getting. That said, I would strongly recommend installing Python.org's MacPython 2.6 and the binary version of numpy.

Answer 3

I had the best luck with the MacPorts version of python, numpy, etc. It was also easy to get a clean 64-bit version.

I followed this outline:

http://stackoverflow.com/questions/2111283/how-to-build-64-bit-python-on-os-x-10-6-only-64-bit-no-universal-nonsense