I have a lot of trouble installing numpy on Mac OS X 10.6. When I try to install it from source, I get the following error:
< p>
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
co mpile 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< br />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 _confi gtest
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 di rectory
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.f ramework/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
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.fram ework/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< br /> 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/Framew orks/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, bu ild_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 have installed Xcode, because I have gcc (version i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1) so these header files seem unlikely to exist. Any idea what might happen?
Thank you.
In the default Python 2.6 installation, Mac OS X A numpy version is already included on 10.6 (albeit a bit outdated). However, if you want a newer version of numpy or want numpy scipy, then I suggest you read my installation instructions: Python2.6+NumPy+SciPy+MatPlotLib on Mac OS X 10.6.
Edit as for the error message you get…. Note that it says “10.4”; numpy hardcodes the Mac OS X 10.4 SDK into it for some reason, so if You have not installed the 10.4 SDK (optional and not installed by default), then you will receive these errors. If you reinstall Xcode, and select Mac OS X 10.4 SDK in order to install it, then this should solve your encounter That is to say, I strongly recommend installing Python.org’s MacPython 2.6 and the binary version of numpy.
I encountered it when I installed numpy on Mac OS X 10.6 A lot of trouble. When I try to install it from source code, 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
cu stomize 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'< br />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 option s:'-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< br />
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/Framewor ks/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,< br /> 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
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 have installed Xcode because I have gcc (version i686-apple-darwin10-gcc-4.2 .1 (GCC) 4.2.1) So these header files seem unlikely to exist. Any idea what might happen?
Thank you.
In the default Python 2.6 installation, Mac OS X 10.6 already includes a numpy version (although a bit outdated ). However, if you want a newer version of numpy or want numpy scipy, then I suggest you read my installation instructions: Python2.6+NumPy+SciPy+MatPlotLib on Mac OS X 10.6.
Edit as for the error message you get…. Note that it says “10.4”; numpy hardcodes the Mac OS X 10.4 SDK into it for some reason, so if you have not installed the 10.4 SDK (optional and by default Not installed), then you will receive these errors. If you reinstall Xcode and choose Mac OS X 10.4 SDK in order to install it, then this should solve your problem. That is, I strongly recommend installing Python .org’s MacPython 2.6 and the binary version of numpy.