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Creating numpy for Lion Python 2.6 with gfortran support

I am trying to install numpy and scipy on pre-installed Python 2.6, which comes with the Lion OS.

Here are the exact steps I'm taking:

  • install a blank copy
    • A lion,
    • updates
    • Xcode (from the app store),
    • Homebrew
    • gfortran
    • pip
    • and numpy.
  • The next step is trying to update numpy.
    Here's what happens: (I could not publish the full journal because I am a limited user.

Downloading/unpacking numpy from http://pypi.python.org/packages/source/n/numpy/numpy-    1.6.2.zip#md5=7e13c931985f90efcfa0408f845d6fee

Downloading numpy-1.6.2.zip (2.9Mb): 2.9Mb downloaded Running setup.py egg_info for package numpy Running from numpy source directory.non-existing path in 'numpy/distutils': 'site.cfg' F2PY Version 2 blas_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-msse3', '- I/System/Library/Frameworks/vecLib.framework/Headers']

lapack_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-msse3'] build_src building py_modules sources building library "npymath" sources 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/local/bin/gfortran customize Gnu95FCompiler customize Gnu95FCompiler using config C compiler: llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno- common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall - Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes - DENABLE_DTRACE -arch i386 -arch x86_64 -pipe 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/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c' llvm-gcc-4.2: _configtest.c sh: llvm-gcc-4.2: command not found sh: llvm-gcc-4.2: command not found failure. removing: _configtest.c _configtest.o Traceback (most recent call last): File "<string>", line 14, in <module> File "/Users/MYUSERNAME/build/numpy/setup.py", line 214, in <module> setup_package() File "/Users/MYUSERNAME/build/numpy/setup.py", line 207, in setup_package configuration=configuration ) File "/Users/MYUSERNAME/build/numpy/numpy/distutils/core.py", line 186, in setup return old_setup(**new_attr) File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/core.py", line 152, in setup File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 975, in run_commands File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 995, in run_command File "/Users/MYUSERNAME/build/numpy/numpy/distutils/command/egg_info.py", line 8, in run self.run_command("build_src") File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/cmd.py", line 333, in run_command File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 995, in run_command File "/Users/MYUSERNAME/build/numpy/numpy/distutils/command/build_src.py", line 152, in run self.build_sources() File "/Users/MYUSERNAME/build/numpy/numpy/distutils/command/build_src.py", line 163, in build_sources self.build_library_sources(*libname_info) File "/Users/MYUSERNAME/build/numpy/numpy/distutils/command/build_src.py", line 298, in build_library_sources sources = self.generate_sources(sources, (lib_name, build_info)) File "/Users/MYUSERNAME/build/numpy/numpy/distutils/command/build_src.py", line 385, in generate_sources source = func(extension, build_dir) File "numpy/core/setup.py", line 696, in get_mathlib_info raise RuntimeError("Broken toolchain: cannot link a simple C program") RuntimeError: Broken toolchain: cannot link a simple C program Complete output from command python setup.py egg_info: Running from numpy source directory.non-existing path in 'numpy/distutils': 'site.cfg' F2PY Version 2 blas_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/vecLib.framework/Headers'] lapack_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-msse3'] running egg_info running build_src build_src building py_modules sources creating build creating build/src.macosx-10.7-intel-2.6 creating build/src.macosx-10.7-intel-2.6/numpy creating build/src.macosx-10.7-intel-2.6/numpy/distutils building library "npymath" sources 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/local/bin/gfortran customize Gnu95FCompiler customize Gnu95FCompiler using config C compiler: llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe 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/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c' llvm-gcc-4.2: _configtest.c sh: llvm-gcc-4.2: command not found sh: llvm-gcc-4.2: command not found failure. removing: _configtest.c _configtest.o Traceback (most recent call last): File "<string>", line 14, in <module> File "/Users/MYUSERNAME/build/numpy/setup.py", line 214, in <module> setup_package() File "/Users/MYUSERNAME/build/numpy/setup.py", line 207, in setup_package configuration=configuration ) File "/Users/MYUSERNAME/build/numpy/numpy/distutils/core.py", line 186, in setup return old_setup(**new_attr) File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/core.py", line 152, in setup File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 975, in run_commands File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 995, in run_command File "/Users/MYUSERNAME/build/numpy/numpy/distutils/command/egg_info.py", line 8, in run self.run_command("build_src") File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/cmd.py", line 333, in run_command File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 995, in run_command File "/Users/MYUSERNAME/build/numpy/numpy/distutils/command/build_src.py", line 152, in run self.build_sources() File "/Users/MYUSERNAME/build/numpy/numpy/distutils/command/build_src.py", line 163, in build_sources self.build_library_sources(*libname_info) File "/Users/MYUSERNAME/build/numpy/numpy/distutils/command/build_src.py", line 298, in build_library_sources sources = self.generate_sources(sources, (lib_name, build_info)) File "/Users/MYUSERNAME/build/numpy/numpy/distutils/command/build_src.py", line 385, in generate_sources source = func(extension, build_dir) File "numpy/core/setup.py", line 696, in get_mathlib_info raise RuntimeError("Broken toolchain: cannot link a simple C program") RuntimeError: Broken toolchain: cannot link a simple C program ---------------------------------------- Command python setup.py egg_info failed with error code 1 in /Users/MYUSERNAME/build/numpy Storing complete log in /Users/MYUSERNAME/Library/Logs/pip.log

I really appreciate any help / comment / guide.

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Have you tried the official installation instructions?

http://www.scipy.org/Installing_SciPy/Mac_OS_X

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