Unable to install rpy2 on Mac OS X 10.9

Question

I have been trying to install rpy2 on Mac OS X 10.9, but I have not been able to do so. I think there is a problem with the R shared library, but I read that R is installed with the shared library option as default. Any help would be very appreciated!

This is the log:

Downloading from URL https://pypi.python.org/packages/source/r/rpy2/rpy2-2.3.9.tar.gz#md5=86851a56f637e7b87709eb2b91dc5075 (from https://pypi.python.org/simple/rpy2/)
Running setup.py (path:/private/tmp/pip_build_root/rpy2/setup.py) egg_info for package rpy2
  running egg_info
  creating pip-egg-info/rpy2.egg-info
  writing dependency_links to pip-egg-info/rpy2.egg-info/dependency_links.txt
  writing pip-egg-info/rpy2.egg-info/PKG-INFO
  writing top-level names to pip-egg-info/rpy2.egg-info/top_level.txt
  writing manifest file 'pip-egg-info/rpy2.egg-info/SOURCES.txt'
  warning: manifest_maker: standard file '-c' not found

  "/opt/local/Library/Frameworks/R.framework/Resources/bin/R" CMD config --ldflags
  "/opt/local/Library/Frameworks/R.framework/Resources/bin/R" CMD config --cppflags
  "/opt/local/Library/Frameworks/R.framework/Resources/bin/R" CMD config LAPACK_LIBS

  returned an empty string.

  "/opt/local/Library/Frameworks/R.framework/Resources/bin/R" CMD config BLAS_LIBS

  returned an empty string.

  Configuration for R as a library:
    include_dirs: ('/opt/local/Library/Frameworks/R.framework/Resources/include',)
    libraries: ()
    library_dirs: ('/opt/local/Library/Frameworks/R.framework/Resources/lib',)
    extra_link_args: ('-F/opt/local/Library/Frameworks/R.framework/..', '-framework R')
   # OSX-specific (included in extra_link_args)
    framework_dirs: ('-F/opt/local/Library/Frameworks/R.framework/..',)
    frameworks: ('-framework R',)
  reading manifest file 'pip-egg-info/rpy2.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  warning: no previously-included files matching '*patch*' found anywhere in distribution
  warning: no previously-included files matching '*diff*' found anywhere in distribution
  warning: no previously-included files matching '.hg' found anywhere in distribution
  no previously-included directories found matching 'dist'
  writing manifest file 'pip-egg-info/rpy2.egg-info/SOURCES.txt'
Source in /private/tmp/pip_build_root/rpy2 has version 2.3.9, which satisfies requirement rpy2
Installing collected packages: rpy2
  Running setup.py install for rpy2
    Running command /usr/bin/python -c "import setuptools, tokenize;__file__='/private/tmp/pip_build_root/rpy2/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-E3rnYf-record/install-record.txt --single-version-externally-managed --compile
  running install
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.9-intel-2.7
  creating build/lib.macosx-10.9-intel-2.7/rpy2
  copying ./rpy/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2
  copying ./rpy/rpy_classic.py -> build/lib.macosx-10.9-intel-2.7/rpy2
  copying ./rpy/tests.py -> build/lib.macosx-10.9-intel-2.7/rpy2
  copying ./rpy/tests_rpy_classic.py -> build/lib.macosx-10.9-intel-2.7/rpy2
  creating build/lib.macosx-10.9-intel-2.7/rpy2/rlike
  copying ./rpy/rlike/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rlike
  copying ./rpy/rlike/container.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rlike
  copying ./rpy/rlike/functional.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rlike
  copying ./rpy/rlike/indexing.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rlike
  creating build/lib.macosx-10.9-intel-2.7/rpy2/rlike/tests
  copying ./rpy/rlike/tests/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rlike/tests
  copying ./rpy/rlike/tests/test_container.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rlike/tests
  copying ./rpy/rlike/tests/test_functional.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rlike/tests
  copying ./rpy/rlike/tests/test_indexing.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rlike/tests
  creating build/lib.macosx-10.9-intel-2.7/rpy2/rinterface
  copying ./rpy/rinterface/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface
  creating build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests
  copying ./rpy/rinterface/tests/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests
  copying ./rpy/rinterface/tests/test_Device.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests
  copying ./rpy/rinterface/tests/test_EmbeddedR.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests
  copying ./rpy/rinterface/tests/test_Sexp.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests
  copying ./rpy/rinterface/tests/test_SexpClosure.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests
  copying ./rpy/rinterface/tests/test_SexpEnvironment.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests
  copying ./rpy/rinterface/tests/test_SexpExtPtr.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests
  copying ./rpy/rinterface/tests/test_SexpVector.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests
  copying ./rpy/rinterface/tests/test_SexpVectorNumeric.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests
  creating build/lib.macosx-10.9-intel-2.7/rpy2/robjects
  copying ./rpy/robjects/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects
  copying ./rpy/robjects/constants.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects
  copying ./rpy/robjects/conversion.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects
  copying ./rpy/robjects/environments.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects
  copying ./rpy/robjects/functions.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects
  copying ./rpy/robjects/help.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects
  copying ./rpy/robjects/language.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects
  copying ./rpy/robjects/methods.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects
  copying ./rpy/robjects/numpy2ri.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects
  copying ./rpy/robjects/packages.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects
  copying ./rpy/robjects/pandas2ri.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects
  copying ./rpy/robjects/robject.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects
  copying ./rpy/robjects/vectors.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects
  creating build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests
  copying ./rpy/robjects/tests/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests
  copying ./rpy/robjects/tests/testArray.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests
  copying ./rpy/robjects/tests/testDataFrame.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests
  copying ./rpy/robjects/tests/testEnvironment.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests
  copying ./rpy/robjects/tests/testFormula.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests
  copying ./rpy/robjects/tests/testFunction.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests
  copying ./rpy/robjects/tests/testHelp.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests
  copying ./rpy/robjects/tests/testLanguage.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests
  copying ./rpy/robjects/tests/testMethods.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests
  copying ./rpy/robjects/tests/testNumpyConversions.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests
  copying ./rpy/robjects/tests/testPackages.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests
  copying ./rpy/robjects/tests/testPandasConversions.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests
  copying ./rpy/robjects/tests/testRObject.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests
  copying ./rpy/robjects/tests/testRobjects.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests
  copying ./rpy/robjects/tests/testVector.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests
  creating build/lib.macosx-10.9-intel-2.7/rpy2/robjects/lib
  copying ./rpy/robjects/lib/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/lib
  copying ./rpy/robjects/lib/ggplot2.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/lib
  copying ./rpy/robjects/lib/grid.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/lib
  creating build/lib.macosx-10.9-intel-2.7/rpy2/robjects/lib/tests
  copying ./rpy/robjects/lib/tests/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/lib/tests
  copying ./rpy/robjects/lib/tests/test_ggplot2.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/lib/tests
  creating build/lib.macosx-10.9-intel-2.7/rpy2/interactive
  copying ./rpy/interactive/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/interactive
  copying ./rpy/interactive/ipython.py -> build/lib.macosx-10.9-intel-2.7/rpy2/interactive
  copying ./rpy/interactive/packages.py -> build/lib.macosx-10.9-intel-2.7/rpy2/interactive
  copying ./rpy/interactive/process_revents.py -> build/lib.macosx-10.9-intel-2.7/rpy2/interactive
  creating build/lib.macosx-10.9-intel-2.7/rpy2/interactive/tests
  copying ./rpy/interactive/tests/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/interactive/tests
  running build_ext
  "/opt/local/Library/Frameworks/R.framework/Resources/bin/R" CMD config --ldflags
  "/opt/local/Library/Frameworks/R.framework/Resources/bin/R" CMD config --cppflags
  "/opt/local/Library/Frameworks/R.framework/Resources/bin/R" CMD config LAPACK_LIBS

  returned an empty string.

  "/opt/local/Library/Frameworks/R.framework/Resources/bin/R" CMD config BLAS_LIBS

  returned an empty string.

  Configuration for R as a library:
    include_dirs: ('/opt/local/Library/Frameworks/R.framework/Resources/include',)
    libraries: ()
    library_dirs: ('/opt/local/Library/Frameworks/R.framework/Resources/lib',)
    extra_link_args: ('-F/opt/local/Library/Frameworks/R.framework/..', '-framework R')
   # OSX-specific (included in extra_link_args)
    framework_dirs: ('-F/opt/local/Library/Frameworks/R.framework/..',)
    frameworks: ('-framework R',)
  building 'rpy2.rinterface._rinterface' extension
  creating build/temp.macosx-10.9-intel-2.7
  creating build/temp.macosx-10.9-intel-2.7/rpy
  creating build/temp.macosx-10.9-intel-2.7/rpy/rinterface
  cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -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 x86_64 -arch i386 -pipe -DR_INTERFACE_PTRS=1 -DHAVE_POSIX_SIGJMP=1 -DRIF_HAS_RSIGHAND=1 -DCSTACK_DEFNS=1 -DHAS_READLINE=1 -I./rpy/rinterface -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/opt/local/Library/Frameworks/R.framework/Resources/include -c ./rpy/rinterface/_rinterface.c -o build/temp.macosx-10.9-intel-2.7/./rpy/rinterface/_rinterface.o
  clang: error: unknown argument: '-mno-fused-madd' [-Wunused-command-line-argument-hard-error-in-future]
  clang: note: this will be a hard error (cannot be downgraded to a warning) in the future
  error: command 'cc' failed with exit status 1
  Complete output from command /usr/bin/python -c "import setuptools, tokenize;__file__='/private/tmp/pip_build_root/rpy2/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-E3rnYf-record/install-record.txt --single-version-externally-managed --compile:
  running install

running build

running build_py

creating build

creating build/lib.macosx-10.9-intel-2.7

creating build/lib.macosx-10.9-intel-2.7/rpy2

copying ./rpy/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2

copying ./rpy/rpy_classic.py -> build/lib.macosx-10.9-intel-2.7/rpy2

copying ./rpy/tests.py -> build/lib.macosx-10.9-intel-2.7/rpy2

copying ./rpy/tests_rpy_classic.py -> build/lib.macosx-10.9-intel-2.7/rpy2

creating build/lib.macosx-10.9-intel-2.7/rpy2/rlike

copying ./rpy/rlike/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rlike

copying ./rpy/rlike/container.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rlike

copying ./rpy/rlike/functional.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rlike

copying ./rpy/rlike/indexing.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rlike

creating build/lib.macosx-10.9-intel-2.7/rpy2/rlike/tests

copying ./rpy/rlike/tests/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rlike/tests

copying ./rpy/rlike/tests/test_container.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rlike/tests

copying ./rpy/rlike/tests/test_functional.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rlike/tests

copying ./rpy/rlike/tests/test_indexing.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rlike/tests

creating build/lib.macosx-10.9-intel-2.7/rpy2/rinterface

copying ./rpy/rinterface/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface

creating build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests

copying ./rpy/rinterface/tests/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests

copying ./rpy/rinterface/tests/test_Device.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests

copying ./rpy/rinterface/tests/test_EmbeddedR.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests

copying ./rpy/rinterface/tests/test_Sexp.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests

copying ./rpy/rinterface/tests/test_SexpClosure.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests

copying ./rpy/rinterface/tests/test_SexpEnvironment.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests

copying ./rpy/rinterface/tests/test_SexpExtPtr.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests

copying ./rpy/rinterface/tests/test_SexpVector.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests

copying ./rpy/rinterface/tests/test_SexpVectorNumeric.py -> build/lib.macosx-10.9-intel-2.7/rpy2/rinterface/tests

creating build/lib.macosx-10.9-intel-2.7/rpy2/robjects

copying ./rpy/robjects/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects

copying ./rpy/robjects/constants.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects

copying ./rpy/robjects/conversion.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects

copying ./rpy/robjects/environments.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects

copying ./rpy/robjects/functions.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects

copying ./rpy/robjects/help.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects

copying ./rpy/robjects/language.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects

copying ./rpy/robjects/methods.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects

copying ./rpy/robjects/numpy2ri.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects

copying ./rpy/robjects/packages.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects

copying ./rpy/robjects/pandas2ri.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects

copying ./rpy/robjects/robject.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects

copying ./rpy/robjects/vectors.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects

creating build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests

copying ./rpy/robjects/tests/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests

copying ./rpy/robjects/tests/testArray.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests

copying ./rpy/robjects/tests/testDataFrame.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests

copying ./rpy/robjects/tests/testEnvironment.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests

copying ./rpy/robjects/tests/testFormula.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests

copying ./rpy/robjects/tests/testFunction.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests

copying ./rpy/robjects/tests/testHelp.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests

copying ./rpy/robjects/tests/testLanguage.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests

copying ./rpy/robjects/tests/testMethods.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests

copying ./rpy/robjects/tests/testNumpyConversions.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests

copying ./rpy/robjects/tests/testPackages.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests

copying ./rpy/robjects/tests/testPandasConversions.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests

copying ./rpy/robjects/tests/testRObject.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests

copying ./rpy/robjects/tests/testRobjects.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests

copying ./rpy/robjects/tests/testVector.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/tests

creating build/lib.macosx-10.9-intel-2.7/rpy2/robjects/lib

copying ./rpy/robjects/lib/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/lib

copying ./rpy/robjects/lib/ggplot2.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/lib

copying ./rpy/robjects/lib/grid.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/lib

creating build/lib.macosx-10.9-intel-2.7/rpy2/robjects/lib/tests

copying ./rpy/robjects/lib/tests/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/lib/tests

copying ./rpy/robjects/lib/tests/test_ggplot2.py -> build/lib.macosx-10.9-intel-2.7/rpy2/robjects/lib/tests

creating build/lib.macosx-10.9-intel-2.7/rpy2/interactive

copying ./rpy/interactive/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/interactive

copying ./rpy/interactive/ipython.py -> build/lib.macosx-10.9-intel-2.7/rpy2/interactive

copying ./rpy/interactive/packages.py -> build/lib.macosx-10.9-intel-2.7/rpy2/interactive

copying ./rpy/interactive/process_revents.py -> build/lib.macosx-10.9-intel-2.7/rpy2/interactive

creating build/lib.macosx-10.9-intel-2.7/rpy2/interactive/tests

copying ./rpy/interactive/tests/__init__.py -> build/lib.macosx-10.9-intel-2.7/rpy2/interactive/tests

running build_ext

"/opt/local/Library/Frameworks/R.framework/Resources/bin/R" CMD config --ldflags

"/opt/local/Library/Frameworks/R.framework/Resources/bin/R" CMD config --cppflags

"/opt/local/Library/Frameworks/R.framework/Resources/bin/R" CMD config LAPACK_LIBS



returned an empty string.



"/opt/local/Library/Frameworks/R.framework/Resources/bin/R" CMD config BLAS_LIBS



returned an empty string.



Configuration for R as a library:

  include_dirs: ('/opt/local/Library/Frameworks/R.framework/Resources/include',)

  libraries: ()

  library_dirs: ('/opt/local/Library/Frameworks/R.framework/Resources/lib',)

  extra_link_args: ('-F/opt/local/Library/Frameworks/R.framework/..', '-framework R')

 # OSX-specific (included in extra_link_args)

  framework_dirs: ('-F/opt/local/Library/Frameworks/R.framework/..',)

  frameworks: ('-framework R',)

building 'rpy2.rinterface._rinterface' extension

creating build/temp.macosx-10.9-intel-2.7

creating build/temp.macosx-10.9-intel-2.7/rpy

creating build/temp.macosx-10.9-intel-2.7/rpy/rinterface

cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -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 x86_64 -arch i386 -pipe -DR_INTERFACE_PTRS=1 -DHAVE_POSIX_SIGJMP=1 -DRIF_HAS_RSIGHAND=1 -DCSTACK_DEFNS=1 -DHAS_READLINE=1 -I./rpy/rinterface -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/opt/local/Library/Frameworks/R.framework/Resources/include -c ./rpy/rinterface/_rinterface.c -o build/temp.macosx-10.9-intel-2.7/./rpy/rinterface/_rinterface.o

clang: error: unknown argument: '-mno-fused-madd' [-Wunused-command-line-argument-hard-error-in-future]

clang: note: this will be a hard error (cannot be downgraded to a warning) in the future

error: command 'cc' failed with exit status 1

----------------------------------------
Cleaning up...
  Removing temporary dir /private/tmp/pip_build_root...
Command /usr/bin/python -c "import setuptools, tokenize;__file__='/private/tmp/pip_build_root/rpy2/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-E3rnYf-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /private/tmp/pip_build_root/rpy2
Exception information:
Traceback (most recent call last):
  File "/Library/Python/2.7/site-packages/pip-1.5.1-py2.7.egg/pip/basecommand.py", line 122, in main
    status = self.run(options, args)
  File "/Library/Python/2.7/site-packages/pip-1.5.1-py2.7.egg/pip/commands/install.py", line 279, in run
    requirement_set.install(install_options, global_options, root=options.root_path)
  File "/Library/Python/2.7/site-packages/pip-1.5.1-py2.7.egg/pip/req.py", line 1380, in install
    requirement.install(install_options, global_options, *args, **kwargs)
  File "/Library/Python/2.7/site-packages/pip-1.5.1-py2.7.egg/pip/req.py", line 699, in install
    cwd=self.source_dir, filter_stdout=self._filter_install, show_stdout=False)
  File "/Library/Python/2.7/site-packages/pip-1.5.1-py2.7.egg/pip/util.py", line 697, in call_subprocess
    % (command_desc, proc.returncode, cwd))
InstallationError: Command /usr/bin/python -c "import setuptools,     tokenize;__file__='/private/tmp/pip_build_root/rpy2/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-E3rnYf-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /private/tmp/pip_build_root/rpy2

Hi @ernestorab, welcome to StackOverflow! In the future, try to format large chunks of code the way Bob Gilmore did for you. You can find out how to format questions and answers here: http://stackoverflow.com/help/formatting — Steve H., Mar 21 '14 at 21:14
Thank you @BobGilmore. I will format the the code in the future. — , Mar 26 '14 at 01:20

score 1 · Answer 1 · edited May 23 '17 at 11:57

1

I had the same problem, this worked for me.

Just set these environment variables before you build rpy2:

export CFLAGS=-Qunused-arguments
export CPPFLAGS=-Qunused-arguments

edited May 23 '17 at 11:57

Community

1
1

answered May 06 '14 at 02:04

hasancc

145
1
9

score 0 · Answer 2 · answered Mar 24 '14 at 22:43

This has to do with the CC compiler (error is right before the Python traceback):

cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -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 x86_64 -arch i386 -pipe -DR_INTERFACE_PTRS=1 -DHAVE_POSIX_SIGJMP=1 -DRIF_HAS_RSIGHAND=1 -DCSTACK_DEFNS=1 -DHAS_READLINE=1 -I./rpy/rinterface -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/opt/local/Library/Frameworks/R.framework/Resources/include -c ./rpy/rinterface/_rinterface.c -o build/temp.macosx-10.9-intel-2.7/./rpy/rinterface/_rinterface.o

clang: error: unknown argument: '-mno-fused-madd' [-Wunused-command-line-argument-hard-error-in-future]

clang: note: this will be a hard error (cannot be downgraded to a warning) in the future

error: command 'cc' failed with exit status 1

Can you provide details regarding the origin of the C compiler (OS X dev tools ? elsewhere ?) and of Python (homebrew ? binary install ? other ?). Do you use specific environment variables (e.g. CFLAGS, or other likely to be picked up by clang) ?

I installed the latest version of the OS X dev tools, but the error continued to appear, maybe I have to reinstall the CC compiler somehow. And the python version I use is the one that came with OS X. I didn't use any specific environment variables, I just wrote `sudo pip install rpy2` on the terminal. — , Mar 26 '14 at 01:25
@ernestorab : some of the flags will come from the way the python you are using was built. Here it would mean incompatibility between clang in XCode and the way the system's python was built. I do not have OS X 10.9; someone who does might be able to comment. In any case, I'd recommend to leave the system's Python alone and install 3rd party packages on a different python (homebrew, python.org, etc...) — lgautier, Mar 28 '14 at 22:56
Thank you for the recommendation. I will give it a try but I think I'll just use another computer to play a little bit with python. — , Mar 30 '14 at 05:02

Unable to install rpy2 on Mac OS X 10.9

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