Having same issues, no fixes work
So I've tried all the suggestions posted here and none of them are working for me.
Running a fresh install of OS X 10.8, XCode 4.6, Python 2.7
- installing with pip > no luck
tried the following with same errors:
$ export CC=llvm-gcc-4.2
$ export CXX=llvm-g++-4.2
$ sudo python setup.py build
running build
running build_py
creating build
creating build/lib.macosx-10.8-intel-2.7
creating build/lib.macosx-10.8-intel-2.7/HTSeq
copying HTSeq/__init__.py -> build/lib.macosx-10.8-intel-2.7/HTSeq
copying HTSeq/_HTSeq_internal.py -> build/lib.macosx-10.8-intel-2.7/HTSeq
copying HTSeq/StepVector.py -> build/lib.macosx-10.8-intel-2.7/HTSeq
copying HTSeq/_version.py -> build/lib.macosx-10.8-intel-2.7/HTSeq
creating build/lib.macosx-10.8-intel-2.7/HTSeq/scripts
copying HTSeq/scripts/__init__.py -> build/lib.macosx-10.8-intel-2.7/HTSeq/scripts
copying HTSeq/scripts/qa.py -> build/lib.macosx-10.8-intel-2.7/HTSeq/scripts
copying HTSeq/scripts/count.py -> build/lib.macosx-10.8-intel-2.7/HTSeq/scripts
running build_ext
building 'HTSeq._HTSeq' extension
creating build/temp.macosx-10.8-intel-2.7
creating build/temp.macosx-10.8-intel-2.7/src
clang -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 -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/_HTSeq.c -o build/temp.macosx-10.8-intel-2.7/src/_HTSeq.o -w
clang: warning: argument unused during compilation: '-Os'
clang: warning: argument unused during compilation: '-mno-fused-madd'
clang -bundle -undefined dynamic_lookup -Wl,-F. -arch i386 -arch x86_64 build/temp.macosx-10.8-intel-2.7/src/_HTSeq.o -o build/lib.macosx-10.8-intel-2.7/HTSeq/_HTSeq.so
building 'HTSeq._StepVector' extension
clang -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 -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/StepVector_wrap.cxx -o build/temp.macosx-10.8-intel-2.7/src/StepVector_wrap.o -w
clang: warning: not using the clang compiler for C++ inputs
clang: warning: not using the clang compiler for C++ inputs
clang: error: unable to execute command: posix_spawn failed: No such file or directory
clang: error: gcc frontend command failed due to signal 1 (use -v to see invocation)
error: command 'clang' failed with exit status 255
$ sudo python setup.py install
running install
running bdist_egg
running egg_info
writing HTSeq.egg-info/PKG-INFO
writing top-level names to HTSeq.egg-info/top_level.txt
writing dependency_links to HTSeq.egg-info/dependency_links.txt
reading manifest file 'HTSeq.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching 'example_data'
no previously-included directories found matching 'test'
warning: no previously-included files found matching 'todo.txt'
writing manifest file 'HTSeq.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.8-intel/egg
running install_lib
running build_py
running build_ext
building 'HTSeq._StepVector' extension
clang -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 -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/StepVector_wrap.cxx -o build/temp.macosx-10.8-intel-2.7/src/StepVector_wrap.o -w
clang: warning: not using the clang compiler for C++ inputs
clang: warning: not using the clang compiler for C++ inputs
clang: error: unable to execute command: posix_spawn failed: No such file or directory
clang: error: gcc frontend command failed due to signal 1 (use -v to see invocation)
error: command 'clang' failed with exit status 255
--------------------------------------
Successfully installed on my Mac running OSX 10.6...super frustrating.
So I've tried all the suggestions posted here and none of them are working for me.
Running a fresh install of OS X 10.8, XCode 4.6, Python 2.7
- installing with pip > no luck
tried the following with same errors:
$ export CC=llvm-gcc-4.2
$ export CXX=llvm-g++-4.2
$ sudo python setup.py build
running build
running build_py
creating build
creating build/lib.macosx-10.8-intel-2.7
creating build/lib.macosx-10.8-intel-2.7/HTSeq
copying HTSeq/__init__.py -> build/lib.macosx-10.8-intel-2.7/HTSeq
copying HTSeq/_HTSeq_internal.py -> build/lib.macosx-10.8-intel-2.7/HTSeq
copying HTSeq/StepVector.py -> build/lib.macosx-10.8-intel-2.7/HTSeq
copying HTSeq/_version.py -> build/lib.macosx-10.8-intel-2.7/HTSeq
creating build/lib.macosx-10.8-intel-2.7/HTSeq/scripts
copying HTSeq/scripts/__init__.py -> build/lib.macosx-10.8-intel-2.7/HTSeq/scripts
copying HTSeq/scripts/qa.py -> build/lib.macosx-10.8-intel-2.7/HTSeq/scripts
copying HTSeq/scripts/count.py -> build/lib.macosx-10.8-intel-2.7/HTSeq/scripts
running build_ext
building 'HTSeq._HTSeq' extension
creating build/temp.macosx-10.8-intel-2.7
creating build/temp.macosx-10.8-intel-2.7/src
clang -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 -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/_HTSeq.c -o build/temp.macosx-10.8-intel-2.7/src/_HTSeq.o -w
clang: warning: argument unused during compilation: '-Os'
clang: warning: argument unused during compilation: '-mno-fused-madd'
clang -bundle -undefined dynamic_lookup -Wl,-F. -arch i386 -arch x86_64 build/temp.macosx-10.8-intel-2.7/src/_HTSeq.o -o build/lib.macosx-10.8-intel-2.7/HTSeq/_HTSeq.so
building 'HTSeq._StepVector' extension
clang -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 -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/StepVector_wrap.cxx -o build/temp.macosx-10.8-intel-2.7/src/StepVector_wrap.o -w
clang: warning: not using the clang compiler for C++ inputs
clang: warning: not using the clang compiler for C++ inputs
clang: error: unable to execute command: posix_spawn failed: No such file or directory
clang: error: gcc frontend command failed due to signal 1 (use -v to see invocation)
error: command 'clang' failed with exit status 255
$ sudo python setup.py install
running install
running bdist_egg
running egg_info
writing HTSeq.egg-info/PKG-INFO
writing top-level names to HTSeq.egg-info/top_level.txt
writing dependency_links to HTSeq.egg-info/dependency_links.txt
reading manifest file 'HTSeq.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching 'example_data'
no previously-included directories found matching 'test'
warning: no previously-included files found matching 'todo.txt'
writing manifest file 'HTSeq.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.8-intel/egg
running install_lib
running build_py
running build_ext
building 'HTSeq._StepVector' extension
clang -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 -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/StepVector_wrap.cxx -o build/temp.macosx-10.8-intel-2.7/src/StepVector_wrap.o -w
clang: warning: not using the clang compiler for C++ inputs
clang: warning: not using the clang compiler for C++ inputs
clang: error: unable to execute command: posix_spawn failed: No such file or directory
clang: error: gcc frontend command failed due to signal 1 (use -v to see invocation)
error: command 'clang' failed with exit status 255
--------------------------------------
Successfully installed on my Mac running OSX 10.6...super frustrating.
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