[tboothby]

Would somebody who has successfully built HTSeq on a Mac mind sharing their build with me? I am getting the same error as in the original post, unfortunately the subsequent suggestions don't seem to be working for me.

[Darwin]

Thanks for the reply, Simon. I installed the newer python because I had the same problems as is listed above, and couldn't solve it.

I have access to a linux cluster, and I will ask the sysadms to install it there until Apple come to their senses and sort this out.

Cheers,
Darwin

[Simon Anders]

When trying to trace C compilation problems, always look at the first error, not the last. In your case:

/Developer/SDKs/MacOSX10.6.sdk/usr/include/c++/4.2.1/exception:42:28: error: bits/c++config.h: No such file or directory

My guess is that your installing a new Python might have messed things up. The root cause of all these problems is, after all, that Apple seemed to have messed up keeping Python and Xcode in sync. Maybe you need to go back to one of the Python/Xcode combinations that people in this thread have reported to work. Maybe this thread helps, too:

http://mail.python.org/pipermail/python-list/2012-October/633352.html

[Darwin]

Has anyone figured this out?

I have for a while tried installing HTSeq on a mac running 10.8.2, Xcode4.6. I installed the newer version of python 2.7.3 and numpy, since I encountered the same problems as is described in this thread.

However, it still fails:
---
lsa-579-005:HTSeq-0.5.4p1 darwin$ python setup.py install
Could not import 'setuptools', falling back to 'distutils'.
running install
running build
running build_py
creating build
creating build/lib.macosx-10.6-intel-2.7
creating build/lib.macosx-10.6-intel-2.7/HTSeq
copying HTSeq/__init__.py -> build/lib.macosx-10.6-intel-2.7/HTSeq
copying HTSeq/_HTSeq_internal.py -> build/lib.macosx-10.6-intel-2.7/HTSeq
copying HTSeq/StepVector.py -> build/lib.macosx-10.6-intel-2.7/HTSeq
copying HTSeq/_version.py -> build/lib.macosx-10.6-intel-2.7/HTSeq
creating build/lib.macosx-10.6-intel-2.7/HTSeq/scripts
copying HTSeq/scripts/__init__.py -> build/lib.macosx-10.6-intel-2.7/HTSeq/scripts
copying HTSeq/scripts/qa.py -> build/lib.macosx-10.6-intel-2.7/HTSeq/scripts
copying HTSeq/scripts/count.py -> build/lib.macosx-10.6-intel-2.7/HTSeq/scripts
running build_ext
building 'HTSeq._HTSeq' extension
creating build/temp.macosx-10.6-intel-2.7
creating build/temp.macosx-10.6-intel-2.7/src
llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/_HTSeq.c -o build/temp.macosx-10.6-intel-2.7/src/_HTSeq.o -w
llvm-gcc-4.2 -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk -isysroot /Developer/SDKs/MacOSX10.6.sdk -g build/temp.macosx-10.6-intel-2.7/src/_HTSeq.o -o build/lib.macosx-10.6-intel-2.7/HTSeq/_HTSeq.so
building 'HTSeq._StepVector' extension
llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/StepVector_wrap.cxx -o build/temp.macosx-10.6-intel-2.7/src/StepVector_wrap.o -w
In file included from /Developer/SDKs/MacOSX10.6.sdk/usr/include/c++/4.2.1/stdexcept:43,
from src/StepVector_wrap.cxx:2996:
/Developer/SDKs/MacOSX10.6.sdk/usr/include/c++/4.2.1/exception:42:28: error: bits/c++config.h: No such file or directory
In file included from /Developer/SDKs/MacOSX10.6.sdk/usr/include/c++/4.2.1/bits/stl_algobase.h:70,
from /Developer/SDKs/MacOSX10.6.sdk/usr/include/c++/4.2.1/bits/char_traits.h:46,
from /Developer/SDKs/MacOSX10.6.sdk/usr/include/c++/4.2.1/string:47,
from /Developer/SDKs/MacOSX10.6.sdk/usr/include/c++/4.2.1/stdexcept:44,
from src/StepVector_wrap.cxx:2996:
---
And a lot of similar errors. In the end I get this:
---

Developer/SDKs/MacOSX10.6.sdk/usr/include/c++/4.2.1/new:47: error: expected declaration before end of line
lipo: can't figure out the architecture type of: /Users/darwin/Temp/cc1blxT1.out
error: command 'llvm-gcc-4.2' failed with exit status 1
----

Any help on this matter is greatly appreciated.

Cheers,
Darwin

[Simon Anders]

In principle, you need sudo only for the 'install', not the 'build'. So what you should have done is:

export CC=llvm-gcc-4.2
export CXX=llvm-g++-4.2
python setup.py build
sudo python setup.py install

The reason that your first try did not work is that the environment variables that you set with 'export' are not seen by the 'python setup.py build' command if you prefix that one with 'sudo', because sudo does not pass on environment variables to its subprocess, for security reasons. The 'setup.py install' command does not need the environment variables, and so the sudo is fine there.

If you want to avoid using 'sudo' altogether, you can also use 'python setup.py install --user', which installs the package within the current user's home directory so that no superuser permissions are required.

[aprilw]

HTSeq installation problem solved...for me

I solved my installation problem the following way:

-when I would run the install without sudo, no clang error was thrown, however I didn't have permission to write
-logged in as root and ran following commands:

# export CC=llvm-gcc-4.2
# export CXX=llvm-g++-4.2
# /usr/bin/python2.7 setup.py build
# /usr/bin/python2.7 setup.py install

Installed with no errors. For some reason logging in as root fixed my problem even though running these same commands using sudo did not?? I'm just glad it's finally installed. Hope this helps someone with the same problem.

[aprilw]

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.

[ryantkoehler]

That did the trick!
Thanks very much,
-Ryan

[Simon Anders]

Change to another directory before trying "import HTSeq".

[ryantkoehler]

Tried it again without the sudo command, but still stuck:

Ryans-MacBook-Pro-2 [HTSeq-0.5.3p9] 668> bash
bash-3.2$ more sham
export CC=llvm-gcc-4.2
export CXX=llvm-g++-4.2
python setup.py build
python setup.py install --user
bash-3.2$ source sham
running build
running build_py
running build_ext
running build_scripts
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
creating build/bdist.macosx-10.8-intel/egg
creating build/bdist.macosx-10.8-intel/egg/HTSeq
copying build/lib.macosx-10.8-intel-2.7/HTSeq/__init__.py -> build/bdist.macosx-10.8-intel/egg/HTSeq
copying build/lib.macosx-10.8-intel-2.7/HTSeq/_HTSeq.so -> build/bdist.macosx-10.8-intel/egg/HTSeq
copying build/lib.macosx-10.8-intel-2.7/HTSeq/_HTSeq_internal.py -> build/bdist.macosx-10.8-intel/egg/HTSeq
copying build/lib.macosx-10.8-intel-2.7/HTSeq/_StepVector.so -> build/bdist.macosx-10.8-intel/egg/HTSeq
copying build/lib.macosx-10.8-intel-2.7/HTSeq/_version.py -> build/bdist.macosx-10.8-intel/egg/HTSeq
creating build/bdist.macosx-10.8-intel/egg/HTSeq/scripts
copying build/lib.macosx-10.8-intel-2.7/HTSeq/scripts/__init__.py -> build/bdist.macosx-10.8-intel/egg/HTSeq/scripts
copying build/lib.macosx-10.8-intel-2.7/HTSeq/scripts/count.py -> build/bdist.macosx-10.8-intel/egg/HTSeq/scripts
copying build/lib.macosx-10.8-intel-2.7/HTSeq/scripts/qa.py -> build/bdist.macosx-10.8-intel/egg/HTSeq/scripts
copying build/lib.macosx-10.8-intel-2.7/HTSeq/StepVector.py -> build/bdist.macosx-10.8-intel/egg/HTSeq
byte-compiling build/bdist.macosx-10.8-intel/egg/HTSeq/__init__.py to __init__.pyc
byte-compiling build/bdist.macosx-10.8-intel/egg/HTSeq/_HTSeq_internal.py to _HTSeq_internal.pyc
byte-compiling build/bdist.macosx-10.8-intel/egg/HTSeq/_version.py to _version.pyc
byte-compiling build/bdist.macosx-10.8-intel/egg/HTSeq/scripts/__init__.py to __init__.pyc
byte-compiling build/bdist.macosx-10.8-intel/egg/HTSeq/scripts/count.py to count.pyc
byte-compiling build/bdist.macosx-10.8-intel/egg/HTSeq/scripts/qa.py to qa.pyc
byte-compiling build/bdist.macosx-10.8-intel/egg/HTSeq/StepVector.py to StepVector.pyc
creating stub loader for HTSeq/_HTSeq.so
creating stub loader for HTSeq/_StepVector.so
byte-compiling build/bdist.macosx-10.8-intel/egg/HTSeq/_HTSeq.py to _HTSeq.pyc
byte-compiling build/bdist.macosx-10.8-intel/egg/HTSeq/_StepVector.py to _StepVector.pyc
creating build/bdist.macosx-10.8-intel/egg/EGG-INFO
installing scripts to build/bdist.macosx-10.8-intel/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/bdist.macosx-10.8-intel/egg/EGG-INFO/scripts
copying build/scripts-2.7/htseq-count -> build/bdist.macosx-10.8-intel/egg/EGG-INFO/scripts
copying build/scripts-2.7/htseq-qa -> build/bdist.macosx-10.8-intel/egg/EGG-INFO/scripts
changing mode of build/bdist.macosx-10.8-intel/egg/EGG-INFO/scripts/htseq-count to 755
changing mode of build/bdist.macosx-10.8-intel/egg/EGG-INFO/scripts/htseq-qa to 755
copying HTSeq.egg-info/PKG-INFO -> build/bdist.macosx-10.8-intel/egg/EGG-INFO
copying HTSeq.egg-info/SOURCES.txt -> build/bdist.macosx-10.8-intel/egg/EGG-INFO
copying HTSeq.egg-info/dependency_links.txt -> build/bdist.macosx-10.8-intel/egg/EGG-INFO
copying HTSeq.egg-info/top_level.txt -> build/bdist.macosx-10.8-intel/egg/EGG-INFO
writing build/bdist.macosx-10.8-intel/egg/EGG-INFO/native_libs.txt
zip_safe flag not set; analyzing archive contents...
HTSeq.StepVector: module references __file__
creating 'dist/HTSeq-0.5.3p9-py2.7-macosx-10.8-intel.egg' and adding 'build/bdist.macosx-10.8-intel/egg' to it
removing 'build/bdist.macosx-10.8-intel/egg' (and everything under it)
Processing HTSeq-0.5.3p9-py2.7-macosx-10.8-intel.egg
removing '/Users/rkoehler/Library/Python/2.7/lib/python/site-packages/HTSeq-0.5.3p9-py2.7-macosx-10.8-intel.egg' (and everything under it)
creating /Users/rkoehler/Library/Python/2.7/lib/python/site-packages/HTSeq-0.5.3p9-py2.7-macosx-10.8-intel.egg
Extracting HTSeq-0.5.3p9-py2.7-macosx-10.8-intel.egg to /Users/rkoehler/Library/Python/2.7/lib/python/site-packages
HTSeq 0.5.3p9 is already the active version in easy-install.pth
Installing htseq-count script to /Users/rkoehler/Library/Python/2.7/bin
Installing htseq-qa script to /Users/rkoehler/Library/Python/2.7/bin

Installed /Users/rkoehler/Library/Python/2.7/lib/python/site-packages/HTSeq-0.5.3p9-py2.7-macosx-10.8-intel.egg
Processing dependencies for HTSeq==0.5.3p9
Finished processing dependencies for HTSeq==0.5.3p9
bash-3.2$ python
Python 2.7.2 (default, Jun 20 2012, 16:23:33)
[GCC 4.2.1 Compatible Apple Clang 4.0 (tags/Apple/clang-418.0.60)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import HTSeq
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "HTSeq/__init__.py", line 8, in <module>
from _HTSeq import *
ImportError: No module named _HTSeq
>>> quit()
bash-3.2$ exit
exit
Ryans-MacBook-Pro-2 [HTSeq-0.5.3p9] 669> python
Python 2.7.2 (default, Jun 20 2012, 16:23:33)
[GCC 4.2.1 Compatible Apple Clang 4.0 (tags/Apple/clang-418.0.60)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import HTSeq
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "HTSeq/__init__.py", line 8, in <module>
from _HTSeq import *
ImportError: No module named _HTSeq
>>> quit()

[Simon Anders]

Note that sboyle in post #23 did _not_ put a "sudo" in fron of the "python setup.py build" command. This is crucial becaue "sudo" resets all environment variables. So, try again without it.

[ryantkoehler]

Hi (and thanks for quick response!)

I normally use tcsh, but I tried the install in bash where I think the correct variables were set(?). I created a short script ("sham") that first sets compiler variables then tries the install. At the end (after it doesn't work), I also checked that the env vars were set (which they appear to be). Here's my try:

Ryans-MacBook-Pro-2 [HTSeq-0.5.3p9] 558> more sham
export CC=llvm-gcc-4.2
export CXX=llvm-g++-4.2
sudo python setup.py build
sudo python setup.py install --user
Ryans-MacBook-Pro-2 [HTSeq-0.5.3p9] 559> bash
bash-3.2$ more sham
export CC=llvm-gcc-4.2
export CXX=llvm-g++-4.2
sudo python setup.py build
sudo python setup.py install --user
bash-3.2$ source sham
running build
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++ -bundle -undefined dynamic_lookup -Wl,-F. -arch i386 -arch x86_64 build/temp.macosx-10.8-intel-2.7/src/StepVector_wrap.o src/step_vector.h -o build/lib.macosx-10.8-intel-2.7/HTSeq/_StepVector.so
clang: warning: treating 'c-header' input as 'c++-header' when in C++ mode, this behavior is deprecated
clang: error: cannot use 'precompiled-header' output with multiple -arch options
clang: error: cannot specify -o when generating multiple output files
error: command 'clang++' failed with exit status 1
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++ -bundle -undefined dynamic_lookup -Wl,-F. -arch i386 -arch x86_64 build/temp.macosx-10.8-intel-2.7/src/StepVector_wrap.o src/step_vector.h -o build/lib.macosx-10.8-intel-2.7/HTSeq/_StepVector.so
clang: warning: treating 'c-header' input as 'c++-header' when in C++ mode, this behavior is deprecated
clang: error: cannot use 'precompiled-header' output with multiple -arch options
clang: error: cannot specify -o when generating multiple output files
error: command 'clang++' failed with exit status 1
bash-3.2$ env | grep CC
CC=llvm-gcc-4.2
bash-3.2$ env | grep CXX
CXX=llvm-g++-4.2

[Simon Anders]

Are you sure you set the environment variable correctly, as shown above. The effect should be that Python's setup call "llvm-gcc-4.2" instead of "clang" but that does not seem to be the case.

Sorry that I cannot offer a more comprehensive solution. I don't have Mac myself, and I have no clue how Apple managed to cause so much chaos with the new Xcode version. I will have to borrow a colleague's Macbook and investigate this thoroughly.

[ryantkoehler]

Hi

Did this ever get fixed? I tried all the above steps but am still stuck (get the same errors; shown below).
I have a Mac book pro OS X 10.8.2 (just upgraded from 10.6), python 2.7.2, and Xcode versions are two versions 3.2 and 4.5.2 (yes, it looks like there are two versions installed... The 3.2 is listed first if that matters. I'm just learning the Mac; Got this via "about this Mac" / Software / Developer).

Any help greatly appreciated :-)

End of install error message:
<<<<<<<<<<<<<<<<<<<<<<<
Installing collected packages: HTSeq
Running setup.py install for HTSeq
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++ -bundle -undefined dynamic_lookup -Wl,-F. -arch i386 -arch x86_64 build/temp.macosx-10.8-intel-2.7/src/StepVector_wrap.o src/step_vector.h -o build/lib.macosx-10.8-intel-2.7/HTSeq/_StepVector.so
clang: warning: treating 'c-header' input as 'c++-header' when in C++ mode, this behavior is deprecated
clang: error: cannot use 'precompiled-header' output with multiple -arch options
clang: error: cannot specify -o when generating multiple output files
error: command 'clang++' failed with exit status 1
Complete output from command /usr/bin/python -c "import setuptools;__file__='/tmp/pip-build/HTSeq/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-N4bYhF-record/install-record.txt --single-version-externally-managed:
running install

running build

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++ -bundle -undefined dynamic_lookup -Wl,-F. -arch i386 -arch x86_64 build/temp.macosx-10.8-intel-2.7/src/StepVector_wrap.o src/step_vector.h -o build/lib.macosx-10.8-intel-2.7/HTSeq/_StepVector.so

clang: warning: treating 'c-header' input as 'c++-header' when in C++ mode, this behavior is deprecated

clang: error: cannot use 'precompiled-header' output with multiple -arch options

clang: error: cannot specify -o when generating multiple output files

error: command 'clang++' failed with exit status 1

----------------------------------------
Command /usr/bin/python -c "import setuptools;__file__='/tmp/pip-build/HTSeq/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-N4bYhF-record/install-record.txt --single-version-externally-managed failed with error code 1 in /tmp/pip-build/HTSeq
Storing complete log in /Users/rkoehler/Library/Logs/pip.log

[sboyle]

Thanks for the suggestion sarmun. I tried installing pip, but it started throwing back errors about not having numpy installed. I did some more looking into this (and bashed my head against the keyboard a few times) and came across and another unrelated post discussing problems getting numpy to install correctly under OSX 10.8. A suggested fix was to specifically call the 2.7 pre-installed version of perl, which already includes numpy) using /usr/bin/python2.7. By combining this with the following it installed correctly:

$ export CC=llvm-gcc-4.2
$ export CXX=llvm-g++-4.2
$ /usr/bin/python2.7 setup.py build
$ sudo /usr/bin/python2.7 setup.py install