[sboyle]

Unfortunately, deleting and starting over with/without sudo did not work.

The specific output was:

$ 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 -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++ -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

[devking]

Well at least you're not getting the write permission error anymore but.... it looks like the compiler issue that Simon alluded to persists. As harlock said it's important to remove EVERYTHING HTseq and then start fresh by re-downloading the source tarball and building with sudo privileges. If you're still not having any luck I'd suggest emailing Dr. Anders and asking for a Mac OSX binary package which you could install with a simple 'python setup.py install --user' command

[harlock0083]

Which xcode version do you have installed?

[sboyle]

Harlock0883, I have the following installed:

Mac Pro (10.8.2)
Python (2.6.6)
xcode (4.5.2)

[harlock0083]

Hi sboyle,

When I first tried to install HTseq on our new mac workstation I got the same clang error.

I have almost the same software versions except my python version is 2.7.2. I followed the directions by devking and was able to install htseq.

I wonder if I could compress my HTseq folder and send it to you. I would think all you would have to do is the python setup.py install command

Winton

[Gadareth]

Mac OS seems to have a habit of subtly messing up its Python installation (or more specifically: the interplay between Python and Xcode) when you update a release.

A user recently reported to me that he managed to solve the problem by typing

export CC=llvm-gcc-4.2
export CXX=llvm-g++-4.2

before calling 'python setup.py install'.

Could somebody please confirm that this solves the issue? (I don't have a Mac so I cannot check.)

Out of curiosity, I would like to know if this problem is really tied to updating from an older Mac OS installation to a current one, or does it also occur with a fresh Mac?

Thank you so much to Dr. Anders and "Dev King" for your posts. I've been searching the net trying to debug this error now for a day!

[sarmun]

Just thought I'd chime in, this might help sboyle, I was having similar issues with installing HTSeq on mountain lion and couldn't get the other suggestions here to work for me.

I ended up using pip to run the install on a downloaded source package (from http://pypi.python.org/pypi/HTSeq/0.5.3p7) and that seemed to work. See below. The first command gets pip for you and then the second command will have pip unpack and install the source package for HTSeq:

> curl https://raw.github.com/pypa/pip/mast...rib/get-pip.py | python

> pip install ../Downloads/HTSeq-0.5.3p9.tar.gz

[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

[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

[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 (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]

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]

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]

Change to another directory before trying "import HTSeq".

[ryantkoehler]

That did the trick!
Thanks very much,
-Ryan