installing htseq on a mac

[harlock0083]

For me it was a fresh Mac OS 10.8 (mountain lion). I installed xcode after the initial setup of the system.

[Simon Anders]

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?

[drdna]

I was able to install just fine on a Mac running Snow Leopard.

[harlock0083]

Not yet, I sent an email to Dr. Anders, but he was out of office on vacation.

[devking]

I have this same problem. Did you figure out any solutions?

[harlock0083]

I also tried install the latest HTseq package and get the same error or mountain lion. I did the install on our linux box running opensuse 11.3 and everything was fine. Anyone have suggestions for a os x install?

[bromo]

I am trying to install htseq 5.3p9 on my mac (mountain lion, xcode 4.4.1) and i have run into a problem with clang? which i tried googling but am not sure how to proceed:

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

Any suggestions would be great! Thanks!