[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

[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!

[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

[sboyle]

Harlock0883, I have the following installed:

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

[harlock0083]

Which xcode version do you have installed?

[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

[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

[harlock0083]

Try deleting the HTseq folder and just start over with the sudo commands.

[sboyle]

Hello Devking,

When I run the suggested commands:
$ export CC=llvm-gcc-4.2
$ export CXX=llvm-g++-4.2
$ sudo python setup.py build
$ sudo python setup.py install --user

I get the following error:
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

Thank you for the help. Any other suggestions?

[devking]

Hi sboyle,

Try the setup.py build as root with sudo

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

[sboyle]

I am also having errors installing HTseq on a brand new Mac Pro.

I have the following system:
Mac Pro (10.8.2)
Python (2.6.6)
xcode (4.5.2)

When attempting to install I get the following error:
$ python setup.py build
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
/usr/bin/lipo: can't create output file: build/temp.macosx-10.8-intel-2.7/src/StepVector_wrap.o (Permission denied)
clang: error: lipo command failed with exit code 1 (use -v to see invocation)
error: command 'clang' failed with exit status 1

When I try to use the suggested addition:
$ export CC=llvm-gcc-4.2
$ export CXX=llvm-g++-4.2
$ python setup.py build

I get the follwoing:
$ python setup.py build
running build
running build_py
running build_ext
building 'HTSeq._StepVector' extension
llvm-gcc-4.2 -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
cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++
cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++
lipo: can't create output file: build/temp.macosx-10.8-intel-2.7/src/StepVector_wrap.o (Permission denied)
error: command 'llvm-gcc-4.2' failed with exit status 1

It is a different error, but I am still not sure how to best progress. Any suggestions? Thank you in advance!

[harlock0083]

I was able HTseq without errors now following devking's procedure.

Thank you!

[devking]

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?

Hi Simon, thanks for the advice. This worked for me. I'm running Mac OS X v 10.8.2, Xcode v. 4.5.2, python v. 2.7.2. I downloaded the source tarball (HTSeq-0.5.3p9.tar.gz) and unpacked. After changing into the directory of the unpacked HTSeq-0.5.3p9 my commands were:

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

To test, I changed out of the directory containing setup.py, started python then typed

>>> import HTSeq
>>>

with no errors

Thanks,
Devin

[dsbreak]

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?

This worked for me. I am running 10.8.1 on a new iMac (i.e. fresh install) with XCode 4.4.1.

[harlock0083]

I did the following commands:

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

but I still get the same error


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


python version is 2.7.2
gcc version 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)
on OS X 10.8

Any help would be appreciated. Thank you!