installing htseq on a mac

[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!

[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?

[devking]

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

[harlock0083]

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

[drdna]

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

[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?

[harlock0083]

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

[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!

[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.

[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

[harlock0083]

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

Thank you!

[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!

[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]

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?

[harlock0083]

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