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Old 10-01-2012, 07:00 AM   #1
bromo
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Exclamation installing htseq on a mac

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:

Code:
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!
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Old 10-10-2012, 07:06 AM   #2
harlock0083
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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?
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Old 11-19-2012, 10:35 AM   #3
devking
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I have this same problem. Did you figure out any solutions?
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Old 11-19-2012, 11:21 AM   #4
harlock0083
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Not yet, I sent an email to Dr. Anders, but he was out of office on vacation.
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Old 11-22-2012, 05:05 AM   #5
drdna
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I was able to install just fine on a Mac running Snow Leopard.
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Old 11-22-2012, 08:42 AM   #6
Simon Anders
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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

Code:
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?
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Old 11-26-2012, 05:49 AM   #7
harlock0083
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For me it was a fresh Mac OS 10.8 (mountain lion). I installed xcode after the initial setup of the system.

Last edited by harlock0083; 11-26-2012 at 09:01 AM.
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Old 11-28-2012, 06:37 AM   #8
harlock0083
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I did the following commands:

Code:
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!
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Old 11-28-2012, 08:02 AM   #9
dsbreak
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Quote:
Originally Posted by Simon Anders View Post
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.
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Old 11-28-2012, 11:03 AM   #10
devking
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Quote:
Originally Posted by Simon Anders View Post

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:

Code:
$ 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
Code:
>>> import HTSeq
>>>
with no errors

Thanks,
Devin
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Old 11-28-2012, 12:45 PM   #11
harlock0083
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I was able HTseq without errors now following devking's procedure.

Thank you!
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Old 12-04-2012, 02:08 PM   #12
sboyle
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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!
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Old 12-04-2012, 04:23 PM   #13
devking
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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

Last edited by devking; 12-04-2012 at 04:28 PM.
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Old 12-06-2012, 01:54 PM   #14
sboyle
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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?
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Old 12-06-2012, 02:05 PM   #15
harlock0083
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Try deleting the HTseq folder and just start over with the sudo commands.
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Old 12-06-2012, 02:55 PM   #16
sboyle
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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
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Old 12-06-2012, 03:58 PM   #17
devking
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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
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Old 12-07-2012, 05:47 AM   #18
harlock0083
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Which xcode version do you have installed?
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Old 12-07-2012, 08:33 AM   #19
sboyle
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Harlock0883, I have the following installed:

Mac Pro (10.8.2)
Python (2.6.6)
xcode (4.5.2)
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Old 12-07-2012, 08:42 AM   #20
harlock0083
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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
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