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  • #16
    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

    Comment


    • #17
      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

      Comment


      • #18
        Which xcode version do you have installed?

        Comment


        • #19
          Harlock0883, I have the following installed:

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

          Comment


          • #20
            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

            Comment


            • #21
              Originally posted by Simon Anders View Post
              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?
              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!

              Comment


              • #22
                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

                Comment


                • #23
                  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

                  Comment


                  • #24
                    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
                    Last edited by ryantkoehler; 01-21-2013, 10:33 AM.

                    Comment


                    • #25
                      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.

                      Comment


                      • #26
                        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
                        Last edited by ryantkoehler; 01-21-2013, 10:57 AM.

                        Comment


                        • #27
                          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.

                          Comment


                          • #28
                            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()

                            Comment


                            • #29
                              Change to another directory before trying "import HTSeq".

                              Comment


                              • #30
                                That did the trick!
                                Thanks very much,
                                -Ryan

                                Comment

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