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  • tboothby
    replied
    Would somebody who has successfully built HTSeq on a Mac mind sharing their build with me? I am getting the same error as in the original post, unfortunately the subsequent suggestions don't seem to be working for me.

    Leave a comment:


  • Darwin
    replied
    Thanks for the reply, Simon. I installed the newer python because I had the same problems as is listed above, and couldn't solve it.

    I have access to a linux cluster, and I will ask the sysadms to install it there until Apple come to their senses and sort this out.

    Cheers,
    Darwin
    Last edited by Darwin; 03-05-2013, 02:43 PM. Reason: clarity.

    Leave a comment:


  • Simon Anders
    replied
    When trying to trace C compilation problems, always look at the first error, not the last. In your case:

    Code:
    /Developer/SDKs/MacOSX10.6.sdk/usr/include/c++/4.2.1/exception:42:28: error: bits/c++config.h: No such file or directory
    My guess is that your installing a new Python might have messed things up. The root cause of all these problems is, after all, that Apple seemed to have messed up keeping Python and Xcode in sync. Maybe you need to go back to one of the Python/Xcode combinations that people in this thread have reported to work. Maybe this thread helps, too:

    Leave a comment:


  • Darwin
    replied
    Has anyone figured this out?

    I have for a while tried installing HTSeq on a mac running 10.8.2, Xcode4.6. I installed the newer version of python 2.7.3 and numpy, since I encountered the same problems as is described in this thread.

    However, it still fails:
    ---
    lsa-579-005:HTSeq-0.5.4p1 darwin$ python setup.py install
    Could not import 'setuptools', falling back to 'distutils'.
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.6-intel-2.7
    creating build/lib.macosx-10.6-intel-2.7/HTSeq
    copying HTSeq/__init__.py -> build/lib.macosx-10.6-intel-2.7/HTSeq
    copying HTSeq/_HTSeq_internal.py -> build/lib.macosx-10.6-intel-2.7/HTSeq
    copying HTSeq/StepVector.py -> build/lib.macosx-10.6-intel-2.7/HTSeq
    copying HTSeq/_version.py -> build/lib.macosx-10.6-intel-2.7/HTSeq
    creating build/lib.macosx-10.6-intel-2.7/HTSeq/scripts
    copying HTSeq/scripts/__init__.py -> build/lib.macosx-10.6-intel-2.7/HTSeq/scripts
    copying HTSeq/scripts/qa.py -> build/lib.macosx-10.6-intel-2.7/HTSeq/scripts
    copying HTSeq/scripts/count.py -> build/lib.macosx-10.6-intel-2.7/HTSeq/scripts
    running build_ext
    building 'HTSeq._HTSeq' extension
    creating build/temp.macosx-10.6-intel-2.7
    creating build/temp.macosx-10.6-intel-2.7/src
    llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/_HTSeq.c -o build/temp.macosx-10.6-intel-2.7/src/_HTSeq.o -w
    llvm-gcc-4.2 -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk -isysroot /Developer/SDKs/MacOSX10.6.sdk -g build/temp.macosx-10.6-intel-2.7/src/_HTSeq.o -o build/lib.macosx-10.6-intel-2.7/HTSeq/_HTSeq.so
    building 'HTSeq._StepVector' extension
    llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/StepVector_wrap.cxx -o build/temp.macosx-10.6-intel-2.7/src/StepVector_wrap.o -w
    In file included from /Developer/SDKs/MacOSX10.6.sdk/usr/include/c++/4.2.1/stdexcept:43,
    from src/StepVector_wrap.cxx:2996:
    /Developer/SDKs/MacOSX10.6.sdk/usr/include/c++/4.2.1/exception:42:28: error: bits/c++config.h: No such file or directory
    In file included from /Developer/SDKs/MacOSX10.6.sdk/usr/include/c++/4.2.1/bits/stl_algobase.h:70,
    from /Developer/SDKs/MacOSX10.6.sdk/usr/include/c++/4.2.1/bits/char_traits.h:46,
    from /Developer/SDKs/MacOSX10.6.sdk/usr/include/c++/4.2.1/string:47,
    from /Developer/SDKs/MacOSX10.6.sdk/usr/include/c++/4.2.1/stdexcept:44,
    from src/StepVector_wrap.cxx:2996:
    ---
    And a lot of similar errors. In the end I get this:
    ---

    Developer/SDKs/MacOSX10.6.sdk/usr/include/c++/4.2.1/new:47: error: expected declaration before end of line
    lipo: can't figure out the architecture type of: /Users/darwin/Temp/cc1blxT1.out
    error: command 'llvm-gcc-4.2' failed with exit status 1
    ----

    Any help on this matter is greatly appreciated.

    Cheers,
    Darwin

    Leave a comment:


  • Simon Anders
    replied
    In principle, you need sudo only for the 'install', not the 'build'. So what you should have done is:

    Code:
    export CC=llvm-gcc-4.2
    export CXX=llvm-g++-4.2
    python setup.py build
    sudo python setup.py install
    The reason that your first try did not work is that the environment variables that you set with 'export' are not seen by the 'python setup.py build' command if you prefix that one with 'sudo', because sudo does not pass on environment variables to its subprocess, for security reasons. The 'setup.py install' command does not need the environment variables, and so the sudo is fine there.

    If you want to avoid using 'sudo' altogether, you can also use 'python setup.py install --user', which installs the package within the current user's home directory so that no superuser permissions are required.
    Last edited by Simon Anders; 02-23-2013, 11:27 AM.

    Leave a comment:


  • aprilw
    replied
    HTSeq installation problem solved...for me

    I solved my installation problem the following way:

    -when I would run the install without sudo, no clang error was thrown, however I didn't have permission to write
    -logged in as root and ran following commands:

    # export CC=llvm-gcc-4.2
    # export CXX=llvm-g++-4.2
    # /usr/bin/python2.7 setup.py build
    # /usr/bin/python2.7 setup.py install

    Installed with no errors. For some reason logging in as root fixed my problem even though running these same commands using sudo did not?? I'm just glad it's finally installed. Hope this helps someone with the same problem.

    Leave a comment:


  • aprilw
    replied
    Having same issues, no fixes work

    So I've tried all the suggestions posted here and none of them are working for me.

    Running a fresh install of OS X 10.8, XCode 4.6, Python 2.7

    - installing with pip > no luck

    tried the following with same errors:

    $ 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: warning: argument unused during compilation: '-Os'
    clang: warning: argument unused during compilation: '-mno-fused-madd'
    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: warning: not using the clang compiler for C++ inputs
    clang: warning: not using the clang compiler for C++ inputs
    clang: error: unable to execute command: posix_spawn failed: No such file or directory
    clang: error: gcc frontend command failed due to signal 1 (use -v to see invocation)
    error: command 'clang' failed with exit status 255
    $ sudo python setup.py install
    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: warning: not using the clang compiler for C++ inputs
    clang: warning: not using the clang compiler for C++ inputs
    clang: error: unable to execute command: posix_spawn failed: No such file or directory
    clang: error: gcc frontend command failed due to signal 1 (use -v to see invocation)
    error: command 'clang' failed with exit status 255

    --------------------------------------
    Successfully installed on my Mac running OSX 10.6...super frustrating.

    Leave a comment:


  • ryantkoehler
    replied
    That did the trick!
    Thanks very much,
    -Ryan

    Leave a comment:


  • Simon Anders
    replied
    Change to another directory before trying "import HTSeq".

    Leave a comment:


  • ryantkoehler
    replied
    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()

    Leave a comment:


  • Simon Anders
    replied
    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.

    Leave a comment:


  • ryantkoehler
    replied
    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.

    Leave a comment:


  • Simon Anders
    replied
    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.

    Leave a comment:


  • ryantkoehler
    replied
    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.

    Leave a comment:


  • sboyle
    replied
    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

    Leave a comment:

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