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  • #31
    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.

    Comment


    • #32
      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.

      Comment


      • #33
        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.

        Comment


        • #34
          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

          Comment


          • #35
            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:

            Comment


            • #36
              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.

              Comment


              • #37
                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.

                Comment

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