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  • 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!

  • #2
    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?

    Comment


    • #3
      I have this same problem. Did you figure out any solutions?

      Comment


      • #4
        Not yet, I sent an email to Dr. Anders, but he was out of office on vacation.

        Comment


        • #5
          I was able to install just fine on a Mac running Snow Leopard.

          Comment


          • #6
            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?

            Comment


            • #7
              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, 10:01 AM.

              Comment


              • #8
                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!

                Comment


                • #9
                  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.

                  Comment


                  • #10
                    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

                    Comment


                    • #11
                      I was able HTseq without errors now following devking's procedure.

                      Thank you!

                      Comment


                      • #12
                        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!

                        Comment


                        • #13
                          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, 05:28 PM.

                          Comment


                          • #14
                            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?

                            Comment


                            • #15
                              Try deleting the HTseq folder and just start over with the sudo commands.

                              Comment

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