Biopython error in mac os x

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    • #1304


        I am new with mac osx and rosetta. I have rosetta 3.3 installed and have trouble with installation of biopython 1.59. on my mac os 10.7, have already installed Xcode 4.3.2. I have pasted the error message. Any help would be highly appreciated.

        $cd biopython-1.59
        $sudo python install
        running install
        running build
        running build_py
        creating build
        creating build/lib.macosx-10.7-intel-2.7
        creating build/lib.macosx-10.7-intel-2.7/Bio
        copying Bio/ -> build/lib.macosx-10.7-intel-2.7/Bio
        copying Bio/ -> build/lib.macosx-10.7-intel-2.7/Bio
        copying Bio/PopGen/SimCoal/data/ssm_2d.par -> build/lib.macosx-10.7-intel-2.7/Bio/PopGen/SimCoal/data
        running build_ext
        building ‘Bio.cpairwise2’ extension
        creating build/temp.macosx-10.7-intel-2.7
        creating build/temp.macosx-10.7-intel-2.7/Bio
        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 -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -IBio -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c Bio/cpairwise2module.c -o build/temp.macosx-10.7-intel-2.7/Bio/cpairwise2module.o
        unable to execute llvm-gcc-4.2: No such file or directory
        error: command ‘llvm-gcc-4.2’ failed with exit status 1

      • #7237

          What do you need biopython for? I wasn’t aware that we had anything that required it. Did you mean to post to a biopython forum?

          It’s failing because llvm-gcc-4.2 doesn’t exist.

        • #7243

            First, thanks for thenprompt reply. Well, I am trying to do a test run of antibody-antigen docking via rosettadock3.3. Reading their manual, its suggested to have biopython as part of setting up the workspace environment.

            Could help to know how to supply llvm-gcc4.2?
            Thanks again,

          • #7245
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