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  • #16
    Originally posted by Krosh View Post
    Hi,
    I can't install bfast in Ubuntu. Thanks for any help.
    Same answer, install the necessary packages listed above. I am adding this to the new BFAST FAQ: https://sourceforge.net/apps/mediawi....php?title=FAQ

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    • #17
      Thank you!

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      • #18
        Hi,

        I am also having some problems building bfast (0.7.0a) on mac osx 10.8.5 with xcode version 3.2.6.

        I am able to run the autogen.sh and ./configure successfully, but I get the following error during the make:

        Undefined symbols for architecture x86_64:
        "_AlignNTSpaceFillInCell", referenced from:
        _AlignNTSpaceGappedBounded in AlignNTSpace.o
        _AlignNTSpaceGappedConstrained in AlignNTSpace.o
        "_ScoringMatrixGetColorScore", referenced from:
        _AlignExact in Align.o
        _AlignColorSpaceUngappedGetBest in AlignColorSpace.o
        _AlignColorSpaceFillInCell in AlignColorSpace.o
        _AlignColorSpaceGappedConstrained in AlignColorSpace.o
        "_ScoringMatrixGetNTScore", referenced from:
        _AlignExact in Align.o
        _AlignNTSpaceUngapped in AlignNTSpace.o
        _AlignNTSpaceGappedConstrained in AlignNTSpace.o
        _AlignColorSpaceUngappedGetBest in AlignColorSpace.o
        _AlignColorSpaceFillInCell in AlignColorSpace.o
        _AlignColorSpaceGappedConstrained in AlignColorSpace.o
        "_ToUpper", referenced from:
        _AlignedReadConvertPrintAlignedEntryToCIGAR in AlignedReadConvert.o
        _RGBinaryRead in RGBinary.o
        _RGMatchCheck in RGMatch.o
        _AlignExact in Align.o
        (maybe you meant: _ToUpperRead)
        ld: symbol(s) not found for architecture x86_64
        clang: error: linker command failed with exit code 1 (use -v to see invocation)
        make[2]: *** [bfast] Error 1
        make[1]: *** [all-recursive] Error 1
        make: *** [all] Error 2

        Searching online leads me to believe that it is a problem in the linking stage, but I don't know how to fix it myself. If anyone has any tips for me, or if I need to post more information, then please let me know.

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