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Patching SSAHA 3.1 so it will compile using GCC 4.0.1

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  • Conrad Halling
    SSAHA users, I attempted to compile SSAHA 3.1 on my Mac OS X computer using the latest compiler, GCC 4.0.1. Unfortunately, GCC 4.0.1 is much more finicky about
    Message 1 of 5 , Dec 29, 2005
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      SSAHA users,

      I attempted to compile SSAHA 3.1 on my Mac OS X computer using the
      latest compiler, GCC 4.0.1. Unfortunately, GCC 4.0.1 is much more
      finicky about C++ standards than the old GCC 2.95 compiler, and there
      were many errors that prevented building the software.

      I updated the SSAHA 3.1 code so it would compile using GCC 4.0.1. At the
      same time, I fixed all compiler warnings (produced by the GCC -Wall
      flag) that I could.

      I have created and tested a patch file for modifying the SSAHA 3.1 code
      so that it can be compiled using GCC 4.0.1 (and, I hope, the GCC 3.3 and
      3.4 compilers). I supply the patch file and detailed directions for
      using it on my web site at http://www.bifx.org/SSAHA/index.html.

      It would be ideal if the developers of SSAHA incorporated some or all of
      my changes into SSAHA 3.1 and distributed an updated release that can be
      compiled with the later GCC compilers.

      -- Conrad

      --
      Conrad Halling
      conrad.halling@...
    • Conrad Halling
      SSAHA users, This is a follow-up to my post on December 29, 2005, about patching SSAHA 3.1 so it will compile using the GCC 4.0.1 compiler. I finally got
      Message 2 of 5 , Jan 12, 2006
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        SSAHA users,

        This is a follow-up to my post on December 29, 2005, about patching
        SSAHA 3.1 so it will compile using the GCC 4.0.1 compiler.

        I finally got around to compiling the patched version of SSAHA 3.1 using
        GCC 4.0.2 under Fedora Core 4. The patched version passes all provided
        test programs under Fedora Core 4.

        However, under Mac OS X 10.4.4, three of the tests fail. Since the
        PowerPC processor uses a different byte ordering than the Pentium
        processor, I suspect the problem is in the SSAHA code that deals with
        byte ordering. I will continue to investigate since I want to run SSAHA
        on a Macintosh.

        Details are provided on my web site at http://www.bifx.org/SSAHA/index.html.

        -- Conrad

        Conrad Halling wrote:
        > SSAHA users,
        >
        > I attempted to compile SSAHA 3.1 on my Mac OS X computer using the
        > latest compiler, GCC 4.0.1. Unfortunately, GCC 4.0.1 is much more
        > finicky about C++ standards than the old GCC 2.95 compiler, and there
        > were many errors that prevented building the software.
        >
        > I updated the SSAHA 3.1 code so it would compile using GCC 4.0.1. At the
        > same time, I fixed all compiler warnings (produced by the GCC -Wall
        > flag) that I could.
        >
        > I have created and tested a patch file for modifying the SSAHA 3.1 code
        > so that it can be compiled using GCC 4.0.1 (and, I hope, the GCC 3.3 and
        > 3.4 compilers). I supply the patch file and detailed directions for
        > using it on my web site at http://www.bifx.org/SSAHA/index.html.
        >
        > It would be ideal if the developers of SSAHA incorporated some or all of
        > my changes into SSAHA 3.1 and distributed an updated release that can be
        > compiled with the later GCC compilers.
        >
        > -- Conrad

        --
        Conrad Halling
        conrad.halling@...
      • Conrad Halling
        SSAHA Users, This is the completion of my one-person thread. After about 24 hours of debugging over three days, I found and corrected the bug that prevented
        Message 3 of 5 , Jan 18, 2006
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          SSAHA Users,

          This is the completion of my one-person thread.

          After about 24 hours of debugging over three days, I found and corrected
          the bug that prevented SSAHA from running correctly on a PowerPC Macintosh.

          On my web site at http://www.bifx.org/SSAHA/index.html you will find a
          patch file that you can use to update the SSAHA 3.1 source code so it
          can be compiled using the GCC 4.0.x compilers available for Mac OS X and
          later distributions of Linux (e.g., Fedora Core 4).

          If the SSAHA developers are still around and reading this list, it would
          be ideal if they tested my patch and then distributed the patched
          version of SSAHA 3.1 from the SSAHA page of the Sanger Institute web site.

          -- Conrad

          Conrad Halling wrote:
          > SSAHA users,
          >
          > This is a follow-up to my post on December 29, 2005, about patching
          > SSAHA 3.1 so it will compile using the GCC 4.0.1 compiler.
          >
          > I finally got around to compiling the patched version of SSAHA 3.1 using
          > GCC 4.0.2 under Fedora Core 4. The patched version passes all provided
          > test programs under Fedora Core 4.
          >
          > However, under Mac OS X 10.4.4, three of the tests fail. Since the
          > PowerPC processor uses a different byte ordering than the Pentium
          > processor, I suspect the problem is in the SSAHA code that deals with
          > byte ordering. I will continue to investigate since I want to run SSAHA
          > on a Macintosh.
          >
          > Details are provided on my web site at http://www.bifx.org/SSAHA/index.html.
          >
          > -- Conrad
          >
          > Conrad Halling wrote:
          > > SSAHA users,
          > >
          > > I attempted to compile SSAHA 3.1 on my Mac OS X computer using the
          > > latest compiler, GCC 4.0.1. Unfortunately, GCC 4.0.1 is much more
          > > finicky about C++ standards than the old GCC 2.95 compiler, and there
          > > were many errors that prevented building the software.
          > >
          > > I updated the SSAHA 3.1 code so it would compile using GCC 4.0.1. At the
          > > same time, I fixed all compiler warnings (produced by the GCC -Wall
          > > flag) that I could.
          > >
          > > I have created and tested a patch file for modifying the SSAHA 3.1 code
          > > so that it can be compiled using GCC 4.0.1 (and, I hope, the GCC 3.3 and
          > > 3.4 compilers). I supply the patch file and detailed directions for
          > > using it on my web site at http://www.bifx.org/SSAHA/index.html.
          > >
          > > It would be ideal if the developers of SSAHA incorporated some or all of
          > > my changes into SSAHA 3.1 and distributed an updated release that can be
          > > compiled with the later GCC compilers.
          > >
          > > -- Conrad

          --
          Conrad Halling
          conrad.halling@...
        • Adam Spargo
          Hi, Thanks for your efforts. I ll put a link to your page from the SSAHA homepage for the time being and hopefully get around to testing your patch soon.
          Message 4 of 5 , Jan 19, 2006
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            Hi,
            Thanks for your efforts. I'll put a link to your page from the SSAHA
            homepage for the time being and hopefully get around to testing your patch
            soon.

            Regards,

            Adam.


            On Wed, 18 Jan 2006, Conrad Halling wrote:

            > SSAHA Users,
            >
            > This is the completion of my one-person thread.
            >
            > After about 24 hours of debugging over three days, I found and corrected
            > the bug that prevented SSAHA from running correctly on a PowerPC Macintosh.
            >
            > On my web site at http://www.bifx.org/SSAHA/index.html you will find a
            > patch file that you can use to update the SSAHA 3.1 source code so it
            > can be compiled using the GCC 4.0.x compilers available for Mac OS X and
            > later distributions of Linux (e.g., Fedora Core 4).
            >
            > If the SSAHA developers are still around and reading this list, it would
            > be ideal if they tested my patch and then distributed the patched
            > version of SSAHA 3.1 from the SSAHA page of the Sanger Institute web site.
            >
            > -- Conrad
            >
            > Conrad Halling wrote:
            > > SSAHA users,
            > >
            > > This is a follow-up to my post on December 29, 2005, about patching
            > > SSAHA 3.1 so it will compile using the GCC 4.0.1 compiler.
            > >
            > > I finally got around to compiling the patched version of SSAHA 3.1 using
            > > GCC 4.0.2 under Fedora Core 4. The patched version passes all provided
            > > test programs under Fedora Core 4.
            > >
            > > However, under Mac OS X 10.4.4, three of the tests fail. Since the
            > > PowerPC processor uses a different byte ordering than the Pentium
            > > processor, I suspect the problem is in the SSAHA code that deals with
            > > byte ordering. I will continue to investigate since I want to run SSAHA
            > > on a Macintosh.
            > >
            > > Details are provided on my web site at http://www.bifx.org/SSAHA/index.html.
            > >
            > > -- Conrad
            > >
            > > Conrad Halling wrote:
            > > > SSAHA users,
            > > >
            > > > I attempted to compile SSAHA 3.1 on my Mac OS X computer using the
            > > > latest compiler, GCC 4.0.1. Unfortunately, GCC 4.0.1 is much more
            > > > finicky about C++ standards than the old GCC 2.95 compiler, and there
            > > > were many errors that prevented building the software.
            > > >
            > > > I updated the SSAHA 3.1 code so it would compile using GCC 4.0.1. At the
            > > > same time, I fixed all compiler warnings (produced by the GCC -Wall
            > > > flag) that I could.
            > > >
            > > > I have created and tested a patch file for modifying the SSAHA 3.1 code
            > > > so that it can be compiled using GCC 4.0.1 (and, I hope, the GCC 3.3 and
            > > > 3.4 compilers). I supply the patch file and detailed directions for
            > > > using it on my web site at http://www.bifx.org/SSAHA/index.html.
            > > >
            > > > It would be ideal if the developers of SSAHA incorporated some or all of
            > > > my changes into SSAHA 3.1 and distributed an updated release that can be
            > > > compiled with the later GCC compilers.
            > > >
            > > > -- Conrad
            >
            >

            --
            Dr Adam Spargo
            High Performance Assembly Group email: aws@...
            Wellcome Trust Sanger Institute Tel: +44 (0)1223 834244 x7728
            Hinxton, Cambridge CB10 1SA Fax: +44 (0)1223 494919
          • Conrad Halling
            Great! Thanks. -- Conrad ... -- Conrad Halling conrad.halling@bifx.org
            Message 5 of 5 , Jan 19, 2006
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              Great! Thanks.

              -- Conrad

              Adam Spargo wrote:
              > Hi,
              > Thanks for your efforts. I'll put a link to your page from the SSAHA
              > homepage for the time being and hopefully get around to testing your patch
              > soon.
              >
              > Regards,
              >
              > Adam.
              >
              >
              > On Wed, 18 Jan 2006, Conrad Halling wrote:
              >
              > > SSAHA Users,
              > >
              > > This is the completion of my one-person thread.
              > >
              > > After about 24 hours of debugging over three days, I found and corrected
              > > the bug that prevented SSAHA from running correctly on a PowerPC
              > Macintosh.
              > >
              > > On my web site at http://www.bifx.org/SSAHA/index.html you will find a
              > > patch file that you can use to update the SSAHA 3.1 source code so it
              > > can be compiled using the GCC 4.0.x compilers available for Mac OS X and
              > > later distributions of Linux (e.g., Fedora Core 4).
              > >
              > > If the SSAHA developers are still around and reading this list, it would
              > > be ideal if they tested my patch and then distributed the patched
              > > version of SSAHA 3.1 from the SSAHA page of the Sanger Institute web
              > site.

              --
              Conrad Halling
              conrad.halling@...
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