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Re: [ssahausers] Patching SSAHA 3.1 so it will compile using GCC 4.0.1

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  • 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 1 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 2 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 3 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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