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Problem building SAMtools 1.2 64-bit under Linux Mint 17

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  • Problem building SAMtools 1.2 64-bit under Linux Mint 17

    I'm using gcc 4.8.2 and the linux-headers-3.13.0-24-generic package in Mint; I've modified the makefile to satisfy the ncurses and zlib dependencies. When I run make, I get a lot of inconsistencies of .h file locations within the linux-headers tree, also some type redefinition errors.

    While continuing to try to resolve thise issues, I can manage with the 0.1.19 version which is the latest available in the Mint repositories. I'd like to know whether anyone has successfully built SAMtools 1.2 for 64-bit Linux and if the binary can be downloaded for installation.

    Thanks in advance for any helpfui responses.

  • #2
    I build it every day on 64-bit Linux without any issues.

    Perhaps you could show us a sampling of these inconsistent .h file location and type redefinition error messages.


    • #3
      I'm almost sure the inconsistency is not due to something in the SAMtools source but is rather within the linux-headers-3.13.0-24-generic package in Linux Mint 17, that it's somehow out of sync with itself and/or with the corresponding headers in gcc 4.8.2. Would using gcc 4.9 likely make a difference?

      I can post again and attach my compilation output, but I was mainly interested in whether you (or someone else) could possibly make available a working binary of version 1.2 for 64-bit Linux - it would be greatly appreciated.