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  • MaSuRCA install error

    I'm attempting to install the MaSuRCA assembly tool using the simple instructions on the quickstart guide. Basically, the instructions say to untar the package, cd into the resulting directory, and then run ./install.sh.

    When I do this, the very end of the output gives a set of errors that apparently have to do with jellyfish. I'm not sure how to interpret this. Has anyone else seen this? I'm pasting just the part of the output that contains the errors and occurs at the very end of the process. There were not any obvious errors before this point:

    # Output
    In file included from sub_commands/count_main.cc:39:
    ./include/jellyfish/mer_qual_iterator.hpp: In member function âvoid jellyfish::mer_qual_iterator<SequencePool, MerType>::init_from_job()â:
    ./include/jellyfish/mer_qual_iterator.hpp:108: error: âstruct std::basic_string<char, std::char_traits<char>, std::allocator<char> >â has no member named âcbeginâ
    ./include/jellyfish/mer_qual_iterator.hpp:109: error: âstruct std::basic_string<char, std::char_traits<char>, std::allocator<char> >â has no member named âcendâ
    ./include/jellyfish/mer_qual_iterator.hpp:111: error: âstruct std::basic_string<char, std::char_traits<char>, std::allocator<char> >â has no member named âcbeginâ
    ./include/jellyfish/mer_qual_iterator.hpp:112: error: âstruct std::basic_string<char, std::char_traits<char>, std::allocator<char> >â has no member named âcendâ
    make[1]: *** [sub_commands/count_main.o] Error 1
    make[1]: *** Waiting for unfinished jobs....
    make[1]: Leaving directory `/raid4/cgrb/MaSuRCA-2.2.0/jellyfish'
    make: *** [install] Error 2

  • #2
    This particular excerpt does not raise any obvious flags. Can you post the earliest instances of "Error" from this output?

    If it is easier, you can paste the whole output via pastebin (http://pastebin.com/). Remember to remove any identifying IP addresses/host names/account names etc.

    Comment


    • #3
      Here's the entire output...

      OK, I tried pasting the entire output in pastebin. How do I link the pastebin page back to this thread?

      I titled the pastebin "MaSuRCA install error output".

      Comment


      • #4
        Here the pastebin link for your output: http://pastebin.com/zLDXsks7 Verify that it is right.

        Comment


        • #5
          Yup, that's the one.

          Comment


          • #6
            Can you tell us what OS you are using and if it is 32- or 64-bit? This is a real server (and not a virtual machine).

            Comment


            • #7
              OS

              The OS is Linux - x86_64 GNU/Linux

              Comment

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