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  • GapFiller compiling problem

    Hey!

    For the last couple of days I've been trying to install GapFiller on linux. Sadly, i failed several times. After I ./configure; make i end up with the following error:

    -------------------------------------------------------------------------------------
    /usr/bin/ld: samtools/GapFiller-bam_import.o: undefined reference to symbol 'gzdopen'
    //usr/local/lib/libz.so.1: error adding symbols: DSO missing from command line
    collect2: error: ld returned 1 exit status
    make[1]: *** [GapFiller] Error 1
    make[1]: Leaving directory `$HOME/ngs/gapfiller-2.1.1/src'
    make: *** [all-recursive] Error 1
    -------------------------------------------------------------------------------------

    Has anyone encountered this error before? I've read quite abit about it, but couldnt find an effective solution. I've compiled a bunch of other softwares and they all worked fine.

    Any input would be appreciated!
    Best,
    Last edited by exo; 11-04-2014, 06:01 AM.

  • #2
    Can you check the Makefile and see if you can find a line that says LIBS? If there is "-lz" in that line, move it to the end of that line.

    One other thing to try would be (if -lz is missing):
    Code:
    $ ./configure LIBS="-lz"

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    • #3
      Wow ok, that worked thank you! Apparently -lz was missing from the Makefile adding your suggestion while running the "./configure" command fixed it!

      Thank you!

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