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  • Installation error (vcftools) due to zlib?

    Hello,

    I'm trying to install vcftools but am getting the following error after following the instructions on the website (up to "make"):

    make[1]: Entering directory `/home/Documents/prog/vcftools_0.1.12b/cpp'
    g++ -O2 -D_FILE_OFFSET_BITS=64 vcftools.o bcf_file.o vcf_file.o variant_file.o header.o bcf_entry.o vcf_entry.o entry.o entry_getters.o entry_setters.o vcf_entry_setters.o bcf_entry_setters.o entry_filters.o variant_file_filters.o variant_file_output.o parameters.o variant_file_format_convert.o variant_file_diff.o output_log.o bgzf.o gamma.o -o vcftools -lz
    bcf_file.o: In function `bcf_file:pen_gz()':
    bcf_file.cpp.text+0x9eb): undefined reference to `gzbuffer'
    vcf_file.o: In function `vcf_file:pen_gz()':
    vcf_file.cpp.text+0x55c): undefined reference to `gzbuffer'
    collect2: ld returned 1 exit status
    make[1]: *** [vcftools] Error 1
    make[1]: Leaving directory `/home/Documents/prog/vcftools_0.1.12b/cpp'
    /bin/sh: 3: cd: can't cd to perl
    The FAQ section on zlib hints at the problem:

    "Why do I get "undefined reference to gzputc"?
    If make test produces something like:
    example.o(.text+0x154): undefined reference to `gzputc'
    check that you don't have old files libz.* in /usr/lib, /usr/local/lib or /usr/X11R6/lib. Remove any old versions, then do make install."
    When I look at the files/directories listed in these /usr/ directories, they are
    /usr/local/lib/libz.a
    /usr/local/lib/libz.so.1
    /usr/local/lib/libz.so
    /usr/local/lib/libz.so.1.2.8

    and all date to when I installed zlib. Do I need to remove these files and reinstall zlib?
    I'm kind of nervous about removing these files (I will need to use the sudo command I think?) as I'm not sure what else depends on zlib...

    Can someone please help me understand what's going on and what I need to do?

    Much thanks in advance!
    Last edited by jullee; 11-27-2014, 07:12 AM.

  • #2
    See if this solution helps: http://stackoverflow.com/questions/1...r-where-lib-lz

    Comment


    • #3
      Thank you GenoMax! That helped.

      Overall I had to do the following:

      As I couldn't find zlib1g-dev using the following command:

      whereis zlib1g-dev

      I first made sure zlib was installed following the instructions here:



      I then made sure tabix was installed.

      I then made the change suggested to the vcftools make file suggested at the link provided (http://stackoverflow.com/questions/1...r-where-lib-lz).

      I should mention, in case others have similar difficulties, after all that, it wasn't over yet! I also had to ensure that I set the following paths before everything worked out:

      export PERL5LIB=/home/path-to-vcftools/vcftools_0.1.12b/perl
      export PATH=$PATH:/home/path-to-tabix/tabix-0.2.6
      export PATH=$PATH:/home/path-to-vcftools/vcftools_0.1.12b/bin

      Cheers

      Comment

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