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  • Error for samtools, `ZLIB_1.2.3.3` not found

    Error:
    Code:
     $./samtools: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by ./samtools)
    I've install zlib and ncurses at first.
    =========================
    Thanks GenoMax for the help, samtools on my server is working.

    Here are what I did.
    1. Replace " -D_CURSES_LIB=1" by " -D_CURSES_LIB=0" in line 4 of Makefile
    2. Comment out "#LIBCURSES= -lcurses # -lXCurses" in Makefile.
    3. Delete the duplicate of "libz*" in /usr/local/lib/.

    I replace the "/lib64/libz.so.1.2.3" by "/usr/local/bin/libz.so.1.2.8". Then result of /lib64/lib and /usr/local/lib/ directory like this:
    Code:
    $ls -l /usr/local/lib/libz*
    -rw-r--r-- 1 root root 126318 Dec 18 12:47 /usr/local/lib/libz.a
    lrwxrwxrwx 1 root root     13 Dec 18 12:47 /usr/local/lib/libz.so.1 -> libz.so.1.2.8
    -rwxr-xr-x 1 root root  99184 Dec 18 12:47 /usr/local/lib/libz.so.1.2.8
    $ls -l  /lib64/libz*
    lrwxrwxrwx 1 root root    13 Dec 19 09:42 /lib64/libz.so.1 -> libz.so.1.2.8
    -rwxr-xr-x 1 root root 99184 Dec 19 09:41 /lib64/libz.so.1.2.8
    =========================


    system info: CentOS 6.3
    Code:
    $head -n 1 /etc/issue CentOS release 6.3 (Final) 
    $uname -a Linux ***** 2.6.32-279.19.1.el6.x86_64 #1 SMP Wed Dec 19 07:05:20 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
    when I download samtools source file "samtools-0.1.19.tar.bz2" from sourceforge.net. The following errors were reported for the first time to compile samtools.

    Error 1:
    Code:
    $make
    ....
    collect2: ld returned 1 exit status
    make[1]: *** [samtools] Error 1
    make[1]: Leaving directory `/home/wangming/Documents/samtools-0.1.19'
    make: *** [all-recur] Error 1
    According to suggestions from online searches. It can be compiled finally after a few changes to the file "Makefile"

    1. Add the "-L/usr/local/lib -I/usr/include/ncurses" to end of line-2 of Makefile under directory of /samtools-0.1.19.
    before:
    Code:
    CFLAGS=     -g -Wall -O2
    after:
    Code:
    CFLAGS=         -g -Wall -O2  -L/usr/local/lib -I/usr/include/ncurses #
    2. change the "-D_CURSES_LIB=1" to "-D_CURSES_LIB=0" in the line-4
    before
    Code:
    DFLAGS=        -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
    after
    Code:
    DFLAGS=        -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0
    Last edited by bakerwm; 12-18-2013, 06:11 PM. Reason: Errors are fixed.

  • #2
    If you do not have "zlib" installed then you would need to install that but if you do have zlib installed then it may be just be a matter of creating a soft-link for the library in /lib64:

    Make sure zlib is installed
    Code:
    $ rpm -qa | grep zlib
    Create the softlink (adjust names/paths according to your system)
    Code:
    $ ln -s /lib64/libz.so.1 /usr/lib/libz.so.1

    Comment


    • #3
      Originally posted by GenoMax View Post
      If you do not have "zlib" installed then you would need to install that but if you do have zlib installed then it may be just be a matter of creating a soft-link for the library in /lib64:

      Make sure zlib is installed
      Code:
      $ rpm -qa | grep zlib
      Create the softlink (adjust names/paths according to your system)
      Code:
      $ ln -s /lib64/libz.so.1 /usr/lib/libz.so.1
      Unfortunately, the problem still there.
      Code:
      $rpm -qa |grep zlib
      zlib-devel-1.2.3-29.el6.x86_64
      zlib-1.2.3-29.el6.x86_64
      
      $file /usr/lib/libz.so.1    
      /usr/lib/libz.so.1: symbolic link to `/lib64/libz.so.1' 
      
      $./samtools 
      ./samtools: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by ./samtools)

      Comment


      • #4
        Do you have /lib64/libz.so.1? Is that readable by "all"?

        Comment


        • #5
          Yes, here are the content in /lib64/

          Code:
          $ll /lib64/libz*
          lrwxrwxrwx 1 root root    13 Dec 17 23:39 /lib64/libz.so.1 -> libz.so.1.2.3
          -rwxrwxrwx 1 root root 91096 Feb 22  2013 /lib64/libz.so.1.2.3

          Comment


          • #6
            That's version 1.2.3, which is < 1.2.3.3.

            Comment


            • #7
              I was able to compile on RedHat 6.5 by doing the following.

              Keep your #2 modification.

              Comment out "#LIBCURSES= -lcurses # -lXCurses" in Makefile.

              "ncurses" library files are in /lib64 in my case. I also have libz.so.1.2.3.

              Comment


              • #8
                Originally posted by dpryan View Post
                That's version 1.2.3, which is < 1.2.3.3.
                Sorry, I cannot fix this error/ the libz is already the latest version.

                Comment


                • #9
                  Originally posted by GenoMax View Post
                  I was able to compile on RedHat 6.5 by doing the following.

                  Keep your #2 modification.

                  Comment out "#LIBCURSES= -lcurses # -lXCurses" in Makefile.

                  "ncurses" library files are in /lib64 in my case. I also have libz.so.1.2.3.
                  I did comment out "LIBCURSES= -lcurses # -lXCurses", and keep #1 & #2 modifications together.
                  compile is OK, but still report the error:
                  Code:
                  $./samtools 
                  ./samtools: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by ./samtools)

                  Comment


                  • #10
                    Samtools is working for me (albeit on RH 6.5 which is probably not fully identical to CentOS).

                    Can you try to use only your mod #2 (i.e. do not use #1) along with commenting the LIBCURSES line out?

                    Post the output of
                    Code:
                    $ ldd samtools

                    Comment


                    • #11
                      Originally posted by GenoMax View Post
                      Samtools is working for me (albeit on RH 6.5 which is probably not fully identical to CentOS).

                      Can you try to use only your mod #2 (i.e. do not use #1) along with commenting the LIBCURSES line out?

                      Post the output of
                      Code:
                      $ ldd samtools

                      #2 + commenting LIBCURSES line, error reported as following when "make"
                      Code:
                      make[1]: *** [samtools] Error 1
                      make[1]: Leaving directory `/home/wangming/Documents/samtools-0.1.19'
                      make: *** [all-recur] Error 1
                      at least using #2 and “-L/usr/local/lib" of #1, then compile is OK.
                      Code:
                      $ldd samtools
                      ./samtools: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by ./samtools)
                              linux-vdso.so.1 =>  (0x00007fffd0ef8000)
                              libm.so.6 => /lib64/libm.so.6 (0x0000003b1a400000)
                              libz.so.1 => /lib64/libz.so.1 (0x0000003547000000)
                              libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003b1ac00000)
                              libc.so.6 => /lib64/libc.so.6 (0x0000003b1a000000)
                              /lib64/ld-linux-x86-64.so.2 (0x0000003b19c00000)

                      Comment


                      • #12
                        Looks like your executable is correctly linked (same libraries as I see).

                        Are there files in your /usr/local/lib? On my server that directory is empty. I wonder if there are duplicate copies of "libz.*" there.

                        Comment


                        • #13
                          Originally posted by GenoMax View Post
                          Looks like your executable is correctly linked (same libraries as I see).

                          Are there files in your /usr/local/lib? On my server that directory is empty. I wonder if there are duplicate copies of "libz.*" there.
                          thanks so much ,i will try your suggestion and report how is going?

                          Comment


                          • #14
                            Originally posted by GenoMax View Post
                            Looks like your executable is correctly linked (same libraries as I see).

                            Are there files in your /usr/local/lib? On my server that directory is empty. I wonder if there are duplicate copies of "libz.*" there.
                            Oh, Yeah, It's done, Samtools works. Thanks GenoMax for the help.

                            Here are what I did last night:
                            1. Replace " -D_CURSES_LIB=1" by " -D_CURSES_LIB=0" in line 4 of Makefile

                            2. Comment out "#LIBCURSES= -lcurses # -lXCurses" in Makefile.

                            3. I do have duplicate of "libz*" in /usr/local/lib/. And then replace the "/lib64/libz.so.1.2.3" by "/usr/local/bin/libz.so.1.2.8". Keep the /lib64/lib and /usr/local/lib/ directory like this.
                            Code:
                            $ls -l /usr/local/lib/libz*
                            -rw-r--r-- 1 root root 126318 Dec 18 12:47 /usr/local/lib/libz.a
                            lrwxrwxrwx 1 root root     13 Dec 18 12:47 /usr/local/lib/libz.so.1 -> libz.so.1.2.8
                            -rwxr-xr-x 1 root root  99184 Dec 18 12:47 /usr/local/lib/libz.so.1.2.8
                            $ls -l  /lib64/libz*
                            lrwxrwxrwx 1 root root    13 Dec 19 09:42 /lib64/libz.so.1 -> libz.so.1.2.8
                            -rwxr-xr-x 1 root root 99184 Dec 19 09:41 /lib64/libz.so.1.2.8

                            Comment


                            • #15
                              Originally posted by dpryan View Post
                              That's version 1.2.3, which is < 1.2.3.3.
                              Thanks, the error was fixed when I replaced the 1.2.3 version by 1.2.8.

                              Comment

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