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  • mosaik-aligner installation problem on redhat 6

    Hi,

    I have downloaded the Mosaik-1.1.0021-source.tar.bz2 on our RedHat6 64 bit system. When running 'make' in the src directory, errors occur. Dependencies (gcc-c++, zlib, zlib-devel) have caused the some of the errors, but now I am stuck.

    Anybody to put me on the right track?

    Code:
    $ make
    Building MOSAIK for the following platform: linux
    =========================================================
    - Building in CommonSource
    - Building in AssemblyFormats
    make[2]: Nothing to be done for `all'.
    
    - Building in DataStructures
    make[2]: Nothing to be done for `all'.
    
    - Building in ExternalReadFormats
    make[2]: Nothing to be done for `all'.
    
    - Building in MosaikReadFormat
    make[2]: Nothing to be done for `all'.
    
    - Building in PairwiseAlignment
    make[2]: Nothing to be done for `all'.
    
    - Building in Utilities
    make[2]: Nothing to be done for `all'.
    
    
    - Building in MosaikBuild
      * linking MosaikBuild
    /usr/bin/ld: cannot find -lz
    collect2: ld returned 1 exit status
    make[1]: *** [MosaikBuild] Error 1
    
    - Building in MosaikAligner
      * linking MosaikAligner
    /usr/bin/ld: cannot find -lpthread
    collect2: ld returned 1 exit status
    make[1]: *** [MosaikAligner] Error 1
    
    - Building in MosaikSort
      * linking MosaikSort
    /usr/bin/ld: cannot find -lpthread
    collect2: ld returned 1 exit status
    make[1]: *** [MosaikSort] Error 1
    
    - Building in MosaikMerge
      * linking MosaikMerge
    /usr/bin/ld: cannot find -lpthread
    collect2: ld returned 1 exit status
    make[1]: *** [MosaikMerge] Error 1
    
    - Building in MosaikAssembler
      * linking MosaikAssembler
    /usr/bin/ld: cannot find -lpthread
    collect2: ld returned 1 exit status
    make[1]: *** [MosaikAssembler] Error 1
    Thanks in advance!
    www.bits.vib.be

  • #2
    Look here for a solution to "-lpthread": http://www.justlinux.com/forum/showthread.php?t=126349

    "-lz" is the zlib which you have installed. Is the Mosaik buildprocess looking in the right folder?

    You can always just google "/usr/bin/ld: cannot find lpthreads" (or whatever library it's missing) for these kinds of things.

    Comment


    • #3
      Sorry, I can't solve the problem

      Hi,

      Thanks for your suggestion to google: that is a new approach.

      zlib is installed, but I am not sure about lpthreads.

      I am learning now about 'ldconfig': apparently this is used to create links to the most up-to-date libraries. Perhaps I should pass a parameter over there.

      Quitting mosaik for now.
      www.bits.vib.be

      Comment


      • #4
        library issue (to some extent)

        I am having the same problem. ("/usr/bin/ld: cannot find -lpthread")
        upgraded my glibc using the add/remove software interface (awesome!) worked great
        then, like you i got the "/usr/bin/ld: cannot find -lz" error
        came across this:
        I am trying to compile Android source code under Ubuntu 10.04. I get an error saying, /usr/bin/ld: cannot find -lz Can you please tell me how can I fix it? What does cannot find -lz mean? Here'...

        which would seem to suggest there's something wrong with the Makefile.in
        However, I looked through several of the Makefile.in and header files for each of the modules and couldn't find anything overtly wrong (plus, i highly doubt the author would release it if it didn't compile). So I started looking around some more and found this:

        i went to my add/remove software interface and searched for zlib1g-dev but couldn't find any package named that, however i *did* find several packages with "zlib" included in the name. so i downloaded them all:
        mingw32-zlib
        perl-IO-Zlib (<--- this was probably the one)
        perl-Archive-Tar
        mingw32-zlib-static
        jzlib
        jzlib-javadoc
        zlib-static (<-- or maybe this one)
        jzlib-demo

        and then the code would compile

        Comment


        • #5
          RHEL 6.0

          I got source distribution to compile/link by modifying the 'includes/linux.inc' as follows:

          # define our processor specific flags
          export PLATFORM_FLAGS = -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -static
          export PLATFORM_LIBS = -L/usr/lib/x86_64-redhat-linux5E/lib64

          Determine library location (PLATFORM_LIBS) with command:
          $ find /usr/lib -name "*pthread*"

          Needs an exact match to 'libpthread.a".

          The GNU_SOURCE define solved linker error for MosaikAlign complaint about C99 version of fscanf().

          Comment


          • #6
            Originally posted by austic View Post
            zlib-static (<-- or maybe this one)
            I was also hit by this issue. I'm using CentOS 6.4. With the help of this thread I was able to solve it by installing these two packages:
            Code:
            sudo yum install zlib-static glibc-static
            No need to modify any source files in my case.

            Best,
            Carlos

            Comment

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