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  • an error when using cufflinks

    hi.
    i have installed samtools and boost librarires.
    after that, i download the cufflinks source code because my linux is 32-bit.

    Everything went fine. However, when I tested using cufflinks test_data.sam, the following error message appears.

    cufflinks: error while loading shared libraries: libboost_thread.so.1.44.0: cann
    ot open shared object file: No such file or directory

    It seems that cufflinks is not seeing the shared object file. However, when I ran the configure, it said as the following:
    checking whether the Boost::Thread library is available... yes

    Can anyone help me solve this problem?

  • #2
    I have the same problem.
    Did anyone manage to get this fixed?

    Or explain what the problem is?
    Last edited by Sparx; 12-15-2010, 03:54 AM.

    Comment


    • #3
      Hi,

      What Linux are you running? I would start by checking the libraries cufflinks is compiled to require by running:

      Code:
      ldd /path/to/cufflinks
      And the location of the installed boost libraries with:

      Code:
      ldconfig -p | grep boost
      Post the output of those if you can.


      Andrew
      Last edited by polyatail; 12-17-2010, 02:29 PM. Reason: better params to run as non-root

      Comment


      • #4
        Thanks for the response.

        What Linux are you running?
        Code:
        $ cat /proc/version 
        Linux version 2.6.18-128.7.1.el5.pdc5noib (gcc version 4.1.2 20080704 (Red Hat 4.1.2-44))
        My setup is a homefolder on afs and I'm trying to run cufflinks on a cluster.


        I would start by checking the libraries cufflinks is compiled to require by running:
        I actually tried to make a local install of boost in $HOME/boost/ and compile cufflinks with the --with-boost and --with-bam flags.
        However it does'nt seem to reflect that in the output of the commands.

        Code:
        $ ldd Data/cufflinks-0.9.3.save/bin/cufflinks 
        	libboost_thread.so.1.45.0 => not found
        	libz.so.1 => /usr/lib64/libz.so.1 (0x00000039f4600000)
        	libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00000039f7200000)
        	libm.so.6 => /lib64/libm.so.6 (0x00000039f3600000)
        	libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000039f4e00000)
        	libpthread.so.0 => /lib64/libpthread.so.0 (0x00000039f3a00000)
        	libc.so.6 => /lib64/libc.so.6 (0x00000039f2e00000)
        	/lib64/ld-linux-x86-64.so.2 (0x00000039f2a00000)
        Code:
        $ /sbin/ldconfig -p | grep boost
        	libboost_wserialization.so.2 (libc6,x86-64) => /usr/lib64/libboost_wserialization.so.2
        	libboost_wserialization.so (libc6,x86-64) => /usr/lib64/libboost_wserialization.so
        	libboost_unit_test_framework.so.2 (libc6,x86-64) => /usr/lib64/libboost_unit_test_framework.so.2
        	libboost_unit_test_framework.so (libc6,x86-64) => /usr/lib64/libboost_unit_test_framework.so
        	libboost_thread.so.2 (libc6,x86-64) => /usr/lib64/libboost_thread.so.2
        	libboost_thread.so (libc6,x86-64) => /usr/lib64/libboost_thread.so
        	libboost_test_exec_monitor.so.2 (libc6,x86-64) => /usr/lib64/libboost_test_exec_monitor.so.2
        	libboost_test_exec_monitor.so (libc6,x86-64) => /usr/lib64/libboost_test_exec_monitor.so
        	libboost_signals.so.2 (libc6,x86-64) => /usr/lib64/libboost_signals.so.2
        	libboost_signals.so (libc6,x86-64) => /usr/lib64/libboost_signals.so
        	libboost_serialization.so.2 (libc6,x86-64) => /usr/lib64/libboost_serialization.so.2
        	libboost_serialization.so (libc6,x86-64) => /usr/lib64/libboost_serialization.so
        	libboost_regex.so.2 (libc6,x86-64) => /usr/lib64/libboost_regex.so.2
        	libboost_regex.so (libc6,x86-64) => /usr/lib64/libboost_regex.so
        	libboost_python.so.2 (libc6,x86-64) => /usr/lib64/libboost_python.so.2
        	libboost_python.so (libc6,x86-64) => /usr/lib64/libboost_python.so
        	libboost_program_options.so.2 (libc6,x86-64) => /usr/lib64/libboost_program_options.so.2
        	libboost_program_options.so (libc6,x86-64) => /usr/lib64/libboost_program_options.so
        	libboost_prg_exec_monitor.so.2 (libc6,x86-64) => /usr/lib64/libboost_prg_exec_monitor.so.2
        	libboost_prg_exec_monitor.so (libc6,x86-64) => /usr/lib64/libboost_prg_exec_monitor.so
        	libboost_iostreams.so.2 (libc6,x86-64) => /usr/lib64/libboost_iostreams.so.2
        	libboost_iostreams.so (libc6,x86-64) => /usr/lib64/libboost_iostreams.so
        	libboost_filesystem.so.2 (libc6,x86-64) => /usr/lib64/libboost_filesystem.so.2
        	libboost_filesystem.so (libc6,x86-64) => /usr/lib64/libboost_filesystem.so
        	libboost_date_time.so.2 (libc6,x86-64) => /usr/lib64/libboost_date_time.so.2
        	libboost_date_time.so (libc6,x86-64) => /usr/lib64/libboost_date_time.so
        Thanks for the help.

        Comment


        • #5
          If you want to use your local installation of boost, I would try:

          Code:
          env LD_LIBRARY_PATH=/path/to/boost /path/to/cufflinks
          This should tell the loader to look for the library in your home directory before the rest of the system.

          You might also try installing the libboost-devel RPM and recompiling cufflinks with that.


          Andrew

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