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  • Cufflinks make 1.3.0 error

    Dear all,
    I have installed Samtools, Bowtie and TopHat as per the instructions. All of those tools work. Then I downloaded the Boost libraries and installed using bjam build. I was able to configure cufflinks 1.3.0 . The boost library version I have is 1.49.0. I tried to run the make on cufflinks and I am getting an error as follows


    libcufflinks.a(assemble.o): In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >erator->() const':
    /usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
    libcufflinks.a(assemble.o): In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >::get() const':
    /usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
    /usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
    /usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
    /usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
    libcufflinks.a(assemble.o):/usr/include/boost/thread/tss.hpp:84: more undefined references to `boost::detail::get_tss_data(void const*)'

    Is there a way around it. I need to download Cufflinks. I ama using a 64bit Ubuntu platform.
    Any solutions/help is really appreciated.
    Thanks,
    Himanshu Sharma.

  • #2
    Hi,

    I had the same problem with cufflinks 2.0.2 and boost-1.50. It seems that the configure script fails to detect the need for two of the binary libraries from boost.

    After running configure, edit src/Makefile (line 163 in my configuration) and change:

    BOOST_THREAD_LIB =

    to

    BOOST_THREAD_LIB = -lboost_thread -lboost_system

    This solved the compilation problem for me.

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