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  • canhu
    Member
    • May 2013
    • 11

    Tophat 2.0.8b installation error

    I install tophat-2.0.8b to rerun the mapping. but when i make it, the error appears like this.
    make[1]: Entering directory `/media/chenzz/software/tophat-2.0.8b'
    Making all in src
    make[2]: Entering directory `/media/chenzz/software/tophat-2.0.8b/src'
    g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/usr/include -I/usr/local/include -I./SeqAn-1.3 -o segment_juncs -L/usr/lib -L/usr/local/lib segment_juncs.o ../src/libtophat.a -lbam -lz
    segment_juncs.o: In function `__static_initialization_and_destruction_0':
    /usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
    /usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
    /usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
    segment_juncs.o: In function `boost::thread::get_id() const':
    /usr/local/include/boost/thread/detail/thread.hpp:725: undefined reference to `boost::thread::native_handle()'
    segment_juncs.o: In function `boost::thread::join()':
    /usr/local/include/boost/thread/detail/thread.hpp:751: undefined reference to `boost::thread::join_noexcept()'
    segment_juncs.o: In function `~thread':
    /usr/local/include/boost/thread/detail/thread.hpp:255: undefined reference to `boost::thread::detach()'
    segment_juncs.o: In function `boost::thread::start_thread()':
    /usr/local/include/boost/thread/detail/thread.hpp:180: undefined reference to `boost::thread::start_thread_noexcept()'
    /usr/local/include/boost/thread/detail/thread.hpp:180: undefined reference to `boost::thread::start_thread_noexcept()'
    segment_juncs.o: In function `boost::thread::get_id() const':
    /usr/local/include/boost/thread/detail/thread.hpp:725: undefined reference to `boost::thread::native_handle()'
    segment_juncs.o: In function `boost::thread::join()':
    /usr/local/include/boost/thread/detail/thread.hpp:751: undefined reference to `boost::thread::join_noexcept()'
    segment_juncs.o: In function `~thread':
    /usr/local/include/boost/thread/detail/thread.hpp:255: undefined reference to `boost::thread::detach()'
    segment_juncs.o: In function `thread_exception':
    /usr/local/include/boost/thread/exceptions.hpp:51: undefined reference to `boost::system::system_category()'
    segment_juncs.o: In function `~thread_data':
    /usr/local/include/boost/thread/detail/thread.hpp:93: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
    /usr/local/include/boost/thread/detail/thread.hpp:93: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
    /usr/local/include/boost/thread/detail/thread.hpp:93: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
    /usr/local/include/boost/thread/detail/thread.hpp:93: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
    segment_juncs.o: In function `thread_data_base':
    /usr/local/include/boost/thread/pthread/thread_data.hpp:142: undefined reference to `vtable for boost::detail::thread_data_base'
    segment_juncs.o: In function `thread_data':
    /usr/local/include/boost/thread/detail/thread.hpp:111: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
    segment_juncs.o.rodata._ZTIN5boost6detail11thread_dataI19SegmentSearchWorkerEE[typeinfo for boost::detail::thread_data<SegmentSearchWorker>]+0x10): undefined reference to `typeinfo for boost::detail::thread_data_base'
    collect2: ld returned 1 exit status
    make[2]: *** [segment_juncs] Error 1
    make[2]: Leaving directory `/media/chenzz/software/tophat-2.0.8b/src'
    make[1]: *** [all-recursive] Error 1
    make[1]: Leaving directory `/media/chenzz/software/tophat-2.0.8b'
    make: *** [all] Error 2
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142

    #2
    You either did not install the "Boost" libraries or if you did, then they did not install correctly.

    Details on the boost installation are included on the tophat getting started page: http://tophat.cbcb.umd.edu/tutorial.shtml

    Comment

    • canhu
      Member
      • May 2013
      • 11

      #3
      Originally posted by GenoMax View Post
      You either did not install the "Boost" libraries or if you did, then they did not install correctly.

      Details on the boost installation are included on the tophat getting started page: http://tophat.cbcb.umd.edu/tutorial.shtml
      Thanks for your reply, it works well until i re-install boost

      Comment

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