while i am making tophat after correct configuring:
make: Warning: File `Makefile' has modification time 1.5e+03 s in the future
make all-recursive
make[1]: Entering directory `/data1/qwu/tophat-2.0.7'
make[1]: Warning: File `Makefile' has modification time 1.5e+03 s in the future
Making all in src
make[2]: Entering directory `/data1/qwu/tophat-2.0.7/src'
make[2]: Warning: File `Makefile' has modification time 1.5e+03 s in the future
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/data1/qwu/boost/boost/boost_1_52_0/boost/include -I/data1/qwu/samtools/include -I./SeqAn-1.3 -o segment_juncs -L/data1/qwu/boost/boost/boost_1_52_0/boost/lib -L/data1/qwu/samtools/lib segment_juncs.o ../src/libtophat.a -lbam -lz -L/data1/qwu/boost/boost/boost_1_52_0/stage/lib
segment_juncs.o: In function `__static_initialization_and_destruction_0':
/data1/qwu/boost/boost/boost_1_52_0/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
/data1/qwu/boost/boost/boost_1_52_0/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
/data1/qwu/boost/boost/boost_1_52_0/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
segment_juncs.o: In function `driver(std::basic_istream<char, std::char_traits<char> >&, _IO_FILE*, _IO_FILE*, _IO_FILE*, _IO_FILE*, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&)':
/data1/qwu/tophat-2.0.7/src/segment_juncs.cpp:4949: undefined reference to `boost::thread::join()'
segment_juncs.o: In function `~thread':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:179: undefined reference to `boost::thread::detach()'
segment_juncs.o: In function `driver(std::basic_istream<char, std::char_traits<char> >&, _IO_FILE*, _IO_FILE*, _IO_FILE*, _IO_FILE*, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&)':
/data1/qwu/tophat-2.0.7/src/segment_juncs.cpp:5026: undefined reference to `boost::thread::join()'
segment_juncs.o: In function `~thread':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:179: undefined reference to `boost::thread::detach()'
segment_juncs.o: In function `thread_exception':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/exceptions.hpp:49: undefined reference to `boost::system::system_category()'
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/exceptions.hpp:49: undefined reference to `boost::system::system_category()'
segment_juncs.o: In function `~thread_data':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:54: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:54: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:54: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:54: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
segment_juncs.o: In function `thread_data_base':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/pthread/thread_data.hpp:125: undefined reference to `vtable for boost::detail::thread_data_base'
segment_juncs.o: In function `thread_exception':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/exceptions.hpp:49: undefined reference to `boost::system::system_category()'
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/exceptions.hpp:49: undefined reference to `boost::system::system_category()'
segment_juncs.o: In function `thread_data':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:72: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
segment_juncs.o: In function `thread<SegmentSearchWorker>':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:223: undefined reference to `boost::thread::start_thread()'
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 `/data1/qwu/tophat-2.0.7/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/data1/qwu/tophat-2.0.7'
make: *** [all] Error 2
i try to add export LD_LIBRARY_PATH=/data1/qwu/bin:$LD_LIBRARY_PATH
to my .bash_profile, but it doesnt work.
desperately ask for help, thanks!
make: Warning: File `Makefile' has modification time 1.5e+03 s in the future
make all-recursive
make[1]: Entering directory `/data1/qwu/tophat-2.0.7'
make[1]: Warning: File `Makefile' has modification time 1.5e+03 s in the future
Making all in src
make[2]: Entering directory `/data1/qwu/tophat-2.0.7/src'
make[2]: Warning: File `Makefile' has modification time 1.5e+03 s in the future
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/data1/qwu/boost/boost/boost_1_52_0/boost/include -I/data1/qwu/samtools/include -I./SeqAn-1.3 -o segment_juncs -L/data1/qwu/boost/boost/boost_1_52_0/boost/lib -L/data1/qwu/samtools/lib segment_juncs.o ../src/libtophat.a -lbam -lz -L/data1/qwu/boost/boost/boost_1_52_0/stage/lib
segment_juncs.o: In function `__static_initialization_and_destruction_0':
/data1/qwu/boost/boost/boost_1_52_0/boost/system/error_code.hpp:214: undefined reference to `boost::system::generic_category()'
/data1/qwu/boost/boost/boost_1_52_0/boost/system/error_code.hpp:215: undefined reference to `boost::system::generic_category()'
/data1/qwu/boost/boost/boost_1_52_0/boost/system/error_code.hpp:216: undefined reference to `boost::system::system_category()'
segment_juncs.o: In function `driver(std::basic_istream<char, std::char_traits<char> >&, _IO_FILE*, _IO_FILE*, _IO_FILE*, _IO_FILE*, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&)':
/data1/qwu/tophat-2.0.7/src/segment_juncs.cpp:4949: undefined reference to `boost::thread::join()'
segment_juncs.o: In function `~thread':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:179: undefined reference to `boost::thread::detach()'
segment_juncs.o: In function `driver(std::basic_istream<char, std::char_traits<char> >&, _IO_FILE*, _IO_FILE*, _IO_FILE*, _IO_FILE*, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&)':
/data1/qwu/tophat-2.0.7/src/segment_juncs.cpp:5026: undefined reference to `boost::thread::join()'
segment_juncs.o: In function `~thread':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:179: undefined reference to `boost::thread::detach()'
segment_juncs.o: In function `thread_exception':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/exceptions.hpp:49: undefined reference to `boost::system::system_category()'
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/exceptions.hpp:49: undefined reference to `boost::system::system_category()'
segment_juncs.o: In function `~thread_data':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:54: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:54: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:54: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:54: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
segment_juncs.o: In function `thread_data_base':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/pthread/thread_data.hpp:125: undefined reference to `vtable for boost::detail::thread_data_base'
segment_juncs.o: In function `thread_exception':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/exceptions.hpp:49: undefined reference to `boost::system::system_category()'
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/exceptions.hpp:49: undefined reference to `boost::system::system_category()'
segment_juncs.o: In function `thread_data':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:72: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
segment_juncs.o: In function `thread<SegmentSearchWorker>':
/data1/qwu/boost/boost/boost_1_52_0/boost/thread/detail/thread.hpp:223: undefined reference to `boost::thread::start_thread()'
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 `/data1/qwu/tophat-2.0.7/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/data1/qwu/tophat-2.0.7'
make: *** [all] Error 2
i try to add export LD_LIBRARY_PATH=/data1/qwu/bin:$LD_LIBRARY_PATH
to my .bash_profile, but it doesnt work.
desperately ask for help, thanks!
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