Hi,
I'm trying to install Tophat. I installed bowtie, samtools and boost (all they are ok, I think).
So, I do:
./configure --prefix=$HOME --with-boost=usr/include/boost --with-bam=$HOME/SAMTools
-- tophat 2.0.4 Configuration Results --
C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -Iusr/include/boost/include -I/home/auri/SAMTools/include -I./SeqAn-1.3
Linker flags:
GCC version: gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Host System type: i686-pc-linux-gnu
Install prefix: /home/auri
Install eprefix: ${prefix}
See config.h for further configuration information.
Email <[email protected]> with questions and bug reports.
make
make all-recursive
make[1]: Entering directory `/home/auri/Downloads/tophat-2.0.4'
Making all in src
make[2]: Entering directory `/home/auri/Downloads/tophat-2.0.4/src'
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/home/auri/Dowloads/boost_1_51_0/include -I/home/auri/SAMTools/include -I./SeqAn-1.3 -o segment_juncs -L/home/auri/Dowloads/boost_1_51_0/lib -L/home/auri/SAMTools/lib segment_juncs.o ../src/libtophat.a -lbam -lz
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> > > >&)':
/home/auri/Downloads/tophat-2.0.4/src/segment_juncs.cpp:4926: undefined reference to `boost::thread::join()'
/home/auri/Downloads/tophat-2.0.4/src/segment_juncs.cpp:4927: undefined reference to `boost::thread::~thread()'
/home/auri/Downloads/tophat-2.0.4/src/segment_juncs.cpp:5003: undefined reference to `boost::thread::join()'
/home/auri/Downloads/tophat-2.0.4/src/segment_juncs.cpp:5004: undefined reference to `boost::thread::~thread()'
segment_juncs.o: In function `thread<SegmentSearchWorker>':
/usr/include/boost/thread/detail/thread.hpp:204: undefined reference to `boost::thread::start_thread()'
/usr/include/boost/thread/detail/thread.hpp:204: undefined reference to `boost::thread::start_thread()'
segment_juncs.o: In function `~thread_data':
/usr/include/boost/thread/detail/thread.hpp:40: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/usr/include/boost/thread/detail/thread.hpp:40: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
segment_juncs.o: In function `thread_data_base':
/usr/include/boost/thread/pthread/thread_data.hpp:67: undefined reference to `vtable for boost::detail::thread_data_base'
segment_juncs.o: In function `thread_data':
/usr/include/boost/thread/detail/thread.hpp:53: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
segment_juncs.o.rodata._ZTIN5boost6detail11thread_dataI19SegmentSearchWorkerEE[typeinfo for boost::detail::thread_data<SegmentSearchWorker>]+0x8): 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 `/home/auri/Downloads/tophat-2.0.4/src'
make[1]: ** [all-recursive] Error 1
make[1]: Leaving directory `/home/auri/Downloads/tophat-2.0.4'
make: ** [all] Error 2
I already tried two paths differents for boost on ./configure, but they finished with this same error when I do make.
--with-boost=usr/include/boost
--with-boost=$HOME/Downloads/boost_1_51_0
If someone can help me I would greatly appreciate it.
I'm trying to install Tophat. I installed bowtie, samtools and boost (all they are ok, I think).
So, I do:
./configure --prefix=$HOME --with-boost=usr/include/boost --with-bam=$HOME/SAMTools
-- tophat 2.0.4 Configuration Results --
C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -Iusr/include/boost/include -I/home/auri/SAMTools/include -I./SeqAn-1.3
Linker flags:
GCC version: gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Host System type: i686-pc-linux-gnu
Install prefix: /home/auri
Install eprefix: ${prefix}
See config.h for further configuration information.
Email <[email protected]> with questions and bug reports.
make
make all-recursive
make[1]: Entering directory `/home/auri/Downloads/tophat-2.0.4'
Making all in src
make[2]: Entering directory `/home/auri/Downloads/tophat-2.0.4/src'
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/home/auri/Dowloads/boost_1_51_0/include -I/home/auri/SAMTools/include -I./SeqAn-1.3 -o segment_juncs -L/home/auri/Dowloads/boost_1_51_0/lib -L/home/auri/SAMTools/lib segment_juncs.o ../src/libtophat.a -lbam -lz
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> > > >&)':
/home/auri/Downloads/tophat-2.0.4/src/segment_juncs.cpp:4926: undefined reference to `boost::thread::join()'
/home/auri/Downloads/tophat-2.0.4/src/segment_juncs.cpp:4927: undefined reference to `boost::thread::~thread()'
/home/auri/Downloads/tophat-2.0.4/src/segment_juncs.cpp:5003: undefined reference to `boost::thread::join()'
/home/auri/Downloads/tophat-2.0.4/src/segment_juncs.cpp:5004: undefined reference to `boost::thread::~thread()'
segment_juncs.o: In function `thread<SegmentSearchWorker>':
/usr/include/boost/thread/detail/thread.hpp:204: undefined reference to `boost::thread::start_thread()'
/usr/include/boost/thread/detail/thread.hpp:204: undefined reference to `boost::thread::start_thread()'
segment_juncs.o: In function `~thread_data':
/usr/include/boost/thread/detail/thread.hpp:40: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/usr/include/boost/thread/detail/thread.hpp:40: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
segment_juncs.o: In function `thread_data_base':
/usr/include/boost/thread/pthread/thread_data.hpp:67: undefined reference to `vtable for boost::detail::thread_data_base'
segment_juncs.o: In function `thread_data':
/usr/include/boost/thread/detail/thread.hpp:53: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
segment_juncs.o.rodata._ZTIN5boost6detail11thread_dataI19SegmentSearchWorkerEE[typeinfo for boost::detail::thread_data<SegmentSearchWorker>]+0x8): 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 `/home/auri/Downloads/tophat-2.0.4/src'
make[1]: ** [all-recursive] Error 1
make[1]: Leaving directory `/home/auri/Downloads/tophat-2.0.4'
make: ** [all] Error 2
I already tried two paths differents for boost on ./configure, but they finished with this same error when I do make.
--with-boost=usr/include/boost
--with-boost=$HOME/Downloads/boost_1_51_0
If someone can help me I would greatly appreciate it.
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