bjam for cufflinks

[masylichu]

Hi, all guys,

Before the install of cufflinks, it need the bjam of boost.

the step i typed is :

(1) ./bootstrap.sh
(2) cp bjam ~/bin
(3) bjam --prefix=/home/wxf/ --toolset=gcc architecture=x86 address-model=64 link=static runtime-link=static stage install

then, i tried to enter the directory of cuffilinks,
(1) ./configure --with-boost=/home/wxf/boost_1_47/boost/
(2) make

errors occur

checking for boostlib >= 1.38.0... configure: error: We could not detect the boost libraries (version 1.38 or higher). If you have a staged boost library (still not installed) please specify $BOOST_ROOT in your environment and do not give a PATH to --with-boost option. If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation.

could some help me to solve it ?

[Jon_Keats]

There was an error in the cufflinks manual for this step not sure if they fixed it but you can follow my instructions on my intro thread which should work.

http://seqanswers.com/forums/showthread.php?t=4589&page=3

[masylichu]

thanks.

I have passed the configure step for cufflinks.

however, the make step did not work. why?

make all-recursive
make[1]: Entering directory `/home/wgf/cufflinks-1.1.0'
Making all in src
make[2]: Entering directory `/home/wgf/cufflinks-1.1.0/src'
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/home/wgf//include -I/home/wgf//include -o cufflinks -L/home/wgf//lib -L/home/wgf//lib cufflinks.o libcufflinks.a libgc.a -lbam -lz
cufflinks.o: In function `sleep<boost:osix_time::milliseconds>':
/home/wgf//include/boost/thread/pthread/thread_data.hpp:138: undefined reference to `boost::this_thread::sleep(boost:osix_time:time const&)'
cufflinks.o: In function `thread_data_base':
/home/wgf//include/boost/thread/pthread/thread_data.hpp:67: undefined reference to `vtable for boost::detail::thread_data_base'
cufflinks.o: In function `thread<void (*)(const RefSequenceTable&, HitBundle*, BiasLearner*, long double, FILE*, FILE*, FILE*, FILE*), boost::reference_wrapper<const RefSequenceTable>, HitBundle*, BiasLearner*, long double, FILE*, FILE*, FILE*, FILE*>':
/home/wgf//include/boost/thread/detail/thread.hpp:300: undefined reference to `boost::thread::start_thread()'
cufflinks.o: In function `assemble_hits(BundleFactory&, BiasLearner*)':
/home/wgf/cufflinks-1.1.0/src/cufflinks.cpp:1391: undefined reference to `boost::thread::~thread()'
cufflinks.o: In function `sleep<boost:osix_time::milliseconds>':
/home/wgf//include/boost/thread/pthread/thread_data.hpp:138: undefined reference to `boost::this_thread::sleep(boost:osix_time:time const&)'
cufflinks.o: In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >::get() const':
/home/wgf//include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/home/wgf//include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/home/wgf//include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/home/wgf//include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/home/wgf//include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
cufflinks.o:/home/wgf//include/boost/thread/tss.hpp:84: more undefined references to `boost::detail::get_tss_data(void const*)' follow
cufflinks.o: In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >::reset(std::basic_string<char, std::char_traits<char>, std::allocator<char> >*)':
/home/wgf//include/boost/thread/tss.hpp:105: undefined reference to `boost::detail::set_tss_data(void const*, boost::shared_ptr<boost::detail::tss_cleanup_function>, void*, bool)'
cufflinks.o: In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >::get() const':
/home/wgf//include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
cufflinks.o: In function `at_thread_exit<void (*)()>':
/home/wgf//include/boost/thread/detail/thread.hpp:521: undefined reference to `boost::detail::add_thread_exit_function(boost::detail::thread_exit_function_base*)'
cufflinks.o: In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >::get() const':
/home/wgf//include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/home/wgf//include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
cufflinks.o: In function `~thread_data':
/home/wgf//include/boost/thread/detail/thread.hpp:42: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/home/wgf//include/boost/thread/detail/thread.hpp:42: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
cufflinks.o.rodata._ZTIN5boost6detail11thread_dataINS_3_bi6bind_tIvPFvRK16RefSequenceTableP9HitBundleP11BiasLearnereP8_IO_FILESC_SC_SC_ENS2_5list8INS_17reference_wrapperIS5_EENS2_5valueIS8_EENSI_ISA_EENSI_IeEENSI_ISC_EESM_SM_SM_EEEEEE[typeinfo for boost::detail::thread_data<boost::_bi::bind_t<void, void (*)(RefSequenceTable const&, HitBundle*, BiasLearner*, long double, _IO_FILE*, _IO_FILE*, _IO_FILE*, _IO_FILE*), boost::_bi::list8<boost::reference_wrapper<RefSequenceTable const>, boost::_bi::value<HitBundle*>, boost::_bi::value<BiasLearner*>, boost::_bi::value<long double>, boost::_bi::value<_IO_FILE*>, boost::_bi::value<_IO_FILE*>, boost::_bi::value<_IO_FILE*>, boost::_bi::value<_IO_FILE*> > > >]+0x10): undefined reference to `typeinfo for boost::detail::thread_data_base'
libcufflinks.a(common.o): In function `~thread_specific_ptr':
/home/wgf//include/boost/thread/tss.hpp:79: undefined reference to `boost::detail::set_tss_data(void const*, boost::shared_ptr<boost::detail::tss_cleanup_function>, void*, bool)'
libcufflinks.a(assemble.o): In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >::get() const':
/home/wgf//include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/home/wgf//include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/home/wgf//include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/home/wgf//include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/home/wgf//include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
libcufflinks.a(assemble.o):/home/wgf//include/boost/thread/tss.hpp:84: more undefined references to `boost::detail::get_tss_data(void const*)' follow
collect2: ld returned 1 exit status
make[2]: *** [cufflinks] Error 1
make[2]: Leaving directory `/home/wgf/cufflinks-1.1.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/wgf/cufflinks-1.1.0'
make: *** [all] Error 2

There was an error in the cufflinks manual for this step not sure if they fixed it but you can follow my instructions on my intro thread which should work.

http://seqanswers.com/forums/showthr...?t=4589&page=3