install tablemaker do make error

[yangfangs]

when i install tablemaker can do ./configure but do make have an error:

$ make make all-recursive make[1]: Entering directory '/home/yangfang/RNA_seq_work/tools/tablemaker-master/tablemaker-2.1.1' Making all in src make[2]: Entering directory '/home/yangfang/RNA_seq_work/tools/tablemaker-master/tablemaker-2.1.1/src' g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/usr/include/boost/include -I/usr/local/include -I/usr/include/eigen3/include -L/usr/include/boost/lib -L/usr/local/lib -o tablemaker cufflinks.o libcufflinks.a libgc.a -lbam -lz cufflinks.o: In function boost::this_thread::sleep(boost::posix_time::ptime const&)': /usr/include/boost/thread/pthread/thread_data.hpp:278: undefined reference toboost::this_thread::hiden::sleep_until(timespec const&)' cufflinks.o: In function boost::thread::~thread()': /usr/include/boost/thread/detail/thread.hpp:254: undefined reference toboost::thread::detach()' cufflinks.o: In function boost::this_thread::sleep(boost::posix_time::ptime const&)': /usr/include/boost/thread/pthread/thread_data.hpp:278: undefined reference toboost::this_thread::hiden::sleep_until(timespec const&)' cufflinks.o: In function boost::thread_specific_ptr<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >::get() const': /usr/include/boost/thread/tss.hpp:84: undefined reference toboost::detail::get_tssdata(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 toboost::detail::get_tss_data(void const)' /usr/include/boost/thread/tss.hpp:84: undefined reference toboost::detail::get_tss_data(void const_)' /usr/include/boost/thread/tss.hpp:84: undefined reference toboost::detail::get_tssdata(void const)' cufflinks.o:/usr/include/boost/thread/tss.hpp:84: more undefined references to `boost::detail::get_tss_data(void const)' follow cufflinks.o: In functionboost::thread_specific_ptr<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >::reset(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >_)': /usr/include/boost/thread/tss.hpp:105: undefined reference toboost::detail::set_tssdata(void const, boost::shared_ptrboost::detail::tss_cleanupfunction, void, bool)' cufflinks.o: In function boost::thread_specific_ptr<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >::get() const': /usr/include/boost/thread/tss.hpp:84: undefined reference toboost::detail::get_tssdata(void const)' cufflinks.o: In function void boost::this_thread::at_thread_exit<void (*)()>(void (*)())': /usr/include/boost/thread/detail/thread.hpp:861: undefined reference toboost::detail::add_thread_exit_function(boost::detail::thread_exit_functionbase)' cufflinks.o: In function boost::thread_specific_ptr<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >::get() const': /usr/include/boost/thread/tss.hpp:84: undefined reference toboost::detail::get_tssdata(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 toboost::detail::get_tssdata(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 toboost::detail::get_tss_data(void const)' cufflinks.o:/usr/include/boost/thread/tss.hpp:84: more undefined references toboost::detail::get_tss_data(void const_)' follow cufflinks.o: In functionboost::thread_exception::threadexception(int, char const)': /usr/include/boost/thread/exceptions.hpp:51: undefined reference to boost::system::system_category()' cufflinks.o: In functionboost::thread::~thread()': /usr/include/boost/thread/detail/thread.hpp:254: undefined reference to boost::thread::detach()' cufflinks.o: In functionboost::detail::thread_data<boost::_bi::bind_t<void, void ()(RefSequenceTable const&, HitBundle, boost::shared_ptr, boost::shared_ptr, _IOFILE, _IOFILE, _IOFILE, _IOFILE), boost::_bi::list8<boost::reference_wrapper, boost::_bi::value<HitBundle>, boost::_bi::valueboost::shared_ptr, boost::_bi::valueboost::shared_ptr, boost::_bi::value<_IO_FILE_>, boost::_bi::value<_IO_FILE_>, boost::_bi::value<_IO_FILE_>, boost::_bi::value<_IO_FILE_> > > >::~thread_data()': /usr/include/boost/thread/detail/thread.hpp:90: undefined reference to boost::detail::thread_data_base::~thread_data_base()' /usr/include/boost/thread/detail/thread.hpp:90: undefined reference toboost::detail::thread_data_base::~thread_data_base()' cufflinks.o: In function boost::detail::thread_data<boost::_bi::bind_t<void, void (*)(RefSequenceTable const&, HitBundle*, boost::shared_ptr<ReadGroupProperties>, boost::shared_ptr<BiasLearner>, _IO_FILE*, _IO_FILE*, _IO_FILE*, _IO_FILE*), boost::_bi::list8<boost::reference_wrapper<RefSequenceTable const>, boost::_bi::value<HitBundle*>, boost::_bi::value<boost::shared_ptr<ReadGroupProperties> >, boost::_bi::value<boost::shared_ptr<BiasLearner> >, boost::_bi::value<_IO_FILE*>, boost::_bi::value<_IO_FILE*>, boost::_bi::value<_IO_FILE*>, boost::_bi::value<_IO_FILE*> > > >::~thread_data()': /usr/include/boost/thread/detail/thread.hpp:90: undefined reference toboost::detail::thread_data_base::~thread_data_base()' /usr/include/boost/thread/detail/thread.hpp:90: undefined reference to boost::detail::thread_data_base::~thread_data_base()' cufflinks.o: In functionboost::detail::thread_data_base::thread_data_base()': /usr/include/boost/thread/pthread/thread_data.hpp:152: undefined reference to vtable for boost::detail::thread_data_base' cufflinks.o: In functionboost::thread::start_thread()': /usr/include/boost/thread/detail/thread.hpp:179: undefined reference to boost::thread::start_thread_noexcept()' cufflinks.o: In functionstatic_initialization_and_destruction_0': /usr/include/boost/system/error_code.hpp:221: undefined reference to boost::system::generic_category()' /usr/include/boost/system/error_code.hpp:222: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:223: undefined reference to boost::system::system_category()' cufflinks.o:(.rodata._ZTIN5boost6detail11thread_dataINS_3_bi6bind_tIvPFvRK16RefSequenceTableP9HitBundleNS_10shared_ptrI19ReadGroupPropertiesEENS9_I11BiasLearnerEEP8_IO_FILESF_SF_SF_ENS2_5list8INS_17reference_wrapperIS5_EENS2_5valueIS8_EENSL_ISB_EENSL_ISD_EENSL_ISF_EESP_SP_SP_EEEEEE[_ZTIN5boost6detail11thread_dataINS_3_bi6bind_tIvPFvRK16RefSequenceTableP9HitBundleNS_10shared_ptrI19ReadGroupPropertiesEENS9_I11BiasLearnerEEP8_IO_FILESF_SF_SF_ENS2_5list8INS_17reference_wrapperIS5_EENS2_5valueIS8_EENSL_ISB_EENSL_ISD_EENSL_ISF_EESP_SP_SP_EEEEEE]+0x10): undefined reference totypeinfo for boost::detail::thread_data_base' libcufflinks.a(clustering.o): In function `static_initialization_and_destruction_0': /usr/include/boost/system/error_code.hpp:221: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:222: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:223: undefined reference toboost::system::system_category()' libcufflinks.a(common.o): In functionstatic_initialization_and_destruction_0': /usr/include/boost/system/error_code.hpp:221: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:222: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:223: undefined reference toboost::system::system_category()' libcufflinks.a(common.o): In functionboost::thread_specific_ptr<std::cxx11::basic_string<char, std::char_traits, std::allocator > >::~thread_specific_ptr()': /usr/include/boost/thread/tss.hpp:79: undefined reference toboost::detail::set_tss_data(void const_, boost::shared_ptrboost::detail::tss_cleanup_function, void_, bool)' libcufflinks.a(assemble.o): In functionboost::thread_specific_ptr<std::cxx11::basic_string<char, std::char_traits, std::allocator > >::get() const': /usr/include/boost/thread/tss.hpp:84: undefined reference toboost::detail::get_tss_data(void const_)' /usr/include/boost/thread/tss.hpp:84: undefined reference toboost::detail::get_tssdata(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 toboost::detail::get_tssdata(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 toboost::detail::get_tss_data(void const*)' follow libcufflinks.a(assemble.o): In function`static_initialization_and_destruction_0': /usr/include/boost/system/error_code.hpp:221: undefined reference to boost::system::generic_category()' /usr/include/boost/system/error_code.hpp:222: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:223: undefined reference to boost::system::system_category()' libcufflinks.a(abundances.o): In functionstatic_initialization_and_destruction_0': /usr/include/boost/system/error_code.hpp:221: undefined reference to boost::system::generic_category()' /usr/include/boost/system/error_code.hpp:222: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:223: undefined reference to boost::system::system_category()' libcufflinks.a(scaffolds.o): In functionstatic_initialization_and_destruction_0': /usr/include/boost/system/error_code.hpp:221: undefined reference to boost::system::generic_category()' /usr/include/boost/system/error_code.hpp:222: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:223: undefined reference to boost::system::system_category()' libcufflinks.a(hits.o): In functionsamread': /usr/local/include/bam/sam.h:95: undefined reference to sam_read1' libcufflinks.a(hits.o): In functionBAMHitFactory::get_hit_frombuf(char const, ReadHit&, bool, char, char)': /home/yangfang/RNA_seq_work/tools/tablemaker-master/tablemaker-2.1.1/src/hits.cpp:555: undefined reference to bam_aux_get' /home/yangfang/RNA_seq_work/tools/tablemaker-master/tablemaker-2.1.1/src/hits.cpp:558: undefined reference tobam_aux2A' /home/yangfang/RNA_seq_work/tools/tablemaker-master/tablemaker-2.1.1/src/hits.cpp:565: undefined reference to bam_aux_get' /home/yangfang/RNA_seq_work/tools/tablemaker-master/tablemaker-2.1.1/src/hits.cpp:568: undefined reference tobam_aux2i' /home/yangfang/RNA_seq_work/tools/tablemaker-master/tablemaker-2.1.1/src/hits.cpp:571: undefined reference to bam_aux_get' /home/yangfang/RNA_seq_work/tools/tablemaker-master/tablemaker-2.1.1/src/hits.cpp:574: undefined reference tobam_aux2i' /home/yangfang/RNA_seq_work/tools/tablemaker-master/tablemaker-2.1.1/src/hits.cpp:578: undefined reference to bam_aux_get' /home/yangfang/RNA_seq_work/tools/tablemaker-master/tablemaker-2.1.1/src/hits.cpp:581: undefined reference tobam_aux2i' libcufflinks.a(hits.o): In function BAMHitFactory::undo_hit()': /home/yangfang/RNA_seq_work/tools/tablemaker-master/tablemaker-2.1.1/src/hits.h:767: undefined reference tobgzf_seek' libcufflinks.a(hits.o): In function BAMHitFactory::reset()': /home/yangfang/RNA_seq_work/tools/tablemaker-master/tablemaker-2.1.1/src/hits.h:780: undefined reference tobgzf_seek' libcufflinks.a(hits.o): In function __static_initialization_and_destruction_0': /usr/include/boost/system/error_code.hpp:221: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:222: undefined reference to boost::system::generic_category()' /usr/include/boost/system/error_code.hpp:223: undefined reference toboost::system::system_category()' libcufflinks.a(genes.o): In function __static_initialization_and_destruction_0': /usr/include/boost/system/error_code.hpp:221: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:222: undefined reference to boost::system::generic_category()' /usr/include/boost/system/error_code.hpp:223: undefined reference toboost::system::system_category()' libcufflinks.a(bundles.o): In function __static_initialization_and_destruction_0': /usr/include/boost/system/error_code.hpp:221: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:222: undefined reference to boost::system::generic_category()' /usr/include/boost/system/error_code.hpp:223: undefined reference toboost::system::system_category()' libcufflinks.a(filters.o): In function __static_initialization_and_destruction_0': /usr/include/boost/system/error_code.hpp:221: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:222: undefined reference to boost::system::generic_category()' /usr/include/boost/system/error_code.hpp:223: undefined reference toboost::system::system_category()' libcufflinks.a(scaffold_graph.o): In function __static_initialization_and_destruction_0': /usr/include/boost/system/error_code.hpp:221: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:222: undefined reference to boost::system::generic_category()' /usr/include/boost/system/error_code.hpp:223: undefined reference toboost::system::system_category()' libcufflinks.a(matching_merge.o): In function __static_initialization_and_destruction_0': /usr/include/boost/system/error_code.hpp:221: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:222: undefined reference to boost::system::generic_category()' /usr/include/boost/system/error_code.hpp:223: undefined reference toboost::system::system_category()' libcufflinks.a(graph_optimize.o): In function boost::thread_specific_ptr<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >::get() const': /usr/include/boost/thread/tss.hpp:84: undefined reference toboost::detail::get_tssdata(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 toboost::detail::get_tssdata(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 toboost::detail::get_tss_data(void const)' libcufflinks.a(graph_optimize.o):/usr/include/boost/thread/tss.hpp:84: more undefined references toboost::detail::get_tss_data(void const_)' follow libcufflinks.a(graph_optimize.o): In functionstatic_initialization_and_destruction_0': /usr/include/boost/system/error_code.hpp:221: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:222: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:223: undefined reference toboost::system::system_category()' libcufflinks.a(biascorrection.o): In functionstatic_initialization_and_destruction_0': /usr/include/boost/system/error_code.hpp:221: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:222: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:223: undefined reference toboost::system::system_category()' libcufflinks.a(replicates.o): In functionstatic_initialization_and_destruction_0': /usr/include/boost/system/error_code.hpp:221: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:222: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:223: undefined reference toboost::system::system_category()' libcufflinks.a(multireads.o): In functionstatic_initialization_and_destruction_0': /usr/include/boost/system/error_code.hpp:221: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:222: undefined reference toboost::system::generic_category()' /usr/include/boost/system/error_code.hpp:223: undefined reference toboost::system::system_category()' /usr/local/lib/libbam.a(sam.o): In functionsamthreads': /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:33: undefined reference tohts_get_format' /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:34: undefined reference tobgzf_mt' /usr/local/lib/libbam.a(sam.o): In functionsamopen': /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:41: undefined reference tohts_open' /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:49: undefined reference tohts_set_fai_filename' /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:55: undefined reference tosam_hdr_read' /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:62: undefined reference tohts_verbose' /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:66: undefined reference tohts_get_format' /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:69: undefined reference tosam_hdr_write' /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:57: undefined reference tohts_close' /usr/local/lib/libbam.a(sam.o): In functionsamclose': /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:78: undefined reference tobam_hdr_destroy' /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:79: undefined reference tohts_close' /usr/local/lib/libbam.a(sam.o): In functionsamfetch': /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:86: undefined reference tobam_init1' /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:87: undefined reference tosam_itr_queryi' /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:89: undefined reference tohts_itr_next' /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:90: undefined reference tohts_itr_destroy' /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:91: undefined reference tobam_destroy1' /usr/local/lib/libbam.a(sam.o): In functionsampileup': /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:100: undefined reference tobam_init1' /usr/local/lib/libbam.a(sam.o): In functionsamread': /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.h:95: undefined reference tosam_read1' /usr/local/lib/libbam.a(sam.o): In functionsampileup': /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:111: undefined reference tobam_destroy1' /usr/local/lib/libbam.a(sam.o): In functionsamfaipath': /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:125: undefined reference tohts_verbose' /home/yangfang/RNA_seq_work/tools/samtools-1.3/sam.c:126: undefined reference tofai_build' /usr/local/lib/libbam.a(bam_plbuf.o): In functionbam_plbuf_init': /home/yangfang/RNA_seq_work/tools/samtools-1.3/bam_plbuf.c:45: undefined reference tobam_plp_init' /usr/local/lib/libbam.a(bam_plbuf.o): In functionbam_plbuf_destroy': /home/yangfang/RNA_seq_work/tools/samtools-1.3/bam_plbuf.c:53: undefined reference tobam_plp_destroy' /usr/local/lib/libbam.a(bam_plbuf.o): In functionbam_plbuf_push': /home/yangfang/RNA_seq_work/tools/samtools-1.3/bam_plbuf.c:61: undefined reference tobam_plp_push' /home/yangfang/RNA_seq_work/tools/samtools-1.3/bam_plbuf.c:63: undefined reference tobam_plp_next' /usr/local/lib/libbam.a(bam_plbuf.o): In functionbam_plbuf_reset': /home/yangfang/RNA_seq_work/tools/samtools-1.3/bam_plbuf.c:38: undefined reference to`bam_plp_reset' collect2: error: ld returned 1 exit status Makefile:608: recipe for target 'tablemaker' failed make[2]: _* [tablemaker] Error 1 make[2]: Leaving directory '/home/yangfang/RNA_seq_work/tools/tablemaker-master/tablemaker-2.1.1/src' Makefile:379: recipe for target 'all-recursive' failed make[1]: * [all-recursive] Error 1 make[1]: Leaving directory '/home/yangfang/RNA_seq_work/tools/tablemaker-master/tablemaker-2.1.1' Makefile:319: recipe for target 'all' failed make: * [all] Error 2

I don't know what's wrong with this error, can you give me some advice?

[JMF47]

Do you have boost installed and have proper pathing to it?

[yangfangs]

yes, i install the boost in my Fedora OS already, then i configure as follow commond ./configure --prefix=~/RNA_seq_work/tools/tablemaker\ --with-boost=/usr/include/boost \ --with-eigen=/usr/include/eigen3

when I do ./configure not have error or warning,but can't make and make install.

I want's use the Linux Binary but can't download because of "404 failed". : (

[gpertea]

Unfortunately the configure scripts are no longer working properly with newer Linux distributions. For the Linux binary you can also try this link: http://ccb.jhu.edu/software/cuffraw/tablemaker-2.1.1.Linux_x86_64.tar.gz

Please note that Tablemaker is no longer maintained, I would suggest using StringTie instead (http://ccb.jhu.edu/software/stringtie), as it can be used as a tablemaker replacement (though it uses a different method of computing FPKMs) and it has been tweaked to work very well with Ballgown recently.

[yangfangs]

Thank you give the link to download Linux binary version and solve my problems, give me some advice. :+1: