Code not building

[svetlanaKalm]

I am on Centos I've installed boost and bamtools with linuxbrew I've installed RInside package to a specific directory as it is said here https://www.r-bloggers.com/installing-r-packages/ Then I tried to compile dropEst and got the massage: "CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function TestTools::testR::test_method()': TestTools.cpp:(.text+0x4df): undefined reference toRInside::parseEval(std::string const&)' TestTools.cpp:(.text+0x571): undefined reference to RInside::parseEval(std::string const&)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In functionboost::unit_test::make_test_case(boost::function<void ()> const&, boost::unit_test::basic_cstring, boost::unit_test::basic_cstring, unsigned long)': TestTools.cpp:(.text._ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m[_ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m]+0x26): undefined reference to boost::unit_test::ut_detail::normalize_test_case_name(boost::unit_test::basic_cstring<char const>)' libDropTools.a(Logs.cpp.o): In functionvoid boost::log::v2_mt_posix::basic_formatting_ostream<char, std::char_traits, std::allocator >::aligned_write(wchar_t const, long)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l[_ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l]+0xdc): undefined reference to `boost::log::v2_mt_posix::aux::code_convert_impl(wchar_t const, unsigned long, std::string&, unsigned long, std::locale const&)' Logs.cpp:(.text._ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l[_ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l]+0x139): undefined reference to boost::log::v2_mt_posix::aux::code_convert_impl(wchar_t const*, unsigned long, std::string&, unsigned long, std::locale const&)' libDropTools.a(Logs.cpp.o): In functionvoid boost::log::v2_mt_posix::type_dispatcher::callback_base::trampoline<boost::log::v2_mt_posix::binder1st<boost::log::v2_mt_posix::output_fun, boost::log::v2_mt_posix::expressions::aux::stream_ref<boost::log::v2_mt_posix::basic_formatting_ostream<char, std::char_traits, std::allocator > >&>, std::basic_string<wchar_t, std::char_traits, std::allocator > >(void, std::basic_string<wchar_t, std::char_traits, std::allocator > const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix15type_dispatcher13callback_base10trampolineINS1_9binder1stINS1_10output_funERNS1_11expressions3aux10stream_refINS1_24basic_formatting_ostreamIcSt11char_traitsIcESaIcEEEEEEESbIwSBIwESaIwEEEEvPvRKT0[_ZN5boost3log11v2_mt_posix15type_dispatcher13callback_base10trampolineINS1_9binder1stINS1_10output_funERNS1_11expressions3aux10stream_refINS1_24basic_formatting_ostreamIcSt11char_traitsIcESaIcEEEEEEESbIwSBIwESaIwEEEEvPvRKT0]+0xf9): undefined reference to `boost::log::v2_mt_posix::aux::code_convert_impl(wchar_t const, unsigned long, std::string&, unsigned long, std::locale const&)' libDropTools.a(Logs.cpp.o): In function boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char> >::consume(boost::log::v2_mt_posix::record_view const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE7consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE7consumeERKNS1_11record_viewE]+0xb8): undefined reference toboost::log::v2_mt_posix::sinks::basic_text_ostream_backend::consume(boost::log::v2_mt_posix::record_view const&, std::string const&)' libDropTools.a(Logs.cpp.o): In function boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char> >::try_consume(boost::log::v2_mt_posix::record_view const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE11try_consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE11try_consumeERKNS1_11record_viewE]+0xde): undefined reference toboost::log::v2_mt_posix::sinks::basic_text_ostream_backend::consume(boost::log::v2_mt_posix::record_view const&, std::string const&)' libDropTools.a(Logs.cpp.o): In function boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::text_file_backend>::consume(boost::log::v2_mt_posix::record_view const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE7consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE7consumeERKNS1_11record_viewE]+0xb8): undefined reference toboost::log::v2_mt_posix::sinks::text_file_backend::consume(boost::log::v2_mt_posix::record_view const&, std::string const&)' libDropTools.a(Logs.cpp.o): In function boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::text_file_backend>::try_consume(boost::log::v2_mt_posix::record_view const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE11try_consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE11try_consumeERKNS1_11record_viewE]+0xde): undefined reference toboost::log::v2_mt_posix::sinks::text_file_backend::consume(boost::log::v2_mt_posix::record_view const&, std::string const&)' libDropTools.a(UtilFunctions.cpp.o): In function Tools::init_r()': UtilFunctions.cpp:(.text+0x5f0): undefined reference toRInside::parseEvalQ(std::string const&)' /home/kalmykova/.linuxbrew/lib/libboost_log_setup-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::replace(unsigned long, unsigned long, char const*, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference tostd::ios_base::failure[abi:cxx11]::what() const@GLIBCXX_3.4.21' //home/kalmykova/.linuxbrew/lib/librt.so.1: undefined reference to __pthread_barrier_init@GLIBC_PRIVATE' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference tostd::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::_M_mutate(unsigned long, unsigned long, wchar_t const*, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to `std::throw_out_of_range_fmt(char const, ...)@GLIBCXX_3.4.20' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits, std::allocator >::find_first_not_of(char const, unsigned long, unsigned long) const@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to std::ios_base::failure[abi:cxx11]::~failure()@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference tostd::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::_M_assign(std::__cxx11::basic_string<wchar_t, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to `std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >::basic_ostringstream(std::_Ios_Openmode)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_create(unsigned long&, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::~basic_string()@GLIBCXX_3.4.21' //home/kalmykova/.linuxbrew/lib/libquadmath.so.0: undefined reference to `signgam@GLIBC_2.23' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_erase(unsigned long, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference tostd::cxx11::collate const& std::use_facet<std::cxx11::collate >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to `std::cxx11::basic_stringstream<char, std::char_traits, std::allocator >::basic_stringstream(std::_Ios_Openmode)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to `std::cxx11::numpunct const& std::use_facet<std::cxx11::numpunct >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace_aux(unsigned long, unsigned long, unsigned long, char)@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_assign(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to typeinfo for std::ios_base::failure[abi:cxx11]@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference tostd::runtime_error::runtime_error(std::runtime_error const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to `std::basic_istream<char, std::char_traits >& std::operator>><char, std::char_traits, std::allocator >(std::basic_istream<char, std::char_traits >&, std::cxx11::basic_string<char, std::char_traits, std::allocator >&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to std::__cxx11::messages<wchar_t> const& std::use_facet<std::__cxx11::messages<wchar_t> >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::append(char const*)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to std::runtime_error::runtime_error(std::runtime_error const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference tostd::__cxx11::basic_stringstream<char, std::char_traits, std::allocator >::~basic_stringstream()@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to `std::logic_error::logic_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log_setup-mt.so: undefined reference to std::basic_istream<wchar_t, std::char_traits<wchar_t> >& std::getline<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >(std::basic_istream<wchar_t, std::char_traits<wchar_t> >&, std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >&, wchar_t)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::compare(char const*) const@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to std::runtime_error::runtime_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference tostd::__cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::swap(std::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >&)@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_append(char const*, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to std::ios_base::failure[abi:cxx11]::failure(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference totypeinfo for std::__cxx11::basic_ostringstream<char, std::char_traits, std::allocator >@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to `std::ios_base::failure[abi:cxx11]::failure(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::rfind(char, unsigned long) const@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference tostd::cxx11::numpunct const& std::use_facet<std::cxx11::numpunct >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_construct(unsigned long, char)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::resize(unsigned long, wchar_t)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference tostd::__cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::_M_replace_aux(unsigned long, unsigned long, unsigned long, wchar_t)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to `std::invalid_argument::invalid_argument(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' //home/kalmykova/.linuxbrew/lib/librt.so.1: undefined reference to __socket@GLIBC_PRIVATE' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference tostd::logic_error::logic_error(std::logic_error const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_replace(unsigned long, unsigned long, wchar_t const*, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference tostd::cxx11::collate const& std::use_facet<std::cxx11::collate >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log_setup-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::compare(unsigned long, unsigned long, char const*) const@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference toVTT for std::cxx11::basic_istringstream<char, std::char_traits, std::allocator >@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to `std::out_of_range::out_of_range(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::reserve(unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference tostd::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to `std::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::_M_erase(unsigned long, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::resize(unsigned long, char)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference tostd::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::reserve(unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::push_back(char)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::find(char, unsigned long) const@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to bool std::has_facet<std::__cxx11::messages<wchar_t> >(std::locale const&)@GLIBCXX_3.4.21' //home/kalmykova/.linuxbrew/lib/librt.so.1: undefined reference toshm_directory@GLIBC_PRIVATE' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_construct(unsigned long, wchar_t)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference tostd::__cxx11::basic_istringstream<char, std::char_traits, std::allocator >::~basic_istringstream()@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::find_last_of(char const, unsigned long, unsigned long) const@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_mutate(unsigned long, unsigned long, char const, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_ostringstream()@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference toVTT for std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to `std::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::compare(wchar_t const) const@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to bool std::has_facet<std::__cxx11::messages<char> >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference tostd::ios_base::failure[abi:cxx11]::~failure()@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_replace(unsigned long, unsigned long, char const, unsigned long)@GLIBCXX_3.4.21' //home/kalmykova/.linuxbrew/lib/librt.so.1: undefined reference to __libc_pread@GLIBC_PRIVATE' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference tostd::cxx11::messages const& std::use_facet<std::cxx11::messages >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::compare(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to `vtable for std::cxx11::basic_istringstream<char, std::char_traits, std::allocator >@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::out_of_range::out_of_range(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference tostd::__cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::compare(std::cxx11::basic_string<wchar_t, std::char_traits, std::allocator > const&) const@GLIBCXX_3.4.21' //home/kalmykova/.linuxbrew/lib/librt.so.1: undefined reference to __pthread_barrier_wait@GLIBC_PRIVATE' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_create(unsigned long&, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to `std::cxx11::basic_stringbuf<char, std::char_traits, std::allocator >::_M_sync(char, unsigned long, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits, std::allocator >::find_first_of(char const, unsigned long, unsigned long) const@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_ostringstream()@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference tostd::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::_M_append(wchar_t const, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to vtable for std::ios_base::failure[abi:cxx11]@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference tostd::__cxx11::basic_string<char, std::char_traits, std::allocator >::find(char const, unsigned long, unsigned long) const@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::logic_error::logic_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference tostd::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::~basic_string()@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to `std::overflow_error::overflow_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' //home/kalmykova/.linuxbrew/lib/librt.so.1: undefined reference to `recv@GLIBC_PRIVATE' /home/kalmykova/.linuxbrew/lib/libboost_thread-mt.so: undefined reference to std::basic_istream<char, std::char_traits<char> >& std::getline<char, std::char_traits<char>, std::allocator<char> >(std::basic_istream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, char)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::swap(std::cxx11::basic_string<char, std::char_traits, std::allocator >&)@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to vtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference tostd::basic_istream<wchar_t, std::char_traits >& std::operator>><wchar_t, std::char_traits, std::allocator >(std::basic_istream<wchar_t, std::char_traits >&, std::__cxx11::basic_string<wchar_t, std::char_traits, std::allocator >&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to `std::__cxx11::basic_stringbuf<char, std::char_traits, std::allocator >::str() const@GLIBCXX_3.4.21' collect2: error: ld returned 1 exit status make[2]: [TestTools] Error 1 make[1]: [CMakeFiles/TestTools.dir/all] Error 2 make: *** [all] Error 2 "

[VPetukhov]

Can you please specify boost and gcc versions? It seems that linuxbrew has boost built with a gcc version different from yours and you have to build boost manually. Here is description of the problem.

[svetlanaKalm]

boost 1.65.1 gcc (Homebrew gcc 5.4.0) 5.4.0

[VPetukhov]

Yes, I've met this problem with these exact versions. I'll add this answer to the troubleshooting section in the README. Manual boost installation should help. Please, contact me if it don't.

[svetlanaKalm]

Thanks I will try

[svetlanaKalm]

I installed boost manyally And again got the error:

CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function TestTools::testR::test_method()': TestTools.cpp:(.text+0x4df): undefined reference toRInside::parseEval(std::string const&)' TestTools.cpp:(.text+0x571): undefined reference to RInside::parseEval(std::string const&)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In functionboost::unit_test::make_test_case(boost::function<void ()> const&, boost::unit_test::basic_cstring, boost::unit_test::basic_cstring, unsigned long)': TestTools.cpp:(.text._ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m[_ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m]+0x26): undefined reference to boost::unit_test::ut_detail::normalize_test_case_name(boost::unit_test::basic_cstring<char const>)' libDropTools.a(Logs.cpp.o): In functionvoid boost::log::v2_mt_posix::basic_formatting_ostream<char, std::char_traits, std::allocator >::aligned_write(wchar_t const, long)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l[_ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l]+0xdc): undefined reference to `boost::log::v2_mt_posix::aux::code_convert_impl(wchar_t const, unsigned long, std::string&, unsigned long, std::locale const&)' Logs.cpp:(.text._ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l[_ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l]+0x139): undefined reference to boost::log::v2_mt_posix::aux::code_convert_impl(wchar_t const*, unsigned long, std::string&, unsigned long, std::locale const&)' libDropTools.a(Logs.cpp.o): In functionvoid boost::log::v2_mt_posix::type_dispatcher::callback_base::trampoline<boost::log::v2_mt_posix::binder1st<boost::log::v2_mt_posix::output_fun, boost::log::v2_mt_posix::expressions::aux::stream_ref<boost::log::v2_mt_posix::basic_formatting_ostream<char, std::char_traits, std::allocator > >&>, std::basic_string<wchar_t, std::char_traits, std::allocator > >(void, std::basic_string<wchar_t, std::char_traits, std::allocator > const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix15type_dispatcher13callback_base10trampolineINS1_9binder1stINS1_10output_funERNS1_11expressions3aux10stream_refINS1_24basic_formatting_ostreamIcSt11char_traitsIcESaIcEEEEEEESbIwSBIwESaIwEEEEvPvRKT0[_ZN5boost3log11v2_mt_posix15type_dispatcher13callback_base10trampolineINS1_9binder1stINS1_10output_funERNS1_11expressions3aux10stream_refINS1_24basic_formatting_ostreamIcSt11char_traitsIcESaIcEEEEEEESbIwSBIwESaIwEEEEvPvRKT0]+0xf9): undefined reference to `boost::log::v2_mt_posix::aux::code_convert_impl(wchar_t const, unsigned long, std::string&, unsigned long, std::locale const&)' libDropTools.a(Logs.cpp.o): In function boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char> >::consume(boost::log::v2_mt_posix::record_view const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE7consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE7consumeERKNS1_11record_viewE]+0xb8): undefined reference toboost::log::v2_mt_posix::sinks::basic_text_ostream_backend::consume(boost::log::v2_mt_posix::record_view const&, std::string const&)' libDropTools.a(Logs.cpp.o): In function boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char> >::try_consume(boost::log::v2_mt_posix::record_view const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE11try_consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE11try_consumeERKNS1_11record_viewE]+0xde): undefined reference toboost::log::v2_mt_posix::sinks::basic_text_ostream_backend::consume(boost::log::v2_mt_posix::record_view const&, std::string const&)' libDropTools.a(Logs.cpp.o): In function boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::text_file_backend>::consume(boost::log::v2_mt_posix::record_view const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE7consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE7consumeERKNS1_11record_viewE]+0xb8): undefined reference toboost::log::v2_mt_posix::sinks::text_file_backend::consume(boost::log::v2_mt_posix::record_view const&, std::string const&)' libDropTools.a(Logs.cpp.o): In function boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::text_file_backend>::try_consume(boost::log::v2_mt_posix::record_view const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE11try_consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE11try_consumeERKNS1_11record_viewE]+0xde): undefined reference toboost::log::v2_mt_posix::sinks::text_file_backend::consume(boost::log::v2_mt_posix::record_view const&, std::string const&)' libDropTools.a(UtilFunctions.cpp.o): In function Tools::init_r()': UtilFunctions.cpp:(.text+0x5f0): undefined reference toRInside::parseEvalQ(std::string const&)' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log_setup.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::replace(unsigned long, unsigned long, char const*, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_iostreams.so: undefined reference tostd::ios_base::failure[abi:cxx11]::what() const@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_mutate(unsigned long, unsigned long, wchar_t const*, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_timer.so.1.65.1: undefined reference toVTT for std::cxx11::basic_stringstream<char, std::char_traits, std::allocator >@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_filesystem.so: undefined reference to `std::throw_out_of_range_fmt(char const, ...)@GLIBCXX_3.4.20' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_filesystem.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits, std::allocator >::find_first_not_of(char const, unsigned long, unsigned long) const@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_iostreams.so: undefined reference to std::ios_base::failure[abi:cxx11]::~cxx11()@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_iostreams.so: undefined reference tostd::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::_M_assign(std::__cxx11::basic_string<wchar_t, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference to `std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >::basic_ostringstream(std::_Ios_Openmode)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_iostreams.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_create(unsigned long&, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_filesystem.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::~basic_string()@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_filesystem.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_erase(unsigned long, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_regex.so: undefined reference tostd::__cxx11::collate const& std::use_facet<std::cxx11::collate >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_unit_test_framework.so: undefined reference to std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >::basic_stringstream(std::_Ios_Openmode)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_regex.so: undefined reference tostd::cxx11::numpunct const& std::use_facet<std::cxx11::numpunct >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_filesystem.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace_aux(unsigned long, unsigned long, unsigned long, char)@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_assign(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_iostreams.so: undefined reference to typeinfo for std::ios_base::failure[abi:cxx11]@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_unit_test_framework.so: undefined reference tostd::runtime_error::runtime_error(std::runtime_error const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference to std::basic_istream<char, std::char_traits<char> >& std::operator>><char, std::char_traits<char>, std::allocator<char> >(std::basic_istream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_regex.so: undefined reference tostd::cxx11::messages const& std::use_facet<std::cxx11::messages >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::append(char const*)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_iostreams.so: undefined reference tostd::runtime_error::runtime_error(std::runtime_error const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_unit_test_framework.so: undefined reference to std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_stringstream()@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_regex.so: undefined reference tostd::logic_error::logic_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log_setup.so: undefined reference to std::basic_istream<wchar_t, std::char_traits<wchar_t> >& std::getline<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >(std::basic_istream<wchar_t, std::char_traits<wchar_t> >&, std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >&, wchar_t)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_filesystem.so: undefined reference tostd::__cxx11::basic_string<char, std::char_traits, std::allocator >::compare(char const*) const@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to `std::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::swap(std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >&)@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference tovtable for std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_iostreams.so: undefined reference tostd::ios_base::failure[abi:cxx11]::cxx11(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_unit_test_framework.so: undefined reference to typeinfo for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_iostreams.so: undefined reference tostd::ios_base::failure[abi:cxx11]::cxx11(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_filesystem.so: undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::rfind(char, unsigned long) const@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference to std::__cxx11::numpunct<char> const& std::use_facet<std::__cxx11::numpunct<char> >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_unit_test_framework.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_construct(unsigned long, char)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference to `std::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::resize(unsigned long, wchar_t)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_replace_aux(unsigned long, unsigned long, unsigned long, wchar_t)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference tostd::invalid_argument::invalid_argument(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference to std::logic_error::logic_error(std::logic_error const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_filesystem.so: undefined reference tostd::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::_M_replace(unsigned long, unsigned long, wchar_t const*, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_regex.so: undefined reference to `std::cxx11::collate const& std::use_facet<std::cxx11::collate >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log_setup.so: undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::compare(unsigned long, unsigned long, char const*) const@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_unit_test_framework.so: undefined reference to VTT for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference tostd::out_of_range::out_of_range(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::reserve(unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_filesystem.so: undefined reference to std::runtime_error::runtime_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_regex.so: undefined reference tostd::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::_M_erase(unsigned long, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_timer.so.1.65.1: undefined reference to vtable for std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::resize(unsigned long, char)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_regex.so: undefined reference to `std::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::reserve(unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::push_back(char)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_filesystem.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find(char, unsigned long) const@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_regex.so: undefined reference tobool std::has_facet<std::cxx11::messages >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_regex.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_construct(unsigned long, wchar_t)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_unit_test_framework.so: undefined reference tostd::__cxx11::basic_istringstream<char, std::char_traits, std::allocator >::~basic_istringstream()@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_filesystem.so: undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::find_last_of(char const, unsigned long, unsigned long) const@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_filesystem.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_mutate(unsigned long, unsigned long, char const, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_unit_test_framework.so: undefined reference to std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_ostringstream()@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference toVTT for std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference to `std::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::compare(wchar_t const) const@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_regex.so: undefined reference to bool std::has_facet<std::__cxx11::messages<char> >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_iostreams.so: undefined reference tostd::ios_base::failure[abi:cxx11]::~cxx11()@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_filesystem.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_replace(unsigned long, unsigned long, char const, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_regex.so: undefined reference to std::__cxx11::messages<char> const& std::use_facet<std::__cxx11::messages<char> >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_regex.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::compare(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_unit_test_framework.so: undefined reference to vtable for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference tostd::out_of_range::out_of_range(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_regex.so: undefined reference to `std::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::compare(std::cxx11::basic_string<wchar_t, std::char_traits, std::allocator > const&) const@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_create(unsigned long&, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference to std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >::_M_sync(char*, unsigned long, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_filesystem.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::find_first_of(char const*, unsigned long, unsigned long) const@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_ostringstream()@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference tostd::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::_M_append(wchar_t const, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_iostreams.so: undefined reference to vtable for std::ios_base::failure[abi:cxx11]@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference tostd::__cxx11::basic_string<char, std::char_traits, std::allocator >::find(char const, unsigned long, unsigned long) const@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference to std::logic_error::logic_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference tostd::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::~basic_string()@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_regex.so: undefined reference to `std::overflow_error::overflow_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_thread.so: undefined reference to std::basic_istream<char, std::char_traits<char> >& std::getline<char, std::char_traits<char>, std::allocator<char> >(std::basic_istream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, char)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::swap(std::cxx11::basic_string<char, std::char_traits, std::allocator >&)@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to vtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference tostd::basic_istream<wchar_t, std::char_traits >& std::operator>><wchar_t, std::char_traits, std::allocator >(std::basic_istream<wchar_t, std::char_traits >&, std::__cxx11::basic_string<wchar_t, std::char_traits, std::allocator >&)@GLIBCXX_3.4.21' /home/kalmykova/boost_1_65_1/boost_lib/lib/libboost_log.so: undefined reference to `std::__cxx11::basic_stringbuf<char, std::char_traits, std::allocator >::str() const@GLIBCXX_3.4.21' collect2: error: ld returned 1 exit status make[2]: [TestTools] Error 1 make[1]: [CMakeFiles/TestTools.dir/all] Error 2

[svetlanaKalm]

by the way the gcc version without brew is 4.8.5

[VPetukhov]

Which version did you use to build boost?

[svetlanaKalm]

when built it manyally - gcc 4.8.5

[VPetukhov]

It's a gcc issue with linkage between 4'th and 5'th versions. Please, see the troubleshooting section.

[larsplus]

Dear Viktor, I run into the same problem. I use gcc 4.8.5 and manually built all requirements except the R packages which were pre-built, I'm unsure about the compiler used. Can you confirm that the problem will be solved if I re-build R and R libraries using gcc 4.8.5 or did I misunderstand anything?

[VPetukhov]

Can you please attach your build logs?

[larsplus]

-- Boost version: 1.66.0 -- Found the following Boost libraries: -- filesystem -- iostreams -- log -- system -- thread -- unit_test_framework -- regex -- date_time -- log_setup -- chrono -- atomic -- Boost Include: /g/steinmetz/velten/Software/boost_1_66_0 -- Boost Libraries: /g/steinmetz/velten/Software/boost_1_66_0/stage/lib -- Boost Link-Libs: /g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_filesystem.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_iostreams.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_log.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_system.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_thread.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_unit_test_framework.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_regex.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_date_time.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_log_setup.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_chrono.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_atomic.so -- Found R: /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R -- Configuring done -- Generating done -- Build files have been written to: /g/steinmetz/velten/Software/dropEst-master [ 11%] Built target DropTools [ 58%] Built target Estimation [ 59%] Linking CXX executable TestTools CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function TestTools::testR::test_method()': TestTools.cpp:(.text+0x4df): undefined reference toRInside::parseEval(std::string const&)' TestTools.cpp:(.text+0x571): undefined reference to RInside::parseEval(std::string const&)' libDropTools.a(UtilFunctions.cpp.o): In functionTools::init_r()': UtilFunctions.cpp:(.text+0x630): undefined reference to RInside::parseEvalQ(std::string const&)' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_assign(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::reserve(unsigned long)@GLIBCXX_3.4.21' /g/steinmetz/velten/Software/lib//libreadline.so.7: undefined reference totgetnum' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference to vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_append(char const, unsigned long)@GLIBCXX_3.4.21' /g/steinmetz/velten/Software/lib//libreadline.so.7: undefined reference to tgetent' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference tostd::runtime_error::runtime_error(char const)@GLIBCXX_3.4.21' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference to `vtable for std::cxx11::basic_stringbuf<char, std::char_traits, std::allocator >@GLIBCXX_3.4.21' /g/steinmetz/velten/Software/lib//libreadline.so.7: undefined reference to tgetstr' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_create(unsigned long&, unsigned long)@GLIBCXX_3.4.21' /g/steinmetz/velten/Software/lib//libreadline.so.7: undefined reference to tgoto' /g/steinmetz/velten/Software/lib//libreadline.so.7: undefined reference toUP' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference to `std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >::~basic_ostringstream()@GLIBCXX_3.4.21' /g/steinmetz/velten/Software/lib//libreadline.so.7: undefined reference to BC' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference toVTT for std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >@GLIBCXX_3.4.21' /g/steinmetz/velten/Software/lib//libreadline.so.7: undefined reference to tputs' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference tooperator delete(void*, unsigned long)@CXXABI_1.3.9' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)@GLIBCXX_3.4.21' /g/steinmetz/velten/Software/lib//libreadline.so.7: undefined reference to PC' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference tostd::runtime_error::runtime_error(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /g/steinmetz/velten/Software/lib//libreadline.so.7: undefined reference to `tgetflag' collect2: error: ld returned 1 exit status make[2]: ** [TestTools] Error 1 make[1]: [CMakeFiles/TestTools.dir/all] Error 2

On 27 Feb 2018, at 18:09, Viktor Petukhov notifications@github.com wrote:

Can you please attach your build logs?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/hms-dbmi/dropEst/issues/8#issuecomment-368952506, or mute the thread https://github.com/notifications/unsubscribe-auth/Ahp880HiFukIatLJh7njaW9uDMeExk24ks5tZDbLgaJpZM4QanQp.

[VPetukhov]

Based on this log I'm quite sure that you need to rebuild RInside. Don't see a reason to rebuild other libraries and especially, whole R system.

[larsplus]

Hi Viktor, thanks for your reply. I cannnot write over the existing RInside install; how can I force cmake to use a different .Library path? I tried setting R_LIBS, R_LIBS_SITE and R_LIBS_USER with no effect. I then even built R from scratch and passed the directory via -D R_ROOT. However the installer still falls back to using the existing R install, see log below.

-- Boost version: 1.66.0 -- Found the following Boost libraries: -- filesystem -- iostreams -- log -- system -- thread -- unit_test_framework -- regex -- date_time -- log_setup -- chrono -- atomic -- Boost Include: /g/steinmetz/velten/Software/boost_1_66_0 -- Boost Libraries: /g/steinmetz/velten/Software/boost_1_66_0/stage/lib -- * Boost Link-Libs: /g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_filesystem.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_iostreams.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_log.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_system.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_thread.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_unit_test_framework.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_regex.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_date_time.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_log_setup.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_chrono.so;/g/steinmetz/velten/Software/boost_1_66_0/stage/lib/libboost_atomic.so -- Found R: /g/steinmetz/velten/Software/R-3.4.3/ -- Configuring done -- Generating done -- Build files have been written to: /g/steinmetz/velten/Software/dropEst-master [ 11%] Built target DropTools [ 58%] Built target Estimation [ 59%] Linking CXX executable TestTools CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function TestTools::testR::test_method()': TestTools.cpp:(.text+0x4df): undefined reference toRInside::parseEval(std::string const&)' TestTools.cpp:(.text+0x571): undefined reference to RInside::parseEval(std::string const&)' libDropTools.a(UtilFunctions.cpp.o): In functionTools::init_r()': UtilFunctions.cpp:(.text+0x630): undefined reference to RInside::parseEvalQ(std::string const&)' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_assign(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::reserve(unsigned long)@GLIBCXX_3.4.21' /g/steinmetz/velten/Software/lib//libreadline.so.7: undefined reference totgetnum' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference to vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference tostd::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_append(char const, unsigned long)@GLIBCXX_3.4.21' /g/steinmetz/velten/Software/lib//libreadline.so.7: undefined reference to tgetent' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference tostd::runtime_error::runtime_error(char const)@GLIBCXX_3.4.21' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference to vtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' /g/steinmetz/velten/Software/lib//libreadline.so.7: undefined reference totgetstr' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)@GLIBCXX_3.4.21' /g/steinmetz/velten/Software/lib//libreadline.so.7: undefined reference totgoto' /g/steinmetz/velten/Software/lib//libreadline.so.7: undefined reference to UP' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference tostd::__cxx11::basic_ostringstream<char, std::char_traits, std::allocator >::~basic_ostringstream()@GLIBCXX_3.4.21' /g/steinmetz/velten/Software/lib//libreadline.so.7: undefined reference to BC' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference toVTT for std::__cxx11::basic_ostringstream<char, std::char_traits, std::allocator >@GLIBCXX_3.4.21' /g/steinmetz/velten/Software/lib//libreadline.so.7: undefined reference to tputs' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference tooperator delete(void, unsigned long)@CXXABI_1.3.9' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)@GLIBCXX_3.4.21' /g/steinmetz/velten/Software/lib//libreadline.so.7: undefined reference toPC' /g/easybuild/x86_64/CentOS/7/nehalem/software/R/3.4.3-foss-2017b-X11-20171023/lib64/R/library/RInside/lib/libRInside.so: undefined reference to std::runtime_error::runtime_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21' /g/steinmetz/velten/Software/lib//libreadline.so.7: undefined reference totgetflag' collect2: error: ld returned 1 exit status

[VPetukhov]

R_PACKAGES_DIRS is variable you're looking for. This directory must contain subfolders "RcppEigen", "Rcpp" and "RInside". Please, keep in mind that you need to clear your build directory after you change cmake variables as cmake caches all found path and ignores changes if cache is not empty.

[larsplus]

Hi Viktor, thanks for all your help. We managed to install it by running cmake with -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc . Just in case this is useful to anyone else running a system with several compilers installed!