Dear community
I am trying to publish my Shiny app but I encounter an error that displays:
"ERROR: compilation failed for package ‘diann’"
I think that It could be related with the fact that this R package is the only one from the packages used that is installed directly from its Github repository (the rest of them are installed through CRAN or Bioconductor).
The files I am trying to publish can be found in the following github repository: TraianProt.
I attach the Error log (previously installation of packages had succeded):
[2025-04-22T07:54:35.168279749+0000] Building R package: diann (1.0.1)
/mnt/packages/build /mnt
g++ -std=gnu++11 -shared -L/opt/R/4.2.3/lib/R/lib -L/usr/local/lib -o diann.so RcppExports.o diann-rcpp.o -L/opt/R/4.2.3/lib/R/lib -lR
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6formatIIiEEESsPKcDpRKT_[_ZN10tinyformat6formatIIiEEESsPKcDpRKT_]+0x362): undefined reference to `std::locale::~locale()'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6formatIIiEEESsPKcDpRKT_[_ZN10tinyformat6formatIIiEEESsPKcDpRKT_]+0x38c): undefined reference to `std::ios_base::~ios_base()'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6formatIIiEEESsPKcDpRKT_[_ZN10tinyformat6formatIIiEEESsPKcDpRKT_]+0x394): undefined reference to `_Unwind_Resume'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp14not_compatibleC1IIiEEEPKcDpOT_[_ZN4Rcpp14not_compatibleC1IIiEEEPKcDpOT_]+0x31): undefined reference to `std::exception::~exception()'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp14not_compatibleC1IIiEEEPKcDpOT_[_ZN4Rcpp14not_compatibleC1IIiEEEPKcDpOT_]+0x3f): undefined reference to `_Unwind_Resume'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp14not_compatibleC1IIiEEEPKcDpOT_[_ZN4Rcpp14not_compatibleC1IIiEEEPKcDpOT_]+0x44): undefined reference to `__cxa_call_unexpected'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC]+0xb): undefined reference to `Rf_length'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC]+0x1c): undefined reference to `TYPEOF'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC]+0x33): undefined reference to `__imp_R_NilValue'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC]+0x40): undefined reference to `Rf_protect'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC]+0x55): undefined reference to `__cxa_guard_acquire'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC]+0x73): undefined reference to `Rf_unprotect'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC]+0x90): undefined reference to `R_GetCCallable'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC]+0xa3): undefined reference to `__cxa_guard_release'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC]+0xaf): undefined reference to `__cxa_allocate_exception'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC]+0xba): undefined reference to `Rf_length'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC]+0xe8): undefined reference to `__cxa_throw'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC]+0xfa): undefined reference to `Rf_unprotect'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC]+0x102): undefined reference to `_Unwind_Resume'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC]+0x111): undefined reference to `__cxa_guard_abort'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC]+0x11e): undefined reference to `__cxa_free_exception'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIiEET_P7SEXPREC]+0x126): undefined reference to `_Unwind_Resume'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC]+0x10): undefined reference to `Rf_length'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC]+0x28): undefined reference to `__imp_R_NilValue'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC]+0x38): undefined reference to `Rf_protect'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC]+0x4d): undefined reference to `__cxa_guard_acquire'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC]+0x6d): undefined reference to `Rf_unprotect'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC]+0x91): undefined reference to `R_GetCCallable'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC]+0xa4): undefined reference to `__cxa_guard_release'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC]+0xb0): undefined reference to `__cxa_allocate_exception'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC]+0xbb): undefined reference to `Rf_length'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC]+0xe9): undefined reference to `__cxa_throw'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC]+0xfb): undefined reference to `Rf_unprotect'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC]+0x103): undefined reference to `_Unwind_Resume'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC]+0x112): undefined reference to `__cxa_guard_abort'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC]+0x11f): undefined reference to `__cxa_free_exception'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC[_ZN4Rcpp8internal12primitive_asIdEET_P7SEXPREC]+0x127): undefined reference to `_Unwind_Resume'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE[_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE]+0x13): undefined reference to `__imp_R_NilValue'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE[_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE]+0x23): undefined reference to `Rf_protect'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE[_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE]+0x38): undefined reference to `__cxa_guard_acquire'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE[_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE]+0x50): undefined reference to `Rf_xlength'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE[_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE]+0x8f): undefined reference to `R_GetCCallable'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE[_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE]+0xa2): undefined reference to `__cxa_guard_release'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE[_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE]+0xd4): undefined reference to `__cxa_guard_abort'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE[_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE]+0xe3): undefined reference to `Rf_unprotect'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE[_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE]+0xeb): undefined reference to `_Unwind_Resume'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE[_ZN4Rcpp8internal18export_range__implIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEEdEEvP7SEXPRECT_NS_6traits17integral_constantIbLb0EEE]+0x74): undefined reference to `Rf_unprotect'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x2b): undefined reference to `std::ios_base::ios_base()'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0xaf): undefined reference to `std::basic_ios<char, std::char_traits<char> >::init(std::basic_streambuf<char, std::char_traits<char> >*)'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x125): undefined reference to `std::locale::locale()'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x14c): undefined reference to `std::string::_S_construct(unsigned long long, char, std::allocator<char> const&)'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x161): undefined reference to `std::basic_ios<char, std::char_traits<char> >::init(std::basic_streambuf<char, std::char_traits<char> >*)'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x16c): undefined reference to `std::ostream::operator<<(int)'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x178): undefined reference to `std::string::_S_construct(unsigned long long, char, std::allocator<char> const&)'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x1bd): undefined reference to `std::string::swap(std::string&)'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x1f4): undefined reference to `std::ostream::write(char const*, long long)'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x263): undefined reference to `std::locale::~locale()'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x295): undefined reference to `std::ios_base::~ios_base()'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x2cb): undefined reference to `std::string::swap(std::string&)'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x2dc): undefined reference to `std::string::_Rep::_M_destroy(std::allocator<char> const&)'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x2ed): undefined reference to `std::string::_Rep::_M_destroy(std::allocator<char> const&)'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x30a): undefined reference to `std::string::_Rep::_M_destroy(std::allocator<char> const&)'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x31d): undefined reference to `std::string::assign(std::string const&)'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x338): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x349): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x351): undefined reference to `std::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_ostringstream()'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x359): undefined reference to `_Unwind_Resume'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x38f): undefined reference to `std::ios_base::~ios_base()'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x397): undefined reference to `_Unwind_Resume'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i[_ZN10tinyformat6detail15formatTruncatedIiEEvRSoRKT_i]+0x3b3): undefined reference to `std::locale::~locale()'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail9FormatArg10formatImplIiEEvRSoPKcS5_iPKv[_ZN10tinyformat6detail9FormatArg10formatImplIiEEvRSoPKcS5_iPKv]+0x2b): undefined reference to `std::ostream::operator<<(int)'
/usr/bin/ld: RcppExports.o:RcppExports.cpp:(.text$_ZN10tinyformat6detail9FormatArg10formatImplIiEEvRSoPKcS5_iPKv[_ZN10tinyformat6detail9FormatArg10formatImplIiEEvRSoPKcS5_iPKv]+0x4c): undefined reference to `std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long long)'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen8internal19throw_std_bad_allocEv[_ZN5Eigen8internal19throw_std_bad_allocEv]+0xa): undefined reference to `__cxa_allocate_exception'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen8internal19throw_std_bad_allocEv[_ZN5Eigen8internal19throw_std_bad_allocEv]+0x18): undefined reference to `std::bad_alloc::~bad_alloc()'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen8internal19throw_std_bad_allocEv[_ZN5Eigen8internal19throw_std_bad_allocEv]+0x2e): undefined reference to `__cxa_throw'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZNSt6vectorIdSaIdEE19_M_emplace_back_auxIIdEEEvDpOT_[_ZNSt6vectorIdSaIdEE19_M_emplace_back_auxIIdEEEvDpOT_]+0x73): undefined reference to `operator delete(void*)'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZNSt6vectorIdSaIdEE19_M_emplace_back_auxIIdEEEvDpOT_[_ZNSt6vectorIdSaIdEE19_M_emplace_back_auxIIdEEEvDpOT_]+0x9e): undefined reference to `operator new(unsigned long long)'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen8internal23triangular_solve_matrixIdxLi2ELi2ELb0ELi1ELi0EE3runExxPKdxPdxRNS0_15level3_blockingIddEE[_ZN5Eigen8internal23triangular_solve_matrixIdxLi2ELi2ELb0ELi1ELi0EE3runExxPKdxPdxRNS0_15level3_blockingIddEE]+0x8c3): undefined reference to `___chkstk_ms'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen8internal23triangular_solve_matrixIdxLi2ELi2ELb0ELi1ELi0EE3runExxPKdxPdxRNS0_15level3_blockingIddEE[_ZN5Eigen8internal23triangular_solve_matrixIdxLi2ELi2ELb0ELi1ELi0EE3runExxPKdxPdxRNS0_15level3_blockingIddEE]+0x927): undefined reference to `_Unwind_Resume'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen8internal23triangular_solve_matrixIdxLi2ELi2ELb0ELi1ELi0EE3runExxPKdxPdxRNS0_15level3_blockingIddEE[_ZN5Eigen8internal23triangular_solve_matrixIdxLi2ELi2ELb0ELi1ELi0EE3runExxPKdxPdxRNS0_15level3_blockingIddEE]+0x93d): undefined reference to `___chkstk_ms'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen8internal40general_matrix_matrix_triangular_productIxdLi0ELb0EdLi1ELb0ELi0ELi1ELi0EE3runExxPKdxS4_xPdxRS3_RNS0_15level3_blockingIddEE[_ZN5Eigen8internal40general_matrix_matrix_triangular_productIxdLi0ELb0EdLi1ELb0ELi0ELi1ELi0EE3runExxPKdxS4_xPdxRS3_RNS0_15level3_blockingIddEE]+0x6f9): undefined reference to `___chkstk_ms'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen8internal40general_matrix_matrix_triangular_productIxdLi0ELb0EdLi1ELb0ELi0ELi1ELi0EE3runExxPKdxS4_xPdxRS3_RNS0_15level3_blockingIddEE[_ZN5Eigen8internal40general_matrix_matrix_triangular_productIxdLi0ELb0EdLi1ELb0ELi0ELi1ELi0EE3runExxPKdxS4_xPdxRS3_RNS0_15level3_blockingIddEE]+0x75d): undefined reference to `_Unwind_Resume'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen8internal40general_matrix_matrix_triangular_productIxdLi0ELb0EdLi1ELb0ELi0ELi1ELi0EE3runExxPKdxS4_xPdxRS3_RNS0_15level3_blockingIddEE[_ZN5Eigen8internal40general_matrix_matrix_triangular_productIxdLi0ELb0EdLi1ELb0ELi0ELi1ELi0EE3runExxPKdxS4_xPdxRS3_RNS0_15level3_blockingIddEE]+0x77b): undefined reference to `___chkstk_ms'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen8internal37evaluateProductBlockingSizesHeuristicIddLi4ExEEvRT2_S3_S3_S2_[_ZN5Eigen8internal37evaluateProductBlockingSizesHeuristicIddLi4ExEEvRT2_S3_S3_S2_]+0x15e): undefined reference to `__cxa_guard_acquire'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen8internal37evaluateProductBlockingSizesHeuristicIddLi4ExEEvRT2_S3_S3_S2_[_ZN5Eigen8internal37evaluateProductBlockingSizesHeuristicIddLi4ExEEvRT2_S3_S3_S2_]+0x1f4): undefined reference to `__cxa_guard_release'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen8internal37evaluateProductBlockingSizesHeuristicIddLi1ExEEvRT2_S3_S3_S2_[_ZN5Eigen8internal37evaluateProductBlockingSizesHeuristicIddLi1ExEEvRT2_S3_S3_S2_]+0x15d): undefined reference to `__cxa_guard_acquire'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen8internal37evaluateProductBlockingSizesHeuristicIddLi1ExEEvRT2_S3_S3_S2_[_ZN5Eigen8internal37evaluateProductBlockingSizesHeuristicIddLi1ExEEvRT2_S3_S3_S2_]+0x1f3): undefined reference to `__cxa_guard_release'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen8internal26triangular_solver_selectorIKNS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEENS2_IdLin1ELi1ELi0ELin1ELi1EEELi1ELi1ELi0ELi1EE3runERS4_RS5_[_ZN5Eigen8internal26triangular_solver_selectorIKNS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEENS2_IdLin1ELi1ELi0ELin1ELi1EEELi1ELi1ELi0ELi1EE3runERS4_RS5_]+0x75): undefined reference to `___chkstk_ms'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen8internal26triangular_solver_selectorIKNS_9TransposeIKNS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEEEENS3_IdLin1ELi1ELi0ELin1ELi1EEELi1ELi2ELi0ELi1EE3runERS7_RS8_[_ZN5Eigen8internal26triangular_solver_selectorIKNS_9TransposeIKNS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEEEENS3_IdLin1ELi1ELi0ELin1ELi1EEELi1ELi2ELi0ELi1EE3runERS7_RS8_]+0x74): undefined reference to `___chkstk_ms'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen3LLTINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi1EE7computeIS2_EERS3_RKNS_9EigenBaseIT_EE[_ZN5Eigen3LLTINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi1EE7computeIS2_EERS3_RKNS_9EigenBaseIT_EE]+0x949): undefined reference to `sqrt'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen3LLTINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi1EE7computeIS2_EERS3_RKNS_9EigenBaseIT_EE[_ZN5Eigen3LLTINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi1EE7computeIS2_EERS3_RKNS_9EigenBaseIT_EE]+0xc8a): undefined reference to `sqrt'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen3LLTINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi1EE7computeIS2_EERS3_RKNS_9EigenBaseIT_EE[_ZN5Eigen3LLTINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi1EE7computeIS2_EERS3_RKNS_9EigenBaseIT_EE]+0xccd): undefined reference to `sqrt'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen3LLTINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi1EE7computeIS2_EERS3_RKNS_9EigenBaseIT_EE[_ZN5Eigen3LLTINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi1EE7computeIS2_EERS3_RKNS_9EigenBaseIT_EE]+0xd31): undefined reference to `sqrt'
/usr/bin/ld: diann-rcpp.o:diann-rcpp.cpp:(.text$_ZN5Eigen3LLTINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi1EE7computeIS2_EERS3_RKNS_9EigenBaseIT_EE[_ZN5Eigen3LLTINS_6MatrixIdLin1ELin1ELi0ELin1ELin1EEELi1EE7computeIS2_EERS3_RKNS_9EigenBaseIT_EE]+0xd6e): undefined reference to `_Unwind_Resume'
/usr/bin/ld: BFD (GNU Binutils for Ubuntu) 2.38 assertion fail ../../bfd/reloc.c:8580
RcppExports.o:RcppExports.cpp:(.pdata$_ZNKSt5ctypeIcE8do_widenEc+0x0): dangerous relocation: collect2: fatal error: ld terminated with signal 11 [Segmentation fault], core dumped
compilation terminated.
make: *** [/opt/R/4.2.3/lib/R/share/make/shlib.mk:10: diann.so] Error 1
ERROR: compilation failed for package ‘diann’
* removing ‘/usr/lib/R/diann’## End Task Log ################################################################
Error: Unhandled Exception: child_task=1535004386 child_task_status=failed: Error building image: Error building diann (1.0.1). Build exited with non-zero status: 1
Execution halted
I do not know how this can be handled, hope someone could enlighten me with this.
Samuel