Error with gcc-7.2

[e-molitor]

Dear PKPDSim creators,

thank you loads for a most useful package. With current versions of gcc-7.2 and stdlib, I ran into an error message. Using the introductory example

p <- list(CL = 1, V = 10, KA = 0.5)
pk1 <- new_ode_model("pk_1cmt_oral")

led to the following list of error messages, each one nagging at ambiguous overload operators:

file4b7eba8cc03.cpp: In Funktion »Rcpp::List sim_wrapper_cpp(Rcpp::NumericVector, Rcpp::List, Rcpp::List, Rcpp::NumericVector, double)«:
file4b7eba8cc03.cpp:89:21: Fehler: ambiguous overload for »operator=« (operand types are »std::vector« and »Rcpp::Vector<19>::NameProxy {aka Rcpp::internal::generic_name_proxy<19>}«)
times = design["t"];
^
In file included from /usr/include/c++/7/vector:69:0,
from /usr/local/lib64/R/library/Rcpp/include/RcppCommon.h:59,
from /usr/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
from file4b7eba8cc03.cpp:8:
/usr/include/c++/7/bits/vector.tcc:179:5: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator]
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/local/lib64/R/library/Rcpp/include/RcppCommon.h:59,
from /usr/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
from file4b7eba8cc03.cpp:8:
/usr/include/c++/7/bits/stl_vector.h:461:7: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(std::vector<_Tp, _Alloc>&&) [with _Tp = double; _Alloc = std::allocator]
operator=(vector&& __x) noexcept(_Alloc_traits::_S_nothrow_move())
^~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:482:7: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(std::initializer_list<_Tp>) [with _Tp = double; _Alloc = std::allocator]
operator=(initializer_list<value_type> __l)
^~~~~~~~
file4b7eba8cc03.cpp:90:24: Fehler: ambiguous overload for »operator=« (operand types are »std::vector« and »Rcpp::Vector<19>::NameProxy {aka Rcpp::internal::generic_name_proxy<19>}«)
doses = design["dose"];
^
In file included from /usr/include/c++/7/vector:69:0,
from /usr/local/lib64/R/library/Rcpp/include/RcppCommon.h:59,
from /usr/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
from file4b7eba8cc03.cpp:8:
/usr/include/c++/7/bits/vector.tcc:179:5: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator]
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/local/lib64/R/library/Rcpp/include/RcppCommon.h:59,
from /usr/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
from file4b7eba8cc03.cpp:8:
/usr/include/c++/7/bits/stl_vector.h:461:7: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(std::vector<_Tp, _Alloc>&&) [with _Tp = double; _Alloc = std::allocator]
operator=(vector&& __x) noexcept(_Alloc_traits::_S_nothrow_move())
^~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:482:7: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(std::initializer_list<_Tp>) [with _Tp = double; _Alloc = std::allocator]
operator=(initializer_list<value_type> __l)
^~~~~~~~
file4b7eba8cc03.cpp:91:23: Fehler: ambiguous overload for »operator=« (operand types are »std::vector« and »Rcpp::Vector<19>::NameProxy {aka Rcpp::internal::generic_name_proxy<19>}«)
evid = design["evid"];
^
In file included from /usr/include/c++/7/vector:69:0,
from /usr/local/lib64/R/library/Rcpp/include/RcppCommon.h:59,
from /usr/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
from file4b7eba8cc03.cpp:8:
/usr/include/c++/7/bits/vector.tcc:179:5: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator]
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/local/lib64/R/library/Rcpp/include/RcppCommon.h:59,
from /usr/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
from file4b7eba8cc03.cpp:8:
/usr/include/c++/7/bits/stl_vector.h:461:7: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(std::vector<_Tp, _Alloc>&&) [with _Tp = int; _Alloc = std::allocator]
operator=(vector&& __x) noexcept(_Alloc_traits::_S_nothrow_move())
^~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:482:7: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(std::initializer_list<_Tp>) [with _Tp = int; _Alloc = std::allocator]
operator=(initializer_list<value_type> __l)
^~~~~~~~
file4b7eba8cc03.cpp:92:23: Fehler: ambiguous overload for »operator=« (operand types are »std::vector« and »Rcpp::Vector<19>::NameProxy {aka Rcpp::internal::generic_name_proxy<19>}«)
dummy = design["dum"];
^
In file included from /usr/include/c++/7/vector:69:0,
from /usr/local/lib64/R/library/Rcpp/include/RcppCommon.h:59,
from /usr/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
from file4b7eba8cc03.cpp:8:
/usr/include/c++/7/bits/vector.tcc:179:5: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator]
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/local/lib64/R/library/Rcpp/include/RcppCommon.h:59,
from /usr/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
from file4b7eba8cc03.cpp:8:
/usr/include/c++/7/bits/stl_vector.h:461:7: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(std::vector<_Tp, _Alloc>&&) [with _Tp = double; _Alloc = std::allocator]
operator=(vector&& __x) noexcept(_Alloc_traits::_S_nothrow_move())
^~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:482:7: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(std::initializer_list<_Tp>) [with _Tp = double; _Alloc = std::allocator]
operator=(initializer_list<value_type> __l)
^~~~~~~~
file4b7eba8cc03.cpp:93:24: Fehler: ambiguous overload for »operator=« (operand types are »std::vector« and »Rcpp::Vector<19>::NameProxy {aka Rcpp::internal::generic_name_proxy<19>}«)
rates = design["rate"];
^
In file included from /usr/include/c++/7/vector:69:0,
from /usr/local/lib64/R/library/Rcpp/include/RcppCommon.h:59,
from /usr/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
from file4b7eba8cc03.cpp:8:
/usr/include/c++/7/bits/vector.tcc:179:5: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator]
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/local/lib64/R/library/Rcpp/include/RcppCommon.h:59,
from /usr/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
from file4b7eba8cc03.cpp:8:
/usr/include/c++/7/bits/stl_vector.h:461:7: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(std::vector<_Tp, _Alloc>&&) [with _Tp = double; _Alloc = std::allocator]
operator=(vector&& __x) noexcept(_Alloc_traits::_S_nothrow_move())
^~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:482:7: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(std::initializer_list<_Tp>) [with _Tp = double; _Alloc = std::allocator]
operator=(initializer_list<value_type> __l)
^~~~~~~~
file4b7eba8cc03.cpp:94:31: Fehler: ambiguous overload for »operator=« (operand types are »std::vector« and »Rcpp::Vector<19>::NameProxy {aka Rcpp::internal::generic_name_proxy<19>}«)
dose_cmt = design["dose_cmt"];
^
In file included from /usr/include/c++/7/vector:69:0,
from /usr/local/lib64/R/library/Rcpp/include/RcppCommon.h:59,
from /usr/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
from file4b7eba8cc03.cpp:8:
/usr/include/c++/7/bits/vector.tcc:179:5: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator]
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/local/lib64/R/library/Rcpp/include/RcppCommon.h:59,
from /usr/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
from file4b7eba8cc03.cpp:8:
/usr/include/c++/7/bits/stl_vector.h:461:7: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(std::vector<_Tp, _Alloc>&&) [with _Tp = int; _Alloc = std::allocator]
operator=(vector&& __x) noexcept(_Alloc_traits::_S_nothrow_move())
^~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:482:7: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(std::initializer_list<_Tp>) [with _Tp = int; _Alloc = std::allocator]
operator=(initializer_list<value_type> __l)
^~~~~~~~
file4b7eba8cc03.cpp:95:28: Fehler: ambiguous overload for »operator=« (operand types are »std::vector« and »Rcpp::Vector<19>::NameProxy {aka Rcpp::internal::generic_name_proxy<19>}«)
dose_type = design["type"];
^
In file included from /usr/include/c++/7/vector:69:0,
from /usr/local/lib64/R/library/Rcpp/include/RcppCommon.h:59,
from /usr/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
from file4b7eba8cc03.cpp:8:
/usr/include/c++/7/bits/vector.tcc:179:5: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = int; _Alloc = std::allocator]
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/local/lib64/R/library/Rcpp/include/RcppCommon.h:59,
from /usr/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
from file4b7eba8cc03.cpp:8:
/usr/include/c++/7/bits/stl_vector.h:461:7: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(std::vector<_Tp, _Alloc>&&) [with _Tp = int; _Alloc = std::allocator]
operator=(vector&& __x) noexcept(_Alloc_traits::_S_nothrow_move())
^~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:482:7: Anmerkung: candidate: std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(std::initializer_list<_Tp>) [with _Tp = int; _Alloc = std::allocator]
operator=(initializer_list<value_type> __l)
^~~~~~~~
make: *** [file4b7eba8cc03.o] Fehler 1
g++ -I/usr/local/lib64/R/include -DNDEBUG -I"/usr/local/lib64/R/library/Rcpp/include" -I"/usr/local/lib64/R/library/BH/include" -I"/tmp/RtmpD8fySg/sourceCpp-x86_64-pc-linux-gnu-0.12.13" -I/usr/local/include -w -fpic -g -O2 -c file4b7eba8cc03.cpp -o file4b7eba8cc03.o
/usr/local/lib64/R/etc/Makeconf:166: die Regel für Ziel „file4b7eba8cc03.o“ scheiterte
Fehler in Rcpp::sourceCpp(code = sim_func, rebuild = TRUE, env = globalenv(), :
Error 1 occurred building shared library.

[ronkeizer]

Can reproduce with this particular compiler version, so seems due to a change in the compiler. Works fine with older gcc (currently using 4.8.2) or clang (any), so please use that for now. Will look for fix a.s.a.p.

[ronkeizer]

Should be fixed with latest revision, please check. Tested with g++ 7.2.0 on Mac.