* installing *source* package 'bayou' ...
** this is package 'bayou' version '2.3.2'
** package 'bayou' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++.exe (GCC) 14.3.0'
using C++17
make[1]: Entering directory '/d/temp/2026_02_15_01_50_00_5770/RtmpYp0kRx/R.INSTALL39e44ca724b6/bayou/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c branches.cpp -o branches.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c threepoint.cpp -o threepoint.o
In file included from D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/RcppCommon.h:188,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:26,
from D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include/RcppArmadillo.h:32,
from threepoint.cpp:1:
In function 'SEXPREC* Rcpp::internal::primitive_wrap__impl__cast(const T&, Rcpp::traits::false_type) [with T = double]',
inlined from 'SEXPREC* Rcpp::internal::primitive_wrap__impl(const T&, Rcpp::traits::r_type_primitive_tag) [with T = double]' at D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/Rcpp/internal/wrap.h:471:46,
inlined from 'SEXPREC* Rcpp::internal::primitive_wrap(const T&) [with T = double]' at D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/Rcpp/internal/wrap.h:495:40,
inlined from 'SEXPREC* Rcpp::internal::wrap_dispatch(const T&, Rcpp::traits::wrap_type_primitive_tag) [with T = double]' at D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/Rcpp/internal/wrap.h:744:34,
inlined from 'SEXPREC* Rcpp::wrap(const T&) [with T = double]' at D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/Rcpp/internal/wrap_end.h:30:38,
inlined from 'static SEXPREC* Rcpp::internal::generic_element_converter<RTYPE>::get(const T&) [with T = double; int RTYPE = 19]' at D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/Rcpp/vector/converter.h:80:23,
inlined from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element__dispatch__isArgument(Rcpp::traits::false_type, iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<double>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' at D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/Rcpp/vector/Vector.h:530:13,
inlined from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element__dispatch(Rcpp::traits::true_type, iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<double>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' at D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/Rcpp/vector/Vector.h:523:46,
inlined from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element(iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<double>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' at D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/Rcpp/vector/Vector.h:512:34,
inlined from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<double>; TArgs = {Rcpp::traits::named_object<arma::Col<double> >}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' at D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/Rcpp/vector/Vector.h:1169:24,
inlined from 'static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<arma::Col<double> >; TArgs = {Rcpp::traits::named_object<double>, Rcpp::traits::named_object<arma::Col<double> >}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' at D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
inlined from 'static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create__dispatch(Rcpp::traits::true_type, const T& ...) [with T = {Rcpp::traits::named_object<arma::Col<double> >, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<arma::Col<double> >}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' at D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/Rcpp/vector/Vector.h:1146:29,
inlined from 'static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T& ...) [with T = {Rcpp::traits::named_object<arma::Col<double> >, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<arma::Col<double> >}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' at D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/Rcpp/vector/Vector.h:1128:50,
inlined from 'SEXPREC* C_transf_branch_lengths(SEXP, int, Rcpp::NumericVector, double)' at threepoint.cpp:148:30:
D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/Rcpp/internal/wrap.h:448:41: warning: 'root' may be used uninitialized [-Wmaybe-uninitialized]
448 | r_vector_start<RTYPE>(x)[0] = object;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
threepoint.cpp: In function 'SEXPREC* C_transf_branch_lengths(SEXP, int, Rcpp::NumericVector, double)':
threepoint.cpp:102:20: note: 'root' was declared here
102 | double d1, d2, root;
| ^~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.5/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.5/RcppArmadillo/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c weightmatrix.cpp -o weightmatrix.o
weightmatrix.cpp: In function 'SEXPREC* C_weightmatrix(SEXP, SEXP)':
weightmatrix.cpp:81:24: warning: comparison of integer expressions of different signedness: 'int' and 'const arma::uword' {aka 'const unsigned int'} [-Wsign-compare]
81 | for(int j=0; j < mstart.n_rows; ++j){
| ~~^~~~~~~~~~~~~~~
g++ -shared -s -static-libgcc -o bayou.dll tmp.def RcppExports.o branches.o threepoint.o weightmatrix.o -LD:/RCompile/recent/R-4.5.2/bin/x64 -lRblas -LD:/RCompile/recent/R-4.5.2/bin/x64 -lRlapack -lgfortran -lquadmath -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.5.2/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2026_02_15_01_50_00_5770/RtmpYp0kRx/R.INSTALL39e44ca724b6/bayou/src'
make[1]: Entering directory '/d/temp/2026_02_15_01_50_00_5770/RtmpYp0kRx/R.INSTALL39e44ca724b6/bayou/src'
make[1]: Leaving directory '/d/temp/2026_02_15_01_50_00_5770/RtmpYp0kRx/R.INSTALL39e44ca724b6/bayou/src'
installing to d:/Rcompile/CRANpkg/lib/4.5/00LOCK-bayou/00new/bayou/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'bayou' as bayou_2.3.2.zip
* DONE (bayou)