* installing *source* package 'GenomeAdmixR' ...
** this is package 'GenomeAdmixR' version '2.1.10'
** using staged installation
** libs
using C++ compiler: 'g++.exe (GCC) 14.2.0'
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include'   -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1   -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c Fish.cpp -o Fish.o
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include'   -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1   -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include'   -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1   -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c helper_functions.cpp -o helper_functions.o
helper_functions.cpp: In function 'arma::mat update_frequency_tibble(const std::vector<Fish>&, double, const std::vector<int>&, int, double)':
helper_functions.cpp:129:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Fish>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  129 |  for (int i = 0; i < v.size(); ++i) {
      |                  ~~^~~~~~~~~~
helper_functions.cpp: In function 'double calculate_fitness(const Fish&, const std::vector<std::array<double, 5> >&, bool)':
helper_functions.cpp:377:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::array<double, 5>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  377 |     if (fitness_index > select[0].size()) {
      |         ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
helper_functions.cpp: In function 'double calculate_fitness(const Fish_emp&, const std::vector<std::array<double, 5> >&, const std::vector<double>&, bool)':
helper_functions.cpp:662:40: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  662 |     if (focal_index < 0 || focal_index > focal.chromosome1.size()) {
      |                            ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
helper_functions.cpp:670:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::array<double, 5>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  670 |     if (fit_index > select[0].size()) {
      |         ~~~~~~~~~~^~~~~~~~~~~~~~~~~~
helper_functions.cpp: In function 'std::vector<std::array<double, 5> > convert_select_from_r(const Rcpp::NumericMatrix&)':
helper_functions.cpp:994:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  994 |   for (size_t i = 0; i < select.nrow(); ++i) {
      |                      ~~^~~~~~~~~~~~~~~
helper_functions.cpp:996:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  996 |     for (size_t j = 0; j < select.ncol(); ++j) {
      |                        ~~^~~~~~~~~~~~~~~
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include'   -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1   -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c simulate.cpp -o simulate.o
simulate.cpp: In function 'std::vector<Fish> simulate_Population(const std::vector<Fish>&, const Rcpp::NumericMatrix&, size_t, int, double, bool, arma::mat&, bool, const Rcpp::NumericVector&, bool, std::vector<double>&, bool, int, const std::vector<int>&, rnd_t&, int)':
simulate.cpp:148:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  148 |     for (size_t i = 0; i < select_r.nrow(); ++i) {
      |                        ~~^~~~~~~~~~~~~~~~~
In file included from D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/tbb.h:32,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/RcppParallel/TBB.h:10,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/RcppParallel.h:24,
                 from util.h:15,
                 from simulate.cpp:19:
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/tbb_thread.h:251:29:   required from here
  251 |             return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
      |                    ~~~~~~~~~^~~~~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/concurrent_hash_map.h:291:31:   required from here
  291 |                   && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
      |                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include'   -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1   -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c simulate_emp.cpp -o simulate_emp.o
simulate_emp.cpp: In function 'Rcpp::List simulate_emp_cpp(const Rcpp::NumericMatrix&, const Rcpp::NumericVector&, const Rcpp::NumericMatrix&, size_t, size_t, double, bool, bool, const Rcpp::NumericVector&, bool, double, const Rcpp::NumericMatrix&, int, const Rcpp::NumericVector&)':
simulate_emp.cpp:291:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  291 |     for (size_t i = 0; i < select.nrow(); ++i) {
      |                        ~~^~~~~~~~~~~~~~~
simulate_emp.cpp:293:28: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  293 |       for (size_t j = 0; j < select.ncol(); ++j) {
      |                          ~~^~~~~~~~~~~~~~~
In file included from D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/tbb.h:32,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/RcppParallel/TBB.h:10,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/RcppParallel.h:24,
                 from util.h:15,
                 from simulate_emp.cpp:23:
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/tbb_thread.h:251:29:   required from here
  251 |             return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
      |                    ~~~~~~~~~^~~~~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/concurrent_hash_map.h:291:31:   required from here
  291 |                   && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
      |                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include'   -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1   -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c simulate_migration.cpp -o simulate_migration.o
simulate_migration.cpp: In function 'std::vector<std::vector<Fish> > simulate_two_populations(const std::vector<Fish>&, const std::vector<Fish>&, const Rcpp::NumericMatrix&, const Rcpp::NumericVector&, int, double, bool, arma::mat&, bool, const Rcpp::NumericVector&, bool, std::vector<double>&, bool, int, const std::vector<int>&, double, int, rnd_t&)':
simulate_migration.cpp:217:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  217 |   for (size_t i = 0; i < select.nrow(); ++i) {
      |                      ~~^~~~~~~~~~~~~~~
simulate_migration.cpp:219:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  219 |     for (size_t j = 0; j < select.ncol(); ++j) {
      |                        ~~^~~~~~~~~~~~~~~
In file included from D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/tbb.h:32,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/RcppParallel/TBB.h:10,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/RcppParallel.h:24,
                 from util.h:15,
                 from simulate_migration.cpp:22:
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/tbb_thread.h:251:29:   required from here
  251 |             return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
      |                    ~~~~~~~~~^~~~~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/concurrent_hash_map.h:291:31:   required from here
  291 |                   && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
      |                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.6/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppArmadillo/include' -I'D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include'   -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1   -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c simulate_migration_emp.cpp -o simulate_migration_emp.o
simulate_migration_emp.cpp: In function 'Rcpp::List simulate_migration_emp_cpp(const Rcpp::NumericMatrix&, const Rcpp::NumericMatrix&, const Rcpp::NumericVector&, Rcpp::NumericMatrix, const Rcpp::NumericVector&, int, double, bool, bool, const Rcpp::NumericVector&, bool, double, double, const Rcpp::NumericMatrix&, int, const Rcpp::NumericVector&)':
simulate_migration_emp.cpp:436:25: warning: comparison of integer expressions of different signedness: 'int' and '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wsign-compare]
  436 |       for (int j = 0; j < pop_size[1]; ++j) {
In file included from D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/tbb.h:32,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/RcppParallel/TBB.h:10,
                 from D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/RcppParallel.h:24,
                 from util.h:15,
                 from simulate_migration_emp.cpp:19:
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/tbb_thread.h:251:29:   required from here
  251 |             return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
      |                    ~~~~~~~~~^~~~~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic<long unsigned int>&' does not use 'constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)' [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]':
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/concurrent_hash_map.h:291:31:   required from here
  291 |                   && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
      |                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&' does not use 'constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
g++ -std=gnu++17 -shared -s -static-libgcc -o GenomeAdmixR.dll tmp.def Fish.o RcppExports.o helper_functions.o simulate.o simulate_emp.o simulate_migration.o simulate_migration_emp.o -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64 -ltbb -ltbbmalloc -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools45/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR
installing to d:/RCompile/CRANincoming/R-devel/lib/00LOCK-GenomeAdmixR/00new/GenomeAdmixR/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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
* DONE (GenomeAdmixR)