* installing *source* package 'simRestore' ...
** using staged installation
** libs
using C++ compiler: 'g++.exe (GCC) 12.3.0'
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include'   -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"     -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/4.4/Rcpp/include'   -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c main_functions.cpp -o main_functions.o
In file included from ./analysis.h:21,
                 from main_functions.cpp:20:
./util.h: In function 'void numericmatrix_to_vector(Rcpp::NumericMatrix*, std::vector<std::vector<double> >*)':
./util.h:35:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   35 |   for (size_t i = 0; i < (*m).nrow(); ++i) {
      |                      ~~^~~~~~~~~~~~~
./util.h:37:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
   37 |     for (size_t j = 0; j < (*m).ncol(); ++j) {
      |                        ~~^~~~~~~~~~~~~
main_functions.cpp: In function 'Rcpp::List simulate_complete(int, float, float, Rcpp::NumericVector, Rcpp::NumericVector, int, int, int, std::vector<double>, Rcpp::NumericVector, double, int, int, int, bool, bool, double, double, double, double, double, double, double, double, double, double, double, bool, double, bool)':
main_functions.cpp:165:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<double> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  165 |     for (int i = 0; i < results.size(); ++i) {
      |                     ~~^~~~~~~~~~~~~~~~
./analysis.h: In instantiation of 'output_data analysis<ANIMAL>::simulate_policy(const std::vector<_RealType>&) [with ANIMAL = organism_simple]':
./analysis.h:232:30:   required from 'output_data analysis<ANIMAL>::do_analysis() [with ANIMAL = organism_simple]'
main_functions.cpp:109:59:   required from here
./analysis.h:278:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<organism_simple>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  278 |     for (int i = num_females; i < base_pop.size(); ++i) {
      |                               ~~^~~~~~~~~~~~~~~~~
./analysis.h: In instantiation of 'output_data analysis<ANIMAL>::simulate_policy(const std::vector<_RealType>&) [with ANIMAL = organism]':
./analysis.h:232:30:   required from 'output_data analysis<ANIMAL>::do_analysis() [with ANIMAL = organism]'
main_functions.cpp:141:59:   required from here
./analysis.h:278:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<organism>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
./analysis.h: In instantiation of 'std::vector<_RealType> analysis<ANIMAL>::admix() [with ANIMAL = organism_simple]':
./analysis.h:629:12:   required from 'std::vector<organism_simple> analysis<ANIMAL>::create_base_pop(tag<organism_simple>) [with ANIMAL = organism_simple]'
./analysis.h:230:53:   required from 'output_data analysis<ANIMAL>::do_analysis() [with ANIMAL = organism_simple]'
main_functions.cpp:109:59:   required from here
./analysis.h:696:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  696 |     for (size_t t = 0; t < params.number_of_generations; ++t) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./analysis.h:698:28: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
  698 |       for (size_t i = 0; i < params.pop_size; ++i) {
      |                          ~~^~~~~~~~~~~~~~~~~
./analysis.h: In instantiation of 'void analysis<ANIMAL>::update_start_season(std::vector<_RealType>*, double, int, int) [with ANIMAL = organism_simple]':
./analysis.h:445:5:   required from 'void analysis<ANIMAL>::update_pop(std::vector<_RealType>*, std::vector<_RealType>*, int, int) [with ANIMAL = organism_simple]'
./analysis.h:292:7:   required from 'output_data analysis<ANIMAL>::simulate_policy(const std::vector<_RealType>&) [with ANIMAL = organism_simple]'
./analysis.h:232:30:   required from 'output_data analysis<ANIMAL>::do_analysis() [with ANIMAL = organism_simple]'
main_functions.cpp:109:59:   required from here
./analysis.h:570:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<organism_simple>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  570 |       if (number_removed >= (*input_pop).size()) {
      |           ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
./analysis.h: In instantiation of 'void analysis<ANIMAL>::mate_random(std::vector<_RealType>*, std::vector<_RealType>*, std::vector<_RealType>*, std::vector<_RealType>*, double) [with ANIMAL = organism_simple]':
./analysis.h:466:7:   required from 'void analysis<ANIMAL>::update_pop(std::vector<_RealType>*, std::vector<_RealType>*, int, int) [with ANIMAL = organism_simple]'
./analysis.h:292:7:   required from 'output_data analysis<ANIMAL>::simulate_policy(const std::vector<_RealType>&) [with ANIMAL = organism_simple]'
./analysis.h:232:30:   required from 'output_data analysis<ANIMAL>::do_analysis() [with ANIMAL = organism_simple]'
main_functions.cpp:109:59:   required from here
./analysis.h:400:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<organism_simple>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  400 |     for (int i = 0; i < (*females).size(); ++i) {
      |                     ~~^~~~~~~~~~~~~~~~~~~
./analysis.h: In instantiation of 'void analysis<ANIMAL>::mate_bonded(std::vector<_RealType>*, std::vector<_RealType>*, std::vector<_RealType>*, std::vector<_RealType>*, double) [with ANIMAL = organism_simple]':
./analysis.h:472:7:   required from 'void analysis<ANIMAL>::update_pop(std::vector<_RealType>*, std::vector<_RealType>*, int, int) [with ANIMAL = organism_simple]'
./analysis.h:292:7:   required from 'output_data analysis<ANIMAL>::simulate_policy(const std::vector<_RealType>&) [with ANIMAL = organism_simple]'
./analysis.h:232:30:   required from 'output_data analysis<ANIMAL>::do_analysis() [with ANIMAL = organism_simple]'
main_functions.cpp:109:59:   required from here
./analysis.h:362:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<organism_simple>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  362 |          i < (*females).size() && j < (*males).size();
      |          ~~^~~~~~~~~~~~~~~~~~~
./analysis.h:362:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<organism_simple>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  362 |          i < (*females).size() && j < (*males).size();
      |                                   ~~^~~~~~~~~~~~~~~~~
./analysis.h: In instantiation of 'void analysis<ANIMAL>::update_start_season(std::vector<_RealType>*, double, int, int) [with ANIMAL = organism]':
./analysis.h:445:5:   required from 'void analysis<ANIMAL>::update_pop(std::vector<_RealType>*, std::vector<_RealType>*, int, int) [with ANIMAL = organism]'
./analysis.h:292:7:   required from 'output_data analysis<ANIMAL>::simulate_policy(const std::vector<_RealType>&) [with ANIMAL = organism]'
./analysis.h:232:30:   required from 'output_data analysis<ANIMAL>::do_analysis() [with ANIMAL = organism]'
main_functions.cpp:141:59:   required from here
./analysis.h:570:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<organism>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  570 |       if (number_removed >= (*input_pop).size()) {
      |           ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
./analysis.h: In instantiation of 'void analysis<ANIMAL>::mate_random(std::vector<_RealType>*, std::vector<_RealType>*, std::vector<_RealType>*, std::vector<_RealType>*, double) [with ANIMAL = organism]':
./analysis.h:466:7:   required from 'void analysis<ANIMAL>::update_pop(std::vector<_RealType>*, std::vector<_RealType>*, int, int) [with ANIMAL = organism]'
./analysis.h:292:7:   required from 'output_data analysis<ANIMAL>::simulate_policy(const std::vector<_RealType>&) [with ANIMAL = organism]'
./analysis.h:232:30:   required from 'output_data analysis<ANIMAL>::do_analysis() [with ANIMAL = organism]'
main_functions.cpp:141:59:   required from here
./analysis.h:400:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<organism>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  400 |     for (int i = 0; i < (*females).size(); ++i) {
      |                     ~~^~~~~~~~~~~~~~~~~~~
./analysis.h: In instantiation of 'void analysis<ANIMAL>::mate_bonded(std::vector<_RealType>*, std::vector<_RealType>*, std::vector<_RealType>*, std::vector<_RealType>*, double) [with ANIMAL = organism]':
./analysis.h:472:7:   required from 'void analysis<ANIMAL>::update_pop(std::vector<_RealType>*, std::vector<_RealType>*, int, int) [with ANIMAL = organism]'
./analysis.h:292:7:   required from 'output_data analysis<ANIMAL>::simulate_policy(const std::vector<_RealType>&) [with ANIMAL = organism]'
./analysis.h:232:30:   required from 'output_data analysis<ANIMAL>::do_analysis() [with ANIMAL = organism]'
main_functions.cpp:141:59:   required from here
./analysis.h:362:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<organism>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  362 |          i < (*females).size() && j < (*males).size();
      |          ~~^~~~~~~~~~~~~~~~~~~
./analysis.h:362:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<organism>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  362 |          i < (*females).size() && j < (*males).size();
      |                                   ~~^~~~~~~~~~~~~~~~~
./analysis.h: In instantiation of 'void analysis<ANIMAL>::old_age(std::vector<_RealType>*) [with ANIMAL = organism_simple]':
./analysis.h:561:5:   required from 'void analysis<ANIMAL>::update_start_season(std::vector<_RealType>*, double, int, int) [with ANIMAL = organism_simple]'
./analysis.h:445:5:   required from 'void analysis<ANIMAL>::update_pop(std::vector<_RealType>*, std::vector<_RealType>*, int, int) [with ANIMAL = organism_simple]'
./analysis.h:292:7:   required from 'output_data analysis<ANIMAL>::simulate_policy(const std::vector<_RealType>&) [with ANIMAL = organism_simple]'
./analysis.h:232:30:   required from 'output_data analysis<ANIMAL>::do_analysis() [with ANIMAL = organism_simple]'
main_functions.cpp:109:59:   required from here
./analysis.h:546:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<organism_simple>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  546 |     for (int i = 0; i < (*pop).size(); ++i) {
      |                     ~~^~~~~~~~~~~~~~~
./analysis.h: In instantiation of 'void analysis<ANIMAL>::additional_death(std::vector<_RealType>*, double, int) [with ANIMAL = organism_simple]':
./analysis.h:564:5:   required from 'void analysis<ANIMAL>::update_start_season(std::vector<_RealType>*, double, int, int) [with ANIMAL = organism_simple]'
./analysis.h:445:5:   required from 'void analysis<ANIMAL>::update_pop(std::vector<_RealType>*, std::vector<_RealType>*, int, int) [with ANIMAL = organism_simple]'
./analysis.h:292:7:   required from 'output_data analysis<ANIMAL>::simulate_policy(const std::vector<_RealType>&) [with ANIMAL = organism_simple]'
./analysis.h:232:30:   required from 'output_data analysis<ANIMAL>::do_analysis() [with ANIMAL = organism_simple]'
main_functions.cpp:109:59:   required from here
./analysis.h:337:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<organism_simple>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  337 |     if (max_num > (*ANIMALs).size()) max_num = (*ANIMALs).size();
      |         ~~~~~~~~^~~~~~~~~~~~~~~~~~~
./analysis.h: In instantiation of 'void analysis<ANIMAL>::old_age(std::vector<_RealType>*) [with ANIMAL = organism]':
./analysis.h:561:5:   required from 'void analysis<ANIMAL>::update_start_season(std::vector<_RealType>*, double, int, int) [with ANIMAL = organism]'
./analysis.h:445:5:   required from 'void analysis<ANIMAL>::update_pop(std::vector<_RealType>*, std::vector<_RealType>*, int, int) [with ANIMAL = organism]'
./analysis.h:292:7:   required from 'output_data analysis<ANIMAL>::simulate_policy(const std::vector<_RealType>&) [with ANIMAL = organism]'
./analysis.h:232:30:   required from 'output_data analysis<ANIMAL>::do_analysis() [with ANIMAL = organism]'
main_functions.cpp:141:59:   required from here
./analysis.h:546:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<organism>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  546 |     for (int i = 0; i < (*pop).size(); ++i) {
      |                     ~~^~~~~~~~~~~~~~~
./analysis.h: In instantiation of 'void analysis<ANIMAL>::additional_death(std::vector<_RealType>*, double, int) [with ANIMAL = organism]':
./analysis.h:564:5:   required from 'void analysis<ANIMAL>::update_start_season(std::vector<_RealType>*, double, int, int) [with ANIMAL = organism]'
./analysis.h:445:5:   required from 'void analysis<ANIMAL>::update_pop(std::vector<_RealType>*, std::vector<_RealType>*, int, int) [with ANIMAL = organism]'
./analysis.h:292:7:   required from 'output_data analysis<ANIMAL>::simulate_policy(const std::vector<_RealType>&) [with ANIMAL = organism]'
./analysis.h:232:30:   required from 'output_data analysis<ANIMAL>::do_analysis() [with ANIMAL = organism]'
main_functions.cpp:141:59:   required from here
./analysis.h:337:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<organism>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  337 |     if (max_num > (*ANIMALs).size()) max_num = (*ANIMALs).size();
      |         ~~~~~~~~^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17  -I"D:/RCompile/recent/R/include" -DNDEBUG  -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include'   -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"     -pedantic -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c organism.cpp -o organism.o
organism.cpp: In member function 'std::vector<std::vector<double> > organism::get_genomic_info(int, int, int) const':
organism.cpp:341:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<junction> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  341 |   for (int i = 0; i < chromosome1.size(); ++i) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~
organism.cpp:354:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<junction> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  354 |   for (int i = 0; i < chromosome2.size(); ++i) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -s -static-libgcc -o simRestore.dll tmp.def RcppExports.o main_functions.o organism.o -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R/bin/x64 -lR
installing to d:/RCompile/CRANincoming/R-devel/lib/00LOCK-simRestore/00new/simRestore/libs/x64
** R
** 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 (simRestore)