* installing *source* package 'adapt3' ... ** this is package 'adapt3' version '2.0.0' ** using staged installation ** libs using C++ compiler: 'g++.exe (GCC) 14.3.0' g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/BH/include' -I'D:/RCompile/CRANpkg/lib/4.6/lefko3/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -I../inst/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 -DARMA_64BIT_WORD=1 -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/BH/include' -I'D:/RCompile/CRANpkg/lib/4.6/lefko3/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -I../inst/include/ -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c projection.cpp -o projection.o In file included from D:/RCompile/CRANpkg/lib/4.6/lefko3/include/LefkoUtils.h:8, from projection.cpp:10: D:/RCompile/CRANpkg/lib/4.6/lefko3/include/basic_funcs/mat_stuff.h: In function 'Rcpp::DataFrame LefkoMats::supp_reassess(Rcpp::DataFrame, bool, Rcpp::Nullable >, Rcpp::Nullable >)': D:/RCompile/CRANpkg/lib/4.6/lefko3/include/basic_funcs/mat_stuff.h:1672:12: warning: variable 'esta2_used' set but not used [-Wunused-but-set-variable] 1672 | bool esta2_used {false}; | ^~~~~~~~~~ In file included from ../inst/include/AdaptUtils.h:8, from projection.cpp:11: ../inst/include/basic_funcs/mats_utils.h: In function 'Rcpp::List AdaptMats::theoldpizzle_adapt3(const Rcpp::DataFrame&, const Rcpp::DataFrame&, const arma::mat&, int, int, int, int, int, int, bool)': ../inst/include/basic_funcs/mats_utils.h:3699:9: warning: unused variable 'nostages_nounborn' [-Wunused-variable] 3699 | int nostages_nounborn = nostages - almostbornstages; | ^~~~~~~~~~~~~~~~~ projection.cpp: In function 'Rcpp::List cleanup3(Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, double, double, int, int, bool, bool, bool)': projection.cpp:3804:29: warning: comparison of integer expressions of different signedness: 'Rcpp::traits::storage_type<13>::type' {aka 'int'} and 'unsigned int' [-Wsign-compare] 3804 | if (year_counter(i) == no_mainyears || j == 0) year_counter(i) = 0; | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ projection.cpp: In function 'void project3_fb_core(Rcpp::NumericMatrix&, Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::LogicalVector, Rcpp::CharacterVector, int, int, int, int, double, double, bool, bool, bool, bool, bool)': projection.cpp:5161:31: warning: comparison of integer expressions of different signedness: 'Rcpp::traits::storage_type<13>::type' {aka 'int'} and 'unsigned int' [-Wsign-compare] 5161 | if (year_counter(i) >= no_mainyears || current_time == 0) year_counter(i) = 0; | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ projection.cpp: In function 'Rcpp::List project3(Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, bool, bool, int, int, int, int, bool, double, double)': projection.cpp:5851:8: warning: variable 'pure_fleslie' set but not used [-Wunused-but-set-variable] 5851 | bool pure_fleslie {false}; // Are all function-based MPMs Leslie MPMs? | ^~~~~~~~~~~~ projection.cpp:5856:7: warning: variable 'stageframe_count' set but not used [-Wunused-but-set-variable] 5856 | int stageframe_count {0}; | ^~~~~~~~~~~~~~~~ projection.cpp:5857:7: warning: variable 'stageframe_notNull_count' set but not used [-Wunused-but-set-variable] 5857 | int stageframe_notNull_count {0}; | ^~~~~~~~~~~~~~~~~~~~~~~~ projection.cpp:5858:7: warning: variable 'supplement_count' set but not used [-Wunused-but-set-variable] 5858 | int supplement_count {0}; | ^~~~~~~~~~~~~~~~ projection.cpp:5859:7: warning: variable 'equivalence_count' set but not used [-Wunused-but-set-variable] 5859 | int equivalence_count {0}; | ^~~~~~~~~~~~~~~~~ projection.cpp:5860:7: warning: variable 'start_count' set but not used [-Wunused-but-set-variable] 5860 | int start_count {0}; | ^~~~~~~~~~~ projection.cpp:5861:7: warning: variable 'tweights_count' set but not used [-Wunused-but-set-variable] 5861 | int tweights_count {0}; | ^~~~~~~~~~~~~~ projection.cpp:5862:7: warning: variable 'density_count' set but not used [-Wunused-but-set-variable] 5862 | int density_count {0}; | ^~~~~~~~~~~~~ projection.cpp:5863:7: warning: variable 'entry_time_count' set but not used [-Wunused-but-set-variable] 5863 | int entry_time_count {0}; | ^~~~~~~~~~~~~~~~ projection.cpp:5864:7: warning: variable 'density_vr_count' set but not used [-Wunused-but-set-variable] 5864 | int density_vr_count {0}; | ^~~~~~~~~~~~~~~~ projection.cpp:5865:7: warning: variable 'sparse_vec_count' set but not used [-Wunused-but-set-variable] 5865 | int sparse_vec_count {0}; | ^~~~~~~~~~~~~~~~ projection.cpp:5866:7: warning: variable 'found_fleslie' set but not used [-Wunused-but-set-variable] 5866 | int found_fleslie {0}; | ^~~~~~~~~~~~~ projection.cpp: In function 'Rcpp::List batch_project3(Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, bool, bool, int, int, int, int, bool, double, double)': projection.cpp:6547:8: warning: unused variable 'sensitivity_bool' [-Wunused-variable] 6547 | bool sensitivity_bool {false}; | ^~~~~~~~~~~~~~~~ projection.cpp: In function 'Rcpp::List cleanup3_inv(Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, double, double, int, unsigned int, unsigned int)': projection.cpp:8404:38: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 8404 | for (unsigned int sfi = 0; sfi < min_age_length; sfi++) { | ~~~~^~~~~~~~~~~~~~~~ projection.cpp:9005:25: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 9005 | for (int i = 0; i < variant_count; i++) { | ~~^~~~~~~~~~~~~~~ projection.cpp:9013:55: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 9013 | if (start_list_length != 1 && start_list_length != variant_count) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ projection.cpp:9092:23: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 9092 | for (int i = 0; i < variant_count; i++) { | ~~^~~~~~~~~~~~~~~ projection.cpp:9516:28: warning: comparison of integer expressions of different signedness: 'Rcpp::traits::storage_type<13>::type' {aka 'int'} and 'unsigned int' [-Wsign-compare] 9516 | if (di_age2(j) < finalage_int) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ projection.cpp:9820:30: warning: comparison of integer expressions of different signedness: 'Rcpp::traits::storage_type<13>::type' {aka 'int'} and 'unsigned int' [-Wsign-compare] 9820 | if (di_age2(j) < finalage_int) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ projection.cpp:9965:53: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 9965 | if (entry_time_count != 1 && entry_time_count != var_per_run) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ projection.cpp:9975:25: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 9975 | for (int i = 0; i < var_per_run; i++) { | ~~^~~~~~~~~~~~~ projection.cpp:10183:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 10183 | for (int i = 0; i < variant_count; i++) { | ~~^~~~~~~~~~~~~~~ projection.cpp:10211:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 10211 | for (int i = 0; i < variant_count; i++) { | ~~^~~~~~~~~~~~~~~ projection.cpp:10235:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 10235 | for (int i = 0; i < variant_count; i++) { | ~~^~~~~~~~~~~~~~~ projection.cpp: In function 'void ESS_optimizer_pre(Rcpp::DataFrame&, Rcpp::DataFrame&, Rcpp::DataFrame&, Rcpp::DataFrame&, Rcpp::IntegerVector&, Rcpp::IntegerVector&, Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::IntegerVector, int, int, int, int, int, int, int, double, double, bool, bool, bool, bool, bool, double, int, int, int, int, int, int, double, bool)': projection.cpp:12183:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 12183 | for (int i = 0; i < total_optima; i++) { | ~~^~~~~~~~~~~~~~ projection.cpp:12801:18: warning: unused variable 'res_fitness_test' [-Wunused-variable] 12801 | double res_fitness_test = current_round_fitness_values(0); | ^~~~~~~~~~~~~~~~ projection.cpp:12431:12: warning: variable 'conv_test' set but not used [-Wunused-but-set-variable] 12431 | double conv_test {0.}; | ^~~~~~~~~ projection.cpp:12433:12: warning: variable 'xE' set but not used [-Wunused-but-set-variable] 12433 | double xE {0.}; // test value to keep in memory from previous expansion round | ^~ projection.cpp:12434:12: warning: variable 'xC_new' set but not used [-Wunused-but-set-variable] 12434 | double xC_new {0.}; // test value to keep in memory from previous contraction round | ^~~~~~ projection.cpp:12993:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 12993 | for (int i = 2; i < total_optima; i++) { | ~~^~~~~~~~~~~~~~ projection.cpp:13016:7: warning: unused variable 'optim_rows' [-Wunused-variable] 13016 | int optim_rows = static_cast(final_output_df.nrows()); | ^~~~~~~~~~ projection.cpp: In function 'void ESS_optimizer_fb(Rcpp::DataFrame&, Rcpp::DataFrame&, Rcpp::DataFrame&, Rcpp::DataFrame&, Rcpp::IntegerVector&, Rcpp::IntegerVector&, arma::vec&, arma::vec&, arma::vec&, arma::vec&, arma::vec&, arma::vec&, arma::vec&, arma::vec&, arma::vec&, arma::vec&, arma::vec&, arma::vec&, arma::vec&, arma::vec&, arma::vec&, arma::vec&, arma::vec&, arma::ivec&, Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List&, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List&, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::DataFrame, Rcpp::DataFrame&, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::DataFrame, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::CharacterVector, Rcpp::CharacterVector, int, int, int, int, int, int, int, int, double, double, bool, bool, bool, bool, bool, double, int, int, int, int, int, int, bool, double, bool)': projection.cpp:14036:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 14036 | for (int i = 0; i < total_optima; i++) { | ~~^~~~~~~~~~~~~~ projection.cpp:14856:18: warning: unused variable 'res_fitness_test' [-Wunused-variable] 14856 | double res_fitness_test = current_round_fitness_values(0); | ^~~~~~~~~~~~~~~~ projection.cpp:14374:12: warning: variable 'conv_test' set but not used [-Wunused-but-set-variable] 14374 | double conv_test {0.}; | ^~~~~~~~~ projection.cpp:14376:12: warning: variable 'xE' set but not used [-Wunused-but-set-variable] 14376 | double xE {0.}; // test value to keep in memory from previous expansion round | ^~ projection.cpp:14377:12: warning: variable 'xC_new' set but not used [-Wunused-but-set-variable] 14377 | double xC_new {0.}; // test value to keep in memory from previous contraction round | ^~~~~~ projection.cpp:15047:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 15047 | for (int i = 2; i < total_optima; i++) { | ~~^~~~~~~~~~~~~~ projection.cpp:15073:7: warning: unused variable 'optim_rows' [-Wunused-variable] 15073 | int optim_rows = static_cast(final_output_df.nrows()); | ^~~~~~~~~~ projection.cpp: In function 'Rcpp::List invade3(Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, Rcpp::Nullable >, int, int, double, int, int, int, double, double, double, int)': projection.cpp:19953:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 19953 | if (!(variant_count >= var_per_run)) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ projection.cpp:19778:7: warning: unused variable 'stageframe_count' [-Wunused-variable] 19778 | int stageframe_count {0}; | ^~~~~~~~~~~~~~~~ projection.cpp:19779:7: warning: variable 'stageframe_notNull_count' set but not used [-Wunused-but-set-variable] 19779 | int stageframe_notNull_count {0}; | ^~~~~~~~~~~~~~~~~~~~~~~~ projection.cpp:19780:7: warning: unused variable 'supplement_count' [-Wunused-variable] 19780 | int supplement_count {0}; | ^~~~~~~~~~~~~~~~ projection.cpp:19781:7: warning: variable 'equivalence_count' set but not used [-Wunused-but-set-variable] 19781 | int equivalence_count {0}; | ^~~~~~~~~~~~~~~~~ projection.cpp:19782:7: warning: variable 'start_count' set but not used [-Wunused-but-set-variable] 19782 | int start_count {0}; | ^~~~~~~~~~~ projection.cpp:19783:7: warning: variable 'tweights_count' set but not used [-Wunused-but-set-variable] 19783 | int tweights_count {0}; | ^~~~~~~~~~~~~~ projection.cpp:19784:7: warning: variable 'density_count' set but not used [-Wunused-but-set-variable] 19784 | int density_count {0}; | ^~~~~~~~~~~~~ projection.cpp:19786:7: warning: variable 'entry_time_count' set but not used [-Wunused-but-set-variable] 19786 | int entry_time_count {0}; | ^~~~~~~~~~~~~~~~ projection.cpp:19787:7: warning: variable 'density_vr_count' set but not used [-Wunused-but-set-variable] 19787 | int density_vr_count {0}; | ^~~~~~~~~~~~~~~~ projection.cpp:19788:7: warning: variable 'sparse_vec_count' set but not used [-Wunused-but-set-variable] 19788 | int sparse_vec_count {0}; | ^~~~~~~~~~~~~~~~ projection.cpp:19800:8: warning: variable 'prebreeding_bool' set but not used [-Wunused-but-set-variable] 19800 | bool prebreeding_bool {true}; | ^~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/BH/include' -I'D:/RCompile/CRANpkg/lib/4.6/lefko3/include' -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -I../inst/include/ -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utilities.cpp -o utilities.o In file included from D:/RCompile/CRANpkg/lib/4.6/lefko3/include/LefkoUtils.h:8, from utilities.cpp:7: D:/RCompile/CRANpkg/lib/4.6/lefko3/include/basic_funcs/mat_stuff.h: In function 'Rcpp::DataFrame LefkoMats::supp_reassess(Rcpp::DataFrame, bool, Rcpp::Nullable >, Rcpp::Nullable >)': D:/RCompile/CRANpkg/lib/4.6/lefko3/include/basic_funcs/mat_stuff.h:1672:12: warning: variable 'esta2_used' set but not used [-Wunused-but-set-variable] 1672 | bool esta2_used {false}; | ^~~~~~~~~~ In file included from ../inst/include/AdaptUtils.h:8, from utilities.cpp:8: ../inst/include/basic_funcs/mats_utils.h: In function 'Rcpp::List AdaptMats::theoldpizzle_adapt3(const Rcpp::DataFrame&, const Rcpp::DataFrame&, const arma::mat&, int, int, int, int, int, int, bool)': ../inst/include/basic_funcs/mats_utils.h:3699:9: warning: unused variable 'nostages_nounborn' [-Wunused-variable] 3699 | int nostages_nounborn = nostages - almostbornstages; | ^~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -shared -s -static-libgcc -o adapt3.dll tmp.def RcppExports.o projection.o utilities.o -fopenmp -LD:/RCompile/recent/R/bin/x64 -lRlapack -LD:/RCompile/recent/R/bin/x64 -lRblas -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/bin/x64 -lR installing to d:/RCompile/CRANincoming/R-devel/lib/00LOCK-adapt3/00new/adapt3/libs/x64 ** R ** data *** moving datasets to lazyload DB ** 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 (adapt3)