* installing *source* package ‘adapt3’ ...
** this is package ‘adapt3’ version ‘2.0.7’
** package ‘adapt3’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/adapt3/src'
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/lefko3/include' -I/usr/local/include -I../inst/include/ -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/lefko3/include' -I/usr/local/include -I../inst/include/ -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c projection.cpp -o projection.o
g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/lefko3/include' -I/usr/local/include -I../inst/include/ -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c utilities.cpp -o utilities.o
In file included from /data/gannet/ripley/R/test-dev/lefko3/include/LefkoUtils.h:8,
from projection.cpp:10:
/data/gannet/ripley/R/test-dev/lefko3/include/basic_funcs/mat_stuff.h: In function ‘Rcpp::DataFrame LefkoMats::supp_reassess(Rcpp::DataFrame, bool, Rcpp::Nullable<Rcpp::DataFrame_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::DataFrame_Impl<Rcpp::PreserveStorage> >)’:
/data/gannet/ripley/R/test-dev/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;
| ^~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/lefko3/include/LefkoUtils.h:8,
from utilities.cpp:7:
/data/gannet/ripley/R/test-dev/lefko3/include/basic_funcs/mat_stuff.h: In function ‘Rcpp::DataFrame LefkoMats::supp_reassess(Rcpp::DataFrame, bool, Rcpp::Nullable<Rcpp::DataFrame_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::DataFrame_Impl<Rcpp::PreserveStorage> >)’:
/data/gannet/ripley/R/test-dev/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};
| ^~~~~~~~~~
projection.cpp: In function ‘Rcpp::List cleanup3(Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, double, double, int, int, bool, bool, bool)’:
projection.cpp:3808:29: warning: comparison of integer expressions of different signedness: ‘Rcpp::traits::storage_type<13>::type’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare]
3808 | 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, bool)’:
projection.cpp:5188:31: warning: comparison of integer expressions of different signedness: ‘Rcpp::traits::storage_type<13>::type’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare]
5188 | if (year_counter(i) >= no_mainyears || current_time == 0) year_counter(i) = 0;
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
projection.cpp: In function ‘Rcpp::List project3(Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, bool, bool, int, int, int, int, bool, double, double)’:
projection.cpp:5880:8: warning: variable ‘pure_fleslie’ set but not used [-Wunused-but-set-variable]
5880 | bool pure_fleslie {false}; // Are all function-based MPMs Leslie MPMs?
| ^~~~~~~~~~~~
projection.cpp:5885:7: warning: variable ‘stageframe_count’ set but not used [-Wunused-but-set-variable]
5885 | int stageframe_count {0};
| ^~~~~~~~~~~~~~~~
projection.cpp:5886:7: warning: variable ‘stageframe_notNull_count’ set but not used [-Wunused-but-set-variable]
5886 | int stageframe_notNull_count {0};
| ^~~~~~~~~~~~~~~~~~~~~~~~
projection.cpp:5887:7: warning: variable ‘supplement_count’ set but not used [-Wunused-but-set-variable]
5887 | int supplement_count {0};
| ^~~~~~~~~~~~~~~~
projection.cpp:5888:7: warning: variable ‘equivalence_count’ set but not used [-Wunused-but-set-variable]
5888 | int equivalence_count {0};
| ^~~~~~~~~~~~~~~~~
projection.cpp:5889:7: warning: variable ‘start_count’ set but not used [-Wunused-but-set-variable]
5889 | int start_count {0};
| ^~~~~~~~~~~
projection.cpp:5890:7: warning: variable ‘tweights_count’ set but not used [-Wunused-but-set-variable]
5890 | int tweights_count {0};
| ^~~~~~~~~~~~~~
projection.cpp:5891:7: warning: variable ‘density_count’ set but not used [-Wunused-but-set-variable]
5891 | int density_count {0};
| ^~~~~~~~~~~~~
projection.cpp:5892:7: warning: variable ‘entry_time_count’ set but not used [-Wunused-but-set-variable]
5892 | int entry_time_count {0};
| ^~~~~~~~~~~~~~~~
projection.cpp:5893:7: warning: variable ‘density_vr_count’ set but not used [-Wunused-but-set-variable]
5893 | int density_vr_count {0};
| ^~~~~~~~~~~~~~~~
projection.cpp:5894:7: warning: variable ‘sparse_vec_count’ set but not used [-Wunused-but-set-variable]
5894 | int sparse_vec_count {0};
| ^~~~~~~~~~~~~~~~
projection.cpp:5895:7: warning: variable ‘found_fleslie’ set but not used [-Wunused-but-set-variable]
5895 | int found_fleslie {0};
| ^~~~~~~~~~~~~
projection.cpp: In function ‘Rcpp::List batch_project3(Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, bool, bool, int, int, int, int, bool, double, double)’:
projection.cpp:6582:8: warning: unused variable ‘sensitivity_bool’ [-Wunused-variable]
6582 | bool sensitivity_bool {false};
| ^~~~~~~~~~~~~~~~
projection.cpp: In function ‘Rcpp::List cleanup3_inv(Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, double, double, int, unsigned int, unsigned int)’:
projection.cpp:8441:38: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
8441 | for (unsigned int sfi = 0; sfi < min_age_length; sfi++) {
| ~~~~^~~~~~~~~~~~~~~~
projection.cpp:9042:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
9042 | for (int i = 0; i < variant_count; i++) {
| ~~^~~~~~~~~~~~~~~
projection.cpp:9050:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
9050 | if (start_list_length != 1 && start_list_length != variant_count) {
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
projection.cpp:9129:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
9129 | for (int i = 0; i < variant_count; i++) {
| ~~^~~~~~~~~~~~~~~
projection.cpp:9553:28: warning: comparison of integer expressions of different signedness: ‘Rcpp::traits::storage_type<13>::type’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare]
9553 | if (di_age2(j) < finalage_int) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~
projection.cpp:9857:30: warning: comparison of integer expressions of different signedness: ‘Rcpp::traits::storage_type<13>::type’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare]
9857 | if (di_age2(j) < finalage_int) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~
projection.cpp:10002:53: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
10002 | if (entry_time_count != 1 && entry_time_count != var_per_run) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
projection.cpp:10012:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
10012 | for (int i = 0; i < var_per_run; i++) {
| ~~^~~~~~~~~~~~~
projection.cpp:10220:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
10220 | for (int i = 0; i < variant_count; i++) {
| ~~^~~~~~~~~~~~~~~
projection.cpp:10248:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
10248 | for (int i = 0; i < variant_count; i++) {
| ~~^~~~~~~~~~~~~~~
projection.cpp:10272:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
10272 | 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:12220:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
12220 | for (int i = 0; i < total_optima; i++) {
| ~~^~~~~~~~~~~~~~
projection.cpp:12838:18: warning: unused variable ‘res_fitness_test’ [-Wunused-variable]
12838 | double res_fitness_test = current_round_fitness_values(0);
| ^~~~~~~~~~~~~~~~
projection.cpp:12468:12: warning: variable ‘conv_test’ set but not used [-Wunused-but-set-variable]
12468 | double conv_test {0.};
| ^~~~~~~~~
projection.cpp:12470:12: warning: variable ‘xE’ set but not used [-Wunused-but-set-variable]
12470 | double xE {0.}; // test value to keep in memory from previous expansion round
| ^~
projection.cpp:12471:12: warning: variable ‘xC_new’ set but not used [-Wunused-but-set-variable]
12471 | double xC_new {0.}; // test value to keep in memory from previous contraction round
| ^~~~~~
projection.cpp:13030:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
13030 | for (int i = 2; i < total_optima; i++) {
| ~~^~~~~~~~~~~~~~
projection.cpp:13053:7: warning: unused variable ‘optim_rows’ [-Wunused-variable]
13053 | int optim_rows = static_cast<int>(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:14073:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
14073 | for (int i = 0; i < total_optima; i++) {
| ~~^~~~~~~~~~~~~~
projection.cpp:14893:18: warning: unused variable ‘res_fitness_test’ [-Wunused-variable]
14893 | double res_fitness_test = current_round_fitness_values(0);
| ^~~~~~~~~~~~~~~~
projection.cpp:14411:12: warning: variable ‘conv_test’ set but not used [-Wunused-but-set-variable]
14411 | double conv_test {0.};
| ^~~~~~~~~
projection.cpp:14413:12: warning: variable ‘xE’ set but not used [-Wunused-but-set-variable]
14413 | double xE {0.}; // test value to keep in memory from previous expansion round
| ^~
projection.cpp:14414:12: warning: variable ‘xC_new’ set but not used [-Wunused-but-set-variable]
14414 | double xC_new {0.}; // test value to keep in memory from previous contraction round
| ^~~~~~
projection.cpp:15084:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
15084 | for (int i = 2; i < total_optima; i++) {
| ~~^~~~~~~~~~~~~~
projection.cpp:15110:7: warning: unused variable ‘optim_rows’ [-Wunused-variable]
15110 | int optim_rows = static_cast<int>(final_output_df.nrows());
| ^~~~~~~~~~
projection.cpp: In function ‘Rcpp::List invade3(Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, Rcpp::Nullable<Rcpp::RObject_Impl<Rcpp::PreserveStorage> >, int, int, double, int, int, int, double, double, double, int)’:
projection.cpp:20034:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
20034 | if (!(variant_count >= var_per_run)) {
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~
projection.cpp:19851:7: warning: unused variable ‘stageframe_count’ [-Wunused-variable]
19851 | int stageframe_count {0};
| ^~~~~~~~~~~~~~~~
projection.cpp:19852:7: warning: variable ‘stageframe_notNull_count’ set but not used [-Wunused-but-set-variable]
19852 | int stageframe_notNull_count {0};
| ^~~~~~~~~~~~~~~~~~~~~~~~
projection.cpp:19853:7: warning: unused variable ‘supplement_count’ [-Wunused-variable]
19853 | int supplement_count {0};
| ^~~~~~~~~~~~~~~~
projection.cpp:19854:7: warning: variable ‘equivalence_count’ set but not used [-Wunused-but-set-variable]
19854 | int equivalence_count {0};
| ^~~~~~~~~~~~~~~~~
projection.cpp:19855:7: warning: variable ‘start_count’ set but not used [-Wunused-but-set-variable]
19855 | int start_count {0};
| ^~~~~~~~~~~
projection.cpp:19856:7: warning: variable ‘tweights_count’ set but not used [-Wunused-but-set-variable]
19856 | int tweights_count {0};
| ^~~~~~~~~~~~~~
projection.cpp:19857:7: warning: variable ‘density_count’ set but not used [-Wunused-but-set-variable]
19857 | int density_count {0};
| ^~~~~~~~~~~~~
projection.cpp:19859:7: warning: variable ‘entry_time_count’ set but not used [-Wunused-but-set-variable]
19859 | int entry_time_count {0};
| ^~~~~~~~~~~~~~~~
projection.cpp:19860:7: warning: variable ‘density_vr_count’ set but not used [-Wunused-but-set-variable]
19860 | int density_vr_count {0};
| ^~~~~~~~~~~~~~~~
projection.cpp:19861:7: warning: variable ‘sparse_vec_count’ set but not used [-Wunused-but-set-variable]
19861 | int sparse_vec_count {0};
| ^~~~~~~~~~~~~~~~
projection.cpp:19873:8: warning: variable ‘prebreeding_bool’ set but not used [-Wunused-but-set-variable]
19873 | bool prebreeding_bool {true};
| ^~~~~~~~~~~~~~~~
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++20 -shared -L/usr/local/lib64 -o adapt3.so RcppExports.o projection.o utilities.o -fopenmp -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/adapt3/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/adapt3/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/adapt3/src'
installing to /data/gannet/ripley/R/packages/tests-devel/adapt3.Rcheck/00LOCK-adapt3/00new/adapt3/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (adapt3)