* installing *source* package ‘Colossus’ ... ** this is package ‘Colossus’ version ‘1.3.0’ ** package ‘Colossus’ 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/Colossus/src' g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/testthat/include' -I/usr/local/include -fopenmp -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 Calc_Repeated.cpp -o Calc_Repeated.o Calc_Repeated.cpp: In function ‘void Make_Match(Rcpp::List&, const Eigen::MatrixXd&, Rcpp::IntegerMatrix&, std::vector<std::vector<int> >&, std::vector<std::vector<double> >&, std::vector<std::vector<std::vector<double> > >&, std::vector<std::vector<std::vector<double> > >&, std::vector<double>&, std::vector<int>&, const int&)’: Calc_Repeated.cpp:361:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 361 | for (int i=0; i< Recur_First[0].size(); i++){ | ~^~~~~~~~~~~~~~~~~~~~~~~ Calc_Repeated.cpp:365:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 365 | for (int i=0; i< Recur_Second[0].size(); i++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~ Calc_Repeated.cpp: In function ‘void Make_Match_Strata(Rcpp::List&, const Eigen::MatrixXd&, Rcpp::IntegerMatrix&, std::vector<std::vector<int> >&, std::vector<std::vector<double> >&, std::vector<std::vector<std::vector<double> > >&, std::vector<std::vector<std::vector<double> > >&, std::vector<double>&, std::vector<int>&, const int&, Rcpp::NumericVector&)’: Calc_Repeated.cpp:496:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 496 | for (int i=0; i< Recur_First[s_ij].size(); i++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~~ Calc_Repeated.cpp:558:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 558 | for (int i=0; i< Recur_First[s_ij].size(); i++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~~ Calc_Repeated.cpp:561:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 561 | for (int i=0; i< Recur_Second[s_ij].size(); i++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ Calc_Repeated.cpp: In function ‘void Make_Match_Time(Rcpp::List&, const int&, const Eigen::MatrixXd&, Rcpp::IntegerMatrix&, std::vector<std::vector<int> >&, std::vector<std::vector<double> >&, std::vector<std::vector<std::vector<double> > >&, std::vector<std::vector<std::vector<double> > >&, std::vector<double>&, std::vector<int>&, const int&, Rcpp::NumericVector&)’: Calc_Repeated.cpp:684:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 684 | for (int i=0; i< Recur_First[ijk].size(); i++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~ Calc_Repeated.cpp:737:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 737 | for (int i=0; i< Recur_First[ijk].size(); i++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~ Calc_Repeated.cpp:740:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 740 | for (int i=0; i< Recur_Second[ijk].size(); i++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~~ Calc_Repeated.cpp: In function ‘void Make_Match_Time_Strata(Rcpp::List&, const int&, const Eigen::MatrixXd&, Rcpp::IntegerMatrix&, std::vector<std::vector<int> >&, std::vector<std::vector<double> >&, std::vector<std::vector<std::vector<double> > >&, std::vector<std::vector<std::vector<double> > >&, std::vector<double>&, std::vector<int>&, const int&, Rcpp::NumericVector&, Rcpp::NumericVector&)’: Calc_Repeated.cpp:876:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 876 | for (int i=0; i< Recur_First[s_ij*ntime+ijk].size(); i++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Calc_Repeated.cpp:941:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 941 | for (int i=0; i< Recur_First[s_ij*ntime+ijk].size(); i++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Calc_Repeated.cpp:944:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 944 | for (int i=0; i< Recur_Second[s_ij*ntime+ijk].size(); i++){ | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Calc_Repeated.cpp: In function ‘void Calc_Recur_LogLik(Rcpp::List&, const int&, const Rcpp::IntegerMatrix&, const std::vector<std::vector<int> >&, const int&, const int&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, const Eigen::MatrixXd&, double&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<std::vector<double> >&, std::vector<std::vector<std::vector<double> > >&, std::vector<std::vector<std::vector<double> > >&, std::vector<double>&, const int&, const Rcpp::IntegerVector&, std::vector<int>&, std::vector<double>&, std::vector<double>&, std::vector<double>&)’: Calc_Repeated.cpp:3365:9: warning: variable ‘reqrdcond’ set but not used [-Wunused-but-set-variable] 3365 | int reqrdcond = 1; | ^~~~~~~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/testthat/include' -I/usr/local/include -fopenmp -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 Main_Functions.cpp -o Main_Functions.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/testthat/include' -I/usr/local/include -fopenmp -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 Omnibus_Pieces.cpp -o Omnibus_Pieces.o Main_Functions.cpp: In function ‘Rcpp::List LogLik_Cox_PH_Omnibus_Log_Bound(Rcpp::IntegerVector, Rcpp::StringVector, Rcpp::NumericVector, Rcpp::NumericMatrix&, Rcpp::IntegerVector, int, std::string, double, Rcpp::NumericVector, int, int, double, double, double, double, Rcpp::NumericMatrix, Rcpp::NumericVector, int, Rcpp::IntegerVector, int, std::string, int, Rcpp::NumericVector&, const Eigen::VectorXd&, Rcpp::List, double, Rcpp::IntegerVector, Eigen::MatrixXd, Eigen::VectorXd, double, int, int, double)’: Main_Functions.cpp:1274:15: warning: unused variable ‘mat_row’ [-Wunused-variable] 1274 | const int mat_row = df0.rows(); | ^~~~~~~ Main_Functions.cpp: In function ‘Rcpp::List LogLik_Cox_PH_Multidose_Omnibus_Serial(Rcpp::IntegerVector, Rcpp::StringVector, Rcpp::NumericVector, Rcpp::NumericMatrix&, Rcpp::NumericMatrix&, Rcpp::IntegerMatrix, Rcpp::IntegerVector, Rcpp::IntegerVector, int, std::string, double, Rcpp::List, int, int, double, double, double, double, Rcpp::NumericMatrix, Rcpp::NumericVector, int, int, Rcpp::IntegerVector, int, std::string, int, Rcpp::NumericVector&, const Eigen::VectorXd&, Rcpp::List, double, Rcpp::IntegerVector, Eigen::MatrixXd, Eigen::VectorXd)’: Main_Functions.cpp:3831:10: warning: unused variable ‘start’ [-Wunused-variable] 3831 | auto start = time_point_cast<microseconds>(start_point).time_since_epoch().count(); | ^~~~~ Main_Functions.cpp:3833:10: warning: unused variable ‘ending’ [-Wunused-variable] 3833 | auto ending = time_point_cast<microseconds>(end_point).time_since_epoch().count(); // the time duration is tracked | ^~~~~~ Main_Functions.cpp: In function ‘Rcpp::List LogLik_CaseCon_Omnibus(Rcpp::IntegerVector, Rcpp::StringVector, Rcpp::NumericMatrix&, Rcpp::NumericMatrix&, Rcpp::IntegerVector, int, std::string, double, Rcpp::List, Rcpp::NumericVector, int, int, double, double, double, double, Rcpp::NumericMatrix, Rcpp::NumericVector, int, int, Rcpp::IntegerVector, int, std::string, int, Rcpp::NumericVector&, Rcpp::List, double, Rcpp::IntegerVector, Eigen::MatrixXd, Eigen::VectorXd)’: Main_Functions.cpp:6257:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6257 | for (int i = 0; i < strata_odds.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~ Main_Functions.cpp:6184:12: warning: unused variable ‘Lstar’ [-Wunused-variable] 6184 | double Lstar = 0.0; | ^~~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/testthat/include' -I/usr/local/include -fopenmp -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 Plot_Extensions.cpp -o Plot_Extensions.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/testthat/include' -I/usr/local/include -fopenmp -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 R_Interface.cpp -o R_Interface.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/testthat/include' -I/usr/local/include -fopenmp -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 R_Interface.cpp: In function ‘Rcpp::List pois_Omnibus_CurveSearch_transition(Rcpp::NumericMatrix, Rcpp::IntegerVector, Rcpp::StringVector, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::NumericMatrix&, int, std::string, Rcpp::List, Rcpp::IntegerVector, int, Rcpp::NumericMatrix, Rcpp::List, Rcpp::NumericMatrix, Rcpp::NumericVector)’: R_Interface.cpp:475:10: warning: unused variable ‘manual’ [-Wunused-variable] 475 | bool manual = model_control["manual"]; | ^~~~~~ g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/testthat/include' -I/usr/local/include -fopenmp -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 Step_Calc.cpp -o Step_Calc.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/testthat/include' -I/usr/local/include -fopenmp -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 Subterms_Risk.cpp -o Subterms_Risk.o g++ -std=gnu++17 -shared -L/usr/local/lib64 -o Colossus.so Calc_Repeated.o Main_Functions.o Omnibus_Pieces.o Plot_Extensions.o R_Interface.o RcppExports.o Step_Calc.o Subterms_Risk.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -fopenmp make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/Colossus/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/Colossus/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/Colossus/src' installing to /data/gannet/ripley/R/packages/tests-devel/Colossus.Rcheck/00LOCK-Colossus/00new/Colossus/libs ** 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 ** 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 (Colossus)