Install log for 'Colossus'

* 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
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 Omnibus_Pieces.cpp -o Omnibus_Pieces.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 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)