* installing *source* package ‘Colossus’ ...
** this is package ‘Colossus’ version ‘1.6.3’
** package ‘Colossus’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++ (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’
using C++17
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/Colossus/src'
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/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
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/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 Grouping.cpp -o Grouping.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/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_Bound.cpp -o Main_Bound.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/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_Logist_Omnibus(const Eigen::Ref<const Eigen::Matrix<double, -1, -1> >&, Rcpp::IntegerVector&, const Rcpp::StringVector&, Rcpp::NumericMatrix&, Eigen::Ref<Eigen::Matrix<double, -1, -1> >, const Rcpp::IntegerVector&, int, const std::string&, Rcpp::List, int, Rcpp::IntegerVector, int, int, Rcpp::List, double, Rcpp::IntegerVector, const Eigen::Ref<const Eigen::Matrix<double, -1, -1> >&, const Eigen::Ref<const Eigen::Matrix<double, -1, 1> >&)’:
Main_Functions.cpp:2233:16: warning: unused variable ‘AIC_val’ [-Wunused-variable]
2233 | double AIC_val = 0;
| ^~~~~~~
Main_Functions.cpp:2234:16: warning: unused variable ‘BIC_val’ [-Wunused-variable]
2234 | double BIC_val = 0;
| ^~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/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_Multi.cpp -o Main_Multi.o
Main_Multi.cpp: In function ‘Rcpp::List LogLik_Logist_Multidose_Omnibus_Serial(Eigen::Ref<Eigen::Matrix<double, -1, -1> >, Rcpp::IntegerVector, Rcpp::StringVector, Eigen::Ref<Eigen::Matrix<double, -1, 1> >, Eigen::Ref<Eigen::Matrix<double, -1, -1> >, const Eigen::Ref<const Eigen::Matrix<double, -1, -1> >&, Rcpp::IntegerMatrix, Rcpp::IntegerVector, Rcpp::IntegerVector, int, const std::string&, Rcpp::List, int, Rcpp::IntegerVector, int, int, Rcpp::List, double, Rcpp::IntegerVector, const Eigen::Ref<const Eigen::Matrix<double, -1, -1> >&, const Eigen::Ref<const Eigen::Matrix<double, -1, 1> >&)’:
Main_Multi.cpp:2199:12: warning: unused variable ‘Lstar’ [-Wunused-variable]
2199 | double Lstar = 0.0;
| ^~~~~
Main_Multi.cpp:2200:9: warning: unused variable ‘ntime’ [-Wunused-variable]
2200 | int ntime = 1.0;
| ^~~~~
Main_Multi.cpp: In function ‘Rcpp::List LogLik_Logist_Multidose_Omnibus_Integrated(Eigen::Ref<Eigen::Matrix<double, -1, -1> >, Rcpp::IntegerVector, Rcpp::StringVector, Eigen::Ref<Eigen::Matrix<double, -1, 1> >, Eigen::Ref<Eigen::Matrix<double, -1, -1> >, const Eigen::Ref<const Eigen::Matrix<double, -1, -1> >&, Rcpp::IntegerMatrix, Rcpp::IntegerVector, Rcpp::IntegerVector, int, const std::string&, Rcpp::List, int, Rcpp::IntegerVector, int, int, Rcpp::List, double, Rcpp::IntegerVector, const Eigen::Ref<const Eigen::Matrix<double, -1, -1> >&, const Eigen::Ref<const Eigen::Matrix<double, -1, 1> >&)’:
Main_Multi.cpp:2601:12: warning: unused variable ‘step_max0’ [-Wunused-variable]
2601 | double step_max0 = step_max;
| ^~~~~~~~~
Main_Multi.cpp:2602:12: warning: unused variable ‘thres_step_max0’ [-Wunused-variable]
2602 | double thres_step_max0 = thres_step_max;
| ^~~~~~~~~~~~~~~
Main_Multi.cpp:2632:12: warning: unused variable ‘Lstar’ [-Wunused-variable]
2632 | double Lstar = 0.0;
| ^~~~~
Main_Multi.cpp:2633:9: warning: unused variable ‘ntime’ [-Wunused-variable]
2633 | int ntime = 1.0;
| ^~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/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
Plot_Extensions.cpp: In function ‘Rcpp::List Assign_Events_Pois(Rcpp::IntegerVector&, const Rcpp::StringVector&, Eigen::Ref<Eigen::Matrix<double, -1, 1> >, Eigen::Ref<Eigen::Matrix<double, -1, -1> >, const Rcpp::IntegerVector&, const Eigen::Ref<const Eigen::Matrix<double, -1, -1> >&, Rcpp::NumericVector&, const Eigen::Ref<const Eigen::Matrix<double, -1, -1> >&, int, const std::string&, int, Rcpp::IntegerVector, int, int, double, Rcpp::IntegerVector, Rcpp::List)’:
Plot_Extensions.cpp:464:15: warning: unused variable ‘mat_row’ [-Wunused-variable]
464 | const int mat_row = df0.rows();
| ^~~~~~~
Plot_Extensions.cpp: In function ‘Rcpp::List Poisson_Residuals(const Eigen::Ref<const Eigen::Matrix<double, -1, -1> >&, Rcpp::IntegerVector&, const Rcpp::StringVector&, Eigen::Ref<Eigen::Matrix<double, -1, 1> >, Eigen::Ref<Eigen::Matrix<double, -1, -1> >, const Rcpp::IntegerVector&, int, const std::string&, double, double, int, Rcpp::IntegerVector, int, int, Rcpp::NumericVector&, const Eigen::Ref<const Eigen::Matrix<double, -1, -1> >&, Rcpp::List, double, Rcpp::IntegerVector, bool, bool)’:
Plot_Extensions.cpp:544:15: warning: unused variable ‘mat_row’ [-Wunused-variable]
544 | const int mat_row = df0.rows();
| ^~~~~~~
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/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/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/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
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/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_Bound.cpp -o Step_Bound.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/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_Grad.cpp -o Step_Grad.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/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_Newton.cpp -o Step_Newton.o
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I'/data/localhost/ripley/R/test-dev/RcppEigen/include' -I'/data/localhost/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
Subterms_Risk.cpp: In function ‘void Make_subterms(const int&, const Rcpp::IntegerVector&, const Rcpp::StringVector&, const Rcpp::IntegerVector&, const int&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, const Eigen::VectorXd&, const Eigen::Ref<const Eigen::Matrix<double, -1, -1> >&, const double&, const double&, const int&, const Rcpp::IntegerVector&)’:
Subterms_Risk.cpp:535:13: warning: unused variable ‘df0_ij’ [-Wunused-variable]
535 | int df0_ij = dfc[ij] - 1;
| ^~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o Colossus.so Calc_Repeated.o Grouping.o Main_Bound.o Main_Functions.o Main_Multi.o Omnibus_Pieces.o Plot_Extensions.o R_Interface.o RcppExports.o Step_Bound.o Step_Grad.o Step_Newton.o Subterms_Risk.o -llapack -L/data/localhost/ripley/R/R-devel/lib -lRblas -lgfortran -lm -latomic_asneeded -lquadmath -fopenmp
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/Colossus/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/Colossus/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/Colossus/src'
installing to /data/localhost/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
*** copying figures
** 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)