Install log for 'Colossus'

* installing *source* package ‘Colossus’ ...
** this is package ‘Colossus’ version ‘1.1.4.2’
** package ‘Colossus’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (GCC) 14.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/Colossus/src'
g++-14 -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  -DR_NO_REMAP -c Calc_Repeated.cpp -o Calc_Repeated.o
g++-14 -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  -DR_NO_REMAP -c Main_Functions.cpp -o Main_Functions.o
g++-14 -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  -DR_NO_REMAP -c Omnibus_Pieces.cpp -o Omnibus_Pieces.o
Omnibus_Pieces.cpp:988:1: warning: multi-line comment [-Wcomment]
  988 | //     #pragma omp declare reduction(vec_double_plus : std::vector<double> : \
      | ^
Omnibus_Pieces.cpp:1091:1: warning: multi-line comment [-Wcomment]
 1091 | //     #pragma omp declare reduction(vec_double_plus : std::vector<double> : \
      | ^
Main_Functions.cpp: In function 'Rcpp::List LogLik_Cox_PH_Omnibus_Log_Bound_Search(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, bool, Rcpp::IntegerVector, int, std::string, int, Rcpp::NumericVector&, const Eigen::VectorXd&, bool, bool, bool, bool, bool, bool, double, Rcpp::IntegerVector, Eigen::MatrixXd, Eigen::VectorXd, double, int, int, double)':
Main_Functions.cpp:2454:10: warning: variable 'convgd' set but not used [-Wunused-but-set-variable]
 2454 |     bool convgd = FALSE;
      |          ^~~~~~
Main_Functions.cpp:2463:9: warning: variable 'guess_abs_best' set but not used [-Wunused-but-set-variable]
 2463 |     int guess_abs_best = - 1;
      |         ^~~~~~~~~~~~~~
Main_Functions.cpp: In function 'Rcpp::List LogLik_Poisson_Omnibus_Log_Bound_Search(const Eigen::MatrixXd&, const Eigen::MatrixXd&, Rcpp::IntegerVector, Rcpp::StringVector, Rcpp::NumericVector, Rcpp::NumericMatrix&, Rcpp::IntegerVector, int, std::string, double, Rcpp::NumericVector, int, int, double, double, double, double, int, bool, Rcpp::IntegerVector, int, int, bool, bool, bool, double, Rcpp::IntegerVector, Eigen::MatrixXd, Eigen::VectorXd, double, int, int, double)':
Main_Functions.cpp:4112:10: warning: variable 'convgd' set but not used [-Wunused-but-set-variable]
 4112 |     bool convgd = FALSE;
      |          ^~~~~~
Main_Functions.cpp:4121:9: warning: variable 'guess_abs_best' set but not used [-Wunused-but-set-variable]
 4121 |     int guess_abs_best = - 1;
      |         ^~~~~~~~~~~~~~
Main_Functions.cpp: In function 'Rcpp::List LogLik_Cox_PH_Multidose_Omnibus(Rcpp::IntegerVector, Rcpp::StringVector, Rcpp::NumericVector, Rcpp::NumericMatrix&, Rcpp::IntegerMatrix, Rcpp::IntegerVector, Rcpp::IntegerVector, int, int, std::string, double, int, int, double, double, double, double, Rcpp::NumericMatrix, Rcpp::NumericVector, int, bool, int, bool, Rcpp::IntegerVector, int, std::string, int, Rcpp::NumericVector&, const Eigen::VectorXd&, bool, bool, bool, bool, bool, bool, double, Rcpp::IntegerVector, Eigen::MatrixXd, Eigen::VectorXd)':
Main_Functions.cpp:5118:10: warning: variable 'convgd' set but not used [-Wunused-but-set-variable]
 5118 |     bool convgd = FALSE;
      |          ^~~~~~
Main_Functions.cpp:5135:9: warning: variable 'guess_abs_best' set but not used [-Wunused-but-set-variable]
 5135 |     int guess_abs_best = - 1;
      |         ^~~~~~~~~~~~~~
Omnibus_Pieces.cpp: In function 'void Cox_Term_Risk_Calc(std::string, const Rcpp::StringVector&, const Rcpp::IntegerVector&, const int&, const int&, const Rcpp::IntegerVector&, int, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::VectorXd, const Eigen::MatrixXd&, const double&, const double&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, const int&, bool, const Rcpp::IntegerVector&, int, bool, bool, double, const Rcpp::IntegerVector&)':
Omnibus_Pieces.cpp:138:9: warning: unused variable 'reqrdnum' [-Wunused-variable]
  138 |     int reqrdnum = totalnum - sum(KeepConstant);
      |         ^~~~~~~~
Omnibus_Pieces.cpp: In function 'void Pois_Term_Risk_Calc(std::string, const Rcpp::StringVector&, const Rcpp::IntegerVector&, const int&, const int&, const Rcpp::IntegerVector&, int, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::VectorXd, const Eigen::MatrixXd&, const double&, const double&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, Eigen::MatrixXd&, const Eigen::MatrixXd&, const int&, bool, const Rcpp::IntegerVector&, int, bool, bool, double, const Rcpp::IntegerVector&)':
Omnibus_Pieces.cpp:577:9: warning: unused variable 'reqrdnum' [-Wunused-variable]
  577 |     int reqrdnum = totalnum - sum(KeepConstant);
      |         ^~~~~~~~
g++-14 -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  -DR_NO_REMAP -c Plot_Extensions.cpp -o Plot_Extensions.o
g++-14 -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  -DR_NO_REMAP -c R_Interface.cpp -o R_Interface.o
R_Interface.cpp:499:1: warning: multi-line comment [-Wcomment]
  499 | //    #pragma omp declare reduction(vec_int_plus : std::vector<int> : \
      | ^
g++-14 -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  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++-14 -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  -DR_NO_REMAP -c Step_Calc.cpp -o Step_Calc.o
g++-14 -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  -DR_NO_REMAP -c Subterms_Risk.cpp -o Subterms_Risk.o
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -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)