* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘hmcdm’ ...
** package ‘hmcdm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpB505TF/R.INSTALL19004c10f4284b/hmcdm/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c basic_functions.cpp -o basic_functions.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c extract_functions.cpp -o extract_functions.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c mcmc_functions.cpp -o mcmc_functions.o
mcmc_functions.cpp: In function ‘Rcpp::List parm_update_HO_RT_joint_g(const arma::cube&, arma::cube&, arma::vec&, arma::vec&, arma::vec&, arma::cube, arma::mat&, arma::vec&, arma::vec&, arma::mat&, arma::cube, arma::mat&, arma::mat, Rcpp::List, int, double, arma::mat, double, arma::vec, double, double)’:
mcmc_functions.cpp:1178:36: warning: ‘t_star’ may be used uninitialized [-Wmaybe-uninitialized]
1178 | Gs.row(i) = G2vec_efficient_g(ETA,J_incidence,alphas.subcube(i,0,0,i,(K-1),(T-1)),
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1179 | t_star,Q_matrix,Design_array,i).t();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mcmc_functions.cpp:1145:61: note: ‘t_star’ was declared here
1145 | double a_alpha, scl_alpha, mu_gamma, sd_gamma, alpha_sqr, t_star;
| ^~~~~~
mcmc_functions.cpp: In function ‘Rcpp::List parm_update_HO_RT_sep_g(arma::cube, arma::cube&, arma::vec&, arma::vec&, arma::vec&, arma::cube, arma::mat&, arma::vec&, arma::vec&, arma::vec&, arma::cube, arma::mat&, arma::mat, Rcpp::List, int, double, double, double, arma::vec, double, double)’:
mcmc_functions.cpp:637:36: warning: ‘t_star’ may be used uninitialized [-Wmaybe-uninitialized]
637 | Gs.row(i) = G2vec_efficient_g(ETA,J_incidence,alphas.subcube(i,0,0,i,(K-1),(T-1)),
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
638 | t_star,Q_matrix,Design_array,i).t();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mcmc_functions.cpp:606:61: note: ‘t_star’ was declared here
606 | double a_alpha, scl_alpha, mu_gamma, sd_gamma, alpha_sqr, t_star;
| ^~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c resp_functions.cpp -o resp_functions.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c rt_functions.cpp -o rt_functions.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/progress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c trans_functions.cpp -o trans_functions.o
trans_functions.cpp: In function ‘arma::cube sim_alphas(std::string, Rcpp::Nullable<arma::Col<double>&>, Rcpp::Nullable<arma::Col<double>&>, Rcpp::Nullable<arma::Mat<double>&>, Rcpp::Nullable<arma::Cube<double>&>, Rcpp::Nullable<arma::Col<double> >, Rcpp::Nullable<arma::Mat<double>&>, int, int, Rcpp::Nullable<arma::Mat<double>&>, Rcpp::Nullable<arma::Mat<double> >)’:
trans_functions.cpp:532:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
532 | for(unsigned int i=0; i<N; i++){
| ~^~
trans_functions.cpp:507:16: warning: ‘K’ may be used uninitialized [-Wmaybe-uninitialized]
507 | unsigned int K;
| ^
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o hmcdm.so RcppExports.o basic_functions.o extract_functions.o mcmc_functions.o resp_functions.o rt_functions.o trans_functions.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpB505TF/R.INSTALL19004c10f4284b/hmcdm/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpB505TF/R.INSTALL19004c10f4284b/hmcdm/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpB505TF/R.INSTALL19004c10f4284b/hmcdm/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-hmcdm/00new/hmcdm/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘hmcdm’
finding HTML links ... done
Design_array html
ETAmat html
L_real_array html
OddsRatio html
Q_list_g html
Q_matrix html
TPmat html
Test_order html
Test_versions html
Y_real_array html
hmcdm-package html
hmcdm html
inv_bijectionvector html
pp_check.hmcdm html
rOmega html
random_Q html
sim_RT html
sim_alphas html
sim_hmcdm html
summary.hmcdm html
** 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 (hmcdm)