* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘epicR’ ...
** this is package ‘epicR’ version ‘1.0.0’
** package ‘epicR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-12) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpviLwtv/R.INSTALL1a094016d4b123/epicR/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/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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c model.cpp -o model.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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c model_events.cpp -o model_events.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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c model_globals.cpp -o model_globals.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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c model_input.cpp -o model_input.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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c model_output.cpp -o model_output.o
model_output.cpp: In function ‘void update_output_ex(agent*)’:
model_output.cpp:176:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
176 | else
| ^~~~
model_output.cpp:183:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’
183 | output_ex.cumul_cost_ctime[time]+=(*ag).cumul_cost;
| ^~~~~~~~~
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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c model_random.cpp -o model_random.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o epicR.so RcppExports.o model.o model_events.o model_globals.o model_input.o model_output.o model_random.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -Wl,-S -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpviLwtv/R.INSTALL1a094016d4b123/epicR/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpviLwtv/R.INSTALL1a094016d4b123/epicR/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpviLwtv/R.INSTALL1a094016d4b123/epicR/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-epicR/00new/epicR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘epicR’
finding HTML links ... done
calc_event_stack_size html
calibrate_COPD_inc html
calibrate_explicit_mortality html
calibrate_explicit_mortality2 html
calibrate_smoking html
copy_configs_to_user html
epicR-config html
epicR-package html
estimate_memory_required html
export_figures html
express_matrix html
get_agent_events html
get_agent_size_bytes html
get_all_events html
get_all_events_matrix html
get_available_memory html
get_default_model_input html
get_default_settings html
get_errors html
get_event html
get_events_by_type html
get_input html
get_inputs html
get_list_elements html
get_n_events html
get_output html
get_output_ex html
get_progress html
get_runtime_stats html
get_sample_output html
get_settings html
get_smith html
get_user_config_dir html
init_session html
list_available_jurisdictions html
mvrnormArma html
report_COPD_by_ctime html
report_exacerbation_by_time html
reset_model_input html
reset_user_configs html
resume html
sanity_COPD html
sanity_check html
set_input_var html
set_settings_var html
simulate html
terminate_session html
test_case_detection html
user_config_exists html
validate_COPD html
validate_config html
validate_diagnosis html
validate_exacerbation html
validate_gpvisits html
validate_lung_function html
validate_medication html
validate_mortality html
validate_overdiagnosis html
validate_payoffs html
validate_population html
validate_smoking html
validate_survival html
validate_symptoms html
validate_treatment 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 (epicR)