* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘PKPDsim’ ...
** package ‘PKPDsim’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/RtmpKC9eZD/R.INSTALL301b2d4be75e6f/PKPDsim/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_HAS_AUTO_PTR_ETC=0 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_HAS_AUTO_PTR_ETC=0 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pk_1cmt_iv_bolus.cpp -o pk_1cmt_iv_bolus.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_HAS_AUTO_PTR_ETC=0 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pk_1cmt_iv_bolus_covariates.cpp -o pk_1cmt_iv_bolus_covariates.o
pk_1cmt_iv_bolus_covariates.cpp: In function ‘Rcpp::DataFrame pk_1cmt_iv_bolus_covariates(Rcpp::DataFrame, Rcpp::List, Rcpp::StringVector, Rcpp::Function)’:
pk_1cmt_iv_bolus_covariates.cpp:8:10: warning: unused variable ‘CLi’ [-Wunused-variable]
8 | double CLi, Vi, tmp;
| ^~~
pk_1cmt_iv_bolus_covariates.cpp:8:15: warning: unused variable ‘Vi’ [-Wunused-variable]
8 | double CLi, Vi, tmp;
| ^~
pk_1cmt_iv_bolus_covariates.cpp:8:19: warning: unused variable ‘tmp’ [-Wunused-variable]
8 | double CLi, Vi, tmp;
| ^~~
pk_1cmt_iv_bolus_covariates.cpp:12:10: warning: unused variable ‘CL’ [-Wunused-variable]
12 | double CL = parameters["CL"];
| ^~
pk_1cmt_iv_bolus_covariates.cpp:13:10: warning: unused variable ‘V’ [-Wunused-variable]
13 | double V = parameters["V"];
| ^
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_HAS_AUTO_PTR_ETC=0 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pk_1cmt_iv_infusion.cpp -o pk_1cmt_iv_infusion.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_HAS_AUTO_PTR_ETC=0 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pk_1cmt_oral.cpp -o pk_1cmt_oral.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_HAS_AUTO_PTR_ETC=0 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pk_2cmt_iv_bolus.cpp -o pk_2cmt_iv_bolus.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_HAS_AUTO_PTR_ETC=0 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pk_2cmt_iv_infusion.cpp -o pk_2cmt_iv_infusion.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_HAS_AUTO_PTR_ETC=0 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pk_2cmt_oral.cpp -o pk_2cmt_oral.o
pk_2cmt_oral.cpp: In function ‘Rcpp::DataFrame pk_2cmt_oral(Rcpp::DataFrame)’:
pk_2cmt_oral.cpp:8:14: warning: unused variable ‘k10’ [-Wunused-variable]
8 | double ka, k10, k20, k30, k23, k32, E1, E2, E3, lambda1, lambda2, t, A1last, A2last, A3last, A2term1, A2term2, A3term1, A3term2;
| ^~~
pk_2cmt_oral.cpp:8:39: warning: unused variable ‘E1’ [-Wunused-variable]
8 | double ka, k10, k20, k30, k23, k32, E1, E2, E3, lambda1, lambda2, t, A1last, A2last, A3last, A2term1, A2term2, A3term1, A3term2;
| ^~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_HAS_AUTO_PTR_ETC=0 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pk_3cmt_iv_bolus.cpp -o pk_3cmt_iv_bolus.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_HAS_AUTO_PTR_ETC=0 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pk_3cmt_iv_infusion.cpp -o pk_3cmt_iv_infusion.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -D_HAS_AUTO_PTR_ETC=0 -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pk_3cmt_oral.cpp -o pk_3cmt_oral.o
pk_3cmt_oral.cpp: In function ‘Rcpp::DataFrame pk_3cmt_oral(Rcpp::DataFrame)’:
pk_3cmt_oral.cpp:8:14: warning: unused variable ‘k10’ [-Wunused-variable]
8 | double ka, k10, k20, k23, k32, k24, k42, k30, k40, E1, E2, E3, E4;
| ^~~
pk_3cmt_oral.cpp:8:54: warning: unused variable ‘E1’ [-Wunused-variable]
8 | double ka, k10, k20, k23, k32, k24, k42, k30, k40, E1, E2, E3, E4;
| ^~
pk_3cmt_oral.cpp:10:42: warning: unused variable ‘A1term1’ [-Wunused-variable]
10 | double A1last, A2last, A3last, A4last, A1term1, A1term2, A2term1, A2term2, A2term3, A3term1, A3term2, A3term3, A4term1, A4term2, A4term3;
| ^~~~~~~
pk_3cmt_oral.cpp:10:51: warning: unused variable ‘A1term2’ [-Wunused-variable]
10 | double A1last, A2last, A3last, A4last, A1term1, A1term2, A2term1, A2term2, A2term3, A3term1, A3term2, A3term3, A4term1, A4term2, A4term3;
| ^~~~~~~
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o PKPDsim.so RcppExports.o pk_1cmt_iv_bolus.o pk_1cmt_iv_bolus_covariates.o pk_1cmt_iv_infusion.o pk_1cmt_oral.o pk_2cmt_iv_bolus.o pk_2cmt_iv_infusion.o pk_2cmt_oral.o pk_3cmt_iv_bolus.o pk_3cmt_iv_infusion.o pk_3cmt_oral.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpKC9eZD/R.INSTALL301b2d4be75e6f/PKPDsim/src'
make[1]: Entering directory '/tmp/RtmpKC9eZD/R.INSTALL301b2d4be75e6f/PKPDsim/src'
make[1]: Leaving directory '/tmp/RtmpKC9eZD/R.INSTALL301b2d4be75e6f/PKPDsim/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-PKPDsim/00new/PKPDsim/libs
** R
** data
*** moving datasets to lazyload DB
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘PKPDsim’
finding HTML links ... done
OneCompIVbolus html
OneCompIVinfusion html
OneCompOral html
PKPDsim-package html
ThreeCompIVbolus html
ThreeCompIVinfusion html
ThreeCompIVinfusionMetab html
ThreeCompOral html
ThreeCompOralMetab html
TwoCompIVbolus html
TwoCompIVinfusion html
TwoCompOral html
add_quotes html
add_ruv html
add_ruv_to_quantile html
adherence_binomial html
adherence_markov html
advan html
advan_create_data html
advan_parse_output html
advan_process_infusion_doses html
analytical_eqn_wrapper html
apply_lagtime html
bioavailability_to_R_code html
calc_dydP html
calc_ss_analytic html
calculate_parameters html
check_iov_specification html
check_mixture_model html
check_obs_input html
compile_sim_cpp html
covariate_last_obs_only html
covariates_table_to_list html
create_event_table html
create_obs_data html
cv_to_omega html
define_tdm_init_model html
detect_ode_syntax html
f_cov html
get_fixed_parameters html
get_ode_model_size html
get_parameters_from_code html
get_t_obs_from_regimen html
get_var_y html
ifelse0 html
is_newer_package html
is_positive_definite html
join_cov_and_par html
join_regimen html
lower_triangle_mat_size html
merge_regimen html
model_from_api html
model_library html
mvrnorm2 html
na_locf html
new_adherence html
new_covariate html
new_covariate_model html
new_ode_model html
new_regimen html
nlmixr_parse_parameters html
nm_to_regimen html
now_utc html
parse_obs_types html
pkdata html
pkpdsim_to_nlmixr html
pop_regimen html
print.PKPDsim html
print.covariate html
print.regimen html
print_list html
read_model_json html
regimen_to_nm html
reparametrize html
search_replace_in_file html
shift_regimen html
shift_state_indices html
sim html
sim_core html
sim_ode html
sim_ode_shiny html
table_to_list html
test_model html
test_pointer html
translate_ode html
triangle_to_full html
vector_to_R_code html
*** 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 (PKPDsim)