* 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 13.2.0-25) 13.2.0’
make[1]: Entering directory '/tmp/RtmpKs97Sp/R.INSTALL2dc65e5461ea2a/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/RtmpKs97Sp/R.INSTALL2dc65e5461ea2a/PKPDsim/src'
make[1]: Entering directory '/tmp/RtmpKs97Sp/R.INSTALL2dc65e5461ea2a/PKPDsim/src'
make[1]: Leaving directory '/tmp/RtmpKs97Sp/R.INSTALL2dc65e5461ea2a/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
* creating tarball
packaged installation of ‘PKPDsim’ as ‘PKPDsim_1.3.0_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (PKPDsim)