* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘pharmr’ ...
** package ‘pharmr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘pharmr’
    finding HTML links ... done
    add_admid                               html  
    add_allometry                           html  
    add_bioavailability                     html  
    add_cmt                                 html  
    add_covariate_effect                    html  
    add_derivative                          html  
    add_effect_compartment                  html  
    add_estimation_step                     html  
    add_iiv                                 html  
    add_indirect_effect                     html  
    add_individual_parameter                html  
    add_iov                                 html  
    add_lag_time                            html  
    add_metabolite                          html  
    add_parameter_uncertainty_step          html  
    add_pd_iiv                              html  
    add_peripheral_compartment              html  
    add_pk_iiv                              html  
    add_population_parameter                html  
    add_predictions                         html  
    add_residuals                           html  
    add_time_after_dose                     html  
    append_estimation_step_options          html  
    bin_observations                        html  
    bump_model_number                       html  
    calculate_aic                           html  
    calculate_bic                           html  
    calculate_corr_from_cov                 html  
    calculate_corr_from_prec                html  
    calculate_cov_from_corrse               html  
    calculate_cov_from_prec                 html  
    calculate_epsilon_gradient_expression   html  
    calculate_eta_gradient_expression       html  
    calculate_eta_shrinkage                 html  
    calculate_individual_parameter_statistics
                                            html  
    calculate_individual_shrinkage          html  
    calculate_parameters_from_ucp           html  
    calculate_pk_parameters_statistics      html  
    calculate_prec_from_corrse              html  
    calculate_prec_from_cov                 html  
    calculate_se_from_cov                   html  
    calculate_se_from_prec                  html  
    calculate_ucp_scale                     html  
    check_dataset                           html  
    check_high_correlations                 html  
    check_parameters_near_bounds            html  
    check_pharmpy                           html  
    cleanup_model                           html  
    convert_model                           html  
    create_basic_pk_model                   html  
    create_config_template                  html  
    create_joint_distribution               html  
    create_report                           html  
    create_rng                              html  
    create_symbol                           html  
    deidentify_data                         html  
    display_odes                            html  
    drop_columns                            html  
    drop_dropped_columns                    html  
    evaluate_epsilon_gradient               html  
    evaluate_eta_gradient                   html  
    evaluate_expression                     html  
    evaluate_individual_prediction          html  
    evaluate_population_prediction          html  
    evaluate_weighted_residuals             html  
    expand_additional_doses                 html  
    filter_dataset                          html  
    find_clearance_parameters               html  
    find_volume_parameters                  html  
    fit                                     html  
    fix_or_unfix_parameters                 html  
    fix_parameters                          html  
    fix_parameters_to                       html  
    get_admid                               html  
    get_baselines                           html  
    get_bioavailability                     html  
    get_central_volume_and_clearance        html  
    get_cmt                                 html  
    get_concentration_parameters_from_data
                                            html  
    get_config_path                         html  
    get_covariate_baselines                 html  
    get_covariate_effects                   html  
    get_doseid                              html  
    get_doses                               html  
    get_dv_symbol                           html  
    get_evid                                html  
    get_ids                                 html  
    get_individual_parameters               html  
    get_individual_prediction_expression    html  
    get_initial_conditions                  html  
    get_lag_times                           html  
    get_mdv                                 html  
    get_model_code                          html  
    get_model_covariates                    html  
    get_number_of_individuals               html  
    get_number_of_observations              html  
    get_number_of_observations_per_individual
                                            html  
    get_number_of_peripheral_compartments   html  
    get_number_of_transit_compartments      html  
    get_observation_expression              html  
    get_observations                        html  
    get_omegas                              html  
    get_parameter_rv                        html  
    get_pd_parameters                       html  
    get_pk_parameters                       html  
    get_population_prediction_expression    html  
    get_rv_parameters                       html  
    get_sigmas                              html  
    get_thetas                              html  
    get_unit_of                             html  
    get_zero_order_inputs                   html  
    greekify_model                          html  
    has_additive_error_model                html  
    has_combined_error_model                html  
    has_covariate_effect                    html  
    has_first_order_absorption              html  
    has_first_order_elimination             html  
    has_instantaneous_absorption            html  
    has_linear_odes                         html  
    has_linear_odes_with_real_eigenvalues   html  
    has_michaelis_menten_elimination        html  
    has_mixed_mm_fo_elimination             html  
    has_odes                                html  
    has_presystemic_metabolite              html  
    has_proportional_error_model            html  
    has_random_effect                       html  
    has_seq_zo_fo_absorption                html  
    has_weighted_error_model                html  
    has_zero_order_absorption               html  
    has_zero_order_elimination              html  
    install_pharmpy                         html  
    install_pharmpy_devel                   html  
    is_linearized                           html  
    is_real                                 html  
    is_strictness_fulfilled                 html  
    list_time_varying_covariates            html  
    load_dataset                            html  
    load_example_model                      html  
    load_example_modelfit_results           html  
    make_declarative                        html  
    mu_reference_model                      html  
    omit_data                               html  
    plot_abs_cwres_vs_ipred                 html  
    plot_cwres_vs_idv                       html  
    plot_dv_vs_ipred                        html  
    plot_dv_vs_pred                         html  
    plot_eta_distributions                  html  
    plot_individual_predictions             html  
    plot_iofv_vs_iofv                       html  
    plot_transformed_eta_distributions      html  
    plot_vpc                                html  
    predict_influential_individuals         html  
    predict_influential_outliers            html  
    predict_outliers                        html  
    print_fit_summary                       html  
    print_model_code                        html  
    print_model_symbols                     html  
    print_pharmpy_version                   html  
    read_dataset_from_datainfo              html  
    read_model                              html  
    read_model_from_string                  html  
    read_modelfit_results                   html  
    read_results                            html  
    remove_bioavailability                  html  
    remove_covariate_effect                 html  
    remove_derivative                       html  
    remove_error_model                      html  
    remove_estimation_step                  html  
    remove_iiv                              html  
    remove_iov                              html  
    remove_lag_time                         html  
    remove_loq_data                         html  
    remove_parameter_uncertainty_step       html  
    remove_peripheral_compartment           html  
    remove_predictions                      html  
    remove_residuals                        html  
    remove_unused_parameters_and_rvs        html  
    rename_symbols                          html  
    replace_non_random_rvs                  html  
    resample_data                           html  
    reset_index                             html  
    reset_indices_results                   html  
    retrieve_models                         html  
    run_allometry                           html  
    run_amd                                 html  
    run_bootstrap                           html  
    run_covsearch                           html  
    run_estmethod                           html  
    run_iivsearch                           html  
    run_iovsearch                           html  
    run_linearize                           html  
    run_modelfit                            html  
    run_modelsearch                         html  
    run_retries                             html  
    run_ruvsearch                           html  
    run_simulation                          html  
    run_structsearch                        html  
    run_tool                                html  
    sample_individual_estimates             html  
    sample_parameters_from_covariance_matrix
                                            html  
    sample_parameters_uniformly             html  
    set_additive_error_model                html  
    set_baseline_effect                     html  
    set_combined_error_model                html  
    set_covariates                          html  
    set_dataset                             html  
    set_direct_effect                       html  
    set_dtbs_error_model                    html  
    set_dvid                                html  
    set_estimation_step                     html  
    set_evaluation_step                     html  
    set_first_order_absorption              html  
    set_first_order_elimination             html  
    set_iiv_on_ruv                          html  
    set_initial_condition                   html  
    set_initial_estimates                   html  
    set_instantaneous_absorption            html  
    set_lloq_data                           html  
    set_lower_bounds                        html  
    set_michaelis_menten_elimination        html  
    set_mixed_mm_fo_elimination             html  
    set_name                                html  
    set_ode_solver                          html  
    set_peripheral_compartments             html  
    set_power_on_ruv                        html  
    set_proportional_error_model            html  
    set_reference_values                    html  
    set_seq_zo_fo_absorption                html  
    set_simulation                          html  
    set_time_varying_error_model            html  
    set_tmdd                                html  
    set_transit_compartments                html  
    set_upper_bounds                        html  
    set_weighted_error_model                html  
    set_zero_order_absorption               html  
    set_zero_order_elimination              html  
    set_zero_order_input                    html  
    simplify_expression                     html  
    solve_ode_system                        html  
    split_joint_distribution                html  
    summarize_modelfit_results              html  
    transform_blq                           html  
    transform_etas_boxcox                   html  
    transform_etas_john_draper              html  
    transform_etas_tdist                    html  
    translate_nmtran_time                   html  
    unconstrain_parameters                  html  
    undrop_columns                          html  
    unfix_parameters                        html  
    unfix_parameters_to                     html  
    unload_dataset                          html  
    update_initial_individual_estimates     html  
    use_thetas_for_error_stdev              html  
    write_csv                               html  
    write_model                             html  
    write_results                           html  
** building package indices
** testing if installed package can be loaded from temporary location
** 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 ‘pharmr’ as ‘pharmr_1.0.0_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (pharmr)