* 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_allometry html
add_covariance_step html
add_covariate_effect html
add_estimation_step html
add_iiv html
add_individual_parameter html
add_iov html
add_lag_time html
add_metabolite html
add_peripheral_compartment html
add_pk_iiv html
add_population_parameter html
add_time_after_dose html
append_estimation_step_options 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_results 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
find_clearance_parameters html
find_volume_parameters html
fit html
fix_or_unfix_parameters html
fix_parameters html
fix_parameters_to html
get_baselines html
get_bioavailability html
get_cmt html
get_concentration_parameters_from_data
html
get_config_path html
get_covariate_baselines 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_observation_expression html
get_observations html
get_omegas 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_elimination 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_proportional_error_model html
has_random_effect 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
list_time_varying_covariates html
load_example_model html
load_example_modelfit_results html
make_declarative html
mu_reference_model html
omit_data html
plot_individual_predictions html
plot_iofv_vs_iofv html
plot_transformed_eta_distributions 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
rank_models html
read_dataset_from_datainfo html
read_model html
read_model_from_string html
read_modelfit_results html
read_results html
remove_covariance_step html
remove_covariate_effect html
remove_error_model html
remove_estimation_step html
remove_iiv html
remove_iov html
remove_lag_time html
remove_loq_data html
remove_peripheral_compartment html
remove_unused_parameters_and_rvs html
rename_symbols html
resample_data html
reset_index html
reset_indices_results html
resume_tool html
retrieve_final_model 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_modelfit html
run_modelsearch html
run_ruvsearch html
run_tool html
sample_individual_estimates html
sample_parameters_from_covariance_matrix
html
sample_parameters_uniformly html
set_additive_error_model html
set_bolus_absorption html
set_combined_error_model html
set_covariates 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_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_seq_zo_fo_absorption 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_errors html
summarize_individuals html
summarize_individuals_count_table 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
update_initial_individual_estimates html
update_inits 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
* DONE (pharmr)