* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘beautier’ ... ** package ‘beautier’ 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 ‘beautier’ finding HTML links ... done alpha_parameter_to_xml html are_clock_models html are_equal_mcmcs html are_equal_screenlogs html are_equal_tracelogs html are_equal_treelogs html are_equal_xml_files html are_equal_xml_lines html are_equivalent_xml_files html are_equivalent_xml_lines html are_equivalent_xml_lines_all html are_equivalent_xml_lines_loggers html are_equivalent_xml_lines_operators html are_equivalent_xml_lines_section html are_fasta_filenames html are_ids html are_init_clock_models html are_init_mrca_priors html are_init_site_models html are_init_tree_priors html are_mrca_align_ids_in_fasta html are_mrca_priors html are_mrca_taxon_names_in_fasta html are_rln_clock_models html are_site_models html are_tree_priors html b_pop_sizes_param_to_xml html b_pop_sizes_parameter_to_xml html bd_tree_prior_to_xml_prior_distr html beautier-package html beta_parameter_to_xml html cbs_tree_prior_to_xml_prior_distr html ccp_tree_prior_to_xml_prior_distr html ccp_tree_prior_to_xml_state html cep_tree_prior_to_xml_prior_distr html check_alignment_id html check_beauti_options html check_clock_model html check_clock_models html check_empty_beautier_folder html check_file_and_model_agree html check_file_exists html check_filename html check_gamma_site_model html check_gamma_site_model_names html check_gtr_site_model html check_gtr_site_model_names html check_inference_model html check_inference_models html check_is_monophyletic html check_log_mode html check_log_sort html check_mcmc html check_mcmc_list_element_names html check_mcmc_values html check_mrca_prior html check_mrca_prior_name html check_mrca_prior_names html check_mrca_prior_taxa_names html check_ns_mcmc html check_param html check_param_names html check_param_types html check_phylogeny html check_rename_fun html check_rln_clock_model html check_screenlog html check_screenlog_names html check_screenlog_values html check_site_model html check_site_model_names html check_site_model_types html check_site_models html check_store_every html check_strict_clock_model html check_tn93_site_model html check_tn93_site_model_names html check_tracelog html check_tracelog_names html check_tracelog_values html check_tree_prior html check_tree_priors html check_treelog html check_treelog_names html check_treelog_values html clock_model_to_xml_operators html clock_model_to_xml_prior_distr html clock_model_to_xml_state html clock_model_to_xml_tracelog html clock_model_to_xml_treelogger html clock_rate_param_to_xml html compare_lines html count_trailing_spaces html create_alpha_param html create_b_pop_sizes_param html create_bd_tree_prior html create_beast2_beast_xml html create_beast2_input html create_beast2_input_beast html create_beast2_input_data html create_beast2_input_data_sequences html create_beast2_input_distr html create_beast2_input_distr_lh html create_beast2_input_distr_prior html create_beast2_input_file html create_beast2_input_file_from_model html create_beast2_input_from_model html create_beast2_input_init html create_beast2_input_map html create_beast2_input_operators html create_beast2_input_run html create_beast2_input_state html create_beauti_options html create_beauti_options_v2_4 html create_beauti_options_v2_6 html create_beautier_tempfolder html create_beta_distr html create_beta_param html create_branch_rate_model_xml html create_cbs_tree_prior html create_ccp_tree_prior html create_cep_tree_prior html create_clock_model html create_clock_model_from_name html create_clock_models html create_clock_models_from_names html create_clock_rate_param html create_clock_rate_state_node_parameter_xml html create_data_xml html create_distr html create_exp_distr html create_freq_param html create_gamma_distr html create_gamma_site_model html create_gtr_site_model html create_gtr_subst_model_xml html create_hky_site_model html create_hky_subst_model_xml html create_inference_model html create_inv_gamma_distr html create_jc69_site_model html create_jc69_subst_model_xml html create_kappa_1_param html create_kappa_2_param html create_kappa_param html create_lambda_param html create_laplace_distr html create_log_normal_distr html create_loggers_xml html create_m_param html create_mcmc html create_mean_param html create_mrca_prior html create_mu_param html create_normal_distr html create_ns_inference_model html create_ns_mcmc html create_one_div_x_distr html create_param html create_poisson_distr html create_rate_ac_param html create_rate_ag_param html create_rate_at_param html create_rate_categories_state_node_xml html create_rate_cg_param html create_rate_ct_param html create_rate_gt_param html create_rln_clock_branch_rate_model_xml html create_rln_clock_model html create_s_param html create_scale_param html create_screenlog html create_screenlog_xml html create_sigma_param html create_site_model html create_site_model_from_name html create_site_model_parameters_xml html create_site_model_xml html create_site_models html create_site_models_from_names html create_strict_clock_branch_rate_model_xml html create_strict_clock_model html create_strict_clock_rate_scaler_operator_xml html create_subst_model_xml html create_temp_screenlog_filename html create_temp_tracelog_filename html create_temp_treelog_filename html create_test_inference_model html create_test_mcmc html create_test_ns_inference_model html create_test_ns_mcmc html create_test_screenlog html create_test_tracelog html create_test_treelog html create_tn93_site_model html create_tn93_subst_model_xml html create_tracelog html create_tracelog_xml html create_trait_set_string html create_tree_likelihood_distr_xml html create_tree_prior html create_tree_priors html create_treelog html create_treelog_xml html create_ucld_mean_state_node_param_xml html create_ucld_stdev_state_node_param_xml html create_uniform_distr html create_xml_declaration html create_yule_tree_prior html default_parameters_doc html default_params_doc html distr_to_xml html distr_to_xml_beta html distr_to_xml_exp html distr_to_xml_inv_gamma html distr_to_xml_laplace html distr_to_xml_log_normal html distr_to_xml_normal html distr_to_xml_one_div_x html distr_to_xml_poisson html distr_to_xml_uniform html extract_xml_loggers_from_lines html extract_xml_operators_from_lines html extract_xml_section_from_lines html fasta_file_to_sequences html find_clock_model html find_first_regex_line html find_first_xml_opening_tag_line html find_last_regex_line html find_last_xml_closing_tag_line html freq_equilibrium_to_xml html freq_param_to_xml html gamma_distr_to_xml html gamma_site_model_to_xml_prior_distr html gamma_site_model_to_xml_state html gamma_site_models_to_xml_prior_distr html get_alignment_id html get_alignment_ids html get_alignment_ids_from_fasta_filenames html get_beautier_folder html get_beautier_path html get_beautier_paths html get_beautier_tempfilename html get_clock_model_name html get_clock_model_names html get_clock_models_ids html get_crown_age html get_default_beast_namespace html get_default_beast_namespace_v2_4 html get_default_beast_namespace_v2_6 html get_distr_n_params html get_distr_names html get_fasta_filename html get_file_base_sans_ext html get_freq_equilibrium_names html get_gamma_site_model_n_distrs html get_gamma_site_model_n_params html get_has_non_strict_clock_model html get_inference_model_filenames html get_log_modes html get_log_sorts html get_mcmc_filenames html get_n_taxa html get_operator_id_pre html get_param_names html get_remove_dir_fun html get_remove_hex_fun html get_replace_dir_fun html get_site_model_n_distrs html get_site_model_n_params html get_site_model_names html get_site_models_n_distrs html get_site_models_n_params html get_taxa_names html get_tree_prior_n_distrs html get_tree_prior_n_params html get_tree_prior_names html get_tree_priors_n_distrs html get_tree_priors_n_params html get_xml_closing_tag html get_xml_opening_tag html gtr_site_model_to_xml_prior_distr html gtr_site_model_to_xml_state html has_mrca_prior html has_mrca_prior_with_distr html has_rln_clock_model html has_strict_clock_model html has_tip_dating html has_xml_closing_tag html has_xml_opening_tag html has_xml_short_closing_tag html hky_site_model_to_xml_prior_distr html hky_site_model_to_xml_state html indent html init_bd_tree_prior html init_beta_distr html init_ccp_tree_prior html init_cep_tree_prior html init_clock_models html init_distr html init_exp_distr html init_gamma_distr html init_gamma_site_model html init_gtr_site_model html init_hky_site_model html init_inference_model html init_inv_gamma_distr html init_jc69_site_model html init_laplace_distr html init_log_normal_distr html init_mrca_prior html init_mrca_priors html init_normal_distr html init_one_div_x_distr html init_param html init_poisson_distr html init_rln_clock_model html init_site_models html init_strict_clock_model html init_tn93_site_model html init_tree_priors html init_uniform_distr html init_yule_tree_prior html interspace html is_alpha_param html is_b_pop_sizes_param html is_bd_tree_prior html is_beauti_options html is_beta_distr html is_beta_param html is_cbs_tree_prior html is_ccp_tree_prior html is_cep_tree_prior html is_clock_model html is_clock_model_name html is_clock_rate_param html is_default_mcmc html is_distr html is_distr_name html is_exp_distr html is_freq_equilibrium_name html is_freq_param html is_gamma_distr html is_gamma_site_model html is_gtr_site_model html is_hky_site_model html is_id html is_in_patterns html is_inference_model html is_init_bd_tree_prior html is_init_beta_distr html is_init_cbs_tree_prior html is_init_ccp_tree_prior html is_init_cep_tree_prior html is_init_clock_model html is_init_distr html is_init_exp_distr html is_init_gamma_distr html is_init_gamma_site_model html is_init_gtr_site_model html is_init_hky_site_model html is_init_inv_gamma_distr html is_init_jc69_site_model html is_init_laplace_distr html is_init_log_normal_distr html is_init_mrca_prior html is_init_normal_distr html is_init_one_div_x_distr html is_init_param html is_init_poisson_distr html is_init_rln_clock_model html is_init_site_model html is_init_strict_clock_model html is_init_tn93_site_model html is_init_tree_prior html is_init_uniform_distr html is_init_yule_tree_prior html is_inv_gamma_distr html is_jc69_site_model html is_kappa_1_param html is_kappa_2_param html is_kappa_param html is_lambda_param html is_laplace_distr html is_log_normal_distr html is_m_param html is_mcmc html is_mcmc_nested_sampling html is_mean_param html is_mrca_align_id_in_fasta html is_mrca_align_ids_in_fastas html is_mrca_prior html is_mrca_prior_with_distr html is_mu_param html is_normal_distr html is_on_appveyor html is_on_ci html is_on_github_actions html is_on_travis html is_one_bool html is_one_div_x_distr html is_one_double html is_one_empty_string html is_one_int html is_one_na html is_one_string html is_one_string_that_is_a_number html is_param html is_param_name html is_phylo html is_poisson_distr html is_rate_ac_param html is_rate_ag_param html is_rate_at_param html is_rate_cg_param html is_rate_ct_param html is_rate_gt_param html is_rln_clock_model html is_s_param html is_scale_param html is_sigma_param html is_site_model html is_site_model_name html is_strict_clock_model html is_tn93_site_model html is_tree_prior html is_tree_prior_name html is_uniform_distr html is_xml html is_yule_tree_prior html jc69_site_model_to_xml_state html kappa_param_to_xml html m_param_to_xml html mcmc_to_xml_run html mcmc_to_xml_run_default html mcmc_to_xml_run_nested_sampling html mrca_prior_to_xml_prior_distr html mrca_prior_to_xml_state html mrca_prior_to_xml_taxonset html mrca_prior_to_xml_tracelog html mrca_priors_to_xml_prior_distr html no_taxa_to_xml_tree html parameter_to_xml html parameter_to_xml_kappa_1 html parameter_to_xml_kappa_2 html parameter_to_xml_lambda html parameter_to_xml_mean html parameter_to_xml_mu html parameter_to_xml_rate_ac html parameter_to_xml_rate_ag html parameter_to_xml_rate_at html parameter_to_xml_rate_cg html parameter_to_xml_rate_ct html parameter_to_xml_rate_gt html parameter_to_xml_scale html parameter_to_xml_sigma html remove_beautier_folder html remove_empty_lines html remove_multiline html rename_inference_model_filenames html rename_mcmc_filenames html rln_clock_model_to_xml_mean_rate_prior html rln_clock_model_to_xml_operators html rln_clock_model_to_xml_prior_distr html rln_clock_model_to_xml_state html rln_clock_model_to_xml_tracelog html rnd_phylo_to_xml_init html s_parameter_to_xml html site_model_to_xml_operators html site_model_to_xml_prior_distr html site_model_to_xml_state html site_model_to_xml_tracelog html site_models_to_xml_operators html site_models_to_xml_prior_distr html site_models_to_xml_tracelog html strict_clock_model_to_xml_operators html strict_clock_model_to_xml_prior_distr html strict_clock_model_to_xml_state html strict_clock_model_to_xml_tracelog html taxa_to_xml_tree html tipdate_taxa_to_xml_trait html tipdate_taxa_to_xml_tree html tn93_site_model_to_xml_prior_distr html tn93_site_model_to_xml_state html tree_model_to_tracelog_xml html tree_prior_to_xml_operators html tree_prior_to_xml_prior_distr html tree_prior_to_xml_state html tree_prior_to_xml_tracelog html tree_priors_to_xml_prior_distr html tree_priors_to_xml_tracelog html unindent html yule_tree_prior_to_xml_operators html yule_tree_prior_to_xml_prior_distr html *** copying figures ** building package indices ** installing vignettes ** 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 (beautier)