* 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  
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    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  
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    are_tree_priors                         html  
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    b_pop_sizes_parameter_to_xml            html  
    bd_tree_prior_to_xml_prior_distr        html  
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    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  
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    check_is_monophyletic                   html  
    check_log_mode                          html  
    check_log_sort                          html  
    check_mcmc                              html  
    check_mcmc_list_element_names           html  
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    check_mrca_prior_name                   html  
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    check_param_types                       html  
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    check_site_model_names                  html  
    check_site_model_types                  html  
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    check_strict_clock_model                html  
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    check_tracelog_names                    html  
    check_tracelog_values                   html  
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    clock_model_to_xml_operators            html  
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    clock_model_to_xml_treelogger           html  
    clock_rate_param_to_xml                 html  
    compare_lines                           html  
    count_trailing_spaces                   html  
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    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  
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    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  
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    create_beast2_input_run                 html  
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    create_beauti_options                   html  
    create_beauti_options_v2_4              html  
    create_beauti_options_v2_6              html  
    create_beautier_tempfolder              html  
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    create_clock_model_from_name            html  
    create_clock_models                     html  
    create_clock_models_from_names          html  
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    create_clock_rate_state_node_parameter_xml
                                            html  
    create_data_xml                         html  
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    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  
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    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  
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    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  
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    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  
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    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  
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    init_param                              html  
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    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  
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    is_beauti_options                       html  
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    is_cep_tree_prior                       html  
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    is_default_mcmc                         html  
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    is_freq_equilibrium_name                html  
    is_freq_param                           html  
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    is_id                                   html  
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    is_init_bd_tree_prior                   html  
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    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  
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    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  
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    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
* creating tarball
packaged installation of ‘beautier’ as ‘beautier_2.6.12_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (beautier)