* 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
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are_equal_xml_lines html
are_equivalent_xml_files html
are_equivalent_xml_lines html
are_equivalent_xml_lines_all html
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are_site_models html
are_tree_priors html
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b_pop_sizes_parameter_to_xml html
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check_mcmc_values html
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check_site_models html
check_store_every html
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check_tracelog_values html
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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
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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
create_beast2_input_state html
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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
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create_hky_site_model html
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create_inference_model html
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create_jc69_subst_model_xml html
create_kappa_1_param html
create_kappa_2_param html
create_kappa_param html
create_lambda_param html
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create_loggers_xml html
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create_mcmc html
create_mean_param html
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create_one_div_x_distr html
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create_poisson_distr html
create_rate_ac_param html
create_rate_ag_param html
create_rate_at_param html
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create_rate_cg_param html
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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
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create_temp_tracelog_filename html
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create_test_inference_model html
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create_test_ns_mcmc html
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create_test_tracelog html
create_test_treelog html
create_tn93_site_model html
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create_treelog_xml html
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create_ucld_stdev_state_node_param_xml
html
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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
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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
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get_remove_dir_fun html
get_remove_hex_fun html
get_replace_dir_fun html
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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_xml_opening_tag html
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gtr_site_model_to_xml_state html
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init_site_models html
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init_tree_priors html
init_uniform_distr html
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interspace html
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kappa_param_to_xml html
m_param_to_xml html
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mcmc_to_xml_run_nested_sampling html
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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)