* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘beastier’ ... ** package ‘beastier’ 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 ‘beastier’ finding HTML links ... done add_quotes_if_has_spaces html are_beast2_input_lines html are_beast2_input_lines_deep html are_beast2_input_lines_fast html are_identical_alignments html beast2_options_to_table html beastier-package html beastier_report html check_beast2 html check_beast2_options html check_beast2_options_data_types html check_beast2_options_do_not_overwrite_existing_files html check_beast2_options_filenames_differ html check_beast2_options_names html check_beast2_optionses html check_beast2_path html check_can_create_dir_for_state_output_file html check_can_create_file html check_can_create_screenlog_file html check_can_create_state_output_file html check_can_create_tracelog_file html check_can_create_treelog_file html check_empty_beastier_folder html check_empty_beaustier_folders html check_input_filename html check_input_filename_validity html check_n_threads html check_os html check_rng_seed html continue_beast2 html create_beast2_continue_cmd_from_options html create_beast2_input_file_folder html create_beast2_options html create_beast2_run_cmd html create_beast2_run_cmd_from_options html create_beast2_screenlog_folder html create_beast2_state_output_file_folder html create_beast2_tracelog_folder html create_beast2_treelog_folder html create_beast2_validate_cmd html create_beast2_validate_cmd_bin html create_beast2_validate_cmd_jar html create_beast2_version_cmd html create_beast2_version_cmd_bin html create_beast2_version_cmd_jar html create_beastier_tempfolder html create_mcbette_beast2_options html create_random_alignment html create_random_fasta html create_random_phylogeny html create_temp_input_filename html create_temp_state_filename html default_params_doc html do_minimal_run html extract_screenlog_filename_from_beast2_input_file html extract_tracelog_filename_from_beast2_input_file html extract_treelog_filename_from_beast2_input_file html get_alignment_ids_from_xml_filename html get_beast2_example_filename html get_beast2_example_filenames html get_beast2_main_class_name html get_beast2_options_filenames html get_beast2_version html get_beastier_folder html get_beastier_path html get_beastier_paths html get_beastier_tempfilename html get_default_beast2_bin_path html get_default_beast2_download_url html get_default_beast2_download_url_linux html get_default_beast2_download_url_win html get_default_beast2_folder html get_default_beast2_jar_path html get_default_beast2_path html get_default_beast2_version html get_default_java_path html get_duplicate_param_ids html get_java_version html get_trees_filenames html gives_beast2_warning html has_unique_ids html install_beast2 html is_alignment html is_beast2_input_file html is_beast2_installed html is_bin_path html is_jar_path html is_on_appveyor html is_on_ci html is_on_travis html is_win_bin_path html print_beast2_options html remove_beastier_folder html remove_beaustier_folders html remove_file_if_present html rename_beast2_options_filenames html run_beast2 html run_beast2_from_options html save_lines html save_nexus_as_fasta html uninstall_beast2 html upgrade_beast2 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 (beastier)