* 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)