* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘Rclade’ ...
** this is package ‘Rclade’ version ‘1.1.5’
** package ‘Rclade’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘Rclade’
finding HTML links ... done
RCLADE_HADEAN_END html
RCLADE_X_MARGIN_FACTOR html
RCLADE_X_MIN_FLOOR html
SUPPORTED_TREE_EXTENSIONS html
add_clip_off html
add_geo_events html
add_geo_timescale html
add_hpd_range html
add_smart_legend html
add_support_labels html
annotate_clade html
batch_plot html
batch_with_interrupt html
build_base_tree html
build_full_taxa_df html
build_group_vec html
build_path html
build_plot_timetree_params html
build_taxonomy_lookup html
check_dependency html
check_example_tree html
check_input_validation html
check_malicious_chars html
check_monophyly html
check_monophyly_logic html
check_special_monophyly html
check_taxonomy_extraction html
cleanup_on_interrupt html
compute_legend_layout html
compute_mrca_map html
compute_time_breaks html
compute_x_min html
convert_unit html
detect_alphabet html
detect_encoding html
detect_sequence_format html
detect_taxonomy_format html
detect_tree_format html
dot-acquire_log_lock html
dot-rclade_extract_config html
dot-release_log_lock html
ensure_dir html
escape_regex html
example_tree html
find_rank_cycles html
format_elapsed html
format_step html
format_timestamp html
generate_colors html
get_dependency_versions html
get_git_hash html
get_level_prefix html
get_progress_summary html
get_rank_name html
get_supported_extensions html
get_taxonomy_levels html
get_version_string html
highlight_clades html
init_progress_tracking html
init_steps html
level_to_num html
log_critical html
log_debug html
log_error html
log_info html
log_keyvalue html
log_memory html
log_message html
log_progress html
log_section html
log_stats html
log_subsection html
log_table html
log_warning html
managed_tempdir html
managed_tempfile html
next_step html
normalize_file_newlines html
normalize_newlines html
normalize_rank html
parse_custom_rank html
parse_custom_regex html
parse_embedded html
parse_gtdb html
parse_ncbi html
parse_plot_params html
parse_semicolon_delimited html
parse_silva html
parse_taxonomy html
parse_taxonomy_with_file html
plot_timetree html
polytomy_tree html
prepare_geo_timescales html
print.rclade_options html
print_version html
pt_single_tree html
pt_step1_prepare_inputs html
pt_step2_resolve_taxonomy html
pt_step3_compute_mrca html
pt_step4_generate_colors html
pt_step5_render_and_collapse html
pt_step6_add_annotations html
pt_step7_finalize_plot html
rclade_logger html
rclade_logo html
rclade_options html
read_file_utf8 html
read_taxonomy_file html
read_tree_auto html
resolve_group html
resolve_special_identifier html
resolve_target_domains html
resolve_taxonomy_source_priority html
run_rclade_cli html
run_rclade_selftest html
run_rclade_shiny html
save_session_info html
save_timetree html
selftest_report html
set_log_enabled html
set_log_file html
set_log_level html
sort_by_depth html
split_legend html
strip_tree_annotations html
summarize_multi_trees html
summarize_taxonomy_quality html
summarize_taxonomy_quality_with_file html
summarize_timetree html
theme_timetree html
timer_start html
timer_stop html
update_progress html
validate_cli_params html
validate_collapse_plan html
validate_custom_groups html
validate_fasta_content html
validate_fastq_content html
validate_file_exists html
validate_file_not_empty html
validate_inputs html
validate_newick_syntax html
validate_sequence_deep html
validate_sequence_file html
validate_taxonomy_no_cycles html
validate_tree_deep html
validate_tree_sequence_match html
validate_tree_structure html
with_graceful_interrupt html
write_file_utf8 html
** 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 (Rclade)