* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘metacoder’ ...
** package ‘metacoder’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/RtmpyqIyRi/R.INSTALL1a01409ce5f8e/metacoder/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c repel_boxes.cpp -o repel_boxes.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o metacoder.so RcppExports.o repel_boxes.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpyqIyRi/R.INSTALL1a01409ce5f8e/metacoder/src'
make[1]: Entering directory '/tmp/RtmpyqIyRi/R.INSTALL1a01409ce5f8e/metacoder/src'
make[1]: Leaving directory '/tmp/RtmpyqIyRi/R.INSTALL1a01409ce5f8e/metacoder/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-metacoder/00new/metacoder/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘metacoder’
finding HTML links ... done
DNAbin_to_char html
add_alpha html
all_functions html
all_names html
ambiguous_patterns html
ambiguous_synonyms html
apply_color_scale html
arrange_obs html
arrange_taxa html
as_id html
as_phyloseq html
finding level-2 HTML links ... done
branches html
calc_diff_abund_deseq2 html
calc_group_mean html
calc_group_median html
calc_group_rsd html
calc_group_stat html
calc_n_samples html
calc_obs_props html
calc_prop_samples html
calc_taxon_abund html
can_be_num html
can_be_used_in_taxmap html
capitalize html
check_class_col html
check_element_length html
check_for_pkg html
check_option_groups html
check_taxmap_data html
classifications html
compare_groups html
complement html
contains html
convert_base html
correct_taxon_names html
count_capture_groups html
counts_to_presence html
data_used html
database_list html
desc_font html
diverging_palette html
do_calc_on_num_cols html
dot-onAttach html
edge_list_depth html
ends_with html
error_font html
everything html
ex_hierarchies html
ex_hierarchy1 html
ex_hierarchy2 html
ex_hierarchy3 html
ex_taxmap html
extract_tax_data html
fasta_headers html
filter_ambiguous_taxa html
filter_obs html
filter_taxa html
filtering-helpers html
get_class_from_el html
get_data html
get_data_frame html
get_database_name html
get_dataset html
get_dots_or_list html
get_edge_children html
get_edge_parents html
get_expected_data html
get_node_children html
get_numeric_cols html
get_numerics html
get_optimal_range html
get_sort_var html
get_taxmap_cols html
get_taxmap_data html
get_taxmap_other_cols html
get_taxmap_table html
get_taxonomy_levels html
grapes-greater-than-grapes html
heat_tree html
heat_tree_matrix html
hierarchies html
hierarchy html
highlight_taxon_ids html
hmp_otus html
hmp_samples html
id_classifications html
init_taxmap_data html
inter_circle_gap html
internodes html
inverse html
is_ambiguous html
is_branch html
is_internode html
is_leaf html
is_root html
is_stem html
label_bounds html
layout_functions html
leaves html
leaves_apply html
length_of_thing html
limited_print html
line_coords html
look_for_na html
lookup_tax_data html
make_dada2_asv_table html
make_dada2_tax_table html
make_fasta_with_u_replaced html
make_plot_legend html
map_data html
map_data_ html
map_unique html
matches html
metacoder html
molten_dist html
multi_sep_split html
mutate_obs html
my_print html
n_leaves html
n_leaves_1 html
n_obs html
n_obs_1 html
n_subtaxa html
n_subtaxa_1 html
n_supertaxa html
n_supertaxa_1 html
name_font html
names_used html
ncbi_sequence html
ncbi_taxon_sample html
num_range html
obs html
obs_apply html
one_of html
parse_dada2 html
parse_dataset html
parse_edge_list html
parse_greengenes html
parse_heirarchies_to_taxonomy html
parse_mothur_tax_summary html
parse_mothur_taxonomy html
parse_newick html
parse_phylo html
parse_phyloseq html
parse_possibly_named_logical html
parse_primersearch html
parse_qiime_biom html
parse_raw_heirarchies_to_taxonomy html
parse_rdp html
parse_seq_input html
parse_silva_fasta html
parse_summary_seqs html
parse_tax_data html
parse_ubiome html
parse_unite_general html
polygon_coords html
prefixed_print html
primersearch html
primersearch_is_installed html
primersearch_raw html
print__character html
print__data.frame html
print__default_ html
print__factor html
print__integer html
print__list html
print__logical html
print__matrix html
print__numeric html
print__ordered html
print__tbl_df html
print__vector html
print_item html
print_tree html
progress_lapply html
punc_font html
qualitative_palette html
quantative_palette html
ranks_ref html
rarefy_obs html
read_fasta html
read_lines_apply html
remove_redundant_names html
replace_taxon_ids html
repo_url html
rescale html
rev_comp html
reverse html
roots html
run_primersearch html
sample_frac_obs html
sample_frac_taxa html
sample_n_obs html
sample_n_taxa html
scale_bar_coords html
select_labels html
select_obs html
simplify html
split_by_level html
starts_with html
startup_msg html
stems html
subtaxa html
subtaxa_apply html
supertaxa html
supertaxa_apply html
taxa html
taxmap html
taxon html
taxon_database html
taxon_id html
taxon_ids html
taxon_indexes html
taxon_name html
taxon_names html
taxon_rank html
taxon_ranks html
taxonomy html
taxonomy_table html
text_grob_length html
tid_font html
to_percent html
transform_data html
transmute_obs html
unique_mapping html
validate_regex_key_pair html
validate_regex_match html
validate_taxmap_funcs html
verify_color_range html
verify_label_count html
verify_size html
verify_size_range html
verify_taxmap html
verify_trans html
write_greengenes html
write_mothur_taxonomy html
write_rdp html
write_silva_fasta html
write_unite_general html
zero_low_counts html
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (metacoder)