* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘Claddis’ ...
** this is package ‘Claddis’ version ‘0.7.0’
** package ‘Claddis’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘Claddis’
finding HTML links ... done
Claddis-package html
add_polymorphisms_to_costmatrix html
add_uncertainties_to_costmatrix html
align_matrix_block html
assign_taxa_to_bins html
bin_changes html
bin_character_completeness html
bin_edge_lengths html
build_cladistic_matrix html
calculate_MPD html
calculate_WMPD html
calculate_g html
calculate_gmax html
calculate_kardashian_index html
calculate_morphological_distances html
calculate_tree_length html
check_cladisticMatrix html
check_costMatrix html
check_stateGraph html
check_taxonGroups html
check_timeBins html
classify_costmatrix html
compactify_cladistic_matrix html
convert_adjacency_matrix_to_costmatrix
html
convert_costmatrix_to_stategraph html
convert_state_tree_to_adjacency_matrix
html
convert_stategraph_to_costmatrix html
count_cherries html
date_nodes html
day_2016 html
drop_time_tip html
estimate_ancestral_states html
estimate_squared_change_ancestors html
find_costmatrix_minimum_span html
find_descendant_edges html
find_linked_edges html
find_minimum_spanning_edges html
find_mrca html
find_shortest_costmatrix_path html
find_stategraph_minimum_span html
find_time_bin_midpoints html
find_unique_trees html
fix_costmatrix html
fix_root_time html
gauthier_1986 html
is.cladisticMatrix html
is.costMatrix html
is.stateGraph html
is.taxonGroups html
is.timeBins html
is_graph_connected html
locate_bracket_positions html
make_costmatrix html
make_labels html
map_dollo_changes html
match_tree_edges html
michaux_1989 html
ordinate_cladistic_matrix html
partition_time_bins html
permute_all_polymorphisms html
permute_all_treeshape_labellings html
permute_all_uncertainties html
permute_connected_graphs html
permute_costmatrices html
permute_graph_splits html
permute_restricted_compositions html
permute_tipstates html
permute_treeshapes html
plot_changes_on_tree html
plot_chronophylomorphospace html
plot_morphospace html
plot_morphospace_stack html
plot_multi_morphospace html
plot_rates_character html
plot_rates_time html
plot_rates_tree html
print.cladisticMatrix html
print.costMatrix html
print.stateGraph html
print.taxonGroups html
print.timeBins html
prune_cladistic_matrix html
read_nexus_matrix html
reconstruct_ancestral_states html
safe_taxonomic_reduction html
safe_taxonomic_reinsertion html
split_out_subgraphs html
test_rates html
trim_marginal_whitespace html
trim_matrix html
write_nexus_matrix html
write_tnt_matrix html
*** copying figures
** building package indices
** 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 (Claddis)