* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘Claddis’ ...
** 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)