* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘cape’ ...
** package ‘cape’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘cape’
    finding HTML links ... done
    Cape-class                              html  
    bin_curve                               html  
    bin_vector                              html  
    calc_delta_errors                       html  
    calc_emp_p                              html  
    calc_m                                  html  
    calc_p                                  html  
    cape2mpp                                html  
    center_std                              html  
    check_bad_markers                       html  
    check_communities                       html  
    check_geno                              html  
    check_underscore                        html  
    chunkV                                  html  
    colors_from_values                      html  
    compare_markers                         html  
    consec_pairs                            html  
    delete_underscore                       html  
    direct_influence                        html  
    draw_pie                                html  
    error_prop                              html  
    exp_color_fun                           html  
    flatten_array                           html  
    genome_wide_threshold_1D                html  
    get_allele_colors                       html  
    get_block_allele                        html  
    get_circle                              html  
    get_col_num                             html  
    get_color                               html  
    get_color2                              html  
    get_concent_circ                        html  
    get_covar                               html  
    get_eigentraits                         html  
    get_geno                                html  
    get_geno_dim                            html  
    get_geno_with_covar                     html  
    get_interaction_error                   html  
    get_layout_mat                          html  
    get_line                                html  
    get_linearly_independent                html  
    get_marker_chr                          html  
    get_marker_covar                        html  
    get_marker_idx                          html  
    get_marker_location                     html  
    get_marker_name                         html  
    get_marker_num                          html  
    get_network                             html  
    get_pairs_for_pairscan                  html  
    get_pheno                               html  
    get_stats_multiallele                   html  
    hist_pheno                              html  
    image_with_text                         html  
    impute_missing_geno                     html  
    kin_adjust                              html  
    kinship                                 html  
    linkage_blocks_network                  html  
    load_input_and_run_cape                 html  
    marker2covar                            html  
    my_image_plot                           html  
    norm_pheno                              html  
    one_pairscan_parallel                   html  
    one_singlescanDO                        html  
    pair_matrix                             html  
    pairscan                                html  
    pairscan_kin                            html  
    pairscan_noKin                          html  
    pairscan_null                           html  
    pairscan_null_kin                       html  
    pheatmap_generate_breaks                html  
    pheatmap_scale_colours                  html  
    pheno2covar                             html  
    plink2cape                              html  
    plot_bars                               html  
    plot_effects                            html  
    plot_full_network                       html  
    plot_int_heat                           html  
    plot_lines                              html  
    plot_network                            html  
    plot_pairscan                           html  
    plot_pheno_cor                          html  
    plot_points                             html  
    plot_singlescan                         html  
    plot_svd                                html  
    plot_trait_circ                         html  
    plot_variant_influences                 html  
    qnorm_pheno                             html  
    qtl2_to_cape                            html  
    read_parameters                         html  
    read_population                         html  
    remove_ind                              html  
    remove_kin_ind                          html  
    remove_markers                          html  
    remove_missing_genotype_data            html  
    remove_unused_markers                   html  
    report_progress                         html  
    rotate_mat                              html  
    run_cape                                html  
    rz_transform                            html  
    segment_region                          html  
    select_eigentraits                      html  
    select_markers_for_pairscan             html  
    select_pheno                            html  
    singlescan                              html  
    sort_by_then_by                         html  
    write_population                        html  
    write_variant_influences                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 (cape)