* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘pepdiff’ ...
** this is package ‘pepdiff’ version ‘1.0.0’
** package ‘pepdiff’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘pepdiff’
    finding HTML links ... done
    apply_fdr_by_comparison                 html  
    assess_missing                          html  
    build_formula                           html  
    build_pairwise_results                  html  
    build_replicate_matrix                  html  
    build_results_tibble                    html  
    calc_rank_product                       html  
    calc_t_statistic                        html  
    check_zeros                             html  
    classify_bf_evidence                    html  
    combine_tech_reps                       html  
    compare                                 html  
    compare.data.frame                      html  
    compare_art                             html  
    compare_calls                           html  
    compare_glm                             html  
    compare_legacy                          html  
    compare_many                            html  
    compare_pairwise                        html  
    compare_pairwise_rankprod               html  
    compare_within_strata                   html  
    compute_design_summary                  html  
    compute_missingness                     html  
    estimate_result_clusters                html  
    extract_contrasts_art                   html  
    extract_contrasts_glm                   html  
    extract_diagnostics                     html  
    extract_stored_residuals                html  
    fc_qqplot                               html  
    fit_and_extract_art                     html  
    fit_and_extract_glm                     html  
    fit_art                                 html  
    fit_glm                                 html  
    fold_change_matrix                      html  
    get_all_residuals                       html  
    get_bootstrap_percentile                html  
    get_comparison                          html  
    get_kruskal_percentile                  html  
    get_peptide                             html  
    get_percentile_lowest_observed_value_iterative
                                            html  
    get_rp_percentile                       html  
    get_sig_rows                            html  
    get_wilcoxon_percentile                 html  
    has_sufficient_variation                html  
    import_data                             html  
    is_useable                              html  
    jzs_bf_approx                           html  
    kmeans_by_selected_cols                 html  
    list2mat                                html  
    log2_fc                                 html  
    long_results                            html  
    matrix_data                             html  
    mean_fold_change                        html  
    metrics                                 html  
    min_peptide_values                      html  
    missing_peptides_plot                   html  
    new_pepdiff_data                        html  
    new_pepdiff_results                     html  
    norm_qqplot                             html  
    p_value_hist                            html  
    pipe                                    html  
    plot.pepdiff_data                       html  
    plot.pepdiff_results                    html  
    plot_bf_distribution                    html  
    plot_distributions_simple               html  
    plot_fc                                 html  
    plot_fc_distribution_new                html  
    plot_fit_diagnostics                    html  
    plot_heatmap                            html  
    plot_kmeans                             html  
    plot_missingness_simple                 html  
    plot_pca                                html  
    plot_pca_simple                         html  
    plot_pvalue_histogram                   html  
    plot_quant_distributions                html  
    plot_result                             html  
    plot_volcano_bf                         html  
    plot_volcano_new                        html  
    print.pepdiff_data                      html  
    print.pepdiff_results                   html  
    print_diagnostic_summary                html  
    read_pepdiff                            html  
    replace_vals                            html  
    run_models                              html  
    select_columns_for_contrast             html  
    significant                             html  
    subset.pepdiff_data                     html  
    summary.pepdiff_data                    html  
    summary.pepdiff_results                 html  
    test_bayes_t                            html  
    test_bootstrap_t                        html  
    test_rankprod                           html  
    test_wilcoxon                           html  
    times_measured                          html  
    times_measured_plot                     html  
    validate_factors                        html  
    validate_pepdiff_data                   html  
    validate_pepdiff_results                html  
    validate_positive                       html  
    volcano_plot                            html  
*** copying figures
** 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 (pepdiff)