* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘HaDeX2’ ...
** this is package ‘HaDeX2’ version ‘1.0.0’
** package ‘HaDeX2’ 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 ‘HaDeX2’
    finding HTML links ... done
    HaDeX2-package                          html  
    HaDeX_GUI                               html  
    HaDeXify                                html  
    add_stat_dependency                     html  
    alpha_dat                               html  
    calculate_MHP                           html  
    calculate_aggregated_diff_uptake        html  
    calculate_aggregated_test_results       html  
    calculate_aggregated_uptake             html  
    calculate_auc                           html  
    calculate_back_exchange                 html  
    calculate_confidence_limit_values       html  
    calculate_diff_uptake                   html  
    calculate_exp_masses                    html  
    calculate_exp_masses_per_replicate      html  
    calculate_kinetics                      html  
    calculate_p_value                       html  
    calculate_peptide_kinetics              html  
    calculate_state_uptake                  html  
    create_aggregated_diff_uptake_dataset   html  
    create_aggregated_uptake_dataset        html  
    create_control_dataset                  html  
    create_diff_uptake_dataset              html  
    create_kinetic_dataset                  html  
    create_overlap_distribution_dataset     html  
    create_p_diff_uptake_dataset            html  
    create_p_diff_uptake_dataset_with_confidence
                                            html  
    create_quality_control_dataset          html  
    create_replicate_dataset                html  
    create_state_comparison_dataset         html  
    create_state_uptake_dataset             html  
    create_uptake_dataset                   html  
    get_n_replicates                        html  
    get_peptide_sequence                    html  
    get_protein_coverage                    html  
    get_protein_redundancy                  html  
    get_replicate_list_sd                   html  
    get_residue_positions                   html  
    get_structure_color                     html  
    hdx_data                                html  
    install_GUI                             html  
    is_GUI_installed                        html  
    new_hdx_data                            html  
    plot_aggregated_differential_uptake     html  
    plot_aggregated_uptake                  html  
    plot_aggregated_uptake_structure        html  
    plot_amino_distribution                 html  
    plot_butterfly                          html  
    plot_chiclet                            html  
    plot_coverage                           html  
    plot_coverage_heatmap                   html  
    plot_differential                       html  
    plot_differential_butterfly             html  
    plot_differential_chiclet               html  
    plot_differential_uptake_curve          html  
    plot_manhattan                          html  
    plot_overlap                            html  
    plot_overlap_distribution               html  
    plot_peptide_charge_measurement         html  
    plot_peptide_mass_measurement           html  
    plot_position_frequency                 html  
    plot_quality_control                    html  
    plot_replicate_histogram                html  
    plot_replicate_mass_uptake              html  
    plot_state_comparison                   html  
    plot_uncertainty                        html  
    plot_uptake_curve                       html  
    plot_volcano                            html  
    prepare_hdxviewer_export                html  
    read_hdx                                html  
    reconstruct_sequence                    html  
    show_aggregated_uptake_data             html  
    show_coverage_heatmap_data              html  
    show_diff_uptake_data                   html  
    show_diff_uptake_data_confidence        html  
    show_overlap_data                       html  
    show_p_diff_uptake_data                 html  
    show_peptide_charge_measurement         html  
    show_peptide_mass_measurement           html  
    show_quality_control_data               html  
    show_replicate_histogram_data           html  
    show_summary_data                       html  
    show_uc_data                            html  
    show_uptake_data                        html  
    update_hdexaminer_file                  html  
    validate_hdx_data                       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 (HaDeX2)