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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL SWATH2stats
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'SWATH2stats' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SWATH2stats'
    finding HTML links ... done
    JPP_update                              html  
    MSstats_data                            html  
    OpenSWATH_data                          html  
    Spyogenes                               html  
    Study_design                            html  
    add_genesymbol                          html  
    assess_decoy_rate                       html  
    assess_fdr_byrun                        html  
    assess_fdr_overall                      html  
    convert4MSstats                         html  
    convert4PECA                            html  
    convert4aLFQ                            html  
    convert4mapDIA                          html  
    convert4pythonscript                    html  
    convert_protein_ids                     html  
    count_analytes                          html  
    disaggregate                            html  
    filter_all_peptides                     html  
    filter_mscore                           html  
    filter_mscore_condition                 html  
    filter_mscore_fdr                       html  
    filter_mscore_freqobs                   html  
    filter_on_max_peptides                  html  
    filter_on_min_peptides                  html  
    filter_proteotypic_peptides             html  
    import_data                             html  
    load_mart                               html  
    mscore4assayfdr                         html  
    mscore4pepfdr                           html  
    mscore4protfdr                          html  
    plot.fdr_cube                           html  
    plot.fdr_table                          html  
    plot_correlation_between_samples        html  
    plot_variation                          html  
    plot_variation_vs_total                 html  
    reduce_OpenSWATH_output                 html  
    removeDecoyProteins                     html  
    rmDecoyProt                             html  
    sample_annotation                       html  
    transform_MSstats_OpenSWATH             html  
    unifyProteinGroupLabels                 html  
    validate_columns                        html  
    write_matrix_peptides                   html  
    write_matrix_proteins                   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 (SWATH2stats)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'TSCAN' is missing or broken
 done