##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL systemPipeR
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'systemPipeR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'systemPipeR'
    finding HTML links ... done
    EnvModules-class                        html  
    GOHyperGAll                             html  
    INTERSECTset-class                      html  
    LineWise-class                          html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-systemPipeR/00new/systemPipeR/help/linewise.html
    ParamFiles                              html  
    SPRproject                              html  
    SYSargs-class                           html  
    SYSargs2-class                          html  
    SYSargsList-class                       html  
    SYSargsList                             html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-systemPipeR/00new/systemPipeR/help/SYSargsList.html
    VENNset-class                           html  
    add-methods                             html  
    alignStats                              html  
    catDB-class                             html  
    catmap                                  html  
    check.output                            html  
    clusterRun                              html  
    config.param                            html  
    configWF                                html  
    countRangeset                           html  
    createParamFiles                        html  
    cwlFilesUpdate                          html  
    evalCode                                html  
    featureCoverage                         html  
    featuretypeCounts                       html  
    filterDEGs                              html  
    filterVars                              html  
    genFeatures                             html  
    importWF                                html  
    loadWorkflow                            html  
    mergeBamByFactor                        html  
    moduleload                              html  
    olBarplot                               html  
    olRanges                                html  
    output_update                           html  
    overLapper                              html  
    plotWF                                  html  
    plotfeatureCoverage                     html  
    plotfeaturetypeCounts                   html  
    predORF                                 html  
    preprocessReads                         html  
    readComp                                html  
    renderLogs                              html  
    renderReport                            html  
    returnRPKM                              html  
    runCommandline                          html  
    runDiff                                 html  
    runWF                                   html  
    run_DESeq2                              html  
    run_edgeR                               html  
    sal2bash                                html  
    sal2rmd                                 html  
    scaleRanges                             html  
    seeFastq                                html  
    showDF                                  html  
    subsetWF                                html  
    symLink2bam                             html  
    sysargs                                 html  
    systemArgs                              html  
    systemPipeR-package                     html  
    targets.as.df                           html  
    tryCMD                                  html  
    tryPath                                 html  
    variantReport                           html  
    vennPlot                                html  
    writeTargetsRef                         html  
    writeTargetsout                         html  
    write_SYSargsList                       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 (systemPipeR)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'ribor' is missing or broken
 done