New R User Configuration

Introduction

This chapters serves as a step-by-step guide for downloading & installing software, setting software configurations, and creating necessary directories. See each section for details

Lets Get Started!

Please read through each section before downloading, installing, and saving to file locations!!

Throughout this document, you will be given code to run. To copy & paste, hover over the code, and click the clipboard icon in the upper right-hand corner. If you have any questions or problems, please contact a CAAT Team member.

Folders & Software

The large chunk of code below will do the following:

Create Required Folders:

Software –>
- GitLocal
- Git
- R

Create Required Files:

.Renviron– creates global environment variables that load during each R session; this file and its contents is important for package management and reproducibility purposes.
Rprofile.site– sets global R options, default package repositories, and download methods; it is also important for package management and reproducibility purposes.

Download & Install Software:

R Version 4.5.1– Currently most compatible version of R
RTOOLS45– necessary to compile packages.
Git– important for version control and collaboration
Download RStudio and redirect you to the DAYS EITS Software Request Page (see Requesting RStudio Installation below for details)

To run the code below:

Type: Win + R to open the Run prompt

Type “powershell” + Enter to open PowerShell

In PowerShell, paste and run the following:


function Start-Countdown {

    param(

        [int]$seconds

    )

    Write-Host "Download and installation of R, Git, and RTOOLS44; and download of RStudio will begin shortly." -ForegroundColor Magenta

    Write-Host "If you need to cancel, please close the window"

    Write-Host "This will take a few minutes!"

    Write-Host "$seconds" -ForegroundColor Magenta

    while ($seconds -gt 0) {

        Start-Sleep -Seconds 1

        $seconds--

        Write-Host "$seconds" -ForegroundColor Magenta

    }

    Write-Host "Initiating..."

    Start-Sleep -Seconds 1

}


Start-Countdown -seconds 10
 

New-Item -Path "$home/Software/GitLocal" -Type Directory

New-Item -Path "$home/Software/R" -Type Directory
 

$softwareDEST = "$home\Software"

$rEnvironPath = "$home\Software\R\.Renviron"

$rProfileSitePath = "$home\Software\R\Rprofile.site"


Add-Content -Path $rProfileSitePath -Value ('local({

    r <- getOption("repos")

    r["CRAN"] <- "http://cran.rstudio.com/"

    options(

      list(

        download.file.method = "libcurl",

        repos = r,

        scipen = 999

      )

    )

    })')


Write-Host "Rprofile.site created and added to file: $rProfileSitePath" -ForegroundColor Green
 

Add-Content -Path $rEnvironPath -Value ('R_USER="' + $softwareDEST + '\R"')

Add-Content -Path $rEnvironPath -Value ('R_PROFILE="' + $softwareDEST + '\R\Rprofile.site"')

Add-Content -Path $rEnvironPath -Value ('RTOOLS45_HOME="' + $softwareDEST + '\R\RTOOLS45"')

Add-Content -Path $rEnvironPath -Value ('PATH="${RTOOLS45_HOME}\usr\bin;${PATH}"')


Write-Host "`n.Renviron created and added to file: $rEnvironPath" -ForegroundColor Green
 

$rURL = "https://cran.r-project.org/bin/windows/base/R-4.5.1-win.exe"

$rDEST = "$home\Downloads\R-4.5.1-win.exe"

$rInstallDirectory = "$softwareDEST\R\R-4.5.1"

$rCommandLine = "$rDEST /SILENT /DIR=$rInstallDirectory"


Write-Host "`nDownloading R from: $rURL"

Write-Host "`nPlease Wait..."

Invoke-WebRequest -Uri $rURL -OutFile $rDEST
 

Write-Host "`nR Download Success" -ForegroundColor Green


Start-Process -FilePath "cmd.exe" -ArgumentList "/c $rCommandLine" -Wait

Write-Host "`nR Installed to: $rInstallDirectory" -ForegroundColor Green


$RTOOLS45URL = "https://cran.r-project.org/bin/windows/Rtools/rtools45/files/rtools45-6608-6492.exe"

$RTOOLS45DEST = "$home\Downloads\rtools45-6608-6492.exe"

$rtoolsInstallDirectory = "$softwareDEST\R\rtools45"

$rtoolsCommandLine = "$RTOOLS45DEST /SILENT /DIR=$rtoolsInstallDirectory"


Write-Host "`nDownloading RTOOLS45 from: $RTOOLS45URL"

Write-Host "`nPlease Wait..."

Invoke-WebRequest -Uri $RTOOLS44URL -OutFile $RTOOLS44DEST

Write-Host "`nRTOOLS45 Download Success" -ForegroundColor Green


Start-Process -FilePath "cmd.exe" -ArgumentList "/c $rtoolsCommandLine" -Wait

Write-Host "`nRTOOLS45 Installed to: $rtoolsInstallDirectory" -ForegroundColor Green

 
$gitURL = "https://github.com/git-for-windows/git/releases/download/v2.51.0.windows.2/Git-2.51.0.2-64-bit.exe"

$gitDEST = "$home\Downloads\Git-2.51.0.2-64-bit.exe"

$gitInstallDirectory = "$softwareDEST\Git"

$gitCommandLine = "$gitDEST /SILENT /DIR=$gitInstallDirectory"


Write-Host "`nDownloading Git from: $gitURL"

Write-Host "`nPlease Wait..."

Invoke-WebRequest -Uri $gitURL -OutFile $gitDEST

Write-Host "`nGit Download Success" -ForegroundColor Green


Start-Process -FilePath "cmd.exe" -ArgumentList "/c $gitCommandLine" -Wait

Write-Host "`nGit Installed to: $gitInstallDirectory" -ForegroundColor Green


$rstudioURL = "https://download1.rstudio.org/electron/windows/RStudio-2025.09.1-401.exe"

$rstudioDEST = "$home\Downloads\RStudio-2025.09.1-401.exe"
 

Write-Host "`nDownloading RStudio from: $rstudioURL. Please note you need admin access to install" -ForegroundColor Magenta


Write-Host "`nPlease Wait..."

Invoke-WebRequest -Uri $rstudioURL -OutFile $rstudioDEST

Write-Host "RStudio Downloaded $rstudioDEST" -ForegroundColor Green
 
Start-Process "https://youtu.be/QB7ACr7pUuE?si=KDnBoztaP3lUbGnv"

Write-Host "All Done! Please close this window" -ForegroundColor Magenta

You should now have:

Software/GitLocal folders

Software/R folders containing .Renviron and Rprofile.site files

R 4.5.1, Git, and {RTOOLS45} installed

Rstudio downloaded, but not yet installed

Requesting RStudio Installation

Configure RStudio

Open RStudio after EITS has installed RStudio

Install Packages Run the following chunk in the console to install these packages

install.packages("curl")   

install.packages("renv")   

install.packages("styler")  

install.packages("usethis")      

install.packages("tidyverse")

install.packages("readxl")

Configure Run the following chunk in the console to configure RStudio correctly

usethis::use_rstudio_preferences(

  check_arguments_to_r_function_calls = TRUE,

  check_for_updates = FALSE,

  check_unexpected_assignment_in_function_call = TRUE,

  default_project_location = Sys.getenv("R_USER"),

  git_exe_path = normalizePath(Sys.which("git"), "/"),

  highlight_r_function_calls = TRUE,

  jobs_tab_visibility = "shown",

  load_workspace = FALSE,

  pdf_previewer = "none",

  restore_last_project = FALSE,

  save_files_before_build = TRUE,

  save_workspace = "never",

  show_diagnostics_other = TRUE,

  source_with_echo = TRUE,

  style_diagnostics = TRUE,

  syntax_color_console = TRUE,

  use_secure_download = FALSE,

  warn_variable_defined_but_not_used = TRUE,

  windows_terminal_shell = "win-git-bash",

  rainbow_parentheses = TRUE

)

 

rstudioapi::executeCommand("restartR")