VSCode- & Cursor-friendly R configuration

Rconfig.R

#!/usr/bin/env Rscript
# R Setup Script
# Author: Christopher Smith
# Date: 2024-10-07

# Prerequisites: Install R and IDE (manual steps, not included in script)

# Define the mirror URL (edit as needed)
cran_mirror <- "https://lib.stat.cmu.edu/R/CRAN/"

# Get the HOME directory, which is where R looks for .Renviron
# Note: gsub is used to replace backslashes with forward slashes
home_dir <- gsub("\\\\", "/", Sys.getenv("HOME"))

# Get the USERPROFILE directory, which on Windows systems with OneDrive
# may be a better choice than HOME for library paths (because R sets
# HOME to the Documents folder like some kind of psychopath)
userprofile_dir <- gsub("\\\\", "/", Sys.getenv("USERPROFILE"))

# Define the library path in a cross-platform compatible way
lib_path <- if (Sys.info()["sysname"] == "Darwin") {
  file.path(home_dir, "Library/R/library")
} else {
  file.path(userprofile_dir, ".R/library")
}

# Define the path to the .Renviron file
renviron_path <- file.path(home_dir, ".Renviron")

# Create the .Renviron file if it doesn't exist
if (!file.exists(renviron_path)) {
  file.create(renviron_path)
}

# Create the R_LIBS_USER line to be added to .Renviron
r_libs_user_line <- sprintf("R_LIBS_USER=%s", lib_path)

# Append the R_LIBS_USER line to .Renviron if it doesn't already exist
if (!any(grepl("^R_LIBS_USER=", readLines(renviron_path)))) {
  cat(r_libs_user_line, file = renviron_path, append = TRUE, sep = "\n")
  cat("Added R_LIBS_USER to .Renviron\n")
} else {
  cat("R_LIBS_USER already exists in .Renviron. Skipping...\n")
}

# Reload .Renviron to apply changes to the current environment
readRenviron(renviron_path)

# Add the library path to .libPaths()
.libPaths(lib_path)

# Create the library directory if it doesn't exist
if (!dir.exists(lib_path)) {
  success <- dir.create(lib_path, recursive = TRUE, showWarnings = TRUE)
  if (!success) {
    stop("Failed to create library directory at: ", lib_path,
         "\nPlease check permissions and ensure parent directories exist.")
  }
  cat("Successfully created library directory at: ", lib_path, "\n")
} else {
  cat("Library directory already exists at: ", lib_path, "\n")
}

# Verify the directory exists and is writable before proceeding
if (!dir.exists(lib_path)) {
  stop("Library directory does not exist: ", lib_path)
}
if (!file.access(lib_path, mode = 2) == 0) {
  stop("Library directory is not writable: ", lib_path)
}

# Define the path to the .Rprofile file
rprofile_path <- file.path(home_dir, ".Rprofile")

# Create the .Rprofile file if it doesn't exist
if (!file.exists(rprofile_path)) {
  file.create(rprofile_path)
}

# Content to be added to .Rprofile
rprofile_content <- sprintf('
if (file.exists("~/.Renviron")) {
  readRenviron("~/.Renviron")
}
options(repos = c(CRAN = "%s"))
', cran_mirror)

# Read existing .Rprofile content
existing_content <- readLines(rprofile_path, warn = FALSE)

# Check if the content already exists
if (!any(grepl("readRenviron\\(\"~/.Renviron\"\\)", existing_content)) &&
      !any(grepl(sprintf("options\\(repos = c\\(CRAN = \"%s\"\\)\\)",
                         cran_mirror), existing_content))) {

  # Append the new content to .Rprofile
  cat(rprofile_content, file = rprofile_path, append = TRUE)
  cat("Added necessary lines to .Rprofile\n")
} else {
  cat("Required content already exists in .Rprofile. Skipping...\n")
}

# Execute the contents of the .Rprofile file
source(rprofile_path)

# Install user-level packages
install.packages(c("devtools", "renv", "httpgd"), lib = lib_path)
install.packages("languageserver", repos = c(
  reditorsupport = "https://reditorsupport.r-universe.dev",
  getOption("repos")
), lib = lib_path)

# Note: Changes to .Rprofile will take effect in the next R session
cat("Note: Restart R for changes in .Rprofile to take effect.\n")
cat("After restart, run print(.libPaths()) to verify the library path\n")
cat("and print(options()$repos) to verify the mirror setting.\n")

When initially running this script it executed partially, creating the parent directories and beginning to download packages. When re-running, it then failed with the error:

"Failed to create library directory at: [path] Please check permissions and ensure parent directories exist."

This happens because the script doesn't handle cases where dir.create() returns FALSE differently, one being when the directory already exists (rather than when it fails be created).

The fix which worked for me was replacing:

# Create the library directory - Added error checking
if (!dir.create(lib_path, recursive = TRUE, showWarnings = FALSE)) {
  stop("Failed to create library directory at: ", lib_path,
       "\nPlease check permissions and ensure parent directories exist.")
}

With:

# Create the library directory if it doesn't exist
if (!dir.exists(lib_path)) {
  success <- dir.create(lib_path, recursive = TRUE, showWarnings = TRUE)
  if (!success) {
    stop("Failed to create library directory at: ", lib_path,
         "\nPlease check permissions and ensure parent directories exist.")
  }
  cat("Successfully created library directory at: ", lib_path, "\n")
} else {
  cat("Library directory already exists at: ", lib_path, "\n")
}

This solved the permission errors that happen if you execute it multiple times (on macOS executing via cursor "Run Source" button). My forked version is here

Thanks; I just updated!

Hi Christopher thanks for making this script, super helpful tutorial! I've tried your script, seems like "httpgd" is removed from CRAN... Is there another way around this?

I also wonder if you have experience creating R package using Cursor? Lots of the bells and whistles of R package creation I learnt was based on RStudio, so I wonder if anyone else tried doing this using Cursor.

Hi Christopher thanks for making this script, super helpful tutorial! I've tried your script, seems like "httpgd" is removed from CRAN... Is there another way around this?

Oh, wow! Well, you can always install from Github: remotes::install_github("nx10/httpgd")

I also wonder if you have experience creating R package using Cursor? Lots of the bells and whistles of R package creation I learnt was based on RStudio, so I wonder if anyone else tried doing this using Cursor.

Yes, I regularly create R packages in Cursor. For the most part, the menu options in RStudio are really just running R commands under the hood. Pretty much everything you need is easily available from the R terminal with usethis and devtools.

Following the instructions in the your video, I cloned your Rconfig.R, which has caused the default URL for my R package installations to always be "https://lib.stat.cmu.edu/R/CRAN/". When I try to modify my default CRAN in the global options, it shows "CRAN repositories modified outside package preferences". Could you tell me how to change it back to my default URL? I have tried many methods, but when I install R packages, it always defaults to opening "https://lib.stat.cmu.edu/R/CRAN/". And two types of installation paths have also appeared. Could you tell me the solution? THANK YOU.

The script adds this CRAN mirror URL to your .Rprofile.

To get the path to the .Rprofile, run:

rprofile_path <- file.path(home_dir, ".Rprofile")
print(rprofile_path)

Open the file in a text editor such as Notepad, RStudio, or VSCode, and remove the line that reads,

options(repos = c(CRAN = "https://lib.stat.cmu.edu/R/CRAN/"))

The script adds this CRAN mirror URL to your .Rprofile.

To get the path to the .Rprofile, run:

rprofile_path <- file.path(home_dir, ".Rprofile")
print(rprofile_path)

Open the file in a text editor such as Notepad, RStudio, or VSCode, and remove the line that reads,

options(repos = c(CRAN = "https://lib.stat.cmu.edu/R/CRAN/"))

Thanks, christopher. I have successfully solved this problem, and I appreciate your reply.