RStudio Server¶

Deep dive into the RStudio Server configuration and features.

Overview¶

RStudio Server provides the full RStudio IDE experience through your web browser. In DataSci Homelab, it's configured with:

• Pre-installed data science packages
• Opinionated but customizable defaults
• Vim keybindings (by default)
• Persistent package storage
• Quarto and LaTeX support

Accessing RStudio¶

URL: http://localhost:8787

Login:

• Username: Value of RSTUDIO_USER in .env (default: rstudio)
• Password: Value of RSTUDIO_PASSWORD in .env

Default Configuration¶

Editor Settings¶

Code Quality¶

Saving & Formatting¶

Diagnostics¶

Workspace¶

Pane Layout¶

The default pane layout is optimized for focused coding:

flowchart TB
    subgraph top[" "]
        direction LR
        A["Source<br>(Primary)"]
        B["Files / Plots<br>Help / Packages"]
    end

    subgraph bottom[" "]
        direction LR
        C["Console"]
        D["Environment<br>History / Git"]
    end

    top ~~~ bottom

    style A fill:#e3f2fd,stroke:#1976d2
    style B fill:#fff3e0,stroke:#f57c00
    style C fill:#e8f5e9,stroke:#388e3c
    style D fill:#fce4ec,stroke:#c2185b

With an additional source column enabled for side-by-side editing.

Package Management¶

Installing Packages¶

# Install from CRAN
install.packages("packagename")

# Install from GitHub
devtools::install_github("user/repo")

# Install from Bioconductor
BiocManager::install("packagename")

Where Packages Are Stored¶

Packages are installed to /usr/local/lib/R/site-library, which is mounted as a Docker volume. This means:

• ✓ Packages persist across container restarts
• ✓ Packages persist across image updates
• ✓ Packages are only lost if you delete the volume

Checking Installed Packages¶

# List all packages
installed.packages()

# Check specific package
packageVersion("tidyverse")

# Load package
library(tidyverse)

Quarto Integration¶

Quarto is pre-installed and integrated with RStudio.

Creating Documents¶

1. File → New File → Quarto Document
2. Choose format (HTML, PDF, Word)
3. Write your content
4. Click "Render" or use keyboard shortcut

Rendering from Console¶

# Render current document
quarto::quarto_render("document.qmd")

# Render to specific format
quarto::quarto_render("document.qmd", output_format = "pdf")

PDF Output¶

TinyTeX is pre-installed for PDF rendering:

# If you need additional LaTeX packages
tinytex::tlmgr_install("packagename")

Database Connections¶

PostgreSQL¶

library(DBI)
library(RPostgres)

con <- dbConnect(
  Postgres(),
  host = "your-host",
  dbname = "your-database",
  user = "your-user",
  password = "your-password"
)

dbListTables(con)
dbGetQuery(con, "SELECT * FROM table LIMIT 10")
dbDisconnect(con)

MySQL¶

library(DBI)
library(RMySQL)

con <- dbConnect(
  MySQL(),
  host = "your-host",
  dbname = "your-database",
  user = "your-user",
  password = "your-password"
)

DuckDB (Embedded)¶

library(duckdb)

con <- dbConnect(duckdb(), dbdir = "my_database.duckdb")
dbWriteTable(con, "mtcars", mtcars)
dbGetQuery(con, "SELECT * FROM mtcars WHERE mpg > 20")
dbDisconnect(con)

Git Integration¶

RStudio has built-in Git support:

Setup¶

# Configure git (first time only)
usethis::use_git_config(
  user.name = "Your Name",
  user.email = "your@email.com"
)

# Set up GitHub credentials
gitcreds::gitcreds_set()

Daily Workflow¶

1. Git pane (top-right by default) shows changed files
2. Stage files by checking boxes
3. Commit with message
4. Push/Pull using toolbar buttons

From Console¶

# Initialize a repo
usethis::use_git()

# Create GitHub repo
usethis::use_github()

Keyboard Shortcuts¶

With Vim keybindings enabled:

Normal Mode¶

Navigation¶

Customization¶

Changing Preferences¶

1. Tools → Global Options
2. Make your changes
3. Click OK

Changes are saved to ~/.config/rstudio/rstudio-prefs.json.

Syncing to Repository¶

To persist your preferences:

cp volumes/home/.config/rstudio/rstudio-prefs.json \
   config-overrides/rstudio-config/
git add config-overrides/rstudio-config/rstudio-prefs.json
git commit -m "Update RStudio preferences"

See Customization for more details.

Troubleshooting¶

RStudio Won't Load¶

# Check if the service is running
docker-compose logs homelab | grep -i rstudio

# Restart the container
docker-compose restart

Package Installation Fails¶

# Check for system dependencies
# Many R packages need system libraries

# Inside container, install system deps:
# sudo apt-get install libcurl4-openssl-dev

Blank Screen / Session Crash¶

# Clear RStudio session files
rm -rf volumes/home/.local/share/rstudio/sessions/*
docker-compose restart

Password Not Working¶

# Reset password
docker-compose exec homelab bash -c 'echo "$RSTUDIO_USER:newpassword" | chpasswd'