Agent skill

r-cli-app

Build command-line apps in R using the Rapp package. Use when creating a CLI tool in R, adding argument parsing to an R script, turning an R script into a command-line app, shipping CLIs in an R package, or using Rapp (the alternative Rscript front-end). Also use for shebang scripts, exec/ directory in R packages, or subcommand-based R tools.

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npx add-skill https://github.com/posit-dev/skills/tree/main/r-lib/r-cli-app

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Additional technical details for this skill

author
Garrick Aden-Buie (@gadenbuie)
version
1.0

SKILL.md

Building CLI Apps with Rapp

Rapp (v0.3.0) is an R package that provides a drop-in replacement for Rscript that automatically parses command-line arguments into R values. It turns simple R scripts into polished CLI apps with argument parsing, help text, and subcommand support — with zero boilerplate.

R ≥ 4.1.0 | CRAN: install.packages("Rapp") | GitHub: r-lib/Rapp

After installing, put the Rapp launcher on PATH:

r
Rapp::install_pkg_cli_apps("Rapp")

This places the Rapp executable in ~/.local/bin (macOS/Linux) or %LOCALAPPDATA%\Programs\R\Rapp\bin (Windows).


Core Concept: Scripts Are the Spec

Rapp scans top-level expressions of an R script and converts specific patterns into CLI constructs. This means:

  1. The same script works identically via source() and as a CLI tool.
  2. You write normal R code — Rapp infers the CLI from what you write.
  3. Default values in your R code become the CLI defaults.

Only top-level assignments are recognized. Assignments inside functions, loops, or conditionals are not parsed as CLI arguments.


Pattern Recognition: R → CLI Mapping

This table is the heart of Rapp — each R pattern automatically maps to a CLI surface:

R Top-Level Expression CLI Surface Notes
foo <- "text" --foo <value> String option
foo <- 1L --foo <int> Integer option
foo <- 3.14 --foo <float> Float option
foo <- TRUE / FALSE --foo / --no-foo Boolean toggle
foo <- NA_integer_ --foo <int> Optional integer (NA = not set)
foo <- NA_character_ --foo <str> Optional string (NA = not set)
foo <- NULL positional arg Required by default
foo... <- NULL variadic positional Zero or more values
foo <- c() repeatable --foo Multiple values as strings
foo <- list() repeatable --foo Multiple values parsed as YAML/JSON
switch("", cmd1={}, cmd2={}) subcommands app cmd1, app cmd2
switch(cmd <- "", ...) subcommands Same; captures command name in cmd

Type behavior

  • Non-string scalars are parsed as YAML/JSON at the CLI and coerced to the R type of the default. n <- 5L means --n 10 gives integer 10L.
  • NA defaults signal optional arguments. Test with !is.na(myvar).
  • Snake case variable names map to kebab-case: n_flips--n-flips.
  • Positional args always arrive as character strings — convert manually.

Script Structure

Shebang line

r
#!/usr/bin/env Rapp

Makes the script directly executable on macOS/Linux after chmod +x. On Windows, call Rapp myscript.R explicitly.

Front matter metadata

Hash-pipe comments (#|) before any code set script-level metadata:

r
#!/usr/bin/env Rapp
#| name: my-app
#| title: My App
#| description: |
#|   A short description of what this app does.
#|   Can span multiple lines using YAML block scalar `|`.

The name: field sets the app name in help output (defaults to filename).

Per-argument annotations

Place #| comments immediately before the assignment they annotate:

r
#| description: Number of coin flips
#| short: 'n'
flips <- 1L

Available annotation fields:

Field Purpose
description: Help text shown in --help
title: Display title (for subcommands and front matter)
short: Single-letter alias, e.g. 'n'-n
required: true/false — for positional args only
val_type: Override type: string, integer, float, bool, any
arg_type: Override CLI type: option, switch, positional
action: For repeatable options: replace or append

Add #| short: for frequently-used options — users expect single-letter shortcuts for common flags like verbose (-v), output (-o), or count (-n).


Named Options

Scalar literal assignments become named options:

r
name <- "world"          # --name <value>    (string, default "world")
count <- 1L              # --count <int>     (integer, default 1)
threshold <- 0.5         # --threshold <flt> (float, default 0.5)
seed <- NA_integer_      # --seed <int>      (optional, NA if omitted)
output <- NA_character_  # --output <str>    (optional, NA if omitted)

For optional arguments, test whether the user supplied them:

r
seed <- NA_integer_
if (!is.na(seed)) set.seed(seed)

Boolean Switches

TRUE/FALSE assignments become toggles:

r
verbose <- FALSE   # --verbose or --no-verbose
wrap <- TRUE       # --wrap (default) or --no-wrap

Values yes/true/1 set TRUE; no/false/0 set FALSE.

Repeatable Options

r
pattern <- c()     # --pattern '*.csv' --pattern 'sales-*'  → character vector
threshold <- list() # --threshold 5 --threshold '[10,20]'   → list of parsed values

Positional Arguments

Assign NULL for positional args (required by default):

r
#| description: The input file to process.
input_file <- NULL

Make optional with #| required: false. Test with is.null(myvar).

Variadic positional args

Use ... suffix to collect multiple positional values:

r
pkgs... <- c()
# install-pkgs dplyr ggplot2 tidyr → pkgs... = c("dplyr", "ggplot2", "tidyr")

Subcommands

Use switch() with a string first argument to declare subcommands. Options before the switch() are global; options inside branches are local to that subcommand.

r
switch(
  command <- "",

  #| title: Display the todos
  list = {
    #| description: Max entries to display (-1 for all).
    limit <- 30L
    # ... list implementation
  },

  #| title: Add a new todo
  add = {
    #| description: Task description to add.
    task <- NULL
    # ... add implementation
  },

  #| title: Mark a task as completed
  done = {
    #| description: Index of the task to complete.
    index <- 1L
    # ... done implementation
  }
)

Help is scoped: myapp --help lists commands; myapp list --help shows list-specific options plus globals. Subcommands can nest by placing another switch() inside a branch.


Built-in Help

Every Rapp automatically gets --help (human-readable) and --help-yaml (machine-readable). These work with subcommands too.


Development and Testing

Use Rapp::run() to test scripts from an R session:

r
Rapp::run("path/to/myapp.R", c("--help"))
Rapp::run("path/to/myapp.R", c("--name", "Alice", "--count", "5"))

It returns the evaluation environment (invisibly) for inspection, and supports browser() for interactive debugging.


Complete Example: Coin Flipper

r
#!/usr/bin/env Rapp
#| name: flip-coin
#| description: |
#|   Flip a coin.

#| description: Number of coin flips
#| short: 'n'
flips <- 1L

sep <- " "
wrap <- TRUE

seed <- NA_integer_
if (!is.na(seed)) {
  set.seed(seed)
}

cat(sample(c("heads", "tails"), flips, TRUE), sep = sep, fill = wrap)
sh
flip-coin            # heads
flip-coin -n 3       # heads tails heads
flip-coin --seed 42 -n 5
flip-coin --help

Generated help:

Usage: flip-coin [OPTIONS]

Flip a coin.

Options:
  -n, --flips <FLIPS>  Number of coin flips [default: 1] [type: integer]
      --sep <SEP>      [default: " "] [type: string]
      --wrap / --no-wrap  [default: true]
      --seed <SEED>    [default: NA] [type: integer]

Complete Example: Todo Manager (Subcommands)

r
#!/usr/bin/env Rapp
#| name: todo
#| description: Manage a simple todo list.

#| description: Path to the todo list file.
#| short: s
store <- ".todo.yml"

switch(
  command <- "",

  list = {
    #| description: Max entries to display (-1 for all).
    limit <- 30L

    tasks <- if (file.exists(store)) yaml::read_yaml(store) else list()
    if (!length(tasks)) {
      cat("No tasks yet.\n")
    } else {
      if (limit >= 0L) tasks <- head(tasks, limit)
      writeLines(sprintf("%2d. %s\n", seq_along(tasks), tasks))
    }
  },

  add = {
    #| description: Task description to add.
    task <- NULL

    tasks <- if (file.exists(store)) yaml::read_yaml(store) else list()
    tasks[[length(tasks) + 1L]] <- task
    yaml::write_yaml(tasks, store)
    cat("Added:", task, "\n")
  },

  done = {
    #| description: Index of the task to complete.
    #| short: i
    index <- 1L

    tasks <- if (file.exists(store)) yaml::read_yaml(store) else list()
    task <- tasks[[as.integer(index)]]
    tasks[[as.integer(index)]] <- NULL
    yaml::write_yaml(tasks, store)
    cat("Completed:", task, "\n")
  }
)
sh
todo add "Write quarterly report"
todo list
todo list --limit 5
todo done 1
todo --store /tmp/work.yml list

Shipping CLIs in an R Package

Place CLI scripts in exec/ and add Rapp to Imports in DESCRIPTION:

mypkg/
├── DESCRIPTION
├── R/
├── exec/
│   ├── myapp       # script with #!/usr/bin/env Rapp shebang
│   └── myapp2
└── man/

Users install the CLI launchers after installing the package:

r
Rapp::install_pkg_cli_apps("mypkg")

Expose a convenience installer so users don't need to know about Rapp:

r
#' Install mypkg CLI apps
#' @export
install_mypkg_cli <- function(destdir = NULL) {
  Rapp::install_pkg_cli_apps(package = "mypkg", destdir = destdir)
}

By default, launchers set --default-packages=base,<pkg>, so only base and the package are auto-loaded. Use library() for other dependencies.


Quick Reference: Common Patterns

NA vs NULL for optional arguments

  • NA (NA_integer_, NA_character_) → optional named option. Test: !is.na(x).
  • NULL + #| required: false → optional positional arg. Test: !is.null(x).

stdin/stdout

r
input_file <- NA_character_
con <- if (is.na(input_file)) file("stdin") else file(input_file, "r")
lines <- readLines(con)
writeLines(lines, stdout())

Exit codes and stderr

r
message("Error: something went wrong")   # writes to stderr
cat("Error:", msg, "\n", file = stderr()) # also stderr
quit(status = 1)                          # non-zero exit

Error handling

r
tryCatch({
  result <- do_work()
}, error = function(e) {
  cat("Error:", conditionMessage(e), "\n", file = stderr())
  quit(status = 1)
})

Additional Reference

For less common topics — launcher customization (#| launcher: front matter), detailed Rapp::install_pkg_cli_apps() API options, and more complete examples (deduplication filter, variadic install-pkg, interactive fallback) — read references/advanced.md.

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