### Install R GitHub Dependency Interactively

Source: https://github.com/lorenzwalthert/precommit/wiki/GitHub-dependencies-can't-be-installed

Use this command to install an R GitHub dependency interactively after ensuring your `GITHUB_PAT` is set. This bypasses pre-commit's vanilla mode limitations.

```r
renv::install("tidyverse/dplyr")
```

--------------------------------

### Install Package Manually with renv

Source: https://github.com/lorenzwalthert/precommit/wiki/Packages-are-not-found-after-R-upgrade

After purging, reinstall the package using `renv::install` to add it to the cache with the correct version. This ensures it is available for pre-commit.

```R
renv::install('docopt')
```

--------------------------------

### Install Pre-commit Hooks

Source: https://github.com/lorenzwalthert/precommit/wiki/Packages-are-not-found-after-R-upgrade

After cleaning the cache, reinstall the pre-commit hooks to ensure they are linked with the correct R version.

```bash
pre-commit install --install-hooks
```

--------------------------------

### Configure CI with pre-commit.ci or GitHub Actions

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Sets up CI for running pre-commit hooks on pull requests. Supports pre-commit.ci ('native') or GitHub Actions ('gha'). Pass NA to skip CI setup.

```r
library(precommit)

# Set up pre-commit.ci (opens browser for GitHub authentication)
use_ci(ci = "native")
#> • Sign in with GitHub to authenticate https://pre-commit.ci and then come back...

# Set up GitHub Actions workflow instead
use_ci(ci = "gha", force = TRUE)
#> ✔ Added GitHub Action template to ".github/workflows/pre-commit.yaml".

# Persist preference in .Rprofile so use_precommit() picks it up automatically
# options(precommit.ci = "gha")
```

--------------------------------

### Set up pre-commit for a git repository

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

The primary onboarding function. Copies a template .pre-commit-config.yaml, runs autoupdate, installs git hooks, and optionally sets up CI. Detects R package vs. generic project for template selection.

```r
library(precommit)

# Basic setup — uses built-in template, sets up pre-commit.ci
use_precommit()

# Supply a custom config file from a URL
use_precommit(
  config_source = "https://raw.githubusercontent.com/org/repo/main/.pre-commit-config.yaml"
)

# Setup without CI, without autoupdate, removing any pre-existing legacy hooks
use_precommit(
  ci            = NA,
  autoupdate    = FALSE,
  legacy_hooks  = "remove",
  install_hooks = TRUE,
  root          = "/path/to/my/git/repo"
)
#>
#> ✔ Copied .pre-commit-config.yaml to /path/to/my/git/repo
#> ✔ Ran pre-commit autoupdate to get the latest version of the hooks.
#> ✔ Sucessfully installed pre-commit for repo.
```

--------------------------------

### Interactive Mode Notice for Programs

Source: https://github.com/lorenzwalthert/precommit/blob/main/LICENSE.md

Display this notice when a program starts in interactive mode to inform users about its licensing, warranty, and redistribution terms.

```text
precommit Copyright (C) 2019 Lorenz Watlhert
This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type 'show c' for details.
```

--------------------------------

### Configure Pre-Commit Hooks in .pre-commit-config.yaml

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Example configuration for an R package using the precommit repository. Pin to a specific release using 'rev' and specify hooks by 'id'. Some hooks accept 'args' or require 'additional_dependencies'.

```yaml
repos:
-   repo: https://github.com/lorenzwalthert/precommit
    rev: v0.4.3   # pin to a specific release
    hooks:
    # Style R/Rmd/Rnw/qmd files using {styler}
    -   id: style-files
        args: [--style_pkg=styler, --style_fun=tidyverse_style]

    # Run roxygen2::roxygenize() when roxygen comments change
    -   id: roxygenize
        additional_dependencies:
        -    your-pkg-dep-1
        -    your-pkg-dep-2

    # Run usethis::use_tidy_description() to normalize DESCRIPTION
    -   id: use-tidy-description

    # Spell check documentation with {spelling}
    -   id: spell-check
        exclude: '(?x)^(.*\[rR\]|.*\.png|.*\.pdf|(.*\/|)NAMESPACE)$'

    # Lint R files with {lintr}
    -   id: lintr

    # Ensure README.md is rendered from README.Rmd
    -   id: readme-rmd-rendered

    # Check R/Rmd files are syntactically valid
    -   id: parsable-R

    # Check roxygen comments are parsable
    -   id: parsable-roxygen

    # Forbid browser() statements
    -   id: no-browser-statement

    # Forbid print() statements
    -   id: no-print-statement

    # Forbid debug() / debugonce() statements
    -   id: no-debug-statement

    # Check package dependencies are declared in DESCRIPTION
    -   id: deps-in-desc

    # Validate pkgdown config with pkgdown::check_pkgdown()
    -   id: pkgdown

    # Keep codemeta.json in sync with DESCRIPTION
    -   id: codemeta-description-updated

    # Validate renv.lock against its JSON schema
    -   id: renv-lockfile-validate

```

--------------------------------

### Install pre-commit executable via conda

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Installs the pre-commit Python executable into the 'r-precommit' conda environment. Requires the reticulate package. Use `force = TRUE` to reinstall if needed.

```r
library(precommit)

# First-time installation (requires reticulate + conda)
install_precommit()
#>
#> ℹ Installing pre-commit into the conda environment `r-precommit`.
#> ✔ Sucessfully installed pre-commit on your system.
#> • To use it with this project, run `precommit::use_precommit()`

# Force reinstall (e.g., after conda environment corruption)
install_precommit(force = TRUE)

# Check the path to the installed executable
path_precommit_exec()
#>
#> [1] "/Users/you/miniforge3/envs/r-precommit/bin/pre-commit"
```

--------------------------------

### Get Path to pre-commit Executable

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Reads the R option `precommit.executable` and returns the path to the pre-commit executable. Optionally checks if the executable exists.

```r
library(precommit)

# Get current executable path (errors if not found)
path_precommit_exec()
#> [1] "/Users/you/miniforge3/envs/r-precommit/bin/pre-commit"

# Get path without existence check (useful for diagnostics)
path_precommit_exec(check_if_exists = FALSE)
#> [1] "/Users/you/miniforge3/envs/r-precommit/bin/pre-commit"

# Override executable path manually
options(precommit.executable = "/usr/local/bin/pre-commit")
path_precommit_exec()
#> [1] "/usr/local/bin/pre-commit"
```

--------------------------------

### use_precommit()

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

The primary function for setting up pre-commit for a git repository. It copies a template `.pre-commit-config.yaml` to the repository root, runs `autoupdate()` to pin hook revisions, installs the git hook script, and optionally sets up CI. It automatically detects whether the repository is an R package or a generic project to select the appropriate template.

```APIDOC
## use_precommit()

### Description
Sets up pre-commit for a git repository by copying a template `.pre-commit-config.yaml`, running `autoupdate()`, installing git hooks, and optionally configuring CI. Detects project type (R package or generic) for template selection.

### Method
`use_precommit(config_source = NULL, ci = TRUE, autoupdate = TRUE, legacy_hooks = "skip", install_hooks = TRUE, root = ".")`

### Parameters
#### Query Parameters
- **config_source** (string or NULL) - Optional - A URL or local path to a custom `.pre-commit-config.yaml` file. If NULL, uses a built-in template.
- **ci** (boolean or NA) - Optional - Whether to set up CI integration. Set to `NA` to disable.
- **autoupdate** (boolean) - Optional - Whether to run `pre-commit autoupdate()` after copying the config. Defaults to `TRUE`.
- **legacy_hooks** (string) - Optional - How to handle legacy hooks. Options: "skip", "remove". Defaults to "skip".
- **install_hooks** (boolean) - Optional - Whether to run `pre-commit install --install-hooks`. Defaults to `TRUE`.
- **root** (string) - Optional - The path to the repository root. Defaults to the current directory.

### Request Example
```r
library(precommit)

# Basic setup — uses built-in template, sets up pre-commit.ci
use_precommit()

# Supply a custom config file from a URL
use_precommit(
  config_source = "https://raw.githubusercontent.com/org/repo/main/.pre-commit-config.yaml"
)

# Setup without CI, without autoupdate, removing any pre-existing legacy hooks
use_precommit(
  ci            = NA,
  autoupdate    = FALSE,
  legacy_hooks  = "remove",
  install_hooks = TRUE,
  root          = "/path/to/my/git/repo"
)
```

### Response
#### Success Response (stdout)
- Informational messages indicating the steps performed (config copied, autoupdate run, hooks installed).

#### Response Example
```
#> ✔ Copied .pre-commit-config.yaml to /path/to/my/git/repo
#> ✔ Ran pre-commit autoupdate to get the latest version of the hooks.
#> ✔ Sucessfully installed pre-commit for repo.
```
```

--------------------------------

### install_precommit()

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Installs the upstream `pre-commit` Python executable into a dedicated conda environment (`r-precommit`). This makes the executable available system-wide for use in any git repository. Requires the `{reticulate}` package. Use `force = TRUE` to reinstall if an executable is already present.

```APIDOC
## install_precommit()

### Description
Installs the upstream `pre-commit` Python executable via conda into the `r-precommit` environment, making it available system-wide. Requires the `{reticulate}` package. Use `force = TRUE` to reinstall even if an executable is already detected.

### Method
`install_precommit(force = FALSE)`

### Parameters
#### Query Parameters
- **force** (boolean) - Optional - Use `TRUE` to force reinstallation even if an executable is already detected.

### Request Example
```r
library(precommit)

# First-time installation (requires reticulate + conda)
install_precommit()

# Force reinstall (e.g., after conda environment corruption)
install_precommit(force = TRUE)
```

### Response
#### Success Response (stdout)
- Informational messages about the installation process and success.

#### Response Example
```
#> ℹ Installing pre-commit into the conda environment `r-precommit`.
#> ✔ Sucessfully installed pre-commit on your system.
#> • To use it with this project, run `precommit::use_precommit()`
```
```

--------------------------------

### Pre-commit GitHub Dependency Installation Error

Source: https://github.com/lorenzwalthert/precommit/wiki/GitHub-dependencies-can't-be-installed

This error occurs when pre-commit exceeds GitHub's API rate limits while trying to download repositories specified in `.pre-commit-config.yaml`.

```text
Error: failed to resolve remote 'r-lib/pkgapi' -- failed to retrieve 'https://api.github.com/repos/r-lib/pkgapi' [error code 22]
In addition: Warning message:
curl: (22) The requested URL returned error: 401 
Traceback (most recent calls last):
```

--------------------------------

### Update pre-commit Executable

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Updates the `pre-commit` Python executable in the conda environment `r-precommit` to the latest version. Only works for conda installations and reports version changes.

```r
library(precommit)

# Update pre-commit executable
update_precommit()
#> ✔ Successfully updated pre-commit from version 3.5.0 to 3.7.1.

# If already at latest version
update_precommit()
#> ℹ Nothing to update, your version 3.7.1 is the latest available.
```

--------------------------------

### path_precommit_exec() — Get path to the pre-commit executable

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Reads the R option `precommit.executable` and returns the path to the pre-commit executable. Optionally checks if the executable exists at that path.

```APIDOC
## `path_precommit_exec()` — Get path to the pre-commit executable

Reads the R option `precommit.executable` and returns the path to the pre-commit executable. Optionally checks whether the executable exists at that path.

```r
library(precommit)

# Get current executable path (errors if not found)
path_precommit_exec()
#> [1] "/Users/you/miniforge3/envs/r-precommit/bin/pre-commit"

# Get path without existence check (useful for diagnostics)
path_precommit_exec(check_if_exists = FALSE)
#> [1] "/Users/you/miniforge3/envs/r-precommit/bin/pre-commit"

# Override executable path manually
options(precommit.executable = "/usr/local/bin/pre-commit")
path_precommit_exec()
#> [1] "/usr/local/bin/pre-commit"
```
```

--------------------------------

### update_precommit() — Update the pre-commit executable

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Updates the `pre-commit` Python executable in the conda environment `r-precommit` to the latest available version. This function only works for conda-based installations.

```APIDOC
## `update_precommit()` — Update the pre-commit executable

Updates the `pre-commit` Python executable in the conda environment `r-precommit` to the latest available version. Only works for conda-based installations. Reports old and new versions.

```r
library(precommit)

# Update pre-commit executable
update_precommit()
#> ✔ Successfully updated pre-commit from version 3.5.0 to 3.7.1.

# If already at latest version
update_precommit()
#> ℹ Nothing to update, your version 3.7.1 is the latest available.
```
```

--------------------------------

### use_ci() — Configure continuous integration for pre-commit

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Sets up CI for running pre-commit hooks on pull requests. Supports pre-commit.ci ('native') or GitHub Actions ('gha').

```APIDOC
## `use_ci()` — Configure continuous integration for pre-commit

Sets up CI for running pre-commit hooks on pull requests. Supports [pre-commit.ci](https://pre-commit.ci) (`"native"`) which requires only browser authentication, or GitHub Actions (`"gha"`) which writes a workflow file to `.github/workflows/pre-commit.yaml`. Pass `NA` to skip CI setup.

```r
library(precommit)

# Set up pre-commit.ci (opens browser for GitHub authentication)
use_ci(ci = "native")
#> • Sign in with GitHub to authenticate https://pre-commit.ci and then come back...

# Set up GitHub Actions workflow instead
use_ci(ci = "gha", force = TRUE)
#> ✔ Added GitHub Action template to `.github/workflows/pre-commit.yaml`.

# Persist preference in .Rprofile so use_precommit() picks it up automatically
# options(precommit.ci = "gha")
```
```

--------------------------------

### Standard Copyright and GPL Notice

Source: https://github.com/lorenzwalthert/precommit/blob/main/LICENSE.md

Include this notice at the beginning of each source file to state the copyright and terms of redistribution under the GNU GPL.

```text
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) 2019 Lorenz Watlhert

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.
```

--------------------------------

### Retrieve pre-commit Executable Version

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Returns the version string of the pre-commit executable by running `pre-commit --version`. Useful for conditional logic based on version.

```r
library(precommit)

version_precommit()
#> [1] "3.7.1"

# Use in conditional logic
if (package_version(version_precommit()) < "2.13.0") {
  warning("Please update pre-commit to >= 2.13.0 for full hook support.")
}
```

--------------------------------

### Open Config Files in RStudio

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Opens `.pre-commit-config.yaml` or `inst/WORDLIST` in the RStudio editor. These helpers wrap `rstudioapi::navigateToFile()` and require an active RStudio session.

```r
library(precommit)

# Open .pre-commit-config.yaml in the RStudio editor
open_config()

# Open inst/WORDLIST for managing spell-check exceptions
open_wordlist()

# Both accept a root argument for non-standard working directories
open_config(root = "/path/to/project")
open_wordlist(root = "/path/to/project")
```

--------------------------------

### version_precommit() — Retrieve the pre-commit executable version

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Returns the version string of the currently configured pre-commit executable by running `pre-commit --version`.

```APIDOC
## `version_precommit()` — Retrieve the pre-commit executable version

Returns the version string of the currently configured pre-commit executable by running `pre-commit --version`.

```r
library(precommit)

version_precommit()
#> [1] "3.7.1"

# Use in conditional logic
if (package_version(version_precommit()) < "2.13.0") {
  warning("Please update pre-commit to >= 2.13.0 for full hook support.")
}
```
```

--------------------------------

### open_config() / open_wordlist() — Open config files in RStudio

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Opens `.pre-commit-config.yaml` or `inst/WORDLIST` in the RStudio editor for interactive editing. These are convenience helpers that wrap `rstudioapi::navigateToFile()`.

```APIDOC
## `open_config()` / `open_wordlist()` — Open config files in RStudio

Opens `.pre-commit-config.yaml` or `inst/WORDLIST` in the RStudio editor for interactive editing. These are convenience helpers that wrap `rstudioapi::navigateToFile()` and require an active RStudio session.

```r
library(precommit)

# Open .pre-commit-config.yaml in the RStudio editor
open_config()

# Open inst/WORDLIST for managing spell-check exceptions
open_wordlist()

# Both accept a root argument for non-standard working directories
open_config(root = "/path/to/project")
open_wordlist(root = "/path/to/project")
```
```

--------------------------------

### use_precommit_config()

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Copies a `.pre-commit-config.yaml` file into the repository root from a specified source (local path, URL, or built-in template). For R packages, it also appends the config filename to `.Rbuildignore`. This function can be used independently to refresh or set up the configuration file.

```APIDOC
## use_precommit_config()

### Description
Copies a `.pre-commit-config.yaml` file into the repository root from a local path, URL, or a built-in template. For R packages, it also appends the config filename to `.Rbuildignore`. Can be called independently to refresh or set up the config file.

### Method
`use_precommit_config(config_source = NULL, force = FALSE, verbose = FALSE)`

### Parameters
#### Query Parameters
- **config_source** (string or NULL) - Optional - A URL, local path, or name of a built-in template for the `.pre-commit-config.yaml` file. If NULL, uses a built-in template.
- **force** (boolean) - Optional - Overwrite an existing `.pre-commit-config.yaml` file if it exists. Defaults to `FALSE`.
- **verbose** (boolean) - Optional - If `TRUE`, prints verbose output during the process. Defaults to `FALSE`.

### Request Example
```r
library(precommit)

# Use the built-in package template (auto-detects pkg vs project)
use_precommit_config()

# Use a custom local config
use_precommit_config(
  config_source = "~/dotfiles/.pre-commit-config.yaml",
  force = TRUE   # overwrite existing config
)

# Download from a remote URL
use_precommit_config(
  config_source = "https://raw.githubusercontent.com/lorenzwalthert/precommit/main/inst/pre-commit-config-proj.yaml",
  verbose = TRUE
)
```

### Response
#### Success Response (stdout)
- Informational messages about copying the config file, including download status if applicable.

#### Response Example
```
#> ℹ Downloading remote config from https://...
#> ✔ Copied .pre-commit-config.yaml to /your/project
```
```

--------------------------------

### Copy a pre-commit config file into a repo

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Copies a .pre-commit-config.yaml from a local path, URL, or built-in template into the repository root. For R packages, it also appends the config filename to .Rbuildignore. Can refresh the config file independently.

```r
library(precommit)

# Use the built-in package template (auto-detects pkg vs project)
use_precommit_config()

# Use a custom local config
use_precommit_config(
  config_source = "~/dotfiles/.pre-commit-config.yaml",
  force = TRUE   # overwrite existing config
)

# Download from a remote URL
use_precommit_config(
  config_source = "https://raw.githubusercontent.com/lorenzwalthert/precommit/main/inst/pre-commit-config-proj.yaml",
  verbose = TRUE
)
#>
#> ℹ Downloading remote config from https://...
#> ✔ Copied .pre-commit-config.yaml to /your/project
```

--------------------------------

### autoupdate()

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Runs the `pre-commit autoupdate` command to update the `rev:` field of each hook repository in the `.pre-commit-config.yaml` file to their latest tagged releases. It also performs validation for renv/pre-commit compatibility before proceeding with the update.

```APIDOC
## autoupdate()

### Description
Runs `pre-commit autoupdate` to update the `rev:` field of each hook repository in `.pre-commit-config.yaml` to the latest tagged release. Validates renv/pre-commit compatibility before updating.

### Method
`autoupdate(root = ".")`

### Parameters
#### Query Parameters
- **root** (string) - Optional - The path to the repository root where the `.pre-commit-config.yaml` file is located. Defaults to the current directory.

### Request Example
```r
library(precommit)

# Update all hook revisions to their latest tags in the current repository
autoupdate()

# Run in a specific repo root
autoupdate(root = "/path/to/project")
```

### Response
#### Success Response (stdout)
- Confirmation message that `pre-commit autoupdate` was run successfully.

#### Response Example
```
#> ✔ Ran pre-commit autoupdate to get the latest version of the hooks.
```
```

--------------------------------

### Generate additional dependencies for roxygenize hook

Source: https://github.com/lorenzwalthert/precommit/blob/main/NEWS.md

Use this snippet to generate the necessary code for the `additional_dependencies` field in `.pre-commit-config.yaml` when using the `roxygenize` hook. This ensures all package dependencies are listed for isolated hook environments.

```r
precommit::snippet_generate("additional-deps-roxygenize")
```

--------------------------------

### Uninstall pre-commit from Repo or System

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Removes pre-commit from the current repository (uninstalls hook, deletes config) or the system (removes conda environment). Interactive prompts can be suppressed.

```r
library(precommit)

# Remove pre-commit from current repo only (keeps system install)
uninstall_precommit(scope = "repo", ask = "none")
#> ✔ Uninstalled pre-commit from repo scope.
#> ✔ Removed .pre-commit-config.yaml.

# Remove the system-level executable too (prompts for confirmation)
uninstall_precommit(scope = "user", ask = "user")
#> You are about to uninstall pre-commit from the conda env r-precommit...
#> Type 'yes' to continue: yes
#> ✔ Removed pre-commit from conda env r-precommit.
```

--------------------------------

### Generate Config Snippets for Hook Dependencies

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Generates YAML snippets for `.pre-commit-config.yaml`, especially for `additional_dependencies` required by hooks that load packages. Reads hard dependencies from DESCRIPTION.

```r
library(precommit)

# Generate additional_dependencies block for the roxygenize hook
snippet_generate("additional-deps-roxygenize")
#>     -   id: roxygenize
#>         # roxygen requires loading pkg -> add dependencies from DESCRIPTION
#>         additional_dependencies:
#>         -    cli
#>         -    dplyr
#>         -    rlang

# Generate additional_dependencies for the lintr hook
snippet_generate("additional-deps-lintr")
#>     -   id: lintr
#>         # lintr requires loading pkg -> add dependencies from DESCRIPTION
#>         additional_dependencies:
#>         -    cli
#>         -    dplyr
```

--------------------------------

### Clean Pre-commit Cache

Source: https://github.com/lorenzwalthert/precommit/wiki/Packages-are-not-found-after-R-upgrade

Run this command to remove the pre-commit cache, which may contain outdated or incompatible binaries after an R upgrade.

```bash
pre-commit clean
```

--------------------------------

### R Hook Script Helpers for Roxygenize and Dependency Checking

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Low-level R functions for use in custom hook scripts. `diff_requires_run_roxygenize` checks staged diffs, `roxygenize_with_cache` wraps `roxygen2::roxygenise` with caching, and `robust_purl` extracts R code from Rmd/Rnw files.

```r
# Used internally by inst/hooks/exported/roxygenize.R — shown for reference
library(precommit)

# Check if staged diff contains roxygen changes
if (diff_requires_run_roxygenize(root = ".")) {
  # Assert all declared dependencies are installed
  roxygen_assert_additional_dependencies()
  # Roxygenize and save a cache timestamp
  key <- list("roxygenize", Sys.getenv("PRE_COMMIT_FROM_REF"))
  roxygenize_with_cache(key = key, dirs = precommit::dirs_R.cache("roxygenize"))
}

# Extract R code from an Rmd for dependency checking
r_code_path <- robust_purl("vignettes/my-vignette.Rmd")
# r_code_path is a tempfile with .R extension, ready for parse()/source()

```

--------------------------------

### Remove Offending Package with renv

Source: https://github.com/lorenzwalthert/precommit/wiki/Packages-are-not-found-after-R-upgrade

If packages are still not found, use `renv::purge` to remove the problematic package from the renv cache. This command can be run from any working directory.

```R
renv::purge('docopt')
```

--------------------------------

### snippet_generate() — Generate config snippets for hook dependencies

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Generates YAML snippets for `.pre-commit-config.yaml`, specifically for `additional_dependencies` required by hooks that load packages.

```APIDOC
## `snippet_generate()` — Generate config snippets for hook dependencies

Generates YAML snippets to paste into `.pre-commit-config.yaml`, particularly for listing `additional_dependencies` required by hooks that load the package (such as `roxygenize` and `lintr`). Reads hard dependencies from the `DESCRIPTION` file automatically.

```r
library(precommit)

# Generate additional_dependencies block for the roxygenize hook
snippet_generate("additional-deps-roxygenize")
#>     -   id: roxygenize
#>         # roxygen requires loading pkg -> add dependencies from DESCRIPTION
#>         additional_dependencies:
#>         -    cli
#>         -    dplyr
#>         -    rlang

# Generate additional_dependencies for the lintr hook
snippet_generate("additional-deps-lintr")
#>     -   id: lintr
#>         # lintr requires loading pkg -> add dependencies from DESCRIPTION
#>         additional_dependencies:
#>         -    cli
#>         -    dplyr
```
```

--------------------------------

### Update hook revisions in .pre-commit-config.yaml

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Runs `pre-commit autoupdate` to update the `rev:` field of each hook repository to the latest tagged release. Validates renv/pre-commit compatibility before updating.

```r
library(precommit)

# Update all hook revisions to their latest tags
autoupdate()
#>
#> ✔ Ran pre-commit autoupdate to get the latest version of the hooks.

# Run in a specific repo root
autoupdate(root = "/path/to/project")
```

--------------------------------

### uninstall_precommit() — Remove pre-commit from a repo or system

Source: https://context7.com/lorenzwalthert/precommit/llms.txt

Removes pre-commit from the current repository (scope = 'repo') or the system entirely (scope = 'user'). Interactive prompts can be suppressed.

```APIDOC
## `uninstall_precommit()` — Remove pre-commit from a repo or system

Removes pre-commit from the current repository (`scope = "repo"`) by uninstalling the git hook script and deleting `.pre-commit-config.yaml`, or from the system entirely (`scope = "user"`) by removing the conda environment installation. Interactive prompts can be suppressed with `ask = "none"`.

```r
library(precommit)

# Remove pre-commit from current repo only (keeps system install)
uninstall_precommit(scope = "repo", ask = "none")
#> ✔ Uninstalled pre-commit from repo scope.
#> ✔ Removed .pre-commit-config.yaml.

# Remove the system-level executable too (prompts for confirmation)
uninstall_precommit(scope = "user", ask = "user")
#> You are about to uninstall pre-commit from the conda env r-precommit...
#> Type 'yes' to continue: yes
#> ✔ Removed pre-commit from conda env r-precommit.
```
```

--------------------------------

### R Package Not Found Error

Source: https://github.com/lorenzwalthert/precommit/wiki/Packages-are-not-found-after-R-upgrade

This error message indicates that a required R package is missing or incompatible after an R upgrade. It often appears during the R package loading process.

```R
Error in loadNamespace(x) : there is no package called ‘docopt’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
```

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