roxygenize hook not accepting --root argument

[wyncster]

I am trying to use the roxygenize hook on an R package that is not located in the repo root. As per the documentation in available hooks, I have used the --root argument to specify the relative path to the package source. However, this alone causes the roxygenize hook to skip saying there are no files to check.

If I add files: to point to the package folder with pass_filenames: false, the roxygenize hook runs but fails with error "Error: Unknown arguments: '--root'".

To Reproduce
The following batch script may be used to reproduce the bug in Windows (tested using the latest version of R, precommit and the hook):

set PACKAGE_NAME=mypackage
set REPO_PATH=repo

mkdir %REPO_PATH%
cd %REPO_PATH%

:: Create new R package structure using package.skeleton
Rscript -e "f <- \(x) x" -e "package.skeleton(name='%PACKAGE_NAME%', list='f')"

:: Initialize git repository in current directory first
git init

:: Create .pre-commit-config.yaml file
echo Creating pre-commit configuration...
(
echo repos:
echo   - repo: https://github.com/lorenzwalthert/precommit
echo     rev: v0.4.3.9013
echo     hooks:
echo       - id: roxygenize
echo         args: [--root=%PACKAGE_NAME%]
echo         files: %PACKAGE_NAME%
echo         pass_filenames: false
) > .pre-commit-config.yaml

:: Add all files to git
git add .
git commit -m "Initial commit: R package setup with pre-commit"

:: Install pre-commit hooks
pre-commit install

:: Run pre-commit on all files
pre-commit run --all-files

This gives the following output:

roxygenize...............................................................Failed
- hook id: roxygenize
- exit code: 1

- The project is out-of-sync -- use `renv::status()` for details.
- The project is out-of-sync -- use `renv::status()` for details.
Run roxygen2::roxygenize()

Obviously, this hook is only activated when any staged file passes the filter
specified in .pre-commit-hooks.yaml. Then, we check the time stamp of the last
time we ran the hook. If any of our R files is younger than that, we consider
running the hook. We next use {git2r} to inspect the cached diff of all .R files
in the R/ directory, and not the files passed to this hook. If we find any
roxygen2 comment in the diff, we run `roxygen2::roxygenize(). The preliminary
use case for this is when we previously attempted to commit but check failed, so
on the second try without any other files changed, it will succeed.
This check should run *after* check that modify the files that are passed to
them (like styler) because they will never modify their input .R files.

Usage:
  roxygenize [--no-warn-cache] [--root=<root_>] <files>...

Options:
  --no-warn-cache  Suppress the warning about a missing permanent cache.
  --root=<root_>  Path relative to the git root that contains the R package root [default: .].


Error: Unknown arguments: '--root'
Execution halted

Expected behavior
I would expect the hook to run on the R package without complaining about an unknown argument --root.

Additional context

• My operating system is: Windows 11 24H2
• R version: 4.5.1
• Rtools version: 4.5

[lorenzwalthert]

Thanks for the comprehensive issue. files: is inherited from the .pre-commit-hooks.yaml you can find here.

In my reprex, I adapted like this

# All available hooks: https://pre-commit.com/hooks.html
# R specific hooks: https://github.com/lorenzwalthert/precommit
repos:
-   repo: https://github.com/lorenzwalthert/precommit
    rev: v0.4.3.9013
    hooks:
    -   id: roxygenize
        args: [--root=rpkg]
        files: '^rpkg/(R|man)/'

When I have my package rpkg sub-folder. This works.

MacBookAir:precommit.root.roxygen2 lorenz$ git commit -m 'add pkg'
roxygenize...............................................................Passed
[main 2d41bdc] add pkg
 2 files changed, 1 insertion(+), 2 deletions(-)
MacBookAir:precommit.root.roxygen2 lorenz$ 

Can you reproduce it? If yes, can you help me adopt the docs so that it's more clear what to do?

[wyncster]

Setting files: like this (to point at the R/man folders within the package) fixes it for me - thanks very much!

I suggest you update the documentation in available hooks - roxygenize to show how files: must also be set in the example of --root to help others who try to use this.

[wyncster]

Note, I also had similar issues with the deps-in-desc hook, which also has a --root argument. But now I understand that files: needs to be modified, I've got that working by pointing it to the DESCRIPTION file within my package folder.

But I suspect this means that every hook with --root needs to have the default files: parameter modified when --root is used. So it would be great if this was at least shown in each of the --root examples in available hooks.

[lorenzwalthert]

Thanks. Do you want to submit a PR to o prove tie docs? You don’t have the bias I have.