modif doc of refresh function

[annasmyk]

No description provided.

[TanguyBarthelemy]

there is a typo:

https://github.com/annasmyk/rjd3x13/blob/b994c7b0d0f3bc4ba81e64296a56f1c770d926ec/R/x13.R#L444

spotted by GHA:

https://github.com/rjdverse/rjd3x13/actions/runs/24138501937/job/70433009193?pr=111#step:10:442

[TanguyBarthelemy]

Currently, the new error arises at line:

https://github.com/annasmyk/rjd3x13/blob/2c620d38c30dcffff5ed5408beadbbfb346e4739/R/x13.R#L517

spotted by GHA:

https://github.com/annasmyk/rjd3x13/actions/runs/24189288323/job/70601915403#step:10:179

Explanation

The object y_new is not found because the part where it's created is in the \donttest{} block and the current check dont run the \donttest{} block in examples:

rjd3x13/.github/workflows/R-CMD-check.yaml

Lines 65 to 69 in f56f935

	- uses: r-lib/actions/check-r-package@v2
	with:
	upload-snapshots: true
	build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
	error-on: '"note"'

unlike the package {rjd3toolkit}:

https://github.com/rjdverse/rjd3toolkit/blob/bc51547deb6197e001ef63fdb1b2cf76c889fa7b/.github/workflows/R-CMD-check.yaml#L81

Action

Currently, what we can do is:

• Ensure that the code running in the examples works both with and without the code in the \donttest sections.

(with running:

devtools::document()
devtools::run_examples()
devtools::run_examples(run_donttest = TRUE)

)

• Add the "--run-donttest" argument to the check-r-package action

Future and other pbs

Example with only a \donttest block

I noticed that when the entire example is inside the donttest block, the following error can occur:

devtools::run_examples(pkg = "/home/onyxia/rjd3x13")
#> Error in srcrefs[[1L]] : subscript out of bounds

^{Created on 2026-04-09 with reprex v2.1.1}

Currently, the only solution I’ve found is to place part of the code (e.g. library("rjd3toolkit")) outside the donttest function so that there is something to test...

Note: I don’t get any errors when running R CMD check in RStudio or via GHA...

I reported the issue in r-lib/pkgload#329.

Loading libraries

Another issue (resolved by @clemasso): when loading the package, you also need to load the JARs using rJava::.jaddClassPath().

I proposed a solution in this commit

https://github.com/TanguyBarthelemy/rjd3x13/blob/7074dccebbefd9e488bcb0bd6e2c38e5d996100f/R/zzz.R#L18-L21