[R-pkg-devel] A simple question regarding examples

On Thu, 21 Sep 2023 00:03:11 +0000

Unfortunately, my_func runs overtime during the CRAN check. To
resolve this, do I simply use the less elegant approach as follows?

#' \dontrun{
#' if (reticulate::py_module_available('ctef')) {
#' res <- my_func(input1, input2)
#' }

\dontrun{} is reserved for things that either cannot be guaranteed to
work (highly dependent on the user's system), involve examples of
interactive input/output (e.g. ?debugger), or are potentially too
destructive in case they break (e.g. ?connections). The \examples
section should include running code, which example(your_func) should
run. If there's only the \dontrun{} section, it won't pass the review.

For things that ought to work, it's best to reduce inputs further until
the example runs within the time limit. One remaining escape hatch is
\donttest{}, but R CMD check --as-cran still involves running
\donttest{} examples. Putting the whole example in a \donttest{}
section doesn't sound like a good idea either.

Best regards,
Ivan

Hello,

I have a simple question about including examples. My code depends on a rarely used Python module, so I am using the @examplesIf tag per Hadley Wickham's advice as follows:

#' @examplesIf reticulate::py_module_available('ctef')
#'  res <- my_func(input1, input2)

Unfortunately, my_func runs overtime during the CRAN check. To resolve this, do I simply use the less elegant approach as follows?

#' \dontrun{
#' if (reticulate::py_module_available('ctef')) {
#' res <- my_func(input1, input2)
#' }

The @examplesIf comments are directed at Roxygen; R checks will never 
look at them.  R will run tests based on what is in the my_func.Rd 
examples section.  I'd guess that's pretty similar to your second 
version (except for the \dontrun part, which you shouldn't use, as Ivan 
said).

Duncan Murdoch

Hello Duncan and Ivan,

Thank you for your prompt response! Perhaps I should add that:

I don't think the Python module "ctef" exists on CRAN. Therefore, I am very surprised that the example below runs overtime, since all it has to do is to run reticulate::py_module_available('ctef'). If even this part is running overtime, I am not quite sure how to deal with it.

#' if (reticulate::py_module_available('ctef')) {
#' res <- my_func(input1, input2)
#' }

Looking forward to your reply.

Best,
Hanyu

On 20/09/2023 8:03 p.m., Hanyu Song wrote:
> Hello,
>
> I have a simple question about including examples. My code depends on a rarely used Python module, so I am using the @examplesIf tag per Hadley Wickham's advice as follows:
>
> #' @examplesIf reticulate::py_module_available('ctef')
> #'  res <- my_func(input1, input2)
>
> Unfortunately, my_func runs overtime during the CRAN check. To resolve this, do I simply use the less elegant approach as follows?
>
> #' \dontrun{
> #' if (reticulate::py_module_available('ctef')) {
> #' res <- my_func(input1, input2)
> #' }
>

The @examplesIf comments are directed at Roxygen; R checks will never
look at them.  R will run tests based on what is in the my_func.Rd
examples section.  I'd guess that's pretty similar to your second
version (except for the \dontrun part, which you shouldn't use, as Ivan
said).

Duncan Murdoch

? Thu, 21 Sep 2023 22:11:37 +0000
Hanyu Song <hanyu.song at duke.edu> ?????:

Therefore, I am very surprised that the example below runs overtime,
since all it has to do is to run
reticulate::py_module_available('ctef'). If even this part is running
overtime, I am not quite sure how to deal with it.

Can you show the precise message given to you by the check?

Are you able to reproduce the problem if you run R CMD check (for
example) in a virtual machine without a working Python installation?

It would explain the situation if the process was stuck asking the user
for (e.g.) permission to install miniconda, but these prompts are all
guarded by tests for interactive() and therefore shouldn't be happening.

Best regards,
Ivan