Skip tests/examples when packages in Suggest section are not installed

[averissimo]

• Part of pre-release activities Pre-release activities #506 (base branch for this PR is pre-release-cleanup@main)
• Rationale on https://github.com/insightsengineering/idr-tasks/issues/713

Changes description

• Handles @examples
  • with @examplesIf requireNamespace("MultiAssayExperiment") as suggested here
  • Conditional clause replacing miniACC with empty data.frame
• Skips tests that use {MAE} or {SE}
• Skips tests that use {withr}

Discussions

• That's not a reason to skip tests. MAE is in Suggests so installing is the responsibility of the person who wants to run tests, i.e. not the end user. If someone uses teal with MAE data, they most likely have the package installed.

• Some generic tests and examples for filter_state_api are complex cases that join together normal data frames with MAE
  • These could be broken down to 2 examples.
• If we merge this it also means tests using {withr} should be skipped
  • Seems silly, but necessary to be a complete compliance

WDYT?

[pawelru]

I think this is the correct way to move forward.

I have one more thing to check that I noticed elsewhere and unfortunately I cannot check it locally for some reason. If a dependent package is missing and there are references in roxygen it will end-up with a following note:

* checking Rd cross-references ... NOTE
Unknown package ‘teal’ in Rd xrefs

Or it might be due to a given package is missing on rdrr.io / CRAN - I'm not 100% sure. I haven't deep dive into this issue but I think it might be related in this context. Will you be able to check it? Just remove package locally and run R CMD CHECK.

[averissimo]

It looks like a rdrr.io / CRAN check. As I've modified the docs to also have some links to {future} and {mistery} (latter doesn't exist) and it only complained about {teal} and {mistery}

(ignore the dev-av warning, it's for local hacking)

[chlebowa]

So I see that @examplesIf prevents the examples from running in checks unless the condition is met but they are still displayed. Sounds good to me.

---

* checking Rd cross-references ... NOTE
Unknown package ‘teal’ in Rd xrefs

I'm not getting this, only

❯ checking package dependencies ... NOTE
  Package suggested but not available for checking: ‘MultiAssayExperiment’

---

examplesIf 👍
remove withr 👍

[chlebowa]

I suppose we will do this in all package, not just teal.slice, correct?

I have uninstalled MultiAssayExperiment to test this and now tests in teal fail, so we don't have to look far.

[chlebowa]

👍