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Add _R_CHECK_SUGGESTS_ONLY_=true to Renviron.bioc #249

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merged 5 commits into from
Mar 29, 2023

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jwokaty
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@jwokaty jwokaty commented Dec 2, 2022

Added to the Renviron.bioc of 3.16 and 3.17. Wait until we check the 3.17 build report as R devel was updated on the 3.17 machines 2022/12/1.

Close #248

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hpages commented Dec 2, 2022

Not for the 3.16 builds please, unless we want to introduce a blood bath on the release build reports 😉 See #248 (comment)

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hpages commented Mar 24, 2023

Thanks for adding the long comment to Renviron.bioc 😉

What about this:

To make the need for this particular setup more prominant and help with reproducibility of the CHECK results on Linux, we could also edit the dotted box displayed at the beginning of each individual report. See for example the "To the developers/maintainers of the Biobase package:" box on this report (i.e. the box that is right below the title of the report "CHECK results for Biobase on nebbiolo1").

Any opinion on that?

Thanks again.

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jwokaty commented Mar 24, 2023

Can you explain your suggestion more? This sounded like a suggestion but it wasn't clear if it is just to make the last line more prominent in some way.

I might reword/shorten/format as

Changes take upto 48 hours to appear on build reports.
See [Troubleshooting Build Reports](https://contributions.bioconductor.org/troubleshooting-build-report.html) and use [Renviron.bioc](https://bioconductor.org/checkResults/3.17/bioc-LATEST/Renviron.bioc) to troubleshoot errors reported on this page.

Or do you mean we should put temporary messaging specifically about the error?

Have a new missing package dependency? We recently updated our [Renviron.bioc](https://bioconductor.org/checkResults/3.17/bioc-LATEST/Renviron.bioc) to detect dependencies missing from Suggests. 

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hpages commented Mar 25, 2023

This was indeed a suggestion, and a pretty vague one, sorry. Was not sure if you saw it. I was thinking of adding something like this:

- If 'R CMD check' started to fail recently on the Linux builder complaining that a dependency is
  missing, it's likely because that dependency is not listed in the Suggests field of your package.
  See _R_CHECK_SUGGESTS_ONLY_=true setting in <A href="../Renviron.bioc">Renviron.bioc</A>
  for how to reproduce this error.

We don't necessarily need to keep this forever but it might help in the context of the upcoming release.

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jwokaty commented Mar 28, 2023

I added a note but did a little rewording, added extra BRs, and removed the center alignment, which I find hard to read.

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hpages commented Mar 29, 2023

sounds good

@jwokaty jwokaty merged commit 60360e2 into Bioconductor:devel Mar 29, 2023
@jwokaty jwokaty deleted the issue/248 branch September 22, 2023 14:48
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WISH: Check with _R_CHECK_SUGGESTS_ONLY_=true to identify missing package dependencies
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