[Bioc-devel] rworkflows temporary CRAN removal and next steps

[Henrik Bengtsson]

Thanks for the update.

Just in case, there is indeed a CRAN check NOTE. On
https://cran-archive.r-project.org/web/checks/2026/2026-03-03_check_results_rworkflows.html,
there's a link to 'donttest' check logs:

https://www.stats.ox.ac.uk/pub/bdr/donttest/rworkflows.out

which reports:

* checking for new files in some other directories ... NOTE
Found the following files/directories:
  ‘~/.cache/R/rworkflows’
  ‘~/.cache/R/rworkflows/versions-manifest.json’

I think the rule is that unless those existed before R CMD check started,
they shouldn't be there afterwards, i.e. running checks shouldn't leave
anything behind.

You can manually check for this, but it's probably easier to set something
like

Sys.setenv(XDG_CACHE_HOME = tempdir())

at the beginning of your test scripts.

Henrik

On Fri, Mar 20, 2026, 05:16 Hiranyamaya Dash <hdash.work using gmail.com> wrote:

> Dear Bioconductor package developers,
>
> Thank you for using rworkflows and for your continued support.
>
> Unfortunately, CRAN has deprecated the package due to unresolved errors,
> despite no errors or warnings being reported in their logs. We are actively
> working to have the package reinstated, but CRAN has not been responsive
> over the past few weeks. As a result, we have initiated a resubmission.
>
> As a temporary measure, we recommend removing rworkflows from Suggests.
> GitHub Actions workflows will remain unaffected. The only change is that
> developers will need to manually install rworkflows from GitHub in order to
> knit the README (if rworkflows functions are used here). While not ideal,
> this does not impact package functionality and can be reverted once
> rworkflows is restored on CRAN.
>
> We appreciate your patience and understanding, and we will keep you updated
> on any progress.
>
> Kind regards,
>
> Hiru
>
> --
>
> *Hiranyamaya (Hiru) Dash*
> Research Assistant in Computational Genomics
> UK Dementia Research Institute at Imperial College London
>
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>
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