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

Dear Henrik,

Thank you for bringing this to my attention.

This NOTE has since been addressed. All instances of cache_dir have been updated to use tempdir(), ensuring the cache is session-scoped.

However, it is unclear whether this NOTE was the cause of the deprecation.

Kind regards,
Hiru

From: Henrik Bengtsson <henrik.bengtsson at gmail.com>
Date: Friday, 20 March 2026 at 2:13?pm
To: Hiranyamaya Dash <hdash.work at gmail.com>
Cc: bioc-devel at r-project.org <bioc-devel at r-project.org>, Skene, Nathan G <n.skene at imperial.ac.uk>
Subject: Re: [Bioc-devel] rworkflows temporary CRAN removal and next steps

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

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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