Problem accessing bioconductor during revdep_check()

[willgearty]

I'm trying to run revdep_check() in a github action, but I'm running into this error:

Error: Error: (converted from warning) unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-x86_64/contrib/4.3:
cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-x86_64/contrib/4.3/PACKAGES'

I get the same error when I try with a windows runner:

Error: Error: (converted from warning) unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/windows/contrib/4.3:
cannot open URL 'https://bioconductor.org/packages/3.17/data/annotation/bin/windows/contrib/4.3/PACKAGES'

I'd appreciate any advice you might have, thanks.

[willgearty]

The weird thing is, I ran this exact same github action for a different R package two weeks ago without any problems, and that other R package has bioconductor dependencies as well.

[willgearty]

I also had no problems running revdep_check() locally.

[dieghernan]

Same issue here on Windows and Mac (local and gh actions).

When running revdep_check() on Linux (local and gh-action) doesn’t happen, so my guess is that something changed in the Bioconductor server setup for binaries (as the error urls suggests).

[etiennebacher]

Same issue here. Note that this is also the case when I use bioc = FALSE

[etiennebacher]

In the meantime, I have a fork where I disabled most of the things that were related to Bioconductor:

pak::pak("etiennebacher/revdepcheck")

It seems to work fine, but of course this won't check for revdep failures on Bioconductor.

[willgearty]

@gaborcsardi any thoughts?

[gaborcsardi]

Try setting the R_BIOC_VERSION env var to 3.18.

[willgearty]

That did it, thanks! Shouldn't revdepcheck always be using the most recent version of bioconductor?

[gaborcsardi]

You always need to use the one that is appropriate for the current R version. Which used to be 3.17, but now it is 3.18, and Bioconductor deleted their 3.17 repository, I don't really understand why.

[dieghernan]

Try setting the R_BIOC_VERSION env var to 3.18.

This solves my issue in GH Actions:

https://github.com/dieghernan/nominatimlite/actions/runs/8537095790

Full action code: https://github.com/dieghernan/nominatimlite/blob/main/.github/workflows/revdepcheck.yaml

[friendly]

If not already done, please handle this internally in the revdepcheck package so that users are not flummoxed by this bioconductor problem. At the minimum, you could use Sys.getenv ("R_BIOC_VERSION") to generate a warning or error that would be comprehensible instead of making maintainers google for this error.

Checking reverse dependencies is now a big part of CRAN submission / verification, that I am also surprised that revdepcheck is not on CRAN