revdepcheck
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r-lib
Problem accessing bioconductor during `revdep_check()`
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.
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.
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).
Same issue here. Note that this is also the case when I use bioc = FALSE
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.
That did it, thanks! Shouldn't revdepcheck always be using the most recent version of bioconductor?
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.
Try setting the
R_BIOC_VERSIONenv 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
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
