search

r-lib / remotes

Install R packages from GitHub, GitLab, Bitbucket, git, svn repositories, URLs
https://remotes.r-lib.org/
Other
331 stars 152 forks source link

Bump Bioc version map for `R v4.1` to `3.14` #664

Closed stufield closed 2 years ago

stufield commented 2 years ago

After the recent Bioconductor release of v3.14 on 2021-10-27, the version map version inside bioc-standalone.R looks like it still points to v3.13, however according to the recently updated BioC docs:

https://www.bioconductor.org/about/release-announcements/#release-versions

R v4.1 should map to Bioconductor v3.14.

After the Bioconductor update in October, this causes bioc_version() (current CRAN v2.4.1 & v2.4.1.9000) to point to the wrong (old) version associated with its R v4.1. I think ...

sapply(c("3.6", "4.0", "4.1", "4.2"), remotes::bioc_version)

If I'm wrong, please feel free to close. Otherwise I'm happy to submit a PR.

riccardoporreca commented 2 years ago

Indeed @stufield, this is now biting as there is a unit test hard-coding the expected Bioconductor release version, see e.g. https://github.com/r-lib/remotes/runs/4086816248?check_suite_focus=true#step:6:148

── Failure (test-bioc.R:40:3): internal map is current ─────────────────────────
bioconductor$get_release_version() not equal to package_version("3.13").
Component 1: Mean relative difference: 0.07142857
stufield commented 2 years ago

I have a GitHub Action that runs rcmdcheck() but first installs a Bioconductor package that alerted me to this issue. Otherwise I may not have noticed.

jimhester commented 2 years ago

A PR updating the mapping would be great, thanks!

bersbersbers commented 2 years ago

Are there plans to make a release for this? I stumbled across this issue in #668. Specifically, a to-be-released package of mine depends on a recent version of some Bioconductor package (present only in 3.14), and I'd like to avoid having to add some BiocManager::install(ask = FALSE) to update outdated packages immediately after installation through remotes.