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

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stufield opened this issue Nov 2, 2021 · 4 comments
Closed

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

stufield opened this issue Nov 2, 2021 · 4 comments

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@stufield
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stufield commented Nov 2, 2021

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
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riccardoporreca commented Nov 2, 2021

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
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stufield commented Nov 3, 2021

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
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A PR updating the mapping would be great, thanks!

@bersbersbers
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bersbersbers commented Nov 11, 2021

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package (present only in 3.14), and I'd like to avoid having to add some BiocManager::install(ask = FALSE) to update outdated packages immediately after installation through remotes.

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