R 3.6.1: How to upgrade from existing Bioconductor 3.9 to 3.10?
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@henrik-bengtsson-4333
Last seen 3 months ago
United States

I realize I don't know what the official way to upgrade an existing Bioconductor 3.9 on R 3.6.1 to Bioconductor 3.10, which was released yesterday (2019-10-30). I've looked at https://bioconductor.org/news/bioc310_release/ and https://bioconductor.org/install/ but I don't think they say how to upgrade - only how to install if you don't already have Bioconductor installed. What's the official go-to approach for upgrading?

Here is what I have:

$ R --vanilla
R version 3.6.1 Patched (2019-09-12 r77183) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
...
> packageVersion("BiocManager")
[1] '1.30.9'
> BiocManager::version()
[1] '3.9'
> packageVersion("BiocVersion")
[1] '3.9.0'
> BiocManager::install()
Bioconductor version 3.9 (BiocManager 1.30.9), R 3.6.1 Patched (2019-09-12 r77183)

PS. https://bioconductor.org/install/ says Bioconductor 3.10 "works with R version 3.6.0" whereas https://bioconductor.org/news/bioc310_release/ suggests it requires "R >=3.6.1".

upgrade BiocManager • 278 views
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@james-w-macdonald-5106
Last seen 8 hours ago
United States
BiocManager::install(version = "3.10")
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Ah... I see. Thxs

I'd like to suggest that a section on 'Upgrading from a previous Bioconductor version' with this is added to https://bioconductor.org/install/

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@martin-morgan-1513
Last seen 10 weeks ago
United States

'Updating' a version is only correct for 1 out of every two release cycles; alternate release cycles require an update to R. It's also a potentially costly operation, both in terms of time and reproducibility.

Consequently, my own practice is to install each Bioconductor version in it's own library. There are additional details in the 'Advanced use' section of the vignette https://github.com/Bioconductor/BiocManager/blob/eece503c8707dd62870150b835dd956c19621cc5/vignettes/BiocManager.Rmd#L171

We'll try to improve the install landing page, which I agree is quite opaque to updating for the current release cycle.

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