Bioconductor: Won't Update to 3.18 with Default Command
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vanbelj ▴ 20
@vanbelj-21216
Last seen 19 days ago
United States

I am in the process of updating everything R-related: R, RStudio, packages.

I noticed that Bioconductor will not update beyond version 3.17 unless I explicitly state the desired version (see below).
Is there a reason for this? Perhaps it is because a package I have installed is not yet compatible with Bioconductor 3.18?

I couldn't post my code due to the presence of ' for instance as it appears in R around version '3.17' ...

BiocManager::version()
[1] 3.17

BiocManager::install()
Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)

BiocManager::install(version = "3.18")
Upgrade 71 packages to Bioconductor version 3.18? [y/n]: 


> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.3.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.22 compiler_4.3.2      tools_4.3.2
Bioconductor • 129 views
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@lluis-revilla-sancho
Last seen 6 days ago
European Union

This is expected and documented on the site. To upgrade from one version to another of Bioconductor you must "force" it.
You don't show the output of BiocManager::version() after making the upgrade by answering yes to Upgrade 71 packages to Bioconductor version 3.18? [y/n]: y, but it should be 3.18

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