Check and Upgrade Bioconductor Packages

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A R version supports more than one version of Bioconductor. To take advantange of new features, users have to update Bioconductor packages regularly.

Before update Bioconductor, upgrade your R to the latest version.

1. Check installed Bioconductor version

if (!require("BiocManager", quietly = TRUE))

In my computer, it output:

Bioconductor version 3.15 (BiocManager 1.30.19), R 4.2.2 (2022-10-31)
Bioconductor version '3.15' is out-of-date; the current release
  version '3.16' is available with R version '4.2'; see

So, I need to update Bioconductor to version 3.16.

2. Update installed Bioconductor packages

BiocManager::install(version = "3.16")

Note Use the argument ask=FALSE to update old packages without being prompted.

3. Tips

Use the commands

BiocManager::valid()     ## R version 3.5 or later

to flag packages that are either out-of-date or too new for your version of Bioconductor. The output suggests ways to solve identified problems.

In my computer, it output:

* sessionInfo()

R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 11 (bullseye)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.19 compiler_4.2.2      tools_4.2.2        

Bioconductor version '3.16'

  * 1 packages out-of-date
  * 0 packages too new

create a valid installation with

  BiocManager::install("ggtree", update = TRUE, ask = FALSE, force = TRUE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message:
1 packages out-of-date; 0 packages too new