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))
install.packages("BiocManager")
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Bioconductor version '3.15' is out-of-date; the current release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
https://bioconductor.org/install
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to flag packages that are either out-of-date or too new for your version of Bioconductor.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/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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* 1 packages out-of-date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1 packages out-of-date; 0 packages too new