This is best done through RStudio which keeps everything up to date.

The old way is

update.packages() 

For BioConductor packages,

BiocManager::install()

This is the same command use to install a new package and its dependencies

BiocManager::install(‘packageName’)

More information on Bioconductor.

Install package from downloaded gz (make sure the file is in tar.gz format)

install.packages(“/path/package.tar.zip", repos=NULL, type="source")