The one true way to install Bioconductor is by using the biocLite script. You get access to this script by sourcing it from the Bioconductor website
source("http://www.bioconductor.org/biocLite.R")The first time you run the script without arguments, it will install a core set of Bioconductor packages.
biocLite()When you run this script, it will autodetect if any of your installed packages are out of date; it will aggressively ask you to update your packages.
Because of this, the way you update a Bioconductor installation, is just by running biocLite() without any argument.
You can check if your installation is fully up-to-date, by running biocValid(); it will return TRUE if everything is current.
You install a new package by using biocLite with the package name, for example
biocLite("limma")The reason why you want to use biocLite - and only this function - to install and update Bioconductor, is because one of the top problems users have is when they mix and match Bioconductor packages from different releases. Using biocLite ensures that everything is synchronized.
The way you update Bioconductor itself when a new release comes out, is by updating R itself and then run biocLite.
Improvements and corrections to this document can be submitted on its GitHub in its repository.