Below are some general tips and tricks for working in R that don’t fit neatly into any articles.
Installing R packages from CRAN vs. Bioconductor vs. GitHub
You can’t use the CRAN instructions to install a BioC package, but you CAN do the reverse. So if you have a bunch of packages to install, and some are in BioC and others are in CRAN, you can install them all in one command if you use the BioC installation mechanism.
When installing the cutting-edge version of package X (where X is available in CRAN or Bioconductor but the latest version is only available in GitHub), it’s recommended to first install the package via CRAN or Bioconductor, then installing the new version of it using
devtools::install_github(X). The reason is that
devtools::install_github()does not always install all the necessary dependencies