Why the apt-get package manager doesn’t contain the latest version of R automatically, I’m not sure. I recently realized I have been downloading a 2+ year old distribution for all of my SDM timing runs by running the standard sudo apt-get install r-base command at the shell. For several weeks, this was fine, but today the package Rcpp, which wraps compiled C++ code in the R environment failed to compile. I spent most of the afternoon trying to figure out what was going on. I didn’t even occur to me that the r-base package I was using was the root cause.

It is not easy to figure out how to update the core R package, but, like most things in linux, it comes down to a correctly ordered set of calls to a package manager.

Note: I am using a Debian 8 Jessie image, version v20160718

###Steps:

  1. sudo apt-get remove r-base. Remove the old version of R.
  2. sudo nano /etc/apt/sources.list. This file holds all of the package repositories for apt-get.
  3. Inside of it, copy and paste:
    deb http://cran.rstudio.com/bin/linux/debian jessie-cran3/
    

    This tells the manager to look in this repository for a copy of the R distribution.

  4. Save and close the text editor.
  5. At the shell, type: gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9 and then gpg -a --export E084DAB9 | sudo apt-key add - What does this do? I’m not exactly sure, but I think it has to do with the package integrity checks down when downloading things from a package manager.

  6. sudo apt-get update. Update the installed packages.
  7. sudo apt-get install r-base. Install the core R functionality, hopefully this time using the newest version.
  8. sudo apt-get install r-base-dev. Install the development headers to allow packages that are not in debian repositories.

At this point, you should have a newly updated R version. You can check with R.version. For me, this worked for updating from R version 3.0.1 to R version 3.3.1.

If you have package install error, it’s definitely worth checking if an update in the r-base package could be responsible.