Updating R on Linux

NB - if on Windows, use Tal Galili's installr (upgrade R from within R!)

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• sudo vim /etc/apt/sources.list
• Add deb https://mirrors.ebi.ac.uk/CRAN/bin/linux/ubuntu trusty/
  • deb MIRROR_URL/bin/linux/ubuntu LINUX_CODENAME/
    ↳ MIRROR_URL : https://mirrors.ebi.ac.uk/CRAN/ — via list of mirrors here
    ↳ LINUX_CODENAME : trusty — via cat /etc/*-release
• sudo apt-get update

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Problem: GPG key has expired (R's Secure APT)

• https://mirrors.ebi.ac.uk/CRAN gave:

  GPG error: https://mirrors.ebi.ac.uk trusty/ Release: The following signatures were invalid: KEYEXPIRED 1445181253 KEYEXPIRED 1445181253 KEYEXPIRED 1445181253
  

  ...switched to https://www.stats.bris.ac.uk/R/ - same there
• switched off HTTPS using http://mirrors.ebi.ac.uk/CRAN/ and problem persisted

Solution: add new key given here

• Via notes at CRAN on Secure APT via this ServerFault question
• run sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys GPG_KEY
  ↳ GPG_KEY : currently E084DAB9 (June 2016, apparently changed mid-Oct '15)
  ↳ sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9

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• sudo apt-get install r-base

Users who need to compile R packages from source [e.g. package maintainers, or anyone installing packages with install.packages()] should also install the r-base-dev package:

sudo apt-get install r-base-dev

* (Followed the system hint to run `sudo apt-get update` again after this step)

```sh
~ $ R

R version 3.3.0 (2016-05-03) -- "Supposedly Educational"

Upgrade complete 😎