This post describes how to properly install multiple versions of R alongside on Ubuntu OS and to set up a properly controlled renv environment.

Preparation

It is better to start with a fresh installation of R. However, if R is already installed, especially if it is installed from the Ubuntu repository, it is better to get rid of the old version first:

sudo apt autoremove --purge r-base r-base-dev r-recommended

In addition, removing the packages is not enough to remove R most of the times. A safe approach is to simply change the binary name in /usr/bin with:

sudo mv /usr/bin/R /usr/bin/R2

(which is an ugly way to solve this issue, indeed).

Installing R from scratch

Inspired by this tutorial, we can now install any R version obtained from the RStudio repository (under the form of a .deb package). The following lines of codes are given for R version 4.0.3 and Ubuntu 20.04 LTS (they have to be adapted for other versions of R and other OS and OS versions):

export R_VERSION=4.0.3
export UBUNTU_YEAR=2004
curl -O https://cdn.rstudio.com/r/ubuntu-${UBUNTU_YEAR}/pkgs/r-${R_VERSION}_1_amd64.deb
sudo dpkg -i r-${R_VERSION}_1_amd64.deb
sudo apt install -f

At this stage, R should be properly installed and work with:

/opt/R/${R_VERSION}/bin/R

The last stage of the installation would ensure that the R binary is properly linked into a bin folder:

sudo ln -s /opt/R/${R_VERSION}/bin/R /usr/local/bin/R
sudo ln -s /opt/R/${R_VERSION}/bin/Rscript /usr/local/bin/Rscript

If you are using RStudio with multiple R versions installed as described here, you can choose between them as described here.

renv environment

Within our project directory, if the renv.lock file is already present and has never been used, the virtual R environment is installed with the following R command lines:

install.packages("renv")
renv::init()

In our case, some packages have shown additional issues:

• nloptr required the installation of an additional Ubuntu library:

  sudo apt install libnlopt-dev
  

• some packages depended on curl and required the installation of:

  sudo apt install libcurl4-openssl-dev
  

• ps had a problem with a wrong installation directory for sed that can be resolved creating a symbolic link:

  ln -s /bin/sed /usr/bin/sed
  

When the renv initialization process is interrupted, it can be resumed with:

renv::restore()

Special case of Bioconductor packages

Bioconductor packages can produce errors at installation within renv. The reason is that the Bioconductor packages are linked to a Bioconductor version that is not itself well handled by renv. Hence, you first have to check that your local Bioconductor version is identical with the Bioconductor version of the initial renv installation (for ASTERICS, it is 3.12). To check your local Bioconductor version, do:

BiocManager::version()

(BiocManager has previously been installed with renv::install("BiocManager") for instance). You have to specify:

BiocManager::install("3.12")

and to install your Bioconductor packages with:

BiocManager::install("pkg_name")

before proceeding to renv::restore(). If it still does not work, check your renv.lock file and replace

"Source": "Repository",
"Repository": "Bioconductor"

by

"Source": "Bioconductor",

for Bioconductor packages.