Install_Linux.md

Notes on installing R and RStudio under Debian-based Linux distributions

About possibly interfering packaging systems

Linux distributions and packaging systems

Programs and libraries (i.e. predefined functionalities that programs can re-use) can be installed in various ways. The hard-core way is to install things directly from the source code provided by the programmers, but this can be sometimes a little complicated. Linux is usually obtained in the form of a "distribution", which includes the core operating system, a variable amount of pre-installed tools, and a database of installable packages (i.e. sets of programs and libraries) together with tools to manage their installation. On Debian-based distributions, this is the apt system.

It is generally recommended to use your distributions' official packaging system to install programs, whenever possible. This should help avoiding incompatibilities between packages.

Language-specific packaging mechanisms

However, programming languages such as R tend to come with their own way to install packages. R has an install.packages function that does precisely that.

Some R packages can then be installed either using your distributions' packaging system, or install.packages, and things may get messy if you use a mix of both approaches. One reason is that your distributions' packaging system has to be used with administrative privileges (typically, prefixing commands with sudo), whereas you should probably avoid using R with such privileges if you want to avoid destroying your system by accident. If you have already dealt with install.packages, you may have noticed error messages about packages that cannot be updated because some place in the disk is not writeable. That's the typical symptom of an interference between R internal mechanisms used as a normal user, and your apt-installed R packages: R is likely trying to update them, but they are not stored in your user directory.

So why not stick to apt, then? Unfortunately, it will eventually happen that some R packages are either not available that way, or not enough up-to-date for your taste or necessities. So it may be wise to avoid as much as possible to install R packages using apt. The r-base-core and r-base-dev packages may actually be sufficient. Another viable alternative might be to install R from source, and would have the benefit that updating your system would not mess with your R installation, but this approach might not be suitable for every user.

Bioconductor

To make things more complicated, there is an effort of the bioinformatics community to provide a set of specialized R packages through it's own system: Bioconductor (which actually uses install.packages under the hood).

Bioconductor strives to provide a set of compatible packages, and can also install R packages that are not specific to bioinformatics. I would therefore suggest to install packages using Bioconductor whenever possible. You may still need to install packages directly with install.packages, and some packages might not build unless you install programs and libraries external to R. In the latter case, try as much as possible to use the apt system.

Installing R

As of November 2020, Bioconductor requires R version 4, which is not the one provided by default by the current stable Debian ("buster" / 10) and Long-Term Support Ubuntu ("bionic" / 18.04 or "focal" / 20.04) distributions.

To make version 4 available in apt's database, you need to provide it's localization through apt's configuration mechanism, which consists in files residing in the /etc/apt/sources.list.d/ directory.

Refer to https://cloud.r-project.org/bin/linux/ to find the exact source for R version 4 (you need to know on which Debian or Ubuntu version your distribution is based). This will consist in some text starting with "deb source=" that you will have to add in a file in /etc/apt/sources.list.d/. The name of the file does not matter but might have to end in ".list". I suggest cran.list (for "Comprehensive R Archive Network"). Either proceed by using your favourite text editor, or on the command-line:

# If you are using Ubuntu 20.04
# deb_source="deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/"
# If you are using Ubuntu 18.04
# deb_source="deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/"
# If you are using MX Linux 19 or Debian 10
deb_source="deb http://cloud.r-project.org/bin/linux/debian buster-cran40/"
# Add the source for R to the source list
echo ${deb_source} | sudo tee -a /etc/apt/sources.list.d/cran.list

In order to avoid some warning messages, you also need to register the authentication key so that apt recognizes the package source as trusted:

# If you are using Ubuntu 18.04 or 20.04
# sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
# If you are using MX Linux 19 or Debian 10
sudo apt-key adv --keyserver keys.gnupg.net --recv-key 'E19F5F87128899B192B1A2C2AD5F960A256A04AF'

Update the package database:

sudo apt update

You may now install R and the necessary tools to install R packages:

sudo apt install r-base-core r-base-dev

If everything worked as expected, you should now have a minimal R installation. Check that you have the desired version with the command R --version. If you get something older than 4, good luck: you may have another version of R interfering with the one you just installed. The present document does not cover the subject of already installed R versions and how to be sure to use the correct one.

Installing RStudio

RStudio does not seem to be provided as a package by the apt system, neither is it an R package. You need to install it "manually" using a package or "installer" provided here: https://www.rstudio.com/products/rstudio/download/#download.

Either download the most relevant "installer" for your distribution, by clicking on the link and continuing the mouse way, or copy the link and proceed to the download and installation the command line way (the actual version number may vary):

# If you are using Debian 10, MX Linux 19 or Ubuntu 18.04 or 20.04:
wget https://download1.rstudio.org/desktop/bionic/amd64/rstudio-1.3.1093-amd64.deb
# For a distribution based on Debian 9, such as MX Linux 18:
# wget https://download1.rstudio.org/desktop/debian9/x86_64/rstudio-1.3.1093-amd64.deb
# Install it (https://unix.stackexchange.com/a/159114/55127):
sudo apt install ./rstudio-1.3.1093-amd64.deb

Note the dot (".") in the last command: it tells apt install that you want to use this exact downloaded file and not a package from the database whose name is "rstudio-1.3.1093-amd64.deb".

If installation fails, it may be due to missing dependencies. Look at error messages for hints, and use help from colleagues or the internet and your package manager to install the missing packages before trying again.

Using Bioconductor to install R packages

As mentioned earlier, one way to install R packages is to do it via the Bioconductor project, which maintains a set of hopefully mutually-compatible packages.

Within an R session, start by installing the BiocManager R package:

install.packages("BiocManager")

Then, whenever you want to install packages, let BiocManager perform some updates:

BiocManager::install()

And finally, use it to install the new packages:

BiocManager::install(c("evaluate", "highr", "markdown", "stringr", "yaml", "htmltools", "caTools", "bitops", "knitr", "jsonlite", "base64enc", "rprojroot", "rmarkdown"))

As already mentioned, installing packages may require other tools, that are not part of R. In particular, you will likely need compilers because R packages sometimes use other programming languages internally, such as C, C++ (that you can get by installing the build-essential package using apt) and Fortran. You might also need development libraries, that you should try to install using apt after consulting the internet. It may be useful to know that development libraries packages often have names that end in "-dev" and provide files with names ending in ".h" (for "header") or ".so" (possibly followed by extra dots and numbers) (for "shared object"). If you see error messages suggesting that such a file is missing, you will be happy to know that the apt system has tools that help finding the name of the package providing the missing file (see https://askubuntu.com/a/1912/129295 and https://wiki.debian.org/apt-file).