Tag: R

Categories
Linux

Update R and Bioconductor

It’s not a straightforward thing to update R and Bioconductor (a bioinformatics package collection for R), especially if you used the R package that comes with your Linux distribution. For example, the R package from Ubuntu package repository is still 3.5, while the latest version from the r-project site is already 4.0.3. While using an older version of R itself for statistics may not be a problem, many of the Bioconductor packages do have updates and bug fixes that require R v4. And to make things worse, updating Bioconductor itself is a painful process. Below is what I did to update R, Bioconductor, and associated packages. The main lesson learned here is not to use the R package from Ubuntu repository.

  1. Remove R installed from the Ubuntu repository;
  2. Install R from r-project by adding it as an apt repository;
  3. Update R packages (system-wide);
  4. Update R packages installed in the user directory;
  5. Update BiocManager
sudo apt-get purge r-base* r-recommended r-cran-*
sudo apt autoremove
sudo apt update
sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo apt update
sudo apt install r-base r-base-core r-recommended r-base-dev
update.packages(ask = FALSE, checkBuilt = TRUE)
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.12")

The R code section may need to run twice once as a sudo user and once as a normal user if you also have packages installed under a user name (that is to say not a system-wide installation from system admin). The last command tells BiocManager (Bioconductor package manager) to install Bioconductor version 3.12 and update all installed Bioconductor pages.

Categories
emacs Linux

Configuration for Developing R code with ESS

It has been close to 10 years since I use R seriously last time. Back then I used ESS in Emacs to do all the editing and interactive sessions. I really liked it back then and I would like to check it out how ESS has evolved through the years. A quick glimpse of the ESS manual suggests it has got a lot of improvements and the Bioconductor project has evolved as well. For example, even the package installation package has changed in Bioconductor.

Unfortunately, I have forgotten the tricks and configurations that I have used to set up my ESS and Emacs environment. Below are a few things that I had to go through.

$sudo apt install -y r-cran-devtools
$sudo apt install libcurl4-gnutls-dev

The above two packages are required for quite some other R packages. To make sure the user library path is loaded correctly, I had to set the following environmental variable:

export R_LIBS="~/.local/R/lib"

The above setting works for starting R in Terminal. To make the local R library (in my home directory with no root privileges required) work with the ESS R session, I had to create a ~/.Rprofile file with the following content:

.libPaths("~/.local/R/lib")

Now my Emacs speaks ESS well. I can install packages to my local libraries by default and use Emacs to edit R code in one frame and run an interactive R session in another frame and use “C-c C-c” to execute a selected region in the R code frame.

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