R Studio - breaking changes in 2023

Issue

I can no longer install packages after June 2023.

The Console will not let me install software (but I can do it in the Terminal)

The cran repo seems to fail while installing packages

Also - R Studio is rebranding to Posit in 2023, see their announcement here:

https://posit.co/blog/rstudio-is-becoming-posit

My use case no longer works unless I specify an upstream repository but I don't want to manually change every installation line in my code:

# This no longer works:
RUN R --no-save -e "install.packages(c('Seurat', 'SingleR', 'celldex'))"
# I needed to change it to
RUN R --no-save -e "install.packages(c('Seurat', 'SingleR', 'celldex'), repos = 'https://cloud.r-project.org')"

Workaround (temporary)

You can change the repositories temporarily inside a Domino RStudio workspace by following the instructions below. Please note that this configuration change must be done every time a workspace is created or restarted.

You can view the current default CRAN mirror to check if it’s set to the old or the new URL:

> getOption("repos")
                           CRAN
"https://cran.us.r-project.org" 

This is the old URL. To change the default mirror, use the following:

> options(repos = c(CRAN="https://cloud.r-project.org/"))

Here is an example of updating the default CARN repo to https://cloud.r-project.org and installing an example package aidar.

Resolution (permanent)

Change the default installation path to the 'cloud' URL. This snippet will modify your Environment and replace the out-dated default mirror. Add to the Dockerfile and rebuild your Environment.

USER ubuntu
# Update default CRAN mirror
RUN sed -i 's/cran.us.r-project.org/cloud.r-project.org/g' /home/ubuntu/.Rprofile

Applies to

Likely to apply to all R Studio Environments/Workspaces and Apps - up to Domino 5.7.

The default CRAN mirror that Domino was using previously (https://cran.us.r-project.org) has recently stopped working, which means you may experience trouble installing packages. To fix this, the default CRAN mirror should be set to https://cloud.r-project.org/. This change has been incorporated in Domino version 5.7