@arnim has a student assistent, @Meet261, doing some research around mybinder.org. @Meet261 was talking with me and I noticed that when we create the Dockerfile and run it, we don't use --vanilla and we end up also running .Rprofile.

Add --vanilla to Dockerfile will break the build of any user expecting their .Rprofile to also run but they can move the code to install.R.

Breaking changes

When R starts a new session as in

R

a couple of files from the current directory are executed, for example .Rprofile and .RData.

For the installation of R packages using install.R, a new R session is used. This means that .Rprofile and .RData and executed during the creation of the container image when install.R is executed.

This pull request will remove disable the execution of .Rprofile during the creation of the container image.

Users that are using .Rprofile to configure things during the creation of the image will observer that their intended changes are no longer present at the container image and the container image might be broken depending of their intended changes.

The .Rprofile is still executed when starting a new R session on Jupyter Notebooks, Jupyter Lab or R Studio.

Example

A user operates their own private mirror of CRAN at https:/cran.private.me and the .Rprofile has

options(repos=c(CRAN="https:/cran.private.me"))

With this pull request, when the user runs

repo2docker ...

the execution of install.R during the creation of the container image will use the official CRAN instead of the private mirror of the user.