Add --vanilla to R call

[rgaiacs]

Closes #1431

Edit: Copied description from #1431

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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.

[rgaiacs]

A release of repo2docker was made in earlier August 2025. I propose that we merge this now so that we can expand a little the number of users for us to be able to re-assess this new feature. We can revert before the next release if we receive too many reports against it. What others thing?

[manics]

It's been a month and no-one's raised any concrete objection on #1431

[consideRatio]

Wieee I'm so glad about your very helpful attention around Jupyter @manics! Thank you @rgaiacs for all your contributions - you are getting a lot done!!! I'm especially glad about your work to fix intermittent CI failures - it makes a project go slower when everyone have to look into what a failure is about.