Hello!

We have noticed that a recent change to setup-r-dependencies, setting R_LIBS_USER if unset, had downstream effects on actions run in the Bioconductor Docker container. For an example, see here, the explicit error is

Error in setwd(libdir) : cannot change working directory

due to the change in R_LIBS_USER.

We are considering options (such as setting the R_LIBS_USER in the container, which may also have an impact on users relying on the current default), but wanted to ask if you would be open to adding a flag to the action, to make it possible for the user to choose whether R_LIBS_USER should be set if missing, or not.

cc @almahmoud

Thanks in advance!