Conditional setting of R_LIBS_USER

[csoneson]

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!

[gaborcsardi]

How exactly does the R_LIBS_USER change cause that check failure?

[LiNk-NY]

It seems like the new folder has different permissions than the previous /__w/_temp.

Folder before the change:

R_LIBS_USER: /__w/_temp/R-lib

Folder after the change:

R_LIBS_USER: /github/home/R/x86_64-pc-linux-gnu-library/4.4

[lcolladotor]

👀

[gaborcsardi]

I am sorry, I don't understand the problem, can you try to explain it and show an example workflow run where it causes problems.

Btw. setup-r-dependencies only sets R_LIBS_USER if it is not set in ${{ env }}, so you can also set it whatever you like in your workflow.