calling `renv` deletes the package `base`

[markjrieke]

So I was following along some of the renv vingettes while trying to setup a github Action & I'm not quite sure what happened. I believe I called:

• renv::status()
• renv::snapshot()
• renv::restore()

I then tried to run the workflow, which depends on the tidyverse, and I got an error along the lines of Warning: there is no installed package called tidyverse

I thought that was a bit strange so I ran install.packages("tidyverse"), and it looks like it installed all the packages into the Repo itself. I tried to open a new studio session & it gave me this error:

Now I can't open RStudio. I think what's going on is that RStudio is trying to reference the library folder that was created in the repo by renv (which just contains tidyverse packages at this point). All my other packages (and tidyverse packages) are still in the expected folder on my computer. I've got a twofold question:

• How do I get RStudio working again?
• What did I do incorrectly beforehand?

Apologies for the lack of a reprex, I can't get into RStudio right now unfortunately!

[markjrieke]

update: I uninstalled/reinstalled R/RStudio & am now back in, but still not sure what I did beforehand (also a bit scared to attempt to recreate the issue!). For the time being, I'm going to just set the workflow to not depend on renv, but I certainly would like to in the future!

[kevinushey]

Unfortunately, without a reproducible example, it's very hard for me to know what went wrong.

[CinnamonJP]

This problem is also happened in my environment repeatedly (6 times). Finish the process as usual and exit Rstudio and the console normally. The next time I launched the console, surprisingly, all the files in the "base" package (which was of course system installed, not under renv) were removed. The result is a "Fatal error" as shown in the image above.

[kevinushey]

Do you see this issue with a prior release of renv (e.g. renv 0.13.2)? https://cran.r-project.org/src/contrib/Archive/renv/

[CinnamonJP]

Thank you for your quick reply. I reinstall prior release (0.13.1). I didn't have this issues when I was using version 0.13.1. Is it a problem specific to 0.14.x?

[kevinushey]

It's possible, but until I'm able to reproduce the issue locally I won't know for sure.

[brianwdavis]

This happened to me while running renv::init() on a new project with a bad wifi connection, so it was doing heavy lifting to populate the project library. Unfortunately I don't know which version of renv I was running at the time because I had to reinstall R and all libs to recover.

R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

[kevinushey]

Unfortunately I still don't have any good ideas as to what could've caused this to happen. If the problem occurs again please let me know and provide as much detail as possible. (Ideally, I would be able to reproduce this myself locally)

[brianwdavis]

I wasn't able to reproduce it a second time either, and my only hunch is that it involved the package installation failing due to the bad wifi connection I was on.

[kevinushey]

#614 made it clear that one way this could happen is if something tries to recursively delete things in the temporary directory when the renv sandbox is active. I've since disabled the sandbox by default to avoid this issue -- hopefully that would imply ultimately fixing the OP's issue as well.

[svethitov]

Hello,

It appears that after re-enabling the sandbox in version 0.16 the problem has returned.

It happened to me after upgrading to renv 0.16 on Windows. I have administrator rights on the server that it happened! Maybe that has something to do with it, as I discovered that the packages' folders in the system library are empty after initiating or activating a renv project.
By disabling the Sandbox the problem disappeared. For some reason renv is deleting the packages from the system library.

[kevinushey]

@svethitov, any chance you could share a set of steps I could use to try and reproduce this locally?

Are you running any tools that try to periodically clean out e.g. temporary directories or anything like that?