Rstudio Hangs git project

#1

Hello RStudio community,

My RStudio hangs when I am trying to work within an Rproject which is version controlled by git. I first noticed the issue a few day ago and I haven't been able to troubleshoot. I have read many requests for similar issues on this website and stackoverflow/exchange that haven't been resolved. In an attempt to fix I have done the following: updated Rstudio to version 1.2.5042, updated R to version 4.0, switched my rendering engine to software, created a new .Rproj.user folder, and investigated my R request log. I do not know much about the log, but it appears the git_all_status is taking a significant amount of time. I am currently waiting for something to run in console (no stop sign or responses to esc or ctrl+c) and the log claims git_all_status is active. I think my problem is possibly related to this thread: https://github.com/rstudio/rstudio/issues/2141, but I do not really know what that thread is suggesting to do as a solution. Also, I am working on a MAC and not Windows. Any advice would be greatly appreciated!

#2

You need to provide some more information for us to help. When do you run into the problem? When setting up a project based on a Git repository, when trying to clone it, or when you are running it? Can you clone the Git repository using the terminal?

#3

That is part of the problem is there is not much consistency in when it occurs except for it appears to only be happening in one of two projects that I frequently work in. My general workflow is as I'm editing in a script I will use CMD+Enter to run something, then when it is sent to the console it hangs up. However, there is no one function that seems to cause the problem to occur.

#4

I can clone the repository from GitHub in terminal

#5

In that case, it is probably unrelated to the fact that you are using Git for the project. I run into the same problem when I, for example, are trying to view a complex data frame. Next time it happens can you check the Activity Manager and whether rsession is running to 100% of CPU.

#6

I have been checking the Activity monitor constantly. I haven't thought that it was an issue because the CPU load has been low. For example currently I have been waiting for at least 30 minutes for Rstudio to respond. The CPU load for User is ~17% and the rsession is using 100% of that. Will it still cause a hang up if I am not maxing my CPU? Also, I have been running larger jobs in terms of object sizes within this project for weeks before this issue started.

#7

To follow up, the R log for the hang up is all saying git_all_status (active). Do you have any resources for understanding this R log? I have tried just googling git_all_status and there are no results.

#8

Not directly. You could try to start a new project without the Git part and see if you run into the same problem. The connection to Git should not represent a problem unless you are actively communicating with the Git repository. This is more likely a problem with the R script and RStudio. Lot of people seem to have things hang, sometime apparently randomly (not that that helps you very much).

#9

I think the git_all_status(active) in the log is indicating that Rstudio is trying to actively communicate with git. I've read on a couple other threads that Rstudio automatically runs git status (e.g., see this comment)

#10

Do you happen to have large files under version control in your project? There are precedents of sessions hanging because of this.

#11

No, I do not. The project folder on my computer is 2.6 MB

#12

But the git status command should not be called when you run a line of code, which is what you said caused the problem. To be certain, set up a new project, copy everything but the Git information over and try whether you get the same problem. If you do, it is definitely not the Git part.

#13

We've had some issues of this form reported when the .git directory became un-hidden, for some reason. Is that directory marked as hidden in your project? (Sorry, this may not be relevant unless you're running on Windows.)

Does git status run in a timely manner from a terminal, outside of RStudio? You might also check whether there is a file .git/index.lock -- if that exists, you might try removing it.

#14

In terminal, git status runs instantly. I have a .git/index file, but it doesn't appear to have an extension.

#15

I will add for completeness that I did have an html file open that is part of the project when the issue happened today and probably for a majority of the other instances, but I can't guarantee.

I appreciate the discussion and agree that it is probably specific to this project so transferring the scripts to a new project space would be the best way forward. It would be nice to be able to troubleshoot, but there are so many inconsistencies that I might not be able to communicate the right information.

#16

Not sure if this is related, or whether this problem has been fixed, but Rstudio can be very slow if your git repo is on a remote server/shared drive. It runs git commands in the background to keep the git pane up to date, and this remote nature can make it very slow. Maybe here a git status that is occurring in the background is lagging?

#17

The repo is not on a remote server or shared drive, but thanks!

#18

I reached out to @lbergmans of this thread and he sent me to a follow up on github where the issue was tracked down to use of the Rfast package. I will be removing all instances of Rfast from project