I am currently running R on a Microsoft Azure instance (Ubuntu virtual machine) using RStudio as my IDE, to which I connect simply through my browser. I am trying to run some commands that take quite some time to complete from within RStudio and figured that I could simply close my tab with RStudio open and the process would keep running. However, when I try to reconnect to see how the process is doing, the page keeps loading but I am unable to see RStudio.
I have a few questions regarding running RStudio on a server:
First, am I correct in thinking that I can close my tab and keep the process running?
Second, is it normal behaviour that I am unable to connect to the server while the process is running?
Third, am I going about this the correct way or are there better ways?
Yes, you can close your tab and keep it running.
RStudio Server waits on updates from the R process to update the UI. This means that if you have a long-running computation, your tab may not fully reload until it's finished. You may also have seen this in the middle of a session: when R is busy, you can have problems saving scripts that are open in the editor pane.
Logging out in the middle of a computation should be safe, but be aware that RStudio will save your workspace and shut R down after a period of inactivity. It then reloads everything when you log back in. But this only extends to objects in memory; if you have any files saved in your temp directory, they'll have disappeared when you come back. They're probably still on the disk, but since your new R session has a new temp directory, you'll have to do a manual search for them.
Related
I have a Desktop Entry that calls a shiny app.
Here's my desktop entry
[Desktop Entry]
Type=Application
Comment=App
Name=App
Exec=/usr/bin/Rscript -e "shiny::runApp('~/raspberry_IP/app.R', launch.browser=TRUE)"
Icon=/home/path/to/logo/rpi_logo.png
Terminal=false
Categories=Utility
StartupNotify=true
This runs well and the Shiny application works as expected. However, when I close my browser tab, I see the process is still running.
I am running this application from Ubuntu 20.04 LTS.
If I change my terminal=false to terminal=true. I see that the output of my terminal freezes (the app no longer updates, hence no diagnostic printing). But the terminal is still active (which makes sense given the process is still running). I can CTRL+C out of it to kill it from my terminal, but that's not the desired user behavior.
I see some strategies to stop the app using stopApp() like here. This strategy uses a separate action button to kill the app, so the user has to "manually" stop it. This might work, but I believe it's natural for the user to try to close the tab or Browser (and there's no way for them to know the process is still running, unless they check).
Using this on the server side, does kill the process, but it's recommended against (see here).
session$onSessionEnded(stopApp)
In this case, because my app is running on a local machine, I think I could potentially get away with this (there is only one user at a time), but I was wondering whether there's better practice to implement.
I have an Rstudio Server installation on a Linux Azure VM that seems frozen and also crashes any browser I try to login with.
I have restarted the VM and separately restarted RStudio Server (similarly to the solution in this post) a number of times, but it does not change the behavior. I didn't think I had it set to reload an environment or operation upon restart, but perhaps I accidentally did. The last thing I was doing with the server was a large sparse matrix operation that turned out to be too much for it.
Since the problem occurs immediately after the app loads, I'm not sure how to reset its state. I tried following these instructions but it didn't work:
I renamed ~/.rstudio to ~/.rstudio.backup while RStudio Server was stopped and it was recreated on the next start, but it still resumed in the same state. I saw mentions of ~/.local/share/rstudio/ and ~/.config/rstudio in the support docs, but they do not seem to exist in this Azure Ubuntu installation.
I also moved and renamed the folder of the last used R project, but it had no effect. There is a .config/R/ folder but it only contains a rsconnect folder and 2 empty subfolders.
I finally got it. After shutting down and restarting RStudio Server it was necessary to run this command immediately after RStudio Server loaded:
sudo rstudio-server suspend-all
I have made a Desktop shiny app for windows using the amazing package RInno but I have been experiencing some inconsistencies with launching the application. Occasionally the application will not quit its session properly, leaving R running in the background. Their github suggests using this chunk of code in the server function to insure R is properly terminated when the session ends. I can tell when the application quits properly because I include a custom function that copies the log files to a new indexed name for records and debugging.
if (!interactive()) {
session$onSessionEnded(function() {
write_logs_out() #My custom function. renames logs and stores backups of session data in .rds files
stopApp()
q("no")
})
}
In these cases a new log file is not made so I assume stopApp() and q("no") are never executed as well, leaving R running in the background. One major issue is I do not know how to reproduce this error. My current guess is that this occurs when the R session locally becomes unresponsive. While R is still running in the background, the shiny app never fully opens to a web browser. I will first need to open task manager and quit any R sessions (usually with the name "R front-end") in order to get the app working again.
Since I dont know how to expect this random error, I was wondering if any windows experts could help me write a script that will check if an R process is running, and then kill it. This would at least
I know that
tasklist | findstr Rscript.exe
will list all the current Rscripts running (which I believe is the "R front-end" i see in task manager), but I don't know if it is bad practice to simply include taskkill /IM "Rscript.exe" /F before the line that calls the .wsf file that starts the app.
The main problem I see with this is that if the session is running fine and the user for some reason clicks the app again, it will force a complete restart.
Any suggestions?
I am used to using R in RStudio. For a new project, I have to use R on the command line, because the data storage and analysis are only allowed to be on a specific server that I connect to using ssh. This server doesn't have rstudio-server to support remote RStudio sessions.
The project involves an extremely large dataset, and some pre-written code to load/format the data that I have been told to run using "source()" before I do anything else. This takes several minutes to run and load the data each time.
What would a good workflow be for something like this? Editing my code in a .r file, saving, then running it would require taking several minutes to load the data each time. But just running R in an interactive session would make it hard to keep track of what I am doing and repeat things if necessary.
Is there some command-line equivalent to RStudio where you can have an interactive session but be editing/saving a file of your code as you go?
Sounds like JuPyteR might be your friend here.
The R kernel works great.
You can use it on a remote server either with exposing an open port (and setting up JuPyteR login credentials)
Or via port forwarding over SSH.
It is a lot like an interactive reply, except it holds state.
And you can go back and rerun cells.
(Of course state can be dangerous for reproduceability)
For RStudio you can launch console and ssh to your remote servers even if your servers don't use expensive RStudio for servers platform. You can then execute all commands from R Studio directly into the ssh with the default shortcut key. This might allow to continue using R studio, track what you're doing in the R script, execute interactively.
I am running rstudio-server on a virtualised (vmware-player) ubuntu machine, and processing lots of data into the ram. I find that after some inactivity that the session suspends the data. The problem is that it takes a VERY long time to resume this session and it is making both the host machine and virtual machine lag very badly.
I just want to kill the session and start a new fresh session of rstudio-server, but so far the only way I have found which does this is to reisub my ubuntu machine. Does anyone know a better solution?
As a side note, I think entering session-timeout-minutes=0 in /etc/rstudio/rsession.conf as per here should fix the problem of the session suspending.
I found this page, which deals with resetting the rstudio-desktop version. In my home directory, I found the folder ~/.rstudio. I renamed/deleted this folder and this loads a new rstudio-server instance.
In fact, there is a folder called suspended session in the ~/.rstudio folder, which I suspect is the thing where suspended data is stored, so maybe deleting this folder is sufficient?
If there is a directory inside ~/.rstudio/sessions/active/, deleting it (in the way like rm -rf ~/.rstudio/sessions/active/session-*) might be sufficient to solve the problem.
Your question is a while back but after running into this problem a zilion times i found a way to reset the Rstudio Shiny Server session without the need for admin rights on Rstudio Shiny Server:
put temporarily as first line in server.r :
quit("yes") # FORCE CLOSE OF SESSION server
go to the site and it will crash (the session closes straight away)
delete or comment out:
# quit("yes") # FORCE CLOSE OF SESSION server
go to the site and you will have the shiny app with a new session =^)
Works for me and saves a lot of time searching through all kind of system folders or the need to enter a part of the system that you are not allowed to go or needing admin rights on Rstudio Shiny Server.
I hope this helps.
I have tried the above solutions which didn't work for me. I tried to kill the rsession which is causing the problem. just run this command to find out pid of user session.
ps -u userid
Find out the pid that is causing the rsession to stall. Kill that process and you're good to go.
Note that with newer versions of Rstudio, this folder is now under
~/.local/share/rstudio/sessions/
while in some older versions, it can also be seen in ~/.rstudio-desktop, see documentation page
A quick solution would be to rename ~/.rstudio and reopen the webpage using rstudio url.