Retrieving Workspace in R - r

I am working with R on Ubuntu. When I was working I accidentally hit Ctrl-Z and
it kicked me out of the workspace and I did not save my variables. Is there
anyway to retrieve my old workspace?
Thank you.

Jump back into the still-running session via
fg
i.e. bring the R session you suspended via Ctrl-Z back to the foreground.

Reconnect and try "jobs" from the terminal to see if the R process is still there. If so, fg should do the trick as #Dirk said (if you have more than 1 suspended jobs, fg %2 would bring back the second one etc).
As far as I know, if you actually terminate the R session and did not save your workspace, it is lost - sorry. S-PLUS would save all variables in your workspace directory as you generated them, but R keeps everything in memory until you explicitly save your workspace - typically at exit, but save.image() can do it mid-session.
/Tommy

Related

Stop submitted lines of code from running

I'm running a long R script, which takes 2 or 3 days to finish. I accidentally run another script, which, if it works as R usually does, will go in some queue and R will run it as soon as the first script is over. I need to stop that, as it would compromise the results from the first script. Is there a visible queue or any other way to stop R from running some code?
I'm working on an interactive session in R studio, on windows 10.
Thanks a lot for any help!
Assuming you're running in console (or interactive session in R studio, that's undetermined from your question) and that what you did was sourcing a script/pasting code and while it was running pasting another chunck of code:
What is ongoing is that you pushed data into R process input stream, it's a buffered input, so it will run each line once the previous line call has ended and free the process.
There's no easy way to play with an input buffer, that's R internal input/output system and mostly it's the Operating system which have those information in cache for now.
Asking R itself is not possible as it already has this buffer to read, any new command would go after.
Last chance thing: If you can spot your another chunck of code starting in your console, you can try pressing the esc key to stop the code running.
You may try messing with the process buffers with procexp but there's a fair chance to just make your R session segfault anyway.
To avoid that in the future, use scripts and run them on the command line separately with Rscript (present in R bin directory under windows too despite the link pointing to a linux manpage).
This would create one session per script and allow to kill them independently. That said if they both write to the same place (database, a file would create an error if accessed by two process) that won't prevent data corruption.
I am guessing OP has below problem:
# my big code, running for a long time
Sys.sleep(10); print("hello 1")
# other big code I dropped in console while R was still busy with above code
print("hello 2")
If this is the case, I don't think it is possible to stop the 2nd process from running.

RStudio Server on Microsoft Azure instance

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.

How to recover RStudio session after crash?

I would like to know how to restore my previous RStudio session after RStudio and the R session crashed.
Background:
I find that my R session crashes very often, at random times for random reasons. I am fine with that I guess.
Most of the time RStudio restarts the R session and I can continue.
But sometimes it just freezes at which time I noticed power cycling the entire machine allows RStudio to recover and even reload my old session.
Stupid me, I don't think power cycling is a good idea so I manually killed the R session, but then RStudio responded but was not really working so I restarted it and it came back with an empty work-space.
I have been backing up with Session->Save Workspace As, but it seems to do nothing as recovering leaves me with the blank empty environment.
I am looking to restore the RStudio display, including the command history , which for a novice like me is precious, and my list of open scripts, some of which were unsaved at the time of the crash.
I am assuming since RStudio can recover itself, there is a file somewhere I can use to recover it.
And if there is no way to recover, how can I completely save my workspace so this cannot happen again?
Also, is there a proper way to recover from an RStudio freeze without a hard reset?
It has been a while since I asked this question. I was never able to fully recover, but I switched to Rprojects which is the recommended way to use Rstudio.
Rprojects are stored in a folder and they remember all files and data from that project in that folder.
This did not help me with my initial problem, but projects prevent it from happening again. The hard part is moving a work-space to a project if it was not in a project to start.
Hi the first step of this article helped me entirely.
https://datacornering.com/how-to-restore-closed-unsaved-script-in-rstudio/
Basically, if on windows, go to C:\Users\xx\AppData\Local\RStudio\sources\s-xx and find a file with "-contents" at the end. This is your unsaved file.

RStudio freezes on "saving workspace image," previously saved .RData file disappears

First, I've also posted this question on the RStudio Support page. If I get a response there, I will post it here for all to see (and vice versa).
I'm enjoying RStudio but am having trouble using Rprojects to save model outputs. I'm running sets of models that take ~1 day to run, so this is really setting me back. This is on an iMac running 10.9.5 (Mavericks).
Here's what happens:
I close the project and allow the "saving workspace image" to go through. (This is taking ~15 min, and the Rdata files are 6GB - this seems surprisingly large to me).
Often there is no problem upon reopening, the Rdata files are restored, and I see the objects I've created in the Global Environment pane. I run another model (or set of them), and close the project again. RStudio now gets hung up on "saving workspace image." Eventually, the wheel showing that this is active stops turning. Sometimes the mouse disappears from the screen and the entire computer freezes.
I either force RStudio to close, or force the computer to shutdown. When I restart and open RStudio, then load the Rproject, the Global Environment is empty. In the Files pane, there are no .RData files shown.
When I check the Rproject directory in Finder, there are multiple .RDataTmp (hidden) files. I'm not clear whether I can use any of them to recover my data, or how to attempt to load them in RStudio.
Solutions I've tried so far:
Updating everything, including R, RStudio, and Safari, per another post on RStudio Support.
Disabling my syncing program (SugarSync) from updating .Rproj.user file, also after reading a post there.
Enabling access for RStudio in the Privacy/Security settings.
I haven't been able to find any other possible solutions, and I am growing frustrated with testing this out, as it seems to happen only intermittently and (sigh) after the problem seems revolved, such that I've run a whole bunch of models and have a good deal of data to lose! This makes me wonder whether (a) the universe is simply cruel, or (b) it's the large file size that is causing the problem. The other option is (c) both.
I read elsewhere on RStudio Support that file compression can be enabled, but that this will slow the process of saving. Since it's already taking quite a long time to save upon closing the project and I'm not clear on why it might help, I'm hesitant to enable file compression until I know more.
Thanks for your help,
MK

Command to open new R Session from R source file

I run some calculations over several hours with R. After a while my memory is full of junk. The gc() and rm() command don't solve the problem. What I did is that I shut down my R session and opend a new one. This solves the memory problem. Now I want to automate this process. Is there a command to open a second R session or RGui form an existing session. Then I want to set the wd in this second session, run some code there and close it after some time. How can I do this? Alternatively, is there another way to get rid of the junk in my memory.
You may want to give Rscript a try, see Rscript --help from command line. Break down your big script into smaller parts and run them in succession using the same workspace with Rscript --restore --save yourscript.r. A new session of R will be opened for each script which may help you to keep memory use under control.

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