I frequently work on a R-server environment. However, whenever come back to my work following the last working day, the system often gets stuck with 'resuming r session'. This might take upwards of 5-15min. I try to terminate R or restart R but often this doesn't really do anything.
I'm looking for a work-around as it is very frustrating to go to the R-server URL and to have to wait forever to get started again. IDEALLY, I'd be able to pick up right where I left off. However, if this can't be done, I guess that is ok….
I was looking around at the folder structure and I noticed that there is a folder called "Suspended-R-Session".
Within this folder are a few files such as:
'options',
'lib paths',
'history',
'environment_vars',
'environment',
and 'settings'.
Should I be deleting these files in order to speed up load time???
As described in this link https://support.rstudio.com/hc/en-us/community/posts/200638878-resuming-session-hangup, in my case for R version 3.5:
cd ~/.rstudio/sessions/active/session-45204d30
rm -rf suspended-session-data
Related
I have a project that I've been working on for several months without a problem. Yesterday I tried to profile a bit of code using the raster package that was taking a very long time to run. I left it running overnight and found RStudio unresponsive in the morning. Now when I open that project, I can't do anything except to force quit RStudio. Other projects appear to work fine.
I suspect something bad is stored in the file(s) that remembers where I was. Is there one or more that I can delete and regain control of the project. Candidates in the project folder would seem to be one or more items in the .Rproj.user directory.
I found a tip on the RStudio website. In a terminal, navigate to the project directory and rename .Rproj.user to something different. I used this command - mv .Rproj.user .Rproj.user_old. This keeps the user-specific information around in case you want to go back to it.
Suddenly, Rstudio is painfully slow, and now it is unusable. This means, I open it up and there is a lag of several seconds if I type anything. I have explored all the options I can come up with:
1. re-installing both R and Rstudio (although I am not 100% sure I could remove all components),
2. trying to reset settings.... the obvious things such as clearing the workspace and the console.
The size of my data is negligible. I cannot think of anything else.... any ideas?
The only observation i can make that shows something could be wrong with the configuration is (sometimes), I see "gctorture false" as a value in the environment.
Just a guess, but ?gctorture says
Provokes garbage collection on (nearly) every memory allocation.
Intended to ferret out memory protection bugs. Also makes R run
_very_ slowly, unfortunately.
which sounds about right for your problem! You could try
gctorture(FALSE)
If that speeds things up, then look for somewhere that this might have been set, e.g., in a .Rprofile (current working directory, or your user home directory, or the installation directory of R; see ?.Rprofile) and make sure that you start R without loading any .Rhistory or .RData files (again in the working directory, your home directory, etc.)
I had a RStudio project with Git Version Control and then it became very slow. I solved the problem by removing the Git Version Control
In RStudio, if you are dealing with a directory that contains a large number of files, and you want to commit and push the recent changes (that you made on all of them) to your repository, the GUI Git component gets super slow and practically doesn't work. Any idea?
Of course you can ignore the GUI and stick to the command-line Git forever, but if you don't want, a quick jump to the command-line git would solve this problem for now.
The temporary solution that I found is as follows:
Click on the blue-gear icon on the GIT panel, inside RStudio.
Select Shell (a terminal window will pup up!)
Write the add and commit command in the terminal:
{ATTENTION: The following command will commit changes on ALL files! You may want to use what is appropriate for your situation!}
git add -A && git commit -m 'staging all files'
Now you can go back to the GUI Git, and click on push button. All files that you staged in the terminal window, will be pushed up to your repository.
My workaround today was to...
create a man1/ directory in my RStudio project (after force-closing and
relaunching RStudio a few times after I had done something that caused it to hang again),
include man1/ in .gitignore,
move just about everything in man/ to man1/,
delete the .git/index.lock file in the repository,
futz around with RStudio, until it was responsive enough to make the (small) commit of files from man/,
pull and push, so that the remote main was once-again fully synched
copy some files from man1/ to man/, commit these
repeat and rinse of steps 6 and 7, until there's nothing left in man1/
Delete man1/ and its entry in .gitignore
My recipe above isn't one-size-fits-all... for example, you may have run into a "diff is too large" difficulty with RStudio because of a single oversized file, rather than (as I had) with "too many" small files. If you're trying to commit a monstrously-big set of diffs from a single file... you should be including this file in your .gitignore, rather than expecting it to be version-controlled without any difficulty by git. Also, if you're locking up RStudio's Git-interface because of "too many" files being committed simultaneously, your first port of call should I think to commit directories one at a time (but do be sure to push & pull after each commit).
And... I'm not going to complain about this defect in how RStudio interacts with git!
Instead I'll close with some kudos. After just a few days of futzing around with RStudio, I'm finding it to be so much easier than what I remember about hacking on S via emacs in the early 1990s. RStudio handles just about everything (especially the ROxygen documentation workflows) than the emacs/eSS setup that I had been struggling to get fully operational earlier this month.
I'm also impressed with how R has developed since the last time I looked at it -- about 20 years ago! The semantics lurking in corner cases are still very "surprising", to put it mildly ;-) But I do appreciate how it has maintained compatibility with the truly-bizarre and primitive semantics of S while allowing its power-users (which will surely never include me!) to write expressively, elegantly, and with an appropriate balance between concision and the write-only alphabet-soup of APL and its ilk (https://en.wikipedia.org/wiki/Write-only_language)
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.
Every time I restart RStudio-it requires me to reload all of the packages that were loaded in the workspace previously. I can't seem to figure out what the problem is, RStudio is saving the projects when it closes them.
How can I make sure that RStudio reloads the necessary packages when I open the project?
I presume you want to say that you have to reload all of the packages that were loaded in the workspace previously. That's not an error, that's by design.
If you want to load some packages at startup in a project, you can do so by creating a file called .Rprofile in the project directory, and specify whatever code you want RStudio to run when loading the project.
For example:
cat("Welcome to this project.\n")
require(ggplot2)
require(zoo)
would print a welcome message in the console, and load ggplot2 and zoo every time you open the project.
See also http://www.rstudio.com/ide/docs/using/projects
In general there's nothing different to default package loading in RStudio than in R (How to load packages in R automatically?). Upon startup R checks for an .Rprofile file in either your local, or fail, that, home or install directory (on Mac/Linux: ./.Rprofile or else ~/.Rprofile) and executes it, and hence any options(defaultPackages...)) or other package-load-related commands it contains.
The only small difference is that RStudio "helpfully" changes your default path before startup see "RStudio: Working with Projects", so you might load a different or missing .Rprofile or the wrong .Rprofile, depending on whether you've opened an RStudio Project or just plain files, and what your RStudio default working directory is set to. It's not always clear what directory you're in, so sometimes this causes real grief.
I tend to use RStudio without defining my code as an RStudio Project, simply because it's heavy-handed and creates more files and directories without adding anything (to my use case, anyway).
So the solution I found to maintaining .Rprofile and making sure the right one gets loaded is a trusty old Unix link from the project directory to my ~
ln -s ~/.Rprofile ./.Rprofile
(If you're on Windows it's more painful.)
You don't need to have one global .Rprofile, you could keep task-specific ones for different types of projects, or trees, or (say) a .Rprofile.nlp, .Rprofile.financial, .Rprofile.bio and so on. As well as options(default.packages, you can gather all your thematically-related settings: scipen, width, data.table/dplyr-specific options, searchpath...
Power tips:
obviously keep backups or SCM of your valuable .Rprofile(s)). Definitely make sure git is tracking it, so don't put it in .gitignore
if you have multiple .Rprofiles, put a cat("Loading .Rprofile.foo") line in each one so you can see from console that the right .Rprofile.xyz got loaded
after every project, revise, trim, tweak your .Rprofile; add new use case stuff, comment out irrelevant stuff, commit the changes to git