I am working on an ubuntu server. I have an R Script which will run for several days. How would I run it in the background - that when I log out it still runs?!
When I try R script.R it says ARGUMENT 'script.R' __ignored__
First off, to run an R script in batch mode, you have several possibilities; I use the following, which works well:
Rscript scriptname.r
This, however, will run the script in the foreground. This isn’t a problem in tmux per se — just run it in a background tab. However, you can of course run it in the background in the usual way — append &:
Rscript scriptname.r &
Again, this needs to be run inside tmux (or similar) to stay alive once you log out.
Related
I try to run an R script at regular intervals to update a webpage. The script runs fine when called from the terminal like this:
/usr/local/bin/Rscript /Users/me/path/myscript.R
However, if I try running it as a cron job, I get an error. I add the job to crontab like this:
46 10 * * * /usr/local/bin/Rscript '/Users/me/path/myscript.R' >> '/Users/me/path/mylog.log' 2>&1
The script does run in R, but aborts due to an error. Specifically, I fit some models using rstan, and get an initialization error. (The error only applies to some models, while others still run fine.) The initialization values are valid by definition, but do not seem to be used properly. It is like rstan is doing math differently (and wrong) when it is run through cron.
The session info from R is identical whether I run the script in the terminal or as a cron job. My question is what else might still differ depending on how the script is run. Could rstan be using a different version of C++ when run as a cron job? Are there other paths I may need to set to get this to work correctly?
Update: The script also works if I run it using R CMD BATCH in terminal, but not if I use R CMD BATCH in a cron job. Using launchd triggers the same issue. I also tried using CmdStan through cmdstanr, and the same same thing happens: Runs fine until added to a cron job.
Edit 2: The models I thought ran fine in cron, were not actually fine. The results were wrong, until I used the fix explained below.
It looks like I finally managed to fix this, and I'm posting my solution here for anyone who encounters the same problem.
I ran env in terminal to see my current user environment. I copy-pasted the full output to the top of my crontab file. (Simply adding the PATH variable was not sufficient. I suppose it was SHELL or perhaps both PATH and SHELL that did the trick, but I haven't explored this further.)
To edit my user's crontab, I ran crontab -e, then pressed i to edit the file, pasted everything from env at the top of the file, stopped editing by pressing ctrl + c, and quit by typing :wq and hitting enter.
I am trying to automate a docker command in R. However, in order to run the command, zscaler must be turned off for it to work.
The R script is as follows:
shell(cmd = "docker some command", shell = "CMD.EXE")
It creates an error because zscaler is on but works when it's off.
I would like to write a command that turns off zscaler before this R script and then another one after to turn it back on. Is such a command possible?
I'm basically looking for any way to automatically run R scripts just like it would run as if I was copy and pasting it into console. I've tried the package 'taskscheduleR' however it just seems to output to a log file in the directory which isn't as if I were to just run it inside the Rstudio application.
An example might be, say I want to get the last closing stock prices of 5 stocks each night, then the script in Rstudio and have the variables there and all of the code would be in the script file.
Any thoughts?
I would suggest the in-built Task Scheduler application if you using Windows.
Create a task that will run a batchscript file. This batchscript file has only 1 line which executes the Rscript you want. Set it to run each night (or whatever time you want).
I am not that well-versed in linux and MacOS but here's what I know:
Linux has cron. Add a job to crontab with your preferred timing and execute your script 'path/to/bin/r /path/to/script.r'
MacOS has Automator + iCal (for scheduling). It also has crontab like Linux.
Like in the topic, I'd like to run shiny app with parameters. I need to specify the database file's path from which I will grab the data. The problem is that the file changes sometimes thus I have to modify the file.path every time.
This is the command I use when running application from terminal
R -e "shiny::runApp('../Shiny_visualization')"
I tried
R -e "shiny::runApp('../Shiny_visualization')" --args 'db_path' yet I got an error.
I want to launch Rcmdr as a command from bash (or any unix shell), perhaps as an alias. R accepts the CMD argument and I could also pipe a script in with <. I would like the R console to stay open, and an interactive RCommander session to be started (Rcmdr is a popular GUI for R, for any newbies reading along, and it seems that you start up R, type library(Rcmdr) and then Commander() to start it up).
I am aware of how to add Rcmdr to my profile, and it appears to always start up if I include library(Rcmdr) in my .Rprofile, on my Linux workstation.
If I pipe my input in with < then this script works up to the point where it says that Commander GUI is launched only in interactive sessions:
library(Rcmdr);
Commander();
However if I run R CMD BATCH ./rcommander.r it just starts up and shuts down immediately, probably giving me some warning about interactive sessions that I didn't see, because CMD BATCH puts R into non-interactive mode and is thus useless for the purpose of "injecting" Rcmdr into an interactive R session.
It appears impossible to "source a file on the command line but run interactively" in R. It also appears that there are command line options to ignore the global and the user profile, but not to specify a custom profile like R --profile-custom ./.Rprofile2
Either I would like to specify a profile that means "Right now I want to start up and use RCmdr" and still be able to run R without it sometimes.
Working on an Ubuntu machine here, I was able to use the advice provided by Dirk in this mailing list post:
nathan#nathan-laptop:~/tmp$ cat rcommander.r
#!/bin/bash
r -lRcmdr -e'while(TRUE) Commander();'
nathan#nathan-laptop:~/tmp$ cat rcommander2.r
#!/bin/bash
Rscript --default-packages=Rcmdr -e 'while(TRUE) Commander();'
The first script uses Dirk's littler package, available on CRAN, and the second uses the standard Rscript executable. As noted, you can kill the process with ctrl + c from your terminal.