I've found a lot of answers on how to run R from a Batch file, but nothing about running a Batch File from R. I know one way to do this is to use system, system2 or shell, but these methods wait for process in the Windows Command Prompt to finish before R accepts another input. I want to run a Batch File which calls a console application that runs indefinitely, and then allow R to do other things. Any help would be greatly appreciated.
The help page ?shell says how to do it. Just run
shell("MyScript.bat", wait=FALSE)
Related
I am creating a function in R and in one step of the function I run a batch file, this batch file in turn runs a different program which creates files that I then want to read in my function.
I am using shell.exec to run the batch file and it runs fine, the problem is that the next line of my code that wants to read in the output from the program ran by the batch file crashes because it hasn't been created yet.
So I get an error the first time I call my function but if I simply call it again it runs fine. Example of code below: Basically what happens is I get an error message when calling the function saying that .../bat_output.txt does not exist, because the batch file hasn't been run yet, but then when I call the function again, it works fine.
shell.exec("run.bat")
readout<-read.table("bat_output.txt")
Any suggestions?
shell.exec returns immediately while the script is running in the background. The reason bat_output.txt is not found the first time is likely that the script has not finished yet. shell.exec does not give you the ability to wait or any information to determine if the process is still running, so it might not be the best tool for this.
Alternatives:
system("cmd /c run.bat")
system2("cmd", c("/c", "run.bat"))
Realize that if you reference a different path, you might want/need to normalizePath and/or dQuote it going into those commands. (R's system* commands are bad at argument forming.)
I'm currently running some queries to a database and getting back some big files as a result. I have encountered the common problem of Windows not freeing the memory, even though I 'rm()' everything and (edit) calling 'gc()'. One workaround i have found is using .rs.restartR() in Rstudio.
This though requires me to constantly watch my script, in order to continue it after the session restart. Is it possible to automate it? If not what other methods do people use to overcome this problem?
You could break the code into 2 files and write a batch file (.bat) that runs the first file through .rs.restartR() and then the remainder of the code in the next file.
You could also skip the .bat and just schedule both .R scripts to run in Task Scheduler.
Also, please see my comment regarding garbage collection (gc()).
Is it possible to Execute a .bat file within the R console? I know I can run R in batch mode, but am wondering if I can start a .bat file from the R code within itself. I have googled it and cannot seem to find an answer. Thanks in advance!
I guess you could use system command for invoking OS commands. Please check here for more info.
I've got a lengthy process running in Rstudio and I would like to open a separate session of Rstudio while the first one is running. I know I can run R from the command line to get as many sessions as I want, but I wanted to know if it is possible for me to do this in Rstudio on a Linux computer. Thanks.
#infominer suggested a good solution, which is to simply type rstudio in the command line. That's what I ended up doing
Another convenient way to deal with this is to start a seperate R-instance in the terminal by typing simply
R
and from there just run the script that has a lengthy process with
source("path-to-your-script/your-script.R")
you can than continue to edit and work with your two scripts in the already opened R-Studio editor window.
I want to execute a R script in the background from the R console.
From the console , i usually run R script as source('~/.active-rstudio-document')
I have to wait until the script is completed to go ahead with my rest of work.
Instead of this i want R to be running in the background while i can continue with my work in the console.
Also i should be somehow notified when R completes the source command.
Is this possible in R ?
This might be quite useful as we often sees jobs taking long time.
PS - i want the source script to be running in the same memory space rather than a new one. Hence solutions like fork , system etc wont work for me. I am seeing if i can run the R script as a separate thread and not a separate process.
You can use system() and Rscript to run your script as an asynchronous background process:
system("Rscript -e 'source(\"your-script.R\")'", wait=FALSE)
At the end of your script, you may save your objects with save.image() in order to load them later, and notify of its completion with cat():
...
save.image("script-output.RData")
cat("Script completed\n\n")
Hope this helps!