I'm running R script in OpenCPU/Docker and looking for the way how I can run the script that will create background process and returning back the message that the process has started. Something like this:
fun1<-function(arg1,arg2){
#calling different function to run in background, using arg1/arg2, no need
#of result now, I will check the result through the file later
fun2(arg1,arg2)
return('Process has started')
}
How can I run the fun2 in the background? All functions are inside the package and I have tried Rscript but with no success. Any ideas or packages for this? I believe a lot of people already went thru this.
Related
I have an R script that's called the following way from the terminal:
Rscript myscript.R param1 param2
When the script finishes it generates an output .csv file that is saved somewhere on my server.
I want to be able to, by using tmux, on different panes, run the same script, just with different values for param1 param2.
How do I go about to do that? Really struggling to find the best way to do it.
So the best solution I managed to get to this problem was to basically start R sessions on each tmux window and from there just input the arguments and run the actual script.
Not the most practical but gets the job done.
Question regarding RStudio. Suppose I am running a code in the console:
> code1()
assume that code1() prints nothing on the console, but code1() above takes an hour to complete. I want to work on something else while I wait for code1(). is it possible? Is there a function like runInBackground which I can use as follows
> runInBackground(code1())
> code2()
The alternatives are running two RStudios or writing a batch file that uses Rscript to run code1(), but I wanted to know if there is something easier that I can do without leaving the RStudio console. I tried to browse through R's help documentation but didn't come up with anything (or may be I didn't use the proper keywords).
The future package (I'm the author) provides this:
library("future")
plan(multisession)
future(code1())
code2()
FYI, if you use
plan(cluster, workers = c("n1", "n3", "remote.server.org"))
then the future expression is resolved on one of those machines. Using
plan(future.BatchJobs::batchjobs_slurm)
will cause it to be resolved via a Slurm job scheduler queue.
This question is closely related to Run asynchronous function in R
You can always do this, which is not ideal but works for most purposes:
shell(cmd = 'Rscript.exe some_script.R', wait=FALSE)
RStudio as of version 1.2 provides this feature. To run a script in the background select "Start Job" in the "Jobs" panel. You also have the option of copying the background job result into the working environment.
The mcparallel() function in the parallel package will do the trick, if you are on Linux, that is ...
library(parallel)
Job1 = mcparallel(code1())
JobResult1 = mccollect(Job1)
I'm trying to call a simple python script from within R using system2(). I've read some information I found vague that said if 'too much' memory is used, it won't work.
If I load a large dataset and use some information in it to use as arguments to pass into system2(), it will only work if I manually click "Restart R" in call Rstudio.
What I want:
df <- read.csv('some_large_file.csv')
###extracting some info called 'args_vec'
for(arg in args_vec){
system2('python', args)
}
This won't work as is. The for loop is simply passed over.
What I need:
df <- read.csv('some_large_file.csv')
###extracting some info called 'args_vec'
###something that 'restarts' R
for(arg in args_vec){
system2('python', args)
}
This answer doesn't quite get what I want. Namely, it doesn't work for me within Rstudio and it calls "system" (which presents the same problem as "system2" in this case). In fact, when I put the answer referenced above in my Rprofile.site file, it just immediately closed rstudio:
I tried the suggestion as a normal function (rather than using "makeActiveBinding", and it didn't quite work.
##restart R in r session -- doesn't work
makeActiveBinding("refresh", function() { system("R --save"); q("no") }, .GlobalEnv)
##nor did this:
refresh <- function() { system("R --save"); q("no") }
I tried a number of variations of these two options above, but this is getting long for what feels like a simple question. There's a lot I don't yet understand about the startup process and "makeActiveBinding" is a bit mysterious. Can anyone point me in the right direction?
In Rstudio, you can restart the R session by:
command/ctrl + shift + F10
You can also use:
.rs.restartR()
RStudio has this undocumented rs.restartR() which is supposed to do just that: restarting R.
However, it does not unload the packages that were loaded, nor does it clean the environment, so that I have some doubts about if it restarts R at all.
If you use RStudio, use the menu item Session > Restart R or the associated keyboard shortcut Ctrl+Shift+F10 (Windows and Linux) or Command+Shift+F10 (Mac OS). Additional keyboard shortcuts make it easy to restart development where you left off, i.e. to say “re-run all the code up to HERE”:
In an R script, use Ctrl+Alt+B (Windows and Linux) or Command+Option+B (Mac OS)
In R markdown, use Ctrl+Alt+P (Windows and Linux) or Command+Option+P (Mac OS)
If you run R from the shell, use Ctrl+D or q() to quit, then restart R.
Have you tried embedding the function call within the apply function, rather than a for loop?
I've had some pieces of code that ran the system out of memory in a for loop run perfectly with apply. It might help?
For those not limited to a command that want something that actually resets the system (no prior state, no loaded packages, no variables, etc.) you can select Terminate R from the Session menu.
It is a bit awkward (asks you if you are sure). If anyone knows something like clear all or really clear classes in MATLAB let me know!
I want an R script to continuously run and check for files in a folder and do something with those files.
The code simply checks for a file, then moves the file to somewhere else and renames it, deleting the old file (in reality it's a bit more elabore than this).
If I run the script it works fine, however I want R to automatically detect for the files. In other words, is there a way to have R run the script continuously so that I don't have to run the script if I put files in that folder?
In pure R you just need an infinite repeat loop...
repeat {
print('Checking files')
# Your code to do file manipulation
Sys.sleep(time=5) # to stop execution for 5 sec
}
However there may be better tools suitable to do this kind of file manipulation depending on your OS.
You can use the function tclTaskSchedule from the tcltk2 package to schedule a function or expression to run on a regular interval. You can have multiple such tasks scheduled and still work in the R session (just be careful not to modify something that the scheduled task could also modify or you can get unpredictable results).
Though an OS based solution that runs a given rscript may still be a better approach.
I am running a set of selected code on R. Like
source("/tmp/r-plugin-honli/Rsource-2704-quantmod.R")
There is no output. Only the prompt '>' flickered there.
I use 'killall' to kill the R session. But I don't know where is wrong on the code. Because R did not give any output. How could I know what's going on about the code.
I'd try two things:
Run the code interactively. As in, open the Rsource-2704 file and run its lines one by one.
If that doesn't replicate the problem or is not possible, you can take Joshua Ulrich's suggestion or use:
R CMD BATCH --vanilla Rsource-2704-quantmod.R out.log
Which will run the code in a batch mode and output the usual console lines to a file called out.log (you can name it whatever you like).
Instead of using print statements, you could also take a look at the browser() command. This drops you into an interactive session at the point where the command is put. This works particularly well when trying to figure out what is happening inside a function, although I don't know if your script contains them.