Is there anyway to capture a SIGINT or SIGTERM from the shell in R so that I can try to execute some graceful exit code?
So far, I haven't found anything in my search.
Related
I am writing an R code on a Linux system using RStudio. At some point in the code, I need to use a system call to a command that will download a few thousand of files from the lines of a text file:
down.command <- paste0("parallel --gnu -a links.txt wget")
system(down.command)
However, this command takes a little while to run (a couple of hours), and the R prompt stays locked while the command runs. I would like to keep using R while the command runs on the background.
I tried to use nohup like this:
down.command <- paste0("nohup parallel --gnu -a links.txt wget > ~/down.log 2>&1")
system(down.command)
but the R prompt still gets "locked" waiting for the end of the command.
Is there any way to circumvent this? Is there a way to submit system commands from R and keep them running on the background?
Using ‘processx’, here’s how to create a new process that redirects both stdout and stderr to the same file:
args = c('--gnu', '-a', 'links.txt', 'wget')
p = processx::process$new('parallel', args, stdout = '~/down.log', stderr = '2>&1')
This launches the process and resumes the execution of the R script. You can then interact with the running process via the p name. Notably you can signal to it, you can query its status (e.g. is_alive()), and you can synchronously wait for its completion (optionally with a timeout after which to kill it):
p$wait()
result = p$get_exit_status()
Based on the comment by #KonradRudolph, I became aware of the processx R package that very smartly deals with system process submissions from within R.
All I had to do was:
library(processx)
down.command <- c("parallel","--gnu", "-a", "links.txt", "wget", ">", "~/down.log", "2>&1")
processx::process$new("nohup", down.comm, cleanup=FALSE)
As simple as that, and very effective.
I am writing an R script as a command to run in terminal, and I found if an error happen when running this script, the command still returns a normal exit signal. So I cannot check the running results by checking [ $? -ne 0 ], it just returns succeed.
This is because R will continue running the next command when it encounters an error in previous command. Is there any way to solve this situation?
Best,
Shixiang
I combine tryCatch() and quit() to solve this problem. I firstly wrap my main function to tryCatch structure to let it detect if an error occurred, once an error is detected, I print the error message and call quit("no", -1) to quit R with exit status signature -1.
The code I am using is:
library(Rmpi)
mpi.spawn.Rslaves(nslaves=mpi.universe.size()-1)
mpi.remote.exec(paste(--))
mpi.close.Rslaves()
mpi.quit()
I tried mpi.exit() but still, it hangs.
Let suppose there is a simple R script with only one statement:
q()
Using the R Script plugin in Pentaho Kettle/Spoon, executing the above R script causes Spoon/Kettle to crash.
How can we stop Kettle/Spoon from crashing abnormally with the above statement in our R script?
Kettle should instead stop executing the script and execution control should return to Kettle.
Try to use a return(value) instead q() to expect kettle handle the value from R script and continue the common kettle row flow.
When I run Pkg.update(), Pkg.status(), sometimes, Julia hangs there. Is there a way to stop the Pkg-related command? I tried C-c, C-c, C-d, C-q, none of them works.
Is there a way to stop those command?
Pkg.xxx() starts a number of detached tasks which are not killed even when the Pkg command is interrupted using Ctrl-C. To kill these tasks, use interrupt(workers()).
It looks like the behaviour of Ctrl-C might be improved in a future version of Julia with RFC14032.