When running a script with a large number of lines RStudio always lags and freezes due to the output/echo that appears in the console. Is there any way to suppress the console messages entirely or at least suppress the repetition of the input that occurs when a script is run?
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I am running a long R script. Is there a way to give me an overview of all the errors that occured after the script has run. (e.g. a function that I could enter after the script has finished running and that extracts me the error notifications from the console)
I would like to run a lot of system commands asynchronously in the first part of my code, but then wait for them to finish in the second part of my code.
Right now I do that in the following way
for(command in commands){
system(command, wait = FALSE, intern = FALSE)
}
Sys.wait(300)
#run second part of my code using the files generated by the commands above
In other words. Right now I just run the commands asynchronously and guess that they will be completed in 300 seconds. Is there a way to explicitly check of the commands are all executed before continuing and at the same time run them asynchronously?
I am trying to run an external code in OpenMDAO 2 that outputs some minor error messages as part of it's run process in windows shell. These error messages does not affect the results of the code and the code runs itself normally. However OpenMDAO raises a fault and stops whenever it detects these error messages. Is it possible for OpenMDAO to ignore such situation and continue running the analysis? I have tried setting fail_hard option to false, but it doesn't seem to change the behavior except that OpenMDAO raises analysis error instead of run-time error.
We can implement a feature to let you specify allowable return codes.. as long as you can enumerate which return codes are not errors, I think this will solve your problem?
Every now and then I have to run a function that takes a lot of time and I need to interrupt the processing before it's complete. To do so, I click on the red sign of "stop" at the top of the console in Rstudio, which quite often returns this message below:
R is not responding to your request to interrupt processing so to stop the current operation you may need to terminate R entirely.
Terminating R will cause your R session to immediately abort. Active computations will be interrupted and unsaved source file changes and workspace objects will be discarded.
Do you want to terminate R now?
The problem is that I click "No" and then Rstudios seems to freeze completely. I would like to know if others face a similar issue and if there is any way to get around this.
Is there a way to stop a process in Rstudio quickly without loosing the objects in the workspace?
Unfortunately, RStudio is currently not able to interrupt R in a couple situations:
R is executing an external program (e.g. you cannot interrupt system("sleep 10")),
R is executing (for example) a C / C++ library call that doesn't provide R an opportunity to check for interrupts.
In such a case, the only option is to forcefully kill the R process -- hopefully this is something that could change in a future iteration of RStudio.
EDIT: RStudio v1.2 should now better handle interrupts in many of these contexts.
This could happen when R is not working within R and is invoking an external library call. The only option is to close the project window. Fortunately, unsaved changes including objects are retained on opening RStudio again.
I'm executing a batch file inside an R script. I'd like to run this and another large section of the R script twice using a foreach loop.
foreach (i=1:2, .combine = rbind)%do%{
shell.exec("\\\\network\\path\\to\\batch\\script.ext")
*rest of the R script*
}
One silly problem though is that this batch file generates data and that data is connected to SQL Server localdb inside the loop. I thought at first that the script would execute the batch file, wait for it to finish and then move on. However, (seems obvious in hindsight) the script instead executes the batch file, tries to grab data that hasn't been created yet (because the file isn't finished running) and the executes the batch file again before it finishes the first time.
I've been trying to find away to delay the rest of the script from executing until the batch script has finished executing but have not come up with anything yet. I'd appreciate any insights anyone has.
Use system2 instead of shell.exe. system2 calls are blocking — meaning, the function waits until the external program has finished running. On most systems, this can be used directly to run scripts. On Windows, you may have to invoke rundll32 to execute a script:
cmd = c('rundll32.exe', 'Shell32.dll,ShellExecute', 'NULL', 'open', scriptpath)
system2(paste(shQuote(cmd), collapse = ' '))
Windows users may use shell, which by default has wait=TRUE, which will cause R to wait for its completion. You may choose whether or not to directly "intern" the result.
On unix-like systems, use system, which also defaults to wait=TRUE.
If your batch file simply launches another process and terminates, then it may need to be modified to either wait for completion or return a suitable process or file indicator that can be monitored.