Background and Problem Statement

When working with system commands in R, it’s common to encounter issues where the R prompt gets locked waiting for the completion of a background task. This can be frustrating, especially when working on Linux systems using RStudio.

In this article, we’ll explore how to release the R prompt while running a system call, which involves downloading files from a text file using the parallel command and wget.

The Issue with nohup

One common approach to resolve this issue is by using the nohup command. However, in the provided example, even with nohup, the R prompt remains locked.

Let’s examine why nohup doesn’t quite solve the problem:

down.command <- paste0("nohup parallel --gnu -a links.txt wget > ~/down.log 2>&1")
system(down.command)

The main reason nohup fails in this case is that it doesn’t change the way R interacts with the child process. The system call blocks until the command completes, which means R is waiting for the output of the nohup command to finish.

Introducing processx

To overcome this limitation, we’ll explore an alternative solution using the processx package in R. This package provides a more sophisticated way to manage processes and their output.

Installing and Loading processx

Before proceeding, you need to install and load the processx package. If you’re working with RStudio, simply type:

install.packages("processx")
library(processx)

Creating a New Process with processx

Let’s see how we can use processx to create a new process that redirects both stdout and stderr to the same file.

First, let’s define the command we want to run:

args = c('--gnu', '-a', 'links.txt', 'wget')

Next, we create a new process using processx::process$new():

p <- processx::process$new('parallel', args, stdout = '~/down.log', stderr = '2>&1')

Here’s what happens in this line of code:

• We define the command to run: parallel --gnu -a links.txt wget. This is similar to our previous example with nohup, but without it.
• We specify the output files for stdout and stderr. In this case, both are redirected to ~/down.log.
• The p variable now holds a reference to the newly created process.

Interacting with the Running Process

Once we’ve launched the new process using processx, we can interact with it in several ways:

Checking the Status

We can check if the process is still running by calling its is_alive() method:

p$wait()
result <- p$get_exit_status()

• The first line calls wait() on the process, which blocks until the process completes. In this context, it’s used to ensure that we’re checking the status of a completed process.
• The second line retrieves the exit status of the process using get_exit_status(). If you run into issues where the command takes too long, you can use a timeout with wait().

Conclusion

In conclusion, we’ve explored how to release the R prompt when running a system command. Using the processx package allows us to create new processes that redirect both stdout and stderr to the same file, enabling background execution without blocking the R prompt.

With this solution, you can interact with your background process via the p object, checking its status, waiting for completion, or even synchronously killing it after a certain time if needed.

Last modified on 2024-04-08