If you are an R programmer, you have likely already experienced the need to run R scripts from the terminal. Running R script from the terminal is a useful skill that can save you a lot of time and effort. Instead of opening an R console or editor, running R script from the terminal allows you to automate tasks, run scripts in batch mode, and integrate R code into shell scripts in a seamless way. In this article, we’ll cover how to run R script from the terminal on different platforms and suggest best practices.
What is the terminal?
The terminal is a command-line interface used to interact with the system operations of a computer. It allows users to access a command prompt and execute various commands to perform tasks like navigating through the file system, modifying file permissions, installing software packages, and running scripts. In the context of running R script, the terminal provides a way to execute R commands from the command line instead of using the R console.
How to run R script from terminal?
To run an R script from the terminal, you need to open the terminal program on your operating system, navigate to the directory where your R script is stored, and execute the command “Rscript filename.R.”
Alternatively, you can also use the command “R CMD BATCH filename.R” to run the script and save the output to a file named “filename.Rout“.
Another option is to use the command “Rscript -e “R command” to run a specific R command from the terminal.
How does Rscript differ from using the R console?
Rscript is a command-line interface that executes R code without displaying the full R startup message. It is useful for running R scripts in batch mode or from other programs that require automated R execution without user intervention.
In contrast, the R console is an interactive interface that allows users to execute R commands line by line and view the output in real-time. It is useful for exploratory data analysis and debugging R code.
What is RStudio?
RStudio is an integrated development environment (IDE) for R that provides a user-friendly interface for writing, testing, and debugging R code. It is available in two formats: RStudio Desktop, which is a standalone application that runs on your local computer, and RStudio Server, which provides remote access to RStudio through a web browser.
RStudio offers many features that enhance the R programming experience, such as code highlighting, auto-completion, debugging tools, package management, and version control integration. It also includes a terminal interface that allows users to access the system shell from within the RStudio IDE.
What is Tmux?
Tmux is a terminal multiplexer that allows multiple terminal sessions to be accessed simultaneously in a single window. It is useful for running more than one command-line program at the same time and for managing long-running tasks that require persistent terminal sessions.
Tmux provides many features that enhance the terminal experience, such as window and pane management, session sharing, and customizable key bindings. It can be integrated with other terminal applications like Vim or Emacs to create a powerful text editing environment.
Why run R script from the terminal?
Running R script from the terminal offers several benefits:
- Allows faster and automated execution of R scripts
- Does not require opening the RStudio IDE
- Simplifies the process of running R scripts on remote servers
- Provides access to full-screen terminal applications like vim and Emacs
- Supports regular command-line operations with line-editing and shell history
How to run an R script from the terminal?
To run an R script from the terminal, follow these steps:
- Open the terminal
- Navigate to the directory containing the R script using the
cdcommand - Type the command
Rscriptfollowed by the name of the R script and hit enterExample:
Rscript my_script.R - The script will then be executed and the output displayed in the terminal
Benefits of using Rscript command to run R scripts from the terminal
The Rscript command is a simple and efficient way to run R scripts from the terminal. Some of its benefits include:
- Printing only the command output and not the full R startup message, which saves time and reduces clutter
- Allows specifying arguments to the script directly in the command line
- Provides a non-interactive way to execute R scripts, which is useful for automated tasks and remote servers
- Supports running scripts that require packages and dependencies, as long as they are installed in the system or specified in the script
Getting started with running R script from the terminal
On a Mac
If you’re a Mac user and want to run an R script from the terminal, the first step is to open the terminal. To do this, you can either search for “Terminal” in the Spotlight search or click on the “Finder” icon and then navigate to “Applications” and then “Utilities” where you’ll find Terminal. Once you’ve opened the terminal, you can type “R” to start the R environment. Then, you can navigate to the directory containing the script you want to run using the “cd” command. Once you’re in the right directory, you can run the script using the “Rscript” command followed by the name of your script. For example, if your script is named “my_script.R”, you’d type “Rscript my_script.R” into the terminal.
On a Windows PC
The process of running an R script from the terminal on a Windows PC is a bit different but still easy to follow. First, you’ll need to open the Command Prompt by searching for “cmd” in the “Start” menu or by using the “Windows Key + R” shortcut and then typing “cmd” in the “Run” dialog box. Once the Command Prompt is open, you can start the R environment by typing “R” and then navigate to the directory where your script is located using the “cd” command. Once you’re in the right directory, you can run the script using the “Rscript” command followed by the name of your script. For example, if your script is named “my_script.R”, you’d type “Rscript my_script.R” into the Command Prompt.
The basics of the terminal
What are commands?
Commands are instructions that the user inputs into the terminal to make the computer perform certain tasks. Commands can be simple or complex, and they can do a wide range of functions, from opening a file to installing software. To use a command, simply type it into the terminal, followed by any necessary arguments or options.
Examples of common commands in the terminal include:
| Command | Function |
| ls | Show contents of current directory |
| cd | Change directory |
| mkdir | Create a new directory |
| cp | Copy a file or directory |
| mv | Move or rename a file or directory |
| rm | Delete a file or directory |
What is the command line?
The command line is a text-based interface for interacting with the computer’s operating system. It allows the user to input commands directly into the terminal, which are then executed by the system. The command line is often used for tasks that cannot be easily performed through a graphical user interface, or for tasks that are more efficiently performed using commands.
Running R script from the terminal
If you are working with R scripts and want to run them from the terminal, here is a step by step guide:
Step 1: Open the terminal
To open the terminal on Windows, press the Windows button + R and type “cmd” in the Run box. On a Mac, go to Applications, then Utilities, and open Terminal.
Use the “cd” command to change directories in the terminal. For example, if your script is saved in the “Documents” folder, type “cd Documents” and press enter.
Step 3: Run the R script using Rscript
Once you are in the correct directory, use the command “Rscript” followed by the name of the R script file to run the script. For instance, if the script file is named “myscript.r”, type “Rscript myscript.r” in the terminal and press enter.
And that’s it! You have now run an R script from the terminal.
Rendering Rmarkdown file from the terminal
Rmarkdown is a file format that allows you to create dynamic documents with R. It is useful for creating reproducible research papers, presentations, and reports. Rmarkdown files can be rendered into different formats such as HTML, PDF, and Word documents. The benefit of rendering Rmarkdown files from the terminal is that it is faster and allows you to automate the process.
Here are the steps to render Rmarkdown files from the terminal:
- Open the terminal
- Navigate to the directory where your Rmarkdown file is located
- Type the following command:Rscript -e “rmarkdown::render(‘yourfile.Rmd’)”
Note that you need to replace ‘yourfile.Rmd’ with the name of your Rmarkdown file. - Press enter and wait until the code finishes rendering your Rmarkdown file.
Troubleshooting errors while running R script from the terminal
Running an R script from the terminal can sometimes lead to errors that interrupt the program’s execution. Here are some of the most common errors that can occur and how to troubleshoot them:
Error: “Command not found”
This error message indicates that the shell couldn’t find the Rscript executable. Make sure that R is installed on your system and, if it is, check whether the Rscript executable is in your search path. You can also try running the command with the full path to Rscript, which is typically /usr/local/bin/Rscript.
Error: “No such file or directory”
This error message indicates that the shell couldn’t find the file specified in your R script command. Make sure that the file exists and that you’ve typed the filename correctly. Check for typos or spaces in the filename or path. It’s also a good idea to use tab completion to avoid any errors typing the full filename.
Error: “Permission denied”
This error message indicates that you don’t have the appropriate permissions to run the command or access the file. Make sure that you have read, write, and execute permissions on the file you’re trying to run. You can also try running the command with sudo to run it with root privileges.
Error: “Invalid syntax”
This error message suggests that the R script command contains a syntax error. Check your code for any missing or incorrect punctuation, misspelled function names, or other coding mistakes.
Error: “Segmentation fault”
This error message usually indicates that there is a problem with memory allocation in your R script command. Check whether you’re using too much memory or whether there is a bug in your code that is causing a memory leak.
These are just a few common errors that can occur while running R scripts from the terminal. It’s important to check your code carefully for any mistakes and to make sure that you have the appropriate permissions and search paths set up to run your commands smoothly.
Conclusion
To run an R script from the terminal, use Rscript -e “command”. This will print the command output without the full R startup message. RStudio also provides a terminal that allows accessing the system shell and running full-screen terminal applications. R Markdown is a file format for making dynamic documents with R. Running functions in rscripts can be done in RStudio. Utilizing the terminal to run R scripts from the command line is beneficial for navigation and accessing other programs.
References
For more information on running an R script from terminal, check out these resources:
