Resolving the `Syntax Error Near Unexpected Token '(' in R's System() Function

Learn how to efficiently extract columns from multiple files in R without encountering syntax errors through the system() function. Explore a straightforward workaround and enhance your scripting skills with this detailed guide. --- This video is based on the question https://stackoverflow.com/q/71618872/ asked by the user 'G.A.7' ( https://stackoverflow.com/u/11741703/ ) and on the answer https://stackoverflow.com/a/71622588/ provided by the user 'Charles Duffy' ( https://stackoverflow.com/u/14122/ ) at 'Stack Overflow' website. Thanks to these great users and Stackexchange community for their contributions. Visit these links for original content and any more details, such as alternate solutions, latest updates/developments on topic, comments, revision history etc. For example, the original title of the Question was: Syntax error near unexpected token `(' when using R system() function Also, Content (except music) licensed under CC BY-SA https://meta.stackexchange.com/help/licensing The original Question post is licensed under the 'CC BY-SA 4.0' ( https://creativecommons.org/licenses/by-sa/4.0/ ) license, and the original Answer post is licensed under the 'CC BY-SA 4.0' ( https://creativecommons.org/licenses/by-sa/4.0/ ) license. If anything seems off to you, please feel free to write me at vlogize [AT] gmail [DOT] com. --- Resolving the `Syntax Error Near Unexpected Token '(' in R's System() Function Have you ever faced the frustrating syntax error near unexpected token '(' while attempting to execute command line operations within R's system() function? This common issue tends to arise when working with shell commands that depend on certain shell features not available in R's default environment. Here, we will explore the problem and guide you through a straightforward solution to extract specific columns from multiple files seamlessly. Understanding the Problem When working in Linux Bash, extracting specific columns from files using commands like awk combined with paste is a breeze. For instance, the following command works perfectly in a standard bash shell: [[See Video to Reveal this Text or Code Snippet]] However, when replicating this command in R using the system() function, you may encounter the dreaded syntax error because <() (process substitution) is not supported in the default /bin/sh shell used by R. This leads to confusion and a halt in productivity when trying to streamline your workflows. The Solution: Using a While Loop in Shell Script To circumvent this issue, you can rewrite your command in a manner that doesn't rely on process substitution. Instead of using <(), a while loop can achieve the same outcome. Here’s how to do it: Step-by-Step Breakdown Setup your command in R: Instead of using process substitutions, you will use file descriptors in a loop. This is more compatible with sh. Use the following code in your R script: [[See Video to Reveal this Text or Code Snippet]] Code Explanation while read: This initiates a loop that reads lines from the three files concurrently. read _ a _ <&3: This reads from the first file (text1.txt) and assigns the second column to variable a. printf: This command formats the output, ensuring that the values from each file are printed in tab-separated format. File descriptors (3, 4, 5): These are used to indicate different input files instead of creating separate processes for each read command. Conclusion By modifying the R script to utilize a while loop and file descriptors, you can effectively extract data from multiple files without encountering syntax errors that halt your progress. This approach not only broadens your understanding of shell scripting but also enhances the functionality of your R scripts. Implement this solution the next time you run into similar problems, and you’ll find yourself efficiently tackling data extraction tasks without the added stress of syntax errors. Happy coding!