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Learn how to run your `Perl script` from R while effectively managing module dependencies, ensuring smooth execution without errors.
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This video is based on the question https://stackoverflow.com/q/65553325/ asked by the user 'Heiko' ( https://stackoverflow.com/u/11609743/ ) and on the answer https://stackoverflow.com/a/65553736/ provided by the user 'Michal T' ( https://stackoverflow.com/u/4253357/ ) at 'Stack Overflow' website. Thanks to these great users and Stackexchange community for their contributions.

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How to Easily Run a Perl Script from R with Specific Modules

If you've ever encountered the challenge of running a Perl script from within R and faced unexpected errors related to module dependencies, you're not alone. Many users, like Heiko, often find themselves frustrated when transitioning from a terminal environment to RStudio for script execution. This guide will walk you through the steps necessary to run your Perl script seamlessly from R, while addressing any module issues that might arise along the way.

Understanding the Problem

When you execute your Perl script from the terminal, it works without a hitch. However, the moment you try to run it from RStudio, you are met with errors indicating missing modules, such as Sort::Fields. These errors usually arise because R is utilizing a different version of Perl than what your script requires. In Heiko's case, the issue stemmed from RStudio using the system-installed Perl (version 5.28) instead of the perlbrew version (5.26.2) where the needed modules were installed.

The Solution

To resolve the issue of running your Perl script in R while ensuring it finds the necessary modules, follow these organized steps:

Step 1: Identify Your Perl Path

First, you need to find the full path to the perlbrew Perl installation that contains your desired modules. This can be done through the terminal:

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This command will return the full path to your perlbrew Perl installation (e.g., /Users/admin/perl5/perlbrew/perls/5.26.2/bin/perl). Keeping this path handy is crucial for the next steps.

Step 2: Modify Your R Code

Next, you have to adjust your R code to utilize this specific Perl installation when executing your script. Instead of calling the default system Perl, you will pass the full path you obtained in Step 1 as the first argument in your system2 call. Your updated R code should look like this:

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Step 3: Test Your Script

With the changes made, run your R code again. This time, R should correctly locate the Sort::Fields module and any other required dependencies, allowing your script to execute without errors.

Additional Tips

Environment Check: Before running your script, ensure your environment is set up correctly in RStudio. Make sure that your Perl modules are available in the specified path.

Module Installation: If you encounter further issues with additional missing modules, consider installing them directly using cpanm or the cpan command within your perlbrew environment.

Documentation: Familiarize yourself with both R and Perl documentation regarding external script calls and module management for a deeper understanding of potential pitfalls and solutions.

Conclusion

Running a Perl script from R can be a straightforward task if you ensure that both the correct version of Perl and its required modules are accessible. By following the steps outlined, you can skirt around issues related to module dependencies and execute your scripts effortlessly. Don't hesitate to reach out if you face any more challenges or need further assistance. Happy coding!