Defining Method On `convert()` Introduces `properties` Global In `R CMD Check`

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Introduction

When developing R packages, it's essential to be aware of the potential issues that can arise when defining methods on generics from other packages. In this article, we'll explore the problem of defining methods on convert() from the S7 package and how it introduces a global variable named properties in R CMD check. We'll also discuss some potential solutions to this issue.

Understanding the Problem

The S7 package defines its own version of @() internally and externally on earlier R versions. When we define methods on S7::convert(), a copy is made. This is because copies of generics are created in a package when we define methods on a generic in another package. As a result, codetools detects the @properties expressions in convert() as introducing a global variable named properties.

The Issue with R CMD check

The introduction of the properties global variable is a problem because it means that any package defining a method for convert() needs to have globalVariables("properties"). This can lead to issues with package namespace management and can make it difficult to track down the source of the problem.

Potential Solutions

There are several potential solutions to this issue:

1. Remove Generics from the Package Namespace

One solution is to remove all generics from the package namespace that originally came from another package. This can be done during or after method registration, which is typically called in .onLoad(). This has the added benefit of keeping the namespace clean and reducing the risk of conflicts with other packages.

2. Delegate to Another Function

Another solution is to have convert() delegate to some other function to access @properties. This can be done by creating a new function that accesses the @properties expressions and then calling that function from convert().

3. Remove Custom @() Function

Finally, we can simply wait until we no longer need compatibility with older versions of R and remove the custom @() function. This will eliminate the need for the properties global variable and will make it easier to manage the package namespace.

Conclusion

Defining methods on convert() from the S7 package can introduce a global variable named properties in R CMD check. This can lead to issues with package namespace management and can make it difficult to track down the source of the problem. However, there are several potential solutions to this issue, including removing generics from the package namespace, delegating to another function, and removing the custom @() function. By understanding the problem and exploring these potential solutions, we can develop more robust and maintainable R packages.

Best Practices for Managing Package Namespaces

When developing R packages, it's essential to follow best practices for managing package namespaces. Here are some tips to help you keep your namespace clean and organized:

  • Use globalVariables(): Use globalVariables() to declare global variables and avoid conflicts with other packages.
  • Remove unused generics: Remove any unused generics from your package namespace to reduce the risk of conflicts with other packages.
  • Use onLoad(): Use onLoad() to register methods and initialize package variables.
  • Test your package: Test your package thoroughly to ensure that it works as expected and doesn't introduce any conflicts with other packages.

Common Issues with Package Namespaces

When developing R packages, it's not uncommon to encounter issues with package namespaces. Here are some common issues to watch out for:

  • Conflicts with other packages: Conflicts with other packages can arise when you use the same function or variable name as another package.
  • Global variable issues: Global variable issues can arise when you use global variables without declaring them using globalVariables().
  • Namespace pollution: Namespace pollution can arise when you add too many functions or variables to your package namespace, making it difficult to track down the source of the problem.

Conclusion

Q: What is the problem with defining methods on convert() from the S7 package?

A: When we define methods on S7::convert(), a copy is made because copies of generics are created in a package when we define methods on a generic in another package. As a result, codetools detects the @properties expressions in convert() as introducing a global variable named properties.

Q: Why is the properties global variable a problem?

A: The properties global variable is a problem because it means that any package defining a method for convert() needs to have globalVariables("properties"). This can lead to issues with package namespace management and can make it difficult to track down the source of the problem.

Q: What are some potential solutions to this issue?

A: There are several potential solutions to this issue:

  • Remove all generics from the package namespace that originally came from another package.
  • Have convert() delegate to some other function to access @properties.
  • Just wait until we no longer need compatibility with older versions of R and remove the custom @() then.

Q: How can I remove generics from the package namespace?

A: You can remove generics from the package namespace during or after method registration, which is typically called in .onLoad(). This has the added benefit of keeping the namespace clean and reducing the risk of conflicts with other packages.

Q: What is the benefit of delegating to another function?

A: Delegating to another function can help to avoid the issue of the properties global variable. By having convert() delegate to another function, you can access the @properties expressions without introducing a global variable.

Q: What is the best approach to take when dealing with this issue?

A: The best approach to take when dealing with this issue is to consider the trade-offs of each potential solution and choose the one that best fits your needs. If you need to maintain compatibility with older versions of R, you may need to use one of the other solutions.

Q: How can I avoid conflicts with other packages?

A: You can avoid conflicts with other packages by following best practices for managing package namespaces. This includes using globalVariables() to declare global variables, removing unused generics, using onLoad() to register methods, and testing your package thoroughly.

Q: What are some common issues with package namespaces?

A: Some common issues with package namespaces include conflicts with other packages, global variable issues, and namespace pollution. By being aware of these issues and following best practices, you can avoid conflicts with other packages and ensure that your packages work as expected.

Q: How can I troubleshoot issues with package namespaces?

A: You can troubleshoot issues with package namespaces by using tools such as R CMD check and R CMD build. You can also use debugging tools such as debug() and browser() to step through your code and identify the source of the problem.

Q: What is the best way to manage package namespaces?

A: The best way to manage package namespaces is to follow best practices and be aware of common issues. This includes using globalVariables() to declare global variables, removing unused generics, using onLoad() to register methods, and testing your package thoroughly. By following these best practices, you can avoid conflicts with other packages and ensure that your packages work as expected.