Understanding .libPaths() and Removing Unwanted Paths in R

When working with multiple libraries or environments in R, it’s common to encounter issues related to conflicting paths. In this article, we’ll explore the Sys.getenv() function, .libPaths(), and how to remove unwanted paths from the library search path.

The Role of .libPaths()

In R, the .libPaths() function returns a list of directories where the user’s libraries are searched for packages. This directory search path is used by R when it loads packages, which can lead to conflicts if multiple versions of the same package exist in different locations.

# Get the current library search path
> .libPaths()
[1] "C:/ProgramFiles/R/R-3.2.5/library"          "X:/R Repository Database"

The Role of Sys.getenv()

The Sys.getenv() function returns the value of an environment variable. In this case, we’re using it to retrieve the values of two specific variables: $R_LIBS_USER and $R_LIBS.

# Get the value of R_LIBS_USER and R_LIBS
> Sys.getenv("R_LIBS_USER")
[1] "X:/R Repository Database"

> Sys.getenv("R_LIBS")
[1] "X:/R Respository Database"

Removing Unwanted Paths from .libPaths()

The main goal is to remove the unwanted paths from the .libPaths() function, so we only have a single non-standard path. This can be achieved using the setenv function in R.

# Set environment variable R_LIBS_USER to point to the desired directory
> setenv(R_LIBS_USER, "X:/R Repository Database")

# Get the updated library search path
> .libPaths()
[1] "X:/R Repository Database"

The Limitations of Changing R_LIBS_USER

It’s essential to understand that changing the value of R_LIBS_USER will not affect the system setting for the package directory ($R_HOME/library). This is because the system setting contains the base packages, including the base package itself, and altering it could lead to issues with package installation and updating.

Using Different R Versions

The main sources of incompatibilities between different versions of user-contributed packages come from using different versions of these packages. By having a site-wide package directory, we can control which version of the package is used across all environments.

# Set environment variable R_LIBS to point to the desired directory
> setenv(R_LIBS, "X:/R Repository Database")

# Get the updated library search path
> .libPaths()
[1] "X:/R Repository Database"

Conclusion

When working with multiple libraries or environments in R, it’s essential to understand how .libPaths() and environment variables interact. By setting R_LIBS_USER to a single non-standard path, we can control which version of user-contributed packages is used across all environments. However, it’s crucial to note that this will not affect the system setting for the package directory ($R_HOME/library) or the base package itself.

Troubleshooting Incompatibilities

If you’re experiencing issues with incompatibilities between different versions of user-contributed packages, try:

• Installing only one version of R.
• Using a site-wide package directory to control which version of the package is used across all environments.

By following these steps and understanding how .libPaths() and environment variables interact, you can maintain a consistent library search path in R while avoiding conflicts between different versions of user-contributed packages.

Last modified on 2023-09-16