The Challenges of Modifying Local Packages in R: A Step-by-Step Guide to Overcoming Installation Issues

Introduction

As a researcher or data scientist, working with packages is an essential part of your daily tasks. When you come across a bug or need to modify the code of a package, updating it can be a straightforward process. However, modifying the package locally and then installing it can be more complex, especially if you’re not familiar with the build process.

In this article, we’ll delve into the world of R package modification, exploring the steps involved in building and installing a modified package from a local zip file. We’ll cover the challenges you might face, provide explanations for technical terms and concepts, and offer practical solutions using popular tools like devtools and installr.

Understanding Package Installation

Before we dive into modifying packages locally, it’s essential to understand how R packages are installed. When you run install.packages("package_name"), R searches for the package in a set of repositories (default ones include CRAN, Bioconductor, and others). If the package is found in one of these repositories, R downloads and installs it.

However, when you modify a package locally, you’re no longer using the package as installed from the repository. Instead, you have a modified version of the code stored on your local machine. This can lead to issues during installation and usage.

Modifying Packages Locally

Modifying packages locally involves making changes to the package’s source code, which is typically stored in a directory structure that follows specific conventions. The simplest way to modify a package locally is to create a new version of the zip file containing your modified files.

Here’s an example:

Create a new directory for your modified package, e.g., modified_package.
Inside this directory, place your modified source files (e.g., .R, .py, etc.) alongside any other required files.
Zip up the entire directory structure into a new zip file.

Now that you have the modified zip file, you can try installing it using R. However, as we’ll see in the next section, this might not be enough to get your package installed successfully.

Building and Installing Packages with devtools

The devtools package provides an easy-to-use interface for building and installing packages locally. With devtools, you don’t need to manually update the package structure or rebuild it from scratch.

Here’s a step-by-step guide on how to use devtools:

Load the devtools package in R: library(devtools)
Build your modified package using the build() function, specifying the path to your package directory: build("path/to/modified_package")
You’ll receive a new built package (a .tar.gz or .zip file) that you can install manually.

library(devtools)

# Build and install on Windows
build("C:/Users/Me/Documents/R/win-library/2.15/modified_package")
install.packages("C:/Users/Me/Documents/R/win-library/2.15/modified_package.tar.gz", repos = NULL, type = "source")

# Build and install on macOS/Linux
build("path/to/modified_package")
install.packages("path/to/built/package.tar.gz", repos = NULL, type = "source")

By using devtools, you can easily modify your package locally, build it from scratch, and then install it without any hassle.

Binary Builds with devtools

When building a binary version of your package (i.e., for Windows), the process is slightly different. The build() function needs to be run with additional options to include the necessary files.

Here’s an example:

library(devtools)

# Build and install on Windows
build("path/to/modified_package", binary = TRUE)
install.packages("C:/Users/Me/Documents/R/win-library/2.15/path/to/built/package.zip", repos = NULL, type = "win.binary")

By using the binary option, you can build a binary version of your package that can be installed on Windows.

Additional Requirements: Rtools for Windows

One crucial requirement when working with packages is having Rtools installed. Rtools is an extension that provides pre-compiled versions of R libraries and tools required by many packages.

On Windows, installing Rtools ensures you have the necessary files to build and install packages successfully.

Here’s how to install Rtools using the installr package:

library(installr)

# Install Rtools for Windows
install.Rtools()

With Rtools installed, you can focus on building and installing your modified package without any further issues.

Conclusion

Modifying local packages in R requires attention to detail when building and installing the package. By using devtools and understanding how packages are installed, you can easily modify your package locally, build it from scratch, and then install it without any hassle.

Remember to keep Rtools installed for Windows users to ensure smooth package installation. With these practical solutions in hand, you’re ready to tackle local package modification challenges head-on!