Installing R Package with libstdc++

Introduction

As a data scientist or statistician, installing third-party packages in R can be a daunting task, especially if you’re using a system with specific compiler settings. In this article, we’ll delve into the world of R package installation and explore how to overcome common issues related to compiling packages with libstdc++.

Background

R is an iconic programming language for statistical computing and graphics. It’s widely used in academia and industry for data analysis, visualization, and modeling. When you install a third-party package in R, it uses the system’s compiler settings to compile the code. However, on macOS systems like OS X Mavericks 10.9.1, the default compiler setting is libc++ instead of libstdc++. This can lead to compilation issues with packages that require libstdc++.

The Problem

The OP (original poster) is trying to install a third-party package called “Zinba” on OS X Mavericks 10.9.1. They encounter an error message from R CMD INSTALL, which indicates that the compilation failed due to missing header files. Specifically, it mentions that the file ext/slist is not found.

The Solution

The recommended solution by Apple is to compile using -stdlib=libstdc++. To achieve this, we’ll use a temporary workaround provided by the withr package in R.

Using withr to Install Zinba

To install the “Zinba” package using libstdc++, we can leverage the withr::with_makevars function. This function creates a temporary file with the desired C++ flags and sets an environment variable (R_MAKEVARS_USER) to point to it.

Here’s the code snippet that does this:

library(withr)

with_makevars(c(CXXFLAGS = "-stdlib=libstdc++"),
              install.packages("zinba", repos = NULL, type = "source"))

In this example, we define a list c() containing only one element: the desired C++ flag -stdlib=libstdc++. The with_makevars function then uses this list to create a temporary file that sets the environment variable R_MAKEVARS_USER with the specified value.

How it Works

When we run install.packages("zinba", repos = NULL, type = "source"), R CMD INSTALL is executed. However, due to our temporary setup using withr::with_makevars, an additional configuration step occurs before compilation begins. This involves creating a temporary file with the desired C++ flags and setting an environment variable (R_MAKEVARS_USER) to point to it.

When R CMD INSTALL starts compiling the package, it inherits this temporary environment variable. As a result, the compiler picks up the correct settings for libstdc++ instead of libc++. This resolves the compilation issues caused by missing header files, such as ext/slist.

Conclusion

Installing third-party packages in R can be challenging, especially when dealing with specific compiler settings like those on OS X Mavericks 10.9.1. By leveraging the withr package and its temporary configuration mechanism (with_makevars), we can overcome common issues related to compiling packages with libstdc++. This approach provides a reliable workaround for resolving compilation errors caused by missing header files or other dependencies.

Additional Tips

Update your Xcode: To resolve any potential issues, ensure that you’re using the latest version of Xcode. Go to Xcode.app > Preferences > Components, and make sure that C++ Compiler is set to Clang 11.0.
Check package dependencies: If a package depends on other packages that aren’t installed, ensure those packages are installed before installing the desired package.
Verify your R environment: Make sure you’re using an up-to-date version of R and its associated dependencies (like R.framework/Versions/3.0).

Last modified on 2024-12-30