Understanding Package Dependencies and Symbolic Links in R

As a data scientist or analyst, you’re likely familiar with the importance of dependencies in software packages. In R, these dependencies can be package-specific or system-wide. In this answer, we’ll delve into how to resolve symbolic link issues related to libgfortran.5.dylib and libquadmath.0.dylib, which are crucial for packages like dm and sf.

The Problem: Package Dependencies and Symbolic Links

When working with R packages that rely on external libraries, you might encounter errors due to missing or corrupted symbolic links. In the provided example, we see that library(dm) and library(sf) throw errors related to these missing symbols.

Resolving Missing Symbolic Links for DM and SF

To resolve these issues, we’ll follow a step-by-step approach:

1. Install Required Packages and Tools

First, install the required packages and tools using Homebrew on macOS:

brew install pkg-config gdal gcc

Next, configure rgdal with the following arguments when installing it from source:

install.packages("rgdal", type = "source", configure.args = c("--with-proj-lib=$(brew --prefix)/lib/", "--with-proj-include=$(brew --prefix)/include/"))

2. Install GNU Fortran on macOS

To fix the missing libgfortran.5.dylib and libquadmath.0.dylib, you need to install GNU Fortran on your system:

# https://github.com/fxcoudert/gfortran-for-macOS/releases
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
brew install gcc

# cf. https://www.kombitz.com/2022/07/28/error-message-usr-local-lib-libgfortran-3-dylib-no-such-file-on-intel-mac-solved/
sudo ln -s /usr/local/Cellar/gcc/13.1.0/lib/gcc/13/libgfortran.5.dylib /usr/local/lib/libgfortran.5.dylib

Repeat the same process for libquadmath.0.dylib:

sudo ln -s /usr/local/Cellar/gcc/13.1.0/lib/gcc/13/libquadmath.0.dylib /usr/local/lib/libquadmath.0.dylib

3. Install and Load All Packages

After resolving the symbolic link issues, re-run devtools::load_all() to ensure that all packages are loaded correctly.

devtools::load_all()

With these steps completed, you should now be able to load packages like dm and sf without encountering errors related to missing symbolic links.

Conclusion

Resolving symbolic link issues for R packages requires attention to detail and a systematic approach. By following the steps outlined in this answer, you’ll be better equipped to handle package dependencies and ensure that your R environment is stable and functional. Remember to check for updates on your system and R packages regularly to avoid encountering similar issues in the future.

Example Use Case:

Suppose you’re working with a project that relies heavily on packages like dm and sf. You’ve encountered errors related to missing symbolic links, but have since resolved these issues using the steps outlined above. Now, you can focus on analyzing your data without worrying about package dependencies.

# Load required packages
library(dm)
library(sf)

# Perform analysis or visualizations

By taking a proactive approach to resolving symbolic link issues, you’ll be able to maintain a stable and efficient R environment that supports your projects effectively.

Last modified on 2024-01-31