Troubleshooting Package Installation with `renv` in RStudio Server

When working with R and renv to manage project dependencies, you might encounter issues during package installation, particularly when using a Conda environment. In this post, I’ll walk through a problem I faced when trying to install the Bioconductor package limma and the steps I took to resolve it.

The Problem: Installation Failure with renv

While attempting to install the limma package using renv, I encountered an error during the installation process. Here’s the full output of the issue:

> renv::install("bioc::limma")
# Downloading packages -------------------------------------------------------
- Downloading limma from BioCsoft ...           OK [file is up to date]
Successfully downloaded 1 package in 0.1 seconds.

The following package(s) will be installed:
- limma [3.60.4]
These packages will be installed into "/data/projects/240814_Popzhelyazkova_Bremer_Neuropathologie_DNAmArray/analysis/renv/library/linux-ubuntu-jammy/R-4.4/x86_64-conda-linux-gnu".

Do you want to proceed? [Y/n]: Y

# Installing packages --------------------------------------------------------
- Installing limma ...                          FAILED
Error: Error installing package 'limma':
=================================

* installing *source* package ‘limma’ ...
 using staged installation
 libs
sh: 1: x86_64-conda-linux-gnu-cc: not found
x86_64-conda-linux-gnu-cc -I"/opt/miniconda3/envs/R4.4.1/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/miniconda3/envs/R4.4.1/include -I/opt/miniconda3/envs/R4.4.1/include -Wl,-rpath-link,/opt/miniconda3/envs/R4.4.1/lib    -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/miniconda3/envs/R4.4.1/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1723488707222/work=/usr/local/src/conda/r-base-4.4.1 -fdebug-prefix-map=/opt/miniconda3/envs/R4.4.1=/usr/local/src/conda-prefix  -c init.c -o init.o
/bin/sh: 1: x86_64-conda-linux-gnu-cc: not found
make: * [/opt/miniconda3/envs/R4.4.1/lib/R/etc/Makeconf:197: init.o] Error 127
ERROR: compilation failed for package ‘limma’
* removing ‘/data/projects/240814_Popzhelyazkova_Bremer_Neuropathologie_DNAmArray/analysis/renv/staging/1/limma’
install of package 'limma' failed [error code 1]

Diagnosing the Issue

The error message indicates that the installation failed because the compiler (x86_64-conda-linux-gnu-cc) could not be found. This pointed to a problem with the system’s PATH environment variable.

When I checked the PATH using:

> Sys.getenv("PATH")
[1] "/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/usr/lib/rstudio-server/bin/quarto/bin:/usr/lib/rstudio-server/bin/postback"

I realized that the path to the Conda environment’s binary directory (/opt/miniconda3/envs/R4.4.1/bin/) was missing. This meant that the necessary compiler, which was installed in the Conda environment, was not available to RStudio, leading to the failure.

The Solution: Updating the PATH Variable

To resolve this, I needed to add the Conda environment’s binary directory to the PATH within R. This can be done temporarily for the current session using the Sys.setenv() function:

Sys.setenv(PATH = paste("/opt/miniconda3/envs/R4.4.1/bin", Sys.getenv("PATH"), sep = ":"))

After updating the PATH, I retried the package installation:

renv::install("bioc::limma")

This time, the installation proceeded without any issues.

Conclusion

If you encounter similar issues when installing packages with renv in RStudio, especially within a Conda environment, make sure the relevant binaries are accessible by checking and updating your PATH. This simple adjustment can save you from installation headaches and keep your R projects running smoothly.

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This blog post captures the problem and the step-by-step solution, making it easy for others facing similar issues to troubleshoot and resolve them effectively.