musserlab/r-renv

R Environment Management

rig: R Version Manager

Use rig to install and switch between multiple R versions.

Essential Commands

rig list              # View installed versions
rig add release       # Install latest stable R
rig add 4.4           # Install specific version
rig default 4.4       # Set system default
rig default           # Show current default

Per-Project R Version (Positron)

Pin the R version in .positron/settings.json (not committed to git):

macOS (Apple Silicon):

{
  "r.rpath.mac": "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/bin/R"
}

macOS (Intel):

{
  "r.rpath.mac": "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/bin/R"
}

Alternative: Use Positron's Command Palette (Cmd+Shift+P) → "R: Select R Binary".

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renv: Package Management

Most R projects use renv for reproducible package management.

Key Commands

renv::status()        # Check sync status
renv::restore()       # Install packages from lockfile
renv::snapshot()      # Record current packages to lockfile
renv::install("pkg")  # Install a package
renv::update()        # Update all packages

How renv Works

• Activates automatically via .Rprofile when R starts in the project directory
• Warnings about "project out-of-sync" are informational, not errors
• When running R scripts via Bash, renv still activates but may show warnings — these don't prevent execution

Workflow

1. If you see "project out-of-sync" warning → run renv::status() to see details
2. To sync packages with lockfile → run renv::restore()
3. After installing new packages → run renv::snapshot() then commit renv.lock to git

Git Tracking

Commit: renv.lock, renv/activate.R, .Rprofile Ignore: renv/library/, renv/staging/, renv/local/

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Bioconductor

Bioconductor packages have coordinated releases tied to R versions.

Installation

install.packages("BiocManager")
BiocManager::install("DESeq2")
BiocManager::install(c("limma", "edgeR", "tximport"))
renv::snapshot()  # Always snapshot after installing

With renv, you can also use:

renv::install("bioc::DESeq2")

Version Synchronization

| R Version | Bioconductor Version | |-----------|---------------------| | R 4.3.x | Bioconductor 3.18 | | R 4.4.x | Bioconductor 3.19–3.20 | | R 4.5.x | Bioconductor 3.21 |

Check your current version:

BiocManager::version()

If renv reports Bioconductor version mismatches, verify that BiocManager::version() matches what's expected for your R version.

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Troubleshooting

"Project out-of-sync"

→ Run renv::status() to see details. Run renv::restore() to sync, or renv::snapshot() if you've installed new packages.

Failed package installation

→ Try renv::install("package", rebuild = TRUE)

Starting fresh

→ renv::deactivate(), remove renv/ and .Rprofile, then renv::init()