Managing Packages in R

# Install a single package

install.packages("ggplot2")

# Install multiple packages at once

install.packages(c("dplyr", "tidyr", "shiny"))

Specify CRAN Mirror: You can choose a specific CRAN mirror if required:

install.packages("ggplot2", repos = "https://cran.r-project.org")

Install from GitHub or other repositories (using devtools or remotes):
install.packages("devtools")

devtools::install_github("hadley/ggplot2")

2. Loading Packages

To use a package in your session, load it with library() or require():

library(ggplot2)   # Preferred, throws error if the package is unavailable

require(ggplot2)   # Returns a warning instead of an error if unavailable

3. Checking Installed Packages

List all installed packages:

installed.packages()

4. Updating Packages

To ensure you’re using the latest version of a package:

# Update all packages

update.packages()

# Update a specific package

install.packages("dplyr")

5. Removing Packages

To uninstall a package:

remove.packages("ggplot2")

6. Checking for Package Availability

To check if a package is already installed:

if (!require("ggplot2")) {

  install.packages("ggplot2")

  library(ggplot2)

}

7. Managing Libraries

R allows multiple library paths. You can check and manage them using:

# View library paths

.libPaths()

# Add a new library path

.libPaths(c(.libPaths(), "/new/library/path"))

8. Installing Bioconductor Packages

Bioconductor packages are widely used in bioinformatics. Install them as follows:

if (!requireNamespace("BiocManager", quietly = TRUE))

    install.packages("BiocManager")

BiocManager::install("GenomicFeatures")

9. Saving and Loading Package Environments

To replicate the package environment of a project:

1. Save Installed Packages:
   installed <- installed.packages()[, "Package"]

save(installed, file = "packages.RData")

2. Load and Install Saved Packages:
   load("packages.RData")

install.packages(installed)

10. Dependency Management

Use tools like packrat or renv to create isolated environments:

packrat:
install.packages("packrat")

packrat::init()  # Initializes a project-specific environment

renv:
install.packages("renv")

• renv::init()     # Creates a reproducible environment for your project

Common Commands Summary