Installation Guide"

In evanverse: Utility Functions for Data Analysis and Visualization

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Overview

This guide covers all installation methods for evanverse, including system requirements, dependencies, and troubleshooting.

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Quick Install

From CRAN (Recommended)

The stable release is available on CRAN:

install.packages("evanverse")

From GitHub (Development Version)

For the latest features and bug fixes:

# Install devtools if needed
install.packages("devtools")

# Install evanverse
devtools::install_github("evanbio/evanverse")

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System Requirements

• R Version: ≥ 4.1.0
• Operating Systems: Windows, macOS, Linux
• Internet Connection: Required for initial installation and some functions

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Dependencies

evanverse depends on several packages that will be automatically installed:

Core Dependencies

• tidyverse — Data manipulation and visualization
• data.table — Fast data processing
• jsonlite — JSON handling for color palettes

Bioinformatics Dependencies

• Biobase — Bioconductor infrastructure
• GSEABase — Gene set analysis
• biomaRt — Gene ID conversion

Visualization Dependencies

• ggplot2 — Plotting framework
• VennDiagram — Venn diagram generation
• ggVennDiagram — Modern Venn diagrams

Utility Dependencies

• cli — Command-line interface
• fs — File system operations
• curl — URL downloads
• openxlsx — Excel file handling

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Installation Options

Minimal Installation

Install without suggested packages:

install.packages("evanverse", dependencies = c("Depends", "Imports"))

Full Installation

Install with all suggested packages for complete functionality:

install.packages("evanverse", dependencies = TRUE)

Install Specific Version

# Install a specific version from CRAN
devtools::install_version("evanverse", version = "0.3.7")

# Install from a specific GitHub release
devtools::install_github("evanbio/evanverse@v0.3.7")

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Bioconductor Dependencies

Some bioinformatics functions require Bioconductor packages. Install them separately:

# Install BiocManager if needed
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# Install Bioconductor dependencies
BiocManager::install(c("Biobase", "GSEABase", "biomaRt", "GEOquery"))

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Verify Installation

After installation, verify that evanverse is working correctly:

# Load the package
library(evanverse)

# Check version
packageVersion("evanverse")

# List available functions
pkg_functions("evanverse")

# Test basic functionality
"Hello" %p% " " %p% "World"

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Update evanverse

Update from CRAN

update.packages("evanverse")

Update from GitHub

devtools::install_github("evanbio/evanverse", force = TRUE)

Using evanverse's Built-in Updater

library(evanverse)
update_pkg("evanverse")

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Troubleshooting

Installation Fails with "package not available"

Solution: Ensure you're using R ≥ 4.1.0

R.version.string

Bioconductor Packages Not Installing

Solution: Install BiocManager first, then retry:

install.packages("BiocManager")
BiocManager::install(c("Biobase", "GSEABase"))

Permission Errors on Linux/macOS

Solution: Install to user library:

install.packages("evanverse", lib = Sys.getenv("R_LIBS_USER"))

Network/Firewall Issues

Solution: Configure proxy if behind a firewall:

Sys.setenv(http_proxy = "http://your-proxy:port")
Sys.setenv(https_proxy = "https://your-proxy:port")

Compilation Issues on Windows

Solution: Install Rtools from CRAN

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Uninstall

To remove evanverse:

remove.packages("evanverse")

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Getting Help

• Documentation: https://evanbio.github.io/evanverse/
• Issues: GitHub Issues
• CRAN: CRAN Package Page

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Next Steps

After installation:

1. Read the Getting Started Guide
2. Explore the Comprehensive Guide
3. Browse the Function Reference
4. Try domain-specific vignettes:
5. Package Management
6. Data Processing
7. Color Palettes
8. Bioinformatics Workflows

evanverse documentation built on March 10, 2026, 5:07 p.m.