# Installation Guide

## Overview

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

## 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")

## System Requirements

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

## 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

## 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")

## 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"))

## Verify Installation

After installation, verify that evanverse is working correctly:

    # Load the package
    library(evanverse)

    # Check version
    packageVersion("evanverse")
    #> [1] '0.4.4'

    # List available functions
    pkg_functions("evanverse")
    #>
    #> ── Package: evanverse ──
    #>
    #> ℹ Matched exported names: 65
    #> %is%
    #> %map%
    #> %match%
    #> %nin%
    #> %p%
    #> any_void
    #> bio_palette_gallery
    #> check_pkg
    #> clear_palette_cache
    #> cols_with_void
    #> comb
    #> combine_logic
    #> compile_palettes
    #> convert_gene_id
    #> create_palette
    #> df2list
    #> download_batch
    #> download_gene_ref
    #> download_geo_data
    #> download_url
    #> drop_void
    #> file_info
    #> file_tree
    #> get_ext
    #> get_palette
    #> gmt2df
    #> gmt2list
    #> hex2rgb
    #> inst_pkg
    #> is_void
    #> list_palettes
    #> map_column
    #> palette_cache_info
    #> perm
    #> pkg_functions
    #> pkg_version
    #> plot_bar
    #> plot_density
    #> plot_forest
    #> plot_pie
    #> plot_venn
    #> preview_palette
    #> quick_anova
    #> quick_chisq
    #> quick_cor
    #> quick_ttest
    #> read_excel_flex
    #> read_table_flex
    #> reload_palette_cache
    #> remind
    #> remove_palette
    #> replace_void
    #> rgb2hex
    #> rows_with_void
    #> safe_execute
    #> scale_color_evanverse
    #> scale_colour_evanverse
    #> scale_fill_evanverse
    #> set_mirror
    #> stat_power
    #> stat_samplesize
    #> update_pkg
    #> view
    #> with_timer
    #> write_xlsx_flex

    # Test basic functionality
    "Hello" %p% " " %p% "World"
    #> [1] "Hello   World"

## 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")

## 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

## Uninstall

To remove evanverse:

    remove.packages("evanverse")

## Getting Help

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

## 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:
   - Package Management
   - Data Processing
   - Color Palettes
   - Bioinformatics Workflows