---
title: "Installation Guide"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Installation Guide}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = FALSE
)
```

## 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:

```{r cran-install}
install.packages("evanverse")
```

### From GitHub (Development Version)

For the latest features and bug fixes:

```{r github-install}
# 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:

```{r minimal-install}
install.packages("evanverse", dependencies = c("Depends", "Imports"))
```

### Full Installation

Install with all suggested packages for complete functionality:

```{r full-install}
install.packages("evanverse", dependencies = TRUE)
```

### Install Specific Version

```{r version-install}
# 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:

```{r bioc-install}
# 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:

```{r verify-install, eval = TRUE}
# Load the package
library(evanverse)

# Check version
packageVersion("evanverse")

# List available functions
pkg_functions("evanverse")

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

---

## Update evanverse

### Update from CRAN

```{r update-cran}
update.packages("evanverse")
```

### Update from GitHub

```{r update-github}
devtools::install_github("evanbio/evanverse", force = TRUE)
```

### Using evanverse's Built-in Updater

```{r update-builtin}
library(evanverse)
update_pkg("evanverse")
```

---

## Troubleshooting

### Installation Fails with "package not available"

**Solution**: Ensure you're using R ≥ 4.1.0

```{r check-r-version}
R.version.string
```

### Bioconductor Packages Not Installing

**Solution**: Install BiocManager first, then retry:

```{r bioc-troubleshoot}
install.packages("BiocManager")
BiocManager::install(c("Biobase", "GSEABase"))
```

### Permission Errors on Linux/macOS

**Solution**: Install to user library:

```{r user-lib-install}
install.packages("evanverse", lib = Sys.getenv("R_LIBS_USER"))
```

### Network/Firewall Issues

**Solution**: Configure proxy if behind a firewall:

```{r proxy-setup}
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](https://cran.r-project.org/bin/windows/Rtools/)

---

## Uninstall

To remove evanverse:

```{r uninstall}
remove.packages("evanverse")
```

---

## Getting Help

- **Documentation**: [https://evanbio.github.io/evanverse/](https://evanbio.github.io/evanverse/)
- **Issues**: [GitHub Issues](https://github.com/evanbio/evanverse/issues)
- **CRAN**: [CRAN Package Page](https://cran.r-project.org/package=evanverse)

---

## Next Steps

After installation:

1. Read the [Getting Started Guide](get-started.html)
2. Explore the [Comprehensive Guide](comprehensive-guide.html)
3. Browse the [Function Reference](https://evanbio.github.io/evanverse/reference/)
4. Try domain-specific vignettes:
   - [Package Management](package-management.html)
   - [Data Processing](data-processing.html)
   - [Color Palettes](color-palettes.html)
   - [Bioinformatics Workflows](bioinformatics-workflows.html)