Installation Guide

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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] '0.4.0'

# 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:

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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