Installation Guide

Overview

This guide covers installation and mirror setup for evanverse. For package installation and updates beyond evanverse itself, we recommend pak.

Area	Tools
Base installation	`install.packages()`, `pak::pkg_install()`
Mirror configuration	`set_mirror()`
Installation and checks	`pak::pkg_install()`, `pak::pkg_status()`
Updates	`pak::pkg_update()`

library(evanverse)

Note: All examples are static (eval = FALSE). Network-dependent commands require internet access.

1 Install evanverse

CRAN release (recommended)

install.packages("evanverse")

GitHub development version

install.packages("devtools")
devtools::install_github("evanbio/evanverse")

Minimal vs full dependency install

# Minimal: Depends + Imports only
install.packages("evanverse", dependencies = c("Depends", "Imports"))

# Full: include Suggests
install.packages("evanverse", dependencies = TRUE)

2 Configure Mirrors

`set_mirror()` - Configure CRAN/Bioconductor mirrors

set_mirror() configures the mirrors used by R’s package system (and respected by pak).

# Set both CRAN + Bioconductor mirrors (default mirror: tuna)
set_mirror()
#> v CRAN mirror set to: https://mirrors.tuna.tsinghua.edu.cn/CRAN
#> v Bioconductor mirror set to: https://mirrors.tuna.tsinghua.edu.cn/bioconductor

# CRAN only
set_mirror("cran", "westlake")

# Bioconductor only
set_mirror("bioc", "official")

Supported mirror names:

Scope	Mirrors
CRAN	`official`, `rstudio`, `tuna`, `ustc`, `aliyun`, `sjtu`, `pku`, `hku`, `westlake`, `nju`, `sustech`
Bioconductor	`official`, `tuna`, `ustc`, `westlake`, `nju`

CRAN-only mirrors cannot be used with repo = "all":

set_mirror("all", "aliyun")
#> Error in `set_mirror()`:
#> ! Mirror "aliyun" is CRAN-only and cannot be used with repo = "all".

3 Installing Other Packages

We recommend pak for all package installation needs. It provides parallel installs, a unified interface for CRAN / GitHub / Bioconductor, and automatic dependency resolution.

# Install pak first (if needed)
install.packages("pak")

# CRAN
pak::pkg_install("dplyr")

# GitHub
pak::pkg_install("hadley/emo")

# Bioconductor
pak::pkg_install("DESeq2")

# Multiple sources at once
pak::pkg_install(c("dplyr", "tidyverse/ggplot2", "bioc::DESeq2"))

Check status and update:

pak::pkg_status(c("ggplot2", "dplyr"))
pak::pkg_update()

4 Troubleshooting

Package not available

R.version.string

If your R version is too old, upgrade R and retry.

Bioconductor install problems

if (!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}
BiocManager::install(c("Biobase", "GSEABase", "biomaRt", "GEOquery"))

Corporate network / proxy issues

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

Local library permission issues

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

5 A Combined Workflow

The following sequence is practical for a fresh environment:

# 1) Install evanverse
install.packages("evanverse")
library(evanverse)

# 2) Set mirrors (especially useful in China)
set_mirror("all", "tuna")

# 3) Install packages via pak
pak::pkg_install(c("dplyr", "ggplot2"))
pak::pkg_install("bioc::DESeq2")

# 4) Verify status
pak::pkg_status(c("dplyr", "ggplot2", "DESeq2"))

# 5) Keep packages updated
pak::pkg_update()