Installation Guide

Overview

This guide covers installation, mirror setup, dependency checks, and updates for evanverse and related packages.

Area Tools
Base installation install.packages(), devtools::install_github()
Mirror configuration set_mirror()
Installation and checks inst_pkg(), check_pkg()
Updates update_pkg() 
library(evanverse)

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

1 Install 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() controls mirror sources used by inst_pkg() and update_pkg().

# 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 Install Other Packages With evanverse

inst_pkg() - Install from CRAN, GitHub, Bioconductor, or local file

inst_pkg("dplyr", source = "CRAN")
inst_pkg("hadley/emo", source = "GitHub")
inst_pkg("DESeq2", source = "Bioconductor")
inst_pkg(source = "Local", path = "mypackage_1.0.0.tar.gz")

Local installation requires path:

inst_pkg(source = "Local")
#> Error in `inst_pkg()`:
#> ! Must provide `path` for local installation.

Already-installed packages are skipped automatically.

4 Verify Installation Status

check_pkg() - Check and optionally auto-install missing packages

check_pkg("ggplot2", source = "CRAN")
#> # A tibble: 1 x 4
#>   package name    installed source
#>   <chr>   <chr>   <lgl>     <chr>
#> 1 ggplot2 ggplot2 TRUE      CRAN
check_pkg(c("ggplot2", "fakepkg123"), source = "CRAN")
#> v Installed: ggplot2
#> ! Missing: fakepkg123
check_pkg(c("ggplot2", "fakepkg123"), source = "CRAN", auto_install = TRUE)
#> i Installing missing packages automatically...

For GitHub source, use "user/repo" format:

check_pkg("r-lib/devtools", source = "GitHub")

5 Update Packages

update_pkg() - Update all packages or specific targets

# Update all CRAN + Bioconductor packages
update_pkg()
# CRAN only
update_pkg(source = "CRAN")
# Specific package(s)
update_pkg("ggplot2", source = "CRAN")
update_pkg("hadley/ggplot2", source = "GitHub")
update_pkg("DESeq2", source = "Bioconductor")

If pkg is provided, source must also be provided (cannot stay at "all").

6 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"))

7 A Combined Workflow

The following sequence is practical for a fresh environment:

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

# 2) Set mirrors
set_mirror("all", "tuna")

# 3) Install key dependencies
inst_pkg(c("dplyr", "ggplot2"), source = "CRAN")
inst_pkg("DESeq2", source = "Bioconductor")

# 4) Verify status
check_pkg(c("dplyr", "ggplot2", "DESeq2"), source = "CRAN")

# 5) Keep packages updated
update_pkg(source = "CRAN")

Getting Help