安裝包及設(shè)置鏡像

安裝包

安裝CRAN軟件

install.packages(pkgs, lib, repos = getOption("repos"), quiet = FALSE)

lib: character vector giving the library directories where to install the packages. Recycled as needed. If missing, defaults to the first element of .libPaths().
repos: character vector, the base URL(s) of the repositories to use, e.g., the URL of a CRAN mirror such as "https://cloud.r-project.org". For more details on supported URL schemes see url.

quiet: logical: if true, reduce the amount of output.

安裝Bioconductor 相關(guān)包

# Source biocLite from web
source("https://bioconductor.org/biocLite.R")
biocLite("package_name")

# Use biocLite under BiocInstaller
install.packages("BiocInstaller")
BiocInstaller::biocLite("package_name")  

biocLite(pkgs=c("Biobase", "IRanges", "AnnotationDbi"),  
         suppressUpdates=FALSE,
         suppressAutoUpdate=FALSE,
         siteRepos=character(),
         ask=TRUE, ...)

Install or update Bioconductor, CRAN, or GitHub packages

if (!requireNamespace("BiocManager", quietly=TRUE)) 
    install.packages("BiocManager")
BiocManager::install("package_name")

Note: BioInstaller and biocLiteare deprecated use the biocmanager cran package instead.

本地安裝源碼包

install.packages("path/to/pkg/package_name.tar.gz", repos = NULL, type = "source")

源碼編譯安裝的時(shí)候，要將源碼壓縮成tar.gz格式再安裝，zip格式會(huì)出奇怪的錯(cuò)誤。

R包相關(guān)操作

# 查看R包安裝位置
.libPaths()

# 查看已安裝的包
installed.packages()

# 查看包版本
packageVersion("package_name")

# 更新包
update.packages("package_name")

# 加載包
library("package_name")
require("package_name")

# 查看加載的包
.packages()

# 移除已加載的包（將包從R運(yùn)行環(huán)境中移除）
detach("package_name")

# 徹底刪除已安裝的包：
remove.packages("package_name", lib = file.path("path/to/library"))

鏡像設(shè)置

常用鏡像地址

CRAN鏡像下載安裝包

# 從CRAN鏡像下載安裝包
install.packages(pkgs, repos = "https://mirrors.ustc.edu.cn/CRAN/")

# 從BioC鏡像安裝包
biocLite(pkg, siteRepos = "http://mirrors.ustc.edu.cn/bioc/")

常用函數(shù)

# 查看當(dāng)前鏡像地址
getOption("repos")

# 查看R_HOME地址
R.home()

R_HOME/doc/CRAN_mirrors.csv
R_HOME/doc/BioC_mirrors.csv

將鏡像添加到配置文件

Bioconductor 鏡像源配置文件之一是 .Rprofile (linux 下位于 ~/.Rprofile )。

在文末添加如下語(yǔ)句:

options(BioC_mirror="https://mirrors.tuna.tsinghua.edu.cn/bioconductor")