R包安装及设置镜像

安装包及设置镜像

安装包

安装CRAN软件

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.

安装Bioconductor 相关包

# 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.

本地安装源码包

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

源码编译安装的时候，要将源码压缩成tar.gz格式再安装，zip格式会出奇怪的错误。

R包相关操作

# 查看R包安装位置
.libPaths()

# 查看已安装的包
installed.packages()

# 查看包版本
packageVersion("package_name")

# 更新包
update.packages("package_name")

# 加载包
library("package_name")
require("package_name")

# 查看加载的包
.packages()

# 移除已加载的包（将包从R运行环境中移除）
detach("package_name")

# 彻底删除已安装的包：
remove.packages("package_name", lib = file.path("path/to/library"))

镜像设置

常用镜像地址

Name	URL	host	type
China (Anhui) [https]	https://mirrors.ustc.edu.cn/bioc/	中科大	CRAN_mirror
China (Anhui)	http://mirrors.ustc.edu.cn/bioc/	中科大	CRAN_mirror
China (Beijing) [https]	https://mirrors.tuna.tsinghua.edu.cn/CRAN/	清华	BioC_mirror
China (Beijing)	http://mirrors.tuna.tsinghua.edu.cn/CRAN/	清华	BioC_mirror

CRAN镜像下载安装包

# 从CRAN镜像下载安装包
install.packages(pkgs, repos = "https://mirrors.ustc.edu.cn/CRAN/")

# 从BioC镜像安装包
biocLite(pkg, siteRepos = "http://mirrors.ustc.edu.cn/bioc/")

常用函数

# 查看当前镜像地址
getOption("repos")

# 查看R_HOME地址
R.home()

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

将镜像添加到配置文件

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

在文末添加如下语句:

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