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:
BioInstallerandbiocLiteare deprecated use thebiocmanagercran 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")
