一、CRAN安装R包：install.packages()函数

1、单个包的安装：install.packages("ggplot2")

• 第一种

> install.packages("ggplot2")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/windows/contrib/3.6/ggplot2_3.2.1.zip'
Content type 'application/zip' length 3976020 bytes (3.8 MB)
downloaded 3.8 MB

package ‘ggplot2’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\xiaoxiaoyi\AppData\Local\Temp\RtmpeufPQo\downloaded_packages

• 第二种：Rstudio上点击操作

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2、批量安装R包:

• 1) sapply()

> pkgs <-  c("tidyr","tibble","dplyr","stringr","ggplot2","ggpubr","factoextra","FactoMineR") 
> sapply(pkgs, install.packages, character.only = T) 
#三个参数：包含要安装的R包的名称的向量
#安装函数install.packages，character.only = T
#它只接受字符串值，它可以接受一个字符串变量

• 2)向量+循环的形式安装包

> cran_packages <- c('tidyr',
                   'tibble',
                   'dplyr',
                   'stringr',
                   'ggplot2',
                   'ggpubr',
                   'factoextra',#包含主成分分析（PCA）h函数
                   'FactoMineR') 
> for (pkg in cran_packages){
  if (! require(pkg,character.only=T) ) {
    install.packages(pkg,ask = F,update = F)
    require(pkg,character.only=T) 
  }
}#以上是向量的形式安装包
###另一种，Biocductor
> Biocductor_packages <- c('GEOquery',
                         'hgu133plus2.db',
                         "KEGG.db",
                         "limma",
                         "impute",
                         "GSEABase",
                         "GSVA",
                         "clusterProfiler",
                         "org.Hs.eg.db",
                         "preprocessCore",
                         "hugene10sttranscriptcluster.db",
                         "enrichplot")
> for (pkg in Biocductor_packages){
  if (! require(pkg,character.only=T) ) {
    BiocManager::install(pkg,ask = F,update = F)
    require(pkg,character.only=T) 
  }
}#cran和bioconductor安装包的形式不一样
#最后，能够加载说明就已经成功。
#前面的所有提示和报错都先不要管。主要看这里
for (pkg in c(Biocductor_packages,cran_packages)){
  require(pkg,character.only=T) 
}#对所有的包进行加载
#没有error就是成功！
#哪个报错，就回去安装哪个。如果你没有安装xx包，却提示你xx包不存在，这也正常，是因为复杂的依赖关系，缺啥补啥。

3、下载到本地安装

1）先下载到本地，并把它放在工作目录中，或者安装时指定软件包的绝对路径。
download.file("http://bioconductor.org/packages/release/bioc/src/contrib/BiocInstaller_1.20.1.tar.gz","BiocInstaller_1.20.1.tar.gz")
install.packages("BiocInstaller_1.20.1.tar.gz", repos = NULL)

---

4、指定网址安装

• Cran

packageurl <- "http://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_0.9.1.tar.gz"
#或者
packageurl <- "http://cran.r-project.org/src/contrib/Archive/gridExtra/gridExtra_0.9.1.tar.gz"
install.packages(packageurl, repos=NULL, type="source")

• bioconductor

packageurl <- "http://www.bioconductor.org/packages/2.11/bioc/src/contrib/ggbio_1.6.6.tar.gz"
#或者
packageurl <- "http://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_1.0.1.tar.gz"
install.packages(packageurl, repos=NULL, type="source")

二、Bioconductor安装R包：BiocManager::install()

1、 单个包安装的方法

> if (!requireNamespace("BiocManager", quietly = TRUE))#用来进行一个特定的行为，如当建议包找不到时抛出一个错误。
> install.packages("BiocManager") # 首先要安装BiocManager包
> BiocManager::install("Biobase") # 再用BiocManager安装

2、 批量安装的方法sapply（）函数

bioanp <- c("pcaMethods", "GO.db", "topGO", "clusterProfiler", "biomaRt")
sapply(anp, BiocManager::install, character.only = T) # 前天你需要安装BiocManager包，方法install.packages("BiocManager")

三、Github安装R包，借助工具包devtools

>install.packages("devtools")
>library(devtools)
>install_github("RevolutionAnalytics/RHadoop")