【原】R包的安装与更新

hucy_Bioinfo 2021-08-19

展开全文

一、R包的安装

0. 设置镜像

R和bioconductor的主服务器都在国外，设置镜像加快下载速度。

## ====修改镜像====options(repos=c(CRAN="https://mirrors.tuna./CRAN/"))options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/")## 检查镜像是否修改成功。options()$BioC_mirroroptions()$repos

1. 批量安装

##====(1)批量安装Packages====# pacman包文档地址 https://www./packages/pacman/versions/0.5.1# pacman conveniently wraps library and package related functions and names them in an intuitive and consistent fashion.

packs = c("haven", "reshape2", "ggplot2", "pheatmap", "openxlsx", "dplyr", "survival", "survminer", "survIDINRI", "LDheatmap", "packHV", "broom", "forestplot", "Hmisc", "CPE", "nricens", "compareC", "gdsfmt","SNPRelate","survcomp", "biomaRt", "validstats", "phenoscanner")

if(! require(pacman)) install.packages("pacman", dependencies = TRUE)pacman::p_load(packs, dependencies=TRUE, character.only = TRUE) # p_load(): Load and Install Packages# checkpacman::p_loaded(packs, character.only = TRUE)all(pacman::p_loaded(packs, character.only = TRUE))

2. 根据不同Repository安装

如果想知道R包的来源，科学上网[1]搜索一下即可。如，ggplot2 R package。

##====(2)根据不同的Repository安装Packages====# 1) CRAN----if(! require(CPE)) install.packages("CPE")# 报错：Failed with error: 'package 'Hmisc’ 4.2.0 was found, but >= 4.3.0 is required by 'rms’’# remove.packages("Hmisc") #版本过低，卸载后重装# if(! require(Hmisc)) install.packages("Hmisc")

if(! require(statmod)) install.packages("statmod")if(! require(rmutil)) install.packages("rmutil")if(! require(haplo.stats)) install.packages("haplo.stats")

# 2) Bioconducter----if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("gdsfmt")BiocManager::install(c("GenomicRanges", "Organism.dplyr"))

# 3) GitHub----if(! require(devtools)) install.packages("devtools")library(devtools)install_github("phenoscanner/phenoscanner") #query the PhenoScanner database# 报错：Error: Failed to install 'phenoscanner' from GitHub: Does not appear to be an R package (no DESCRIPTION)# 解决参考：https://github.com/r-lib/devtools/issues/1939

# You seem to have a non-standard tar on your PATH. You could try setting Sys.setenv("TAR" = "internal") to use R's internal tar instead.

Sys.setenv("TAR" = "internal") # install_github("phenoscanner/phenoscanner")library(phenoscanner)

3. 本地安装

# ====(3)本地下载安装Packages====# 1)下载Rtools工具(安装过程默认自动配置环境变量)https://cran./bin/windows/Rtools/ ；# 2) 指定安装包所在目录（待安装包下载到本地的位置）。# 示例R包下载地址：http://individual./osaarela/

install.packages("D:/Program Files/R/R-3.5.2/bin/x64/validstats_1.4.tar.gz", repos = NULL, type = "source") # 注意R包的编码类型

install.packages("D:/Program Files/R/R-3.6.1/bin/x64/phenoscanner.zip", repos = NULL,type = "win.binary")

二、R包的更新

0. 常用查看基本信息的函数

# 加载R包

require("ggplot2") # 能够返回逻辑值，若包能够被加载利用，则返回T，否则返回F；常用于条件判断

library("ggplot2") # 不返回逻辑值

# 压缩R包加载信息，使显示更加简洁suppressPackageStartupMessages({ library(statmod) library(rmutil) library(haplo.stats) library(gdsfmt)})

# 查看使用示例??gdsfmtbrowseVignettes("gdsfmt")R.version.string #查看R版本信息sessionInfo() #查看R版本号、R运行的平台、加载的包及其安装的包和版本号

.libPaths() # 查看R包的安装位置library() # 查看所有已安装的R包packageVersion("ggplot2") #查看某个包的版本号#查看已经安装的包及其版本号和安装路径installed.packages()[,c('Package','Version','LibPath')]available.packages() # 查看CRAN可以安装哪些包BiocManager::available() # 搜索可用Bioconductor R包#查看ggplot2包及其版本号和安装路径installed.packages()["ggplot2",c('Package','Version','LibPath')]

#查看已经加载的包(.packages())search()

#查看某个包的详细信息packageDescription("ggplot2")library(help="ggplot2")

help("ggplot") #查看某个函数属于哪个包args(lm) #查看函数的参数example(lm) #自动运行该函数帮助文档中的例子

1. 更新R包