R包的安装与更新
一、R包的安装
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.tsinghua.edu.cn/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Packages====# pacman包文档地址 https://www.rdocumentation.org/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))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.r-project.org/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.utoronto.ca/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
# 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# 升级Rif(! require(installr)) install.packages("installr")updateR()
# install Rtoolsinstall.Rtools()
# 重新安装ggplot2包，是安装最新R包版本install.packages("ggplot2")update.packages("ggplot2") # 更新ggplot2包
update.packages(ask = F) #更新所有R包BiocManager::install() # 更新所有已安装的 R 包到最新版本
BiocManager::version() # 查看 Bioconductor 的版本BiocManager::available("BSgenome.Hsapiens") # 根据正则表达式过滤包名称
# 安装特定版本的R包devtools::install_version("survminer", version = "0.4.2")packageVersion("survminer") # 当前版本查看
packageurl = "https://cran.r-project.org/src/contrib/Archive/survminer/survminer_0.4.2.tar.gz"install.packages(packageurl, repos = NULL, type = "source")
# 使用rvcheck::update_all()可以自动更新CRAN, Bioconductor和Github上的R包rvcheck::update_all()#从环境中移除R包detach(name="package:plyr")
#从下载库中卸载R包remove.packages("plyr")# 注意：移除R包，可以library()重新加载到Ｒ环境中，# 卸载Ｒ包，则不能重新加载进来，必须重新下载该包才能重新加载到Ｒ环境中。 赞 (0)