r - R：从终端安装软件包时出错

Question

我正在尝试使用 shell 命令在 R 中安装一些包。我写了一个 R 文件“ installDependencies.R”来安装包。该文件如下：

packages <- c("xts","stringr","log4r")

# Function to check whether package is installed
is.installed <- function(mypkg){
  is.element(mypkg, installed.packages()[,1])
}

for(package in packages){
  # check if package is installed
  if (!is.installed(package)){
    install.packages(package)
  }
}

现在我正在尝试使用终端运行这个文件。我创建了一个shell脚本文件inst.sh，它如下：

#!/bin/bash

Rscript installDependencies.R

每当我使用./inst.sh命令运行文件时，都会生成以下错误：

algotree@algotree-900X3C-900X4C-900X4D:~$ ./inst.sh
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
Error in contrib.url(repos, type) : 
  trying to use CRAN without setting a mirror
Calls: install.packages -> grep -> contrib.url
Execution halted
algotree@algotree-900X3C-900X4C-900X4D:~$ 

Answer 1

在设置 CRAN 镜像之前我遇到了类似的问题

for(x in pkgs){
  if(!is.element(x, installed.packages()[,1]))
    {install.packages(x, repos="http://cran.fhcrc.org")
  } else {print(paste(x, " library already installed"))}
}