ubuntu中运行r脚本解决r包下载问题

Question

在ubuntu中运行./rarepng.R后，出现以下报错

Error in loadNamespace(x) : there is no package called ‘prettyunits’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted

检查后发现，是因为r包未安装导致，在ubuntu中安装r包r脚本会面临镜像源选择的问题，如果以下：

--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors

 1: 0-Cloud [https]                       2: Australia (Canberra) [https]
 3: Australia (Melbourne 1) [https]       4: Australia (Melbourne 2) [https]
 5: Austria [https]                       6: Belgium (Brussels) [https]
 7: Brazil (PR) [https]                   8: Brazil (RJ) [https]
 9: Brazil (SP 1) [https]                10: Brazil (SP 2) [https]
11: Bulgaria [https]                     12: Canada (MB) [https]
13: Canada (ON 1) [https]                14: Canada (ON 2) [https]
15: Chile (Santiago) [https]             16: China (Beijing 2) [https]
17: China (Beijing 3) [https]            18: China (Hefei) [https]
19: China (Hong Kong) [https]            20: China (Guangzhou) [https]
21: China (Jinan) [https]                22: China (Lanzhou) [https]
23: China (Nanjing) [https]              24: China (Shanghai 2) [https]
25: China (Shenzhen) [https]             26: Colombia (Cali) [https]
27: Costa Rica [https]                   28: Cyprus [https]
29: Czech Republic [https]               30: Denmark [https]
31: East Asia [https]                    32: Ecuador (Cuenca) [https]
33: France (Lyon 1) [https]              34: France (Lyon 2) [https]
35: France (Marseille) [https]           36: France (Paris 1) [https]
37: Germany (Erlangen) [https]           38: Germany (Göttingen) [https]
39: Germany (Leipzig) [https]            40: Germany (Münster) [https]
41: Greece [https]                       42: Iceland [https]
43: India (Bengaluru) [https]            44: India (Bhubaneswar) [https]
45: Indonesia (Banda Aceh) [https]       46: Iran (Mashhad) [https]
47: Italy (Milano) [https]               48: Italy (Padua) [https]
49: Japan (Yonezawa) [https]             50: Korea (Gyeongsan-si) [https]
51: Mexico (Mexico City) [https]         52: Mexico (Texcoco) [https]
53: Morocco [https]                      54: Netherlands (Dronten) [https]
55: New Zealand [https]                  56: Norway [https]
57: South Africa (Johannesburg) [https]  58: Spain (A Coruña) [https]
59: Spain (Madrid) [https]               60: Sweden (Umeå) [https]
61: Switzerland (Zurich 1) [https]       62: Taiwan (Taipei) [https]
63: Turkey (Denizli) [https]             64: Turkey (Istanbul) [https]
65: UK (Bristol) [https]                 66: UK (London 1) [https]
67: USA (IA) [https]                     68: USA (MI) [https]
69: USA (MO) [https]                     70: USA (OH) [https]
71: USA (OR) [https]                     72: USA (PA 1) [https]
73: USA (TN) [https]                     74: United Arab Emirates [https]
75: Uruguay [https]                      76: (other mirrors)

我的r脚本中使用的是以下代码安装并加载r包，

load_or_install_packages <- function(package_names) {
  for (pkg in package_names) {
    if (!requireNamespace(pkg, quietly = TRUE)) {
      install.packages(pkg, dependencies = TRUE)
      library(pkg, character.only = TRUE)
    } else {
      library(pkg, character.only = TRUE)
    }
  }
}
Packages <- c("microeco", "magrittr", "vegan", "tidyr")
load_or_install_packages(Packages)

请问如何解决脚本运行中选择镜像源的自动化问题

Answer 1

以下内容由CHATGPT及阿里嘎多学长共同生成、有用望采纳：

---

在Ubuntu系统中运行R脚本时遇到需要选择CRAN镜像源的问题，可以通过设置R的配置文件来实现自动化选择。以下是一些步骤来解决你的问题：

1. 设置R的配置文件：你可以在R会话中设置默认的镜像源，这样在安装包时就不需要手动选择。

   options(repos = c(CRAN = "https://cran.rstudio.com/"))
   

   这里我使用了RStudio的镜像源作为例子，你可以根据你的地理位置和网络情况选择一个更近的镜像源。

2. 修改.Renviron文件：R会读取用户主目录下的.Renviron文件来设置环境变量。你可以在这个文件中设置默认的CRAN镜像源。

   打开终端，使用文本编辑器创建或修改.Renviron文件：

   echo 'options(repos = c(CRAN = "https://cran.rstudio.com/"))' >> ~/.Renviron
   

   这样设置后，每次启动R会话时都会自动应用这个配置。

3. 在R脚本中设置：你也可以在R脚本的开始部分添加设置默认镜像源的代码，这样每次运行脚本时都会自动设置。

   options(repos = c(CRAN = "https://cran.rstudio.com/"))
   

4. 使用install.packages的repos参数：如果你只想在安装特定包时使用特定的镜像源，可以在调用install.packages时指定repos参数。

   install.packages("prettyunits", repos = "https://cran.rstudio.com/")
   

5. 自动化脚本：如果你希望完全自动化这个过程，可以在脚本中添加逻辑来检测特定包是否已安装，如果没有，则自动安装。

   install_needed_packages <- function(packages) {
     to_install <- packages[!packages %in% rownames(installed.packages()[,"Package"])]
     if (length(to_install)) {
       install.packages(to_install, repos = "https://cran.rstudio.com/")
     }
   }
   

   然后使用这个函数来安装你的包：

   Packages <- c("microeco", "magrittr", "vegan", "tidyr", "prettyunits")
   install_needed_packages(Packages)
   

6. 注意：确保你选择的镜像源是可靠和可用的。如果你在中国大陆，可能需要选择一个国内镜像源，比如中国科学技术大学的镜像源。

通过上述方法，你可以避免在安装R包时手动选择CRAN镜像源，提高脚本的自动化程度。希望这些信息对你有帮助！

如果你需要更多帮助，或者想要了解特定的CRAN镜像源，请随时告诉我。