RStudio 显示不同的 $PATH 变量 [英] RStudio shows a different $PATH variable

问题描述

可能的重复问题，但是不知道RStudio的启动过程来判断问题是否相同.我在 Linux 上使用 RStudio Desktop v0.99.442.从 RStudio 内的控制台，我运行

Possible duplicate question, but I don't know the startup process of RStudio to tell if the problems are the same. I'm using RStudio Desktop v0.99.442 on Linux. From the console inside RStudio, I run

system("echo $PATH")
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games

然而，我真正的 $PATH(当我从控制台 echo $PATH 时看到的)上面有很多我想要的其他程序能够使用 R 中的 system() 进行调用.例如，在我的 .bashrc 中，我将 tabix 附加到 $PATH.

However, my real $PATH (which I see when I echo $PATH from the console) has a lot of other programs on it that I'd like to be able to call using system() from R. For example, in my .bashrc, I have tabix appended to $PATH.

奇怪的是，当我从控制台中的 R 会话运行相同的命令时，我得到

The weird thing is when I run the same command from a R session within the console, I get

system("echo $PATH")
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games;/path/to/bcftools-1.2/htslib-1.2.1/tabix

这是正确的.因此，RStudio 中的 R 会话和控制台中的 R 会话之间存在差异.它们不加载相同的环境变量.如何让 RStudio 使用正确版本的 $PATH?

which is correct. So there is a difference between a R session inside RStudio and a R session in the console. They do not load the same environment variables. How do I get RStudio to use the correct version of $PATH?

推荐答案

当你从命令行启动 R 然后运行 ​​system(echo $PATH) 时，你从你的命令行会话.例如，当您从 Mac 上的 Dock 或 Finder 或作为 Ubuntu 中的系统应用程序而不是从命令行启动 RStudio 时，RStudio 不会从您的 /.bashrc 获取其环境.相反，它将从系统范围的设置中获取环境变量.它如何找到这些系统设置将取决于操作系统.

When you start R from the command line and then run system(echo $PATH), you are inheriting the Bash environment from your command line session. When you launch RStudio from, say, the Dock or Finder on a Mac or as a system application in Ubuntu, and not from the command line, RStudio does not gets its environment from your /.bashrc. Instead it will get the environment variables from system-wide settings. How it finds those system settings will depend on the operating system.

在Ubuntu中查看环境变量的解释，尤其是桌面应用程序部分.

See this explanation of environment variables in Ubuntu, especially the section on desktop applications.

根据那个解释:

您可以通过编辑应用程序的 .desktop 文件向应用程序添加环境变量.例如，要运行环境变量为 APPMENU_DISPLAY_BOTH=1 的digiKam"，找到对应的 digikam.desktop 文件，并通过 env 命令将变量的设置添加到Exec"条目中:

You can add an environment variable to an application by editing its .desktop file. For example, to run "digiKam" with the environment variable APPMENU_DISPLAY_BOTH=1, find the corresponding digikam.desktop file and add the setting of the variable, via the env command, to the entry "Exec":

RStudio .desktop 文件将位于 ~/.local/share/applications/ 或 /usr/share/applications/ (最有可能是后者).编辑该文件以包含此行:

The RStudio .desktop file will be in ~/.local/share/applications/ or /usr/share/applications/ (most likely the latter). Edit that file to include this line:

PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games;/path/to/bcftools-1.2/htslib-1.2.1/tabix

Mac

系统范围的环境变量由启动代理设置，而不是由 Bash 设置.为从 Finder 启动的应用程序设置环境变量的确切方式取决于您的 Mac OS X 版本.这个 答案可能有帮助.

我这样做的方法是添加一个文件，~/Library/LaunchAgents/com.username.envvariables.plist，其中包含以下内容:

The way that I do this is to add a file, ~/Library/LaunchAgents/com.username.envvariables.plist with these contents:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
  <dict>
    <key>Label</key>
    <string>com.username.envvariables</string>
    <key>ProgramArguments</key>
    <array>
      <string>sh</string>
      <string>-c</string>
      <string>
        launchctl setenv PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games;/path/to/bcftools-1.2/htslib-1.2.1/tabix
      </string>
    </array>
    <key>RunAtLoad</key>
    <true/>
  </dict>
</plist>

然后您必须加载该文件:

You will then have to load that file:

launchctl load ~/Library/LaunchAgents/com.username.envvariables.plist

您可能需要重新启动 Finder:

You may have to restart the Finder:

killall -KILL Dock

然后重新启动 RStudio.

Then restart RStudio.

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