Installing R & Rmarkdown integrated in VSCode

1 Install and configure R on remote system

• R (>= 3.4.0) should be installed via conda (miniconda or anaconda)

• Install “radian”, via conda, as an alternative interface for default R (strongly recommended)

• After “radian” is installed, add this line in .bashrc or .bash_profile

  alias r="radian"

• Install following packages (always try to install R packages via conda first):

  • httpgd
  • languageserver
  • devtools
  • knitr
  • rmarkdown

• For example:

  conda install -c conda-forge r-languageserver

• If the required package cannot be found on conda, try to install from github (devtools packages is required)

• Create or add the following lines to “~/.Rprofile”

  source(file.path(Sys.getenv(
      if (.Platform$OS.type == "windows") "USERPROFILE" else "HOME"
  ), ".vscode-R", "init.R"))

• Create or add the following contents to “~/.vscode/settings.json”

  {
      "r.rpath.linux": "[link_to_R_execute_file]",
      "r.rterm.linux": "[link_to_R_execute_file]"
      "files.associations": {
          "*.Rmd": "rmd"
      }
  }

• NOTE:

  • R execute file can be found by “which R”
  • From now, always open R via “radian” (which is aliased as “r”)

2 Install VSCode

• Download the installation from following link: https://code.visualstudio.com/download

3 Install extensions

• Extension for remote SSH connection

  1. Remote - SSH & Remote - SSH: Editing Configuration
  2. R (by Yuki Ueda)
  3. Other recommended extensions:
     • Dracula Official
     • Vim
     • vscode-icons
     • Bracket Pairs Colorizer

• For Mac OS (and linux): should add all SSH configurations in : /Users/[idname]/.ssh/config

• Sample of config file:

  Host *
      ServerAliveInterval 300
      ForwardAgent yes
      ForwardX11 yes
      ForwardX11Trusted yes
      XAuthLocation /opt/local/bin/xauth
  
  Host [Host_address_1]
      HostName [Host_name_1]
      User [User_name]
      Compression yes
      Ciphers aes128-ctr,aes128-cbc
  
  Host [A_host_address_jump_from_Address_1]
      Hostname [Host_name_2]
      ProxyJump [Host_address_1]
  
  Host [A_special_host_address]
      HostName [A_special_host_name]
      UserKnownHostsFile=/dev/null
      StrictHostKeyChecking=no
  

• TRICK: Setup ssh connection without password

  1. Create public and private keys: ssh-keygen ==> By default, the key file is stored in /home/[user_id]/.ssh/id_rsa.pub
  2. Copy the public key to remote-host: ssh-copy-id ~/.ssh/id_rsa/pub remote-host
  3. Log in for the first time (have to)
  4. Ref: https://www.thegeekstuff.com/2008/11/3-steps-to-perform-ssh-login-without-password-using-ssh-keygen-ssh-copy-id/

4 Configure on local computer

• Press F1 to open “settings.json”

• The following options MUST be noticed:

  • “r.alwaysUseActiveTerminal”: true,
  • “r.bracketedPaste”: true,
  • “r.sessionWatcher”: true,
  • “r.lsp.diagnostics”: false,
  • “r.plot.useHttpgd”: true,

• Other options can be found in below example of “settings.json”

  {
    "workbench.iconTheme": "vscode-icons",
    "workbench.editor.highlightModifiedTabs": true,
    "r.alwaysUseActiveTerminal": true,
    "r.bracketedPaste": true,
    "r.sessionWatcher": true,
    "r.lsp.diagnostics": false,
    "r.plot.useHttpgd": true,
    "editor.minimap.enabled": false,
    "editor.renderWhitespace": "all",
    "editor.fontFamily": "Fira Code",
    "editor.fontLigatures": true,
    "editor.fontSize": 13,
    "editor.letterSpacing": -0.5,
    "editor.cursorStyle": "underline",
    "editor.quickSuggestions": {
        "comments": "off",
        "strings": "off",
        "other": "off"
    },
    "editor.acceptSuggestionOnEnter": "off",
    "editor.quickSuggestionsDelay": 10,
    "editor.wordBasedSuggestions": false,
    "editor.suggestOnTriggerCharacters": false,
    "editor.parameterHints.enabled": false,
    "editor.tabSize": 2,
    "editor.insertSpaces": true,
    "editor.detectIndentation": false,
    "terminal.integrated.fontFamily": "Fira Code",
    "terminal.integrated.fontSize":12,
    "terminal.integrated.gpuAcceleration": "off",
    "files.autoSave": "afterDelay",
    "files.autoSaveDelay": 13000,
    "workbench.colorTheme": "Dracula",
    "vsicons.dontShowNewVersionMessage": true,
    "editor.rulers": [
        80
    ],
    "remote.SSH.connectTimeout": 131,
    "remote.SSH.remotePlatform": {
        "101.96.72.101": "linux"
    },
    "window.zoomLevel": -0.28133422777602873,
    "workbench.layoutControl.enabled": false,
    "window.commandCenter": false,
  } 

5 References

• https://renkun.me/2019/12/11/writing-r-in-vscode-a-fresh-start/
• https://renkun.me/2019/12/26/writing-r-in-vscode-interacting-with-an-r-session/
• https://code.visualstudio.com/docs/languages/r
• https://github-wiki-see.page/m/Ikuyadeu/vscode-R/wiki/R-Session-watcher
• https://github.com/REditorSupport/vscode-R/wiki/R-Markdown
• https://github.com/REditorSupport/vscode-R/wiki/R-Session-watcher
• https://github.com/REditorSupport/vscode-R/issues/1013
• https://stackoverflow.com/questions/52284345/how-to-show-r-graph-from-visual-studio-code