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Initial Setup

Documentation

R in Visual Studio Code

MacOS Setup Details

  1. Install R if it is not already installed on your system.
  2. Install the R extension for VSCode
  3. Install XQuartz prior to installing the httpgd package.
  4. Install the following packages:
## start R
R

## Install packages to allow plot viewing
install.packages("httpgd")
install.packages("languageserver)
install.packages("lintr")
  1. Type CMD + , to open Settings. Type httpgd. Check the option to use httpgd for R plot viewing: image
  2. Also in Settings, type rpath. Enter the following for macOS:
/usr/local/bin/R
  1. If you plan to use R Markdown documents, install Pandoc and install the following packages:
install.packages("rmarkdown")
install.packages("knitr")
  1. Add keybindings for arrow(<-) and pipe(|> or %>%) to your keybindings.json file. Press Cmd+Shift+P to open the Command Palette. Type Preferences: Open Keyboard Shortcuts (JSON) and select it. Add the following blocks between the [ ] brackets:
    // Insert pipe-operator
    {
        "description": "R Pipe Operator",
        "key": "ctrl+shift+m",
        "command": "type",
        "args": {"text": " |> "},
        "when": "editorTextFocus",
    },
    // Insert <- assignment
    {
        "description": "R Assignment Arrow",
        "key": "alt+-",
        "command": "type",
        "args": {"text": " <- "},
        "when": "editorTextFocus",
    }

See here for other useful keybindings.

  1. Restart VSCode

HTCF Seput

  1. Connect via SSH
  2. Start an interactive session
sml
  1. Install the VSCode R extension here as well.
  2. In Settings, type rpath. Enter the path to the lab R installation for linux:
/ref/dblab/software/spack-0.21.0/opt/spack/linux-rocky8-x86_64/gcc-8.5.0/r-4.3.0-3ggwaqrtfpe2t627qhwaknvsifz6dk5n/rlib/R/bin/R

Type R: Lib Paths and enter /ref/dblab/software/r-envs/4.1.3. Check the Use Renv Lib Path checkbox.

Type Terminal integrated profiles and update the settings.json for Linux. Add an entry for R.

{
    "terminal.integrated.profiles.linux": {
        "R": {
            "path": "/bin/bash",
            "args": ["-c", "eval `spack load --sh /3ggwaqr"]
        }
    }
}
  1. Install XQuartz prior to installing the httpgd package.
  2. Install the following packages:
## Start R
labr
runr

## Install packages to allow plot viewing
install.packages("httpgd")
install.packages("languageserver)
install.packages("lintr")

Daily Use

Load R

labr
runr

Open an R terminal

image

Start the plot viewer

# Load the httpgd library
library(httpgd)

# Start the httpgd graphics device
hgd()

Copy the URL. Type R Plot: Open Httpgd URL and select it. Paste in the URL and press enter.

Open the Command Palette (Cmd+Shift+P). Type R: Show Plot Viewer and select it to open the httpgd viewer.

Run a line by or selection using CMD + ENTER.

Troubleshooting

How do I make this work with a different R installation?

  1. Install R using spack (it has already been installed in the lab spack instance using the following commands):
spack create env r_430
spack install r@4.3.0 X=True
spack env activate r_430
spack add r@4.3.0 X=True
  1. Enter the following commands, replacing r@4.3.0 with your spec name:
spack location -i r@4.3.0

Add /rlib/R/bin/R to the path that is returned to get the path to the R executable. Update the rpath Linux setting with this path.