Interactive R Terminal using System Default R instead of R in a Conda Environment

Overview

In this article, we will explore how to use the interactive R terminal with system default R (4.1.2) installed on a remote server running Ubuntu 16.04.2 LTS, while also utilizing an R environment created within a conda environment.

Background

The question arises from a scenario where VSCode is running on a macOS machine, and the R version being used by the interactive terminal is different from the one installed in the local conda environment. We aim to utilize the R environment within the conda environment as the interactive terminal.

R in Conda Environment

When an R environment is created within a conda environment, it uses the system default R path for execution. This can sometimes lead to issues with using specific versions of R or custom paths for the R interpreter.

The r.rpath.linux setting in VSCode’s settings.json file is used to specify the path where the R interpreter will be executed from. However, this setting may not always work as expected due to various reasons such as permissions issues or incorrect syntax.

Specifying R Binary Path

One possible solution to this issue is to specify the R binary path using the --r-binary launching option in the radian executable. This can be done by adding a new key-value pair under the "r.rterm.option" parameter in VSCode’s settings.json file.

Here’s an example of how you might set up your settings.json file to achieve this:

{
    "r.rterm.linux": "/your/conda/env/bin/radian",
    "r.rterm.option": [
        "--no-save",
        "--no-restore",
        "--r-binary=/your/conda/env/bin/R"
    ]
}

In this example, we’re using the --r-binary option to specify the path of the R executable within our conda environment.

Radian and Radjutsu

For those unfamiliar with radian, it’s a command-line interface for the R programming language. The radian package provides a more modern and efficient way to run R commands compared to the traditional R interpreter.

In order to use the radian package, we need to install it first using pip:

pip install radjutsu

Note: In addition to installing the radian package, you may also want to consider adding an alias for radian in your shell configuration file. For example, on a macOS machine, you could add the following line to your ~/.bashrc file:

alias rad=radian

This allows us to simply type r instead of radian when running R commands.

Using Interactive R Terminal with Conda Environment

Once we have set up our settings.json file, we can use the interactive R terminal within VSCode. Here are some steps you might need to follow:

1. Open the Command Palette

Press Ctrl+Shift+P on Windows/Linux or Cmd+Shift+P on macOS to open the command palette.

2. Select “Terminal: Create New Terminal”

Select this option from the command palette to create a new terminal within VSCode.

3. Set Up Conda Environment

Make sure you are in your project directory and that your conda environment has been activated:

conda activate myenv

Replace myenv with the name of your conda environment.

4. Open Interactive R Terminal

Open a new terminal within VSCode by selecting “Terminal: Create New Terminal” from the command palette.

In this terminal, you should see an interactive R prompt:

> 
>

You can now use r instead of radian to run R commands.

Troubleshooting and Best Practices

Here are some additional tips for troubleshooting common issues with using an interactive R terminal within a conda environment:

Check Conda Environment Status

conda info –envs


    This will show you the current status of your conda environments.

*   **Verify R Binary Path**

    Make sure that the `--r-binary` option is set correctly in your `settings.json` file. You can verify this by opening a new terminal and running:

    ```markdown
conda run --envs myenv python -c "import sys; print(sys.executable)"

This should print the path to the R executable within your conda environment.

Use Radjutsu
Installing radian using pip is a good practice. Make sure you also add an alias for radian in your shell configuration file if needed.

By following these steps and best practices, you should be able to use the interactive R terminal with system default R installed on a remote server running Ubuntu 16.04.2 LTS, while also utilizing an R environment created within a conda environment.

Last modified on 2023-10-30