mirror of https://github.com/docker/docs.git
add guide for R language (#19787)
Add R language with sample repository --------- Co-authored-by: David Karlsson <35727626+dvdksn@users.noreply.github.com>
This commit is contained in:
Marco Franzon
GitHub
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@ -1,6 +1,6 @@
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---
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description: Language-specific guides overview
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keywords: guides, docker, language, node, java, python, go, golang, .net
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keywords: guides, docker, language, node, java, python, R, go, golang, .net
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title: Language-specific guides overview
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toc_min: 1
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toc_max: 2
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@ -30,6 +30,9 @@ Learn how to containerize your applications and start developing using Docker. C
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<div class="flex items-center flex-1 shadow p-4">
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<a href="/language/python/"><img class="m-auto rounded" src="/language/images/python.webp" alt="Develop with Python"></a>
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</div>
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<div class="flex items-center flex-1 shadow p-4">
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<a href="/language/r/"><img class="m-auto rounded" src="/language/images/r.webp" alt="Develop with R"></a>
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</div>
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<div class="flex items-center flex-1 shadow p-4">
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<a href="/language/java/"><img class="m-auto rounded" src="/language/images/java.webp" alt="Develop with Java"></a>
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</div>
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@ -0,0 +1,17 @@
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---
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description: Containerize R apps using Docker
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keywords: Docker, getting started, R, language
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title: R language-specific guide
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toc_min: 1
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toc_max: 2
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---
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The R language-specific guide teaches you how to containerize a R application using Docker. In this guide, you’ll learn how to:
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* Containerize and run a R application
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* Set up a local environment to develop a R application using containers
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* Configure a CI/CD pipeline for a containerized R application using GitHub Actions
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* Deploy your containerized R application locally to Kubernetes to test and debug your deployment
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Start by containerizing an existing R application.
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{{< button text="Containerize a R app" url="containerize.md" >}}
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---
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title: Configure CI/CD for your R application
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keywords: ci/cd, github actions, R, shiny
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description: Learn how to configure CI/CD using GitHub Actions for your R application.
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---
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## Prerequisites
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Complete all the previous sections of this guide, starting with [Containerize a R application](containerize.md). You must have a [GitHub](https://github.com/signup) account and a [Docker](https://hub.docker.com/signup) account to complete this section.
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## Overview
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In this section, you'll learn how to set up and use GitHub Actions to build and test your Docker image as well as push it to Docker Hub. You will complete the following steps:
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1. Create a new repository on GitHub.
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2. Define the GitHub Actions workflow.
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3. Run the workflow.
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## Step one: Create the repository
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Create a GitHub repository, configure the Docker Hub secrets, and push your source code.
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1. [Create a new repository](https://github.com/new) on GitHub.
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2. Open the repository **Settings**, and go to **Secrets and variables** >
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**Actions**.
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3. Create a new secret named `DOCKER_USERNAME` and your Docker ID as value.
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4. Create a new [Personal Access Token (PAT)](../../security/for-developers/access-tokens.md/#create-an-access-token) for Docker Hub. You can name this token `r-docker`.
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5. Add the PAT as a second secret in your GitHub repository, with the name
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`DOCKERHUB_TOKEN`.
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6. In your local repository on your machine, run the following command to change
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the origin to the repository you just created. Make sure you change
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`your-username` to your GitHub username and `your-repository` to the name of
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the repository you created.
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```console
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$ git remote set-url origin https://github.com/your-username/your-repository.git
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```
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7. Run the following commands to stage, commit, and push your local repository to GitHub.
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```console
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$ git add -A
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$ git commit -m "my commit"
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$ git push -u origin main
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```
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## Step two: Set up the workflow
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Set up your GitHub Actions workflow for building, testing, and pushing the image
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to Docker Hub.
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1. Go to your repository on GitHub and then select the **Actions** tab.
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2. Select **set up a workflow yourself**.
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This takes you to a page for creating a new GitHub actions workflow file in
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your repository, under `.github/workflows/main.yml` by default.
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3. In the editor window, copy and paste the following YAML configuration.
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```yaml
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name: ci
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on:
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push:
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branches:
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- main
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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-
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name: Checkout
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uses: actions/checkout@v4
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-
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name: Login to Docker Hub
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uses: docker/login-action@v3
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with:
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username: ${{ secrets.DOCKER_USERNAME }}
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password: ${{ secrets.DOCKERHUB_TOKEN }}
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-
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name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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-
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name: Build and push
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uses: docker/build-push-action@v5
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with:
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context: .
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push: true
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tags: ${{ secrets.DOCKER_USERNAME }}/${{ github.event.repository.name }}:latest
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```
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For more information about the YAML syntax used here, see [Workflow syntax for GitHub Actions](https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions).
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## Step three: Run the workflow
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Save the workflow file and run the job.
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1. Select **Commit changes...** and push the changes to the `main` branch.
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After pushing the commit, the workflow starts automatically.
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2. Go to the **Actions** tab. It displays the workflow.
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Selecting the workflow shows you the breakdown of all the steps.
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3. When the workflow is complete, go to your
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[repositories on Docker Hub](https://hub.docker.com/repositories).
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If you see the new repository in that list, it means the GitHub Actions
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successfully pushed the image to Docker Hub.
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## Summary
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In this section, you learned how to set up a GitHub Actions workflow for your R application.
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Related information:
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- [Introduction to GitHub Actions](../../build/ci/github-actions/index.md)
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- [Workflow syntax for GitHub Actions](https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions)
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## Next steps
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Next, learn how you can locally test and debug your workloads on Kubernetes before deploying.
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{{< button text="Test your deployment" url="./deploy.md" >}}
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---
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title: Containerize a R application
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keywords: R, containerize, initialize
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description: Learn how to containerize a R application.
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aliases:
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- /language/R/build-images/
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- /language/R/run-containers/
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---
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## Prerequisites
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* You have a [git client](https://git-scm.com/downloads). The examples in this section use a command-line based git client, but you can use any client.
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## Overview
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This section walks you through containerizing and running a R application.
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## Get the sample application
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The sample application uses the popular [Shiny](https://shiny.posit.co/) framework.
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Clone the sample application to use with this guide. Open a terminal, change directory to a directory that you want to work in, and run the following command to clone the repository:
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```console
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$ git clone https://github.com/mfranzon/r-docker-dev.git
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```
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You should now have the following contents in your `r-docker`
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directory.
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```text
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├── r-docker/
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│ ├── src/
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│ │ └── app.R
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│ ├── src_db/
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│ │ └── app_db.R
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│ ├── compose.yaml
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│ ├── Dockerfile
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│ └── README.md
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```
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To learn more about the files in the repository, see the following:
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- [Dockerfile](../../reference/dockerfile.md)
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- [.dockerignore](../../reference/dockerfile.md#dockerignore-file)
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- [compose.yaml](../../compose/compose-file/_index.md)
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## Run the application
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Inside the `r-docker` directory, run the following command in a
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terminal.
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```console
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$ docker compose up --build
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```
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Open a browser and view the application at [http://localhost:3838](http://localhost:3838). You should see a simple Shiny application.
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In the terminal, press `ctrl`+`c` to stop the application.
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### Run the application in the background
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You can run the application detached from the terminal by adding the `-d`
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option. Inside the `r-docker` directory, run the following command
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in a terminal.
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```console
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$ docker compose up --build -d
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```
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Open a browser and view the application at [http://localhost:3838](http://localhost:3838).
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You should see a simple Shiny application.
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In the terminal, run the following command to stop the application.
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```console
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$ docker compose down
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```
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For more information about Compose commands, see the [Compose CLI
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reference](../../compose/reference/_index.md).
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|
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## Summary
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|
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In this section, you learned how you can containerize and run your R
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application using Docker.
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Related information:
|
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- [Build with Docker guide](../../build/guide/index.md)
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- [Docker Compose overview](../../compose/_index.md)
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|
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## Next steps
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|
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In the next section, you'll learn how you can develop your application using
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containers.
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{{< button text="Develop your application" url="develop.md" >}}
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|
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---
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title: Test your R deployment
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keywords: deploy, kubernetes, R
|
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description: Learn how to develop locally using Kubernetes
|
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---
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|
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## Prerequisites
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|
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- Complete all the previous sections of this guide, starting with [Containerize a R application](containerize.md).
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- [Turn on Kubernetes](/desktop/kubernetes/#install-and-turn-on-kubernetes) in Docker Desktop.
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|
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## Overview
|
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|
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In this section, you'll learn how to use Docker Desktop to deploy your application to a fully-featured Kubernetes environment on your development machine. This allows you to test and debug your workloads on Kubernetes locally before deploying.
|
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|
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## Create a Kubernetes YAML file
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|
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In your `r-docker-dev` directory, create a file named
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`docker-r-kubernetes.yaml`. Open the file in an IDE or text editor and add
|
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the following contents. Replace `DOCKER_USERNAME/REPO_NAME` with your Docker
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username and the name of the repository that you created in [Configure CI/CD for
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your R application](configure-ci-cd.md).
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|
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```yaml
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apiVersion: apps/v1
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kind: Deployment
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metadata:
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name: docker-r-demo
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namespace: default
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spec:
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replicas: 1
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selector:
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matchLabels:
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service: shiny
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template:
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metadata:
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labels:
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service: shiny
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spec:
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containers:
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- name: shimy-service
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image: DOCKER_USERNAME/REPO_NAME
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imagePullPolicy: Always
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env:
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- name: POSTGRES_PASSWORD
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value: mysecretpassword
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---
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apiVersion: v1
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kind: Service
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metadata:
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name: service-entrypoint
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namespace: default
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spec:
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type: NodePort
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selector:
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service: shiny
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ports:
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- port: 3838
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targetPort: 3838
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nodePort: 30001
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```
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|
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In this Kubernetes YAML file, there are two objects, separated by the `---`:
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|
||||
- A Deployment, describing a scalable group of identical pods. In this case,
|
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you'll get just one replica, or copy of your pod. That pod, which is
|
||||
described under `template`, has just one container in it. The
|
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container is created from the image built by GitHub Actions in [Configure CI/CD for
|
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your R application](configure-ci-cd.md).
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- A NodePort service, which will route traffic from port 30001 on your host to
|
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port 3838 inside the pods it routes to, allowing you to reach your app
|
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from the network.
|
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|
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To learn more about Kubernetes objects, see the [Kubernetes documentation](https://kubernetes.io/docs/home/).
|
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|
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## Deploy and check your application
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|
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1. In a terminal, navigate to `r-docker-dev` and deploy your application to
|
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Kubernetes.
|
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|
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```console
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$ kubectl apply -f docker-r-kubernetes.yaml
|
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```
|
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|
||||
You should see output that looks like the following, indicating your Kubernetes objects were created successfully.
|
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|
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```text
|
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deployment.apps/docker-r-demo created
|
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service/service-entrypoint created
|
||||
```
|
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|
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2. Make sure everything worked by listing your deployments.
|
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|
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```console
|
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$ kubectl get deployments
|
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```
|
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|
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Your deployment should be listed as follows:
|
||||
|
||||
```shell
|
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NAME READY UP-TO-DATE AVAILABLE AGE
|
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docker-r-demo 1/1 1 1 15s
|
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```
|
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|
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This indicates all one of the pods you asked for in your YAML are up and running. Do the same check for your services.
|
||||
|
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```console
|
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$ kubectl get services
|
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```
|
||||
|
||||
You should get output like the following.
|
||||
|
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```shell
|
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NAME TYPE CLUSTER-IP EXTERNAL-IP PORT(S) AGE
|
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kubernetes ClusterIP 10.96.0.1 <none> 443/TCP 23h
|
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service-entrypoint NodePort 10.99.128.230 <none> 3838:30001/TCP 75s
|
||||
```
|
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|
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In addition to the default `kubernetes` service, you can see your `service-entrypoint` service, accepting traffic on port 30001/TCP.
|
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|
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3. In a browser, visit the following address. Note that a database was not deployed in
|
||||
this example.
|
||||
|
||||
```console
|
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http://localhost:30001/
|
||||
```
|
||||
|
||||
4. Run the following command to tear down your application.
|
||||
|
||||
```console
|
||||
$ kubectl delete -f docker-r-kubernetes.yaml
|
||||
```
|
||||
|
||||
## Summary
|
||||
|
||||
In this section, you learned how to use Docker Desktop to deploy your application to a fully-featured Kubernetes environment on your development machine.
|
||||
|
||||
Related information:
|
||||
- [Kubernetes documentation](https://kubernetes.io/docs/home/)
|
||||
- [Deploy on Kubernetes with Docker Desktop](../../desktop/kubernetes.md)
|
||||
- [Swarm mode overview](../../engine/swarm/_index.md)
|
||||
|
|
@ -0,0 +1,221 @@
|
|||
---
|
||||
title: Use containers for R development
|
||||
keywords: R, local, development
|
||||
description: Learn how to develop your R application locally.
|
||||
---
|
||||
|
||||
## Prerequisites
|
||||
|
||||
Complete [Containerize a R application](containerize.md).
|
||||
|
||||
## Overview
|
||||
|
||||
In this section, you'll learn how to set up a development environment for your containerized application. This includes:
|
||||
|
||||
- Adding a local database and persisting data
|
||||
- Configuring Compose to automatically update your running Compose services as you edit and save your code
|
||||
|
||||
## Get the sample application
|
||||
|
||||
You'll need to clone a new repository to get a sample application that includes logic to connect to the database.
|
||||
|
||||
Change to a directory where you want to clone the repository and run the following command.
|
||||
|
||||
```console
|
||||
$ git clone https://github.com/mfranzon/r-docker-dev.git
|
||||
```
|
||||
|
||||
## Configure the application to use the database
|
||||
|
||||
To try the connection between the Shiny application and the local database you have to modify the `Dockerfile` changing the `COPY` instruction:
|
||||
|
||||
```diff
|
||||
-RUN src/ .
|
||||
+RUN src_db/ .
|
||||
```
|
||||
|
||||
|
||||
|
||||
## Add a local database and persist data
|
||||
|
||||
You can use containers to set up local services, like a database. In this section, you'll update the `compose.yaml` file to define a database service and a volume to persist data.
|
||||
|
||||
In the cloned repository's directory, open the `compose.yaml` file in an IDE or text editor.
|
||||
|
||||
In the `compose.yaml` file, you need to un-comment the properties for configuring the database. You must also mount the database password file and set an environment variable on the `shiny-app` service pointing to the location of the file in the container.
|
||||
|
||||
The following is the updated `compose.yaml` file.
|
||||
|
||||
```yaml
|
||||
services:
|
||||
shiny-app:
|
||||
build:
|
||||
context: .
|
||||
dockerfile: Dockerfile
|
||||
ports:
|
||||
- 3838:3838
|
||||
environment:
|
||||
- POSTGRES_PASSWORD_FILE=/run/secrets/db-password
|
||||
depends_on:
|
||||
db:
|
||||
condition: service_healthy
|
||||
secrets:
|
||||
- db-password
|
||||
db:
|
||||
image: postgres
|
||||
restart: always
|
||||
user: postgres
|
||||
secrets:
|
||||
- db-password
|
||||
volumes:
|
||||
- db-data:/var/lib/postgresql/data
|
||||
environment:
|
||||
- POSTGRES_DB=example
|
||||
- POSTGRES_PASSWORD_FILE=/run/secrets/db-password
|
||||
expose:
|
||||
- 5432
|
||||
healthcheck:
|
||||
test: [ "CMD", "pg_isready" ]
|
||||
interval: 10s
|
||||
timeout: 5s
|
||||
retries: 5
|
||||
volumes:
|
||||
db-data:
|
||||
secrets:
|
||||
db-password:
|
||||
file: db/password.txt
|
||||
```
|
||||
|
||||
> **Note**
|
||||
>
|
||||
> To learn more about the instructions in the Compose file, see [Compose file
|
||||
> reference](/compose/compose-file/).
|
||||
|
||||
Before you run the application using Compose, notice that this Compose file specifies a `password.txt` file to hold the database's password. You must create this file as it's not included in the source repository.
|
||||
|
||||
In the cloned repository's directory, create a new directory named `db` and inside that directory create a file named `password.txt` that contains the password for the database. Using your favorite IDE or text editor, add the following contents to the `password.txt` file.
|
||||
|
||||
```text
|
||||
mysecretpassword
|
||||
```
|
||||
|
||||
Save and close the `password.txt` file.
|
||||
|
||||
You should now have the following contents in your `r-docker-dev`
|
||||
directory.
|
||||
|
||||
```text
|
||||
├── r-docker-dev/
|
||||
│ ├── db/
|
||||
│ │ └── password.txt
|
||||
│ ├── src/
|
||||
│ │ └── app.R
|
||||
│ ├── src_db/
|
||||
│ │ └── app_db.R
|
||||
│ ├── requirements.txt
|
||||
│ ├── .dockerignore
|
||||
│ ├── compose.yaml
|
||||
│ ├── Dockerfile
|
||||
│ ├── README.Docker.md
|
||||
│ └── README.md
|
||||
```
|
||||
|
||||
Now, run the following `docker compose up` command to start your application.
|
||||
|
||||
```console
|
||||
$ docker compose up --build
|
||||
```
|
||||
|
||||
Now test your DB connection opening a browser at:
|
||||
|
||||
```console
|
||||
http://localhost:3838
|
||||
```
|
||||
|
||||
You should see a pop-up message:
|
||||
|
||||
```text
|
||||
DB CONNECTED
|
||||
```
|
||||
|
||||
|
||||
Press `ctrl+c` in the terminal to stop your application.
|
||||
|
||||
## Automatically update services
|
||||
|
||||
Use Compose Watch to automatically update your running Compose services as you
|
||||
edit and save your code. For more details about Compose Watch, see [Use Compose
|
||||
Watch](../../compose/file-watch.md).
|
||||
|
||||
Open your `compose.yaml` file in an IDE or text editor and then add the Compose
|
||||
Watch instructions. The following is the updated `compose.yaml` file.
|
||||
|
||||
```yaml {hl_lines="15-18"}
|
||||
services:
|
||||
shiny-app:
|
||||
build:
|
||||
context: .
|
||||
dockerfile: Dockerfile
|
||||
ports:
|
||||
- 3838:3838
|
||||
environment:
|
||||
- POSTGRES_PASSWORD_FILE=/run/secrets/db-password
|
||||
depends_on:
|
||||
db:
|
||||
condition: service_healthy
|
||||
secrets:
|
||||
- db-password
|
||||
develop:
|
||||
watch:
|
||||
- action: rebuild
|
||||
path: .
|
||||
db:
|
||||
image: postgres
|
||||
restart: always
|
||||
user: postgres
|
||||
secrets:
|
||||
- db-password
|
||||
volumes:
|
||||
- db-data:/var/lib/postgresql/data
|
||||
environment:
|
||||
- POSTGRES_DB=example
|
||||
- POSTGRES_PASSWORD_FILE=/run/secrets/db-password
|
||||
expose:
|
||||
- 5432
|
||||
healthcheck:
|
||||
test: [ "CMD", "pg_isready" ]
|
||||
interval: 10s
|
||||
timeout: 5s
|
||||
retries: 5
|
||||
volumes:
|
||||
db-data:
|
||||
secrets:
|
||||
db-password:
|
||||
file: db/password.txt
|
||||
```
|
||||
|
||||
Run the following command to run your application with Compose Watch.
|
||||
|
||||
```console
|
||||
$ docker compose watch
|
||||
```
|
||||
|
||||
Now, if you modify your `app.R` you will see the changes in real time without re-building the image!
|
||||
|
||||
Press `ctrl+c` in the terminal to stop your application.
|
||||
|
||||
## Summary
|
||||
|
||||
In this section, you took a look at setting up your Compose file to add a local
|
||||
database and persist data. You also learned how to use Compose Watch to automatically rebuild and run your container when you update your code.
|
||||
|
||||
Related information:
|
||||
- [Compose file reference](/compose/compose-file/)
|
||||
- [Compose file watch](../../compose/file-watch.md)
|
||||
- [Multi-stage builds](../../build/building/multi-stage.md)
|
||||
|
||||
## Next steps
|
||||
|
||||
In the next section, you'll take a look at how to set up a CI/CD pipeline using GitHub Actions.
|
||||
|
||||
{{< button text="Configure CI/CD" url="configure-ci-cd.md" >}}
|
||||
|
|
@ -90,6 +90,18 @@ Guides:
|
|||
path: /language/python/configure-ci-cd/
|
||||
- title: "Test your deployment"
|
||||
path: /language/python/deploy/
|
||||
- sectiontitle: R
|
||||
section:
|
||||
- title: "Overview"
|
||||
path: /language/r/
|
||||
- title: "Containerize your app"
|
||||
path: /language/r/containerize/
|
||||
- title: "Develop your app"
|
||||
path: /language/r/develop/
|
||||
- title: "Configure CI/CD"
|
||||
path: /language/r/configure-ci-cd/
|
||||
- title: "Test your deployment"
|
||||
path: /language/r/deploy/
|
||||
- sectiontitle: Java
|
||||
section:
|
||||
- title: "Overview"
|
||||
|
|
|
|||
Loading…
Reference in New Issue