使用github操作运行r rmd文件

Question

我有两个存储库每天只需在Rstudio打开项目并编织RMD文件，然后将结果推向存储库，可以每天更新。

我很想通过github动作自动化这一点，但是我发现文档很困惑。

在做这件事时，是否有“像我5岁的人”来解释吗？

因此，我制作了一个bash文件，位于./ bash/data_refresh.sh.sh和一个github操作文件data_refresh.yaml

bash文件：

#!/bin/bash

echo "Rendering the page..."

Rscript -e "rmarkdown::render(input = 'README.Rmd')"

if [[ "$(git status --porcelain)" != "" ]]; then
    git config --global user.name 'my_user_name'
    git config --global user.email 'my_email_address'
    git add *
    git commit -m "Auto update Report"
    git push
fi

这是我的yaml：

# This is a basic workflow to help you get started with Actions

name: Package Data Refresh

# Controls when the workflow will run
on:
  # Triggers the workflow on push or pull request events but only for the "master" branch
  schedule:
    - cron: '0  12 * * *'

  # Allows you to run this workflow manually from the Actions tab
  workflow_dispatch:

# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
  # This workflow contains a single job called "build"
  build:
    name: refresh the dashboard
    # The type of runner that the job will run on
    runs-on: ubuntu-latest

    # Steps represent a sequence of tasks that will be executed as part of the job
    steps:
      - name: checkout_repo
        uses: actions/checkout@v2
        with:
          ref:  'master'
      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
      - name: Render Rmarkdown
        run: bash ./bash/data_refresh.sh

我遇到以下错误，不确定如何纠正它。

Run bash ./bash/data_refresh.sh
  bash ./bash/data_refresh.sh
  shell: /usr/bin/bash -e {0}
Rendering the page...
Error in loadNamespace(x) : there is no package called ‘rmarkdown’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted

Answer 1

您可以取从r-lib 作为起点并添加您的零件（渲染＆amp; cron作业）。

当手动触发时，这起作用了，我尚未测试cron作业：

# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
  # Triggers the workflow on push or pull request events but only for the "master" branch
  schedule:
    - cron: '0  12 * * *'

  # Allows you to run this workflow manually from the Actions tab
  workflow_dispatch:

name: Package Data Refresh

jobs:
  render-rmarkdown:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    steps:
      - name: Checkout repo
        uses: actions/checkout@v2
        with:
          fetch-depth: 0

      - uses: r-lib/actions/setup-pandoc@v2

      - uses: r-lib/actions/setup-r@v2

      - uses: r-lib/actions/setup-renv@v2
      
      - name: Render Rmarkdown Readme file and Commit Results
        run: |
          echo "Rendering the page..."
          Rscript -e 'rmarkdown::render(input = "README.Rmd")'
          if [[ "$(git status --porcelain)" != "" ]]; then
            git config --local user.name "$GITHUB_ACTOR"
            git config --local user.email "[email protected]"
            git add *
            git commit -m "Auto update Report"
            git push origin
          fi

这使用renv安装依赖项并缓存GHA中的依赖项（据我了解）。因此，您需要在存储库中使用renv。只需使用renv :: init（）并提交结果文件。当您使用.rmd时，这包括rmarkDown。有关更多信息，请检查 renv rentv文档。

使其起作用的关键部分是，您必须在参数周围使用rscript的单个引号，而不是双引号。否则它将无法正常工作。

另外，我是GHA的新手，因此您可能还可以优化其他方面。

在此处编辑

是一个无需renv的版本，但是我建议使用renv，因为它允许缓存依赖关系（套件）。

# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
  # Triggers the workflow on push or pull request events but only for the "master" branch
  schedule:
    - cron: '0  12 * * *'

  # Allows you to run this workflow manually from the Actions tab
  workflow_dispatch:

name: Package Data Refresh 2

jobs:
  render-rmarkdown:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    steps:
      - name: Checkout repo
        uses: actions/checkout@v2
        with:
          fetch-depth: 0

      - uses: r-lib/actions/setup-pandoc@v2

      - uses: r-lib/actions/setup-r@v2
      
      - name: Install packages, render Rmarkdown Readme file and Commit Results
        run: |
          echo "Rendering the page..."
          Rscript -e 'install.packages(c("knitr", "rmarkdown"))'
          Rscript -e 'rmarkdown::render(input = "README.Rmd")'
          if [[ "$(git status --porcelain)" != "" ]]; then
            git config --local user.name "$GITHUB_ACTOR"
            git config --local user.email "[email protected]"
            git add *
            git commit -m "Auto update Report"
            git push origin
          fi