How can I deploy a quarto book using renv and github actions when the renv.lock file doesn't capture all the dependencies?

[luifrancgom]

Description

I am deploying a book using quarto, github actions and renv. I am locally using:

• quarto 1.4.550
• Windows 11 Pro 23H2

Also I have try locally using:

• Ubuntu 22.04.4 LTS (Jammy Jellyfish)

In the book I am using tikz as a language through knitr to create a diagram, where one of the packages needed is magick. I install the package using renv::install("magick"). However when I deploy the book in a github page I get the following error: ! there is no package called 'magick' in relation to the step Render and Publish

I create a minimal reproducible example in this repository: https://github.com/luifrancgom/question_magick_quarto

The code that is failing when deploying is in the intro.qmd file and corresponds to the following content:

# Introduction

This is a book created from markdown and executable code.

See @knuth84 for additional discussion of literate programming.

# Diagram

```{r}
1 + 1
```

```{tikz}
#| out-width: 50%
\begin{tikzpicture}
  \draw (-1,0) circle (1.5);
\end{tikzpicture}
```

The renv.lock has the following content where I don't understand why magick is not included even if a use renv::install("magick") and all its dependencies have been installed locally in the renv/library folder:

{
  "R": {
    "Version": "4.3.3",
    "Repositories": [
      {
        "Name": "CRAN",
        "URL": "https://cloud.r-project.org"
      }
    ]
  },
  "Packages": {
    "R6": {
      "Package": "R6",
      "Version": "2.5.1",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R"
      ],
      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
    },
    "base64enc": {
      "Package": "base64enc",
      "Version": "0.1-3",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R"
      ],
      "Hash": "543776ae6848fde2f48ff3816d0628bc"
    },
    "bslib": {
      "Package": "bslib",
      "Version": "0.6.1",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "base64enc",
        "cachem",
        "grDevices",
        "htmltools",
        "jquerylib",
        "jsonlite",
        "lifecycle",
        "memoise",
        "mime",
        "rlang",
        "sass"
      ],
      "Hash": "c0d8599494bc7fb408cd206bbdd9cab0"
    },
    "cachem": {
      "Package": "cachem",
      "Version": "1.0.8",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "fastmap",
        "rlang"
      ],
      "Hash": "c35768291560ce302c0a6589f92e837d"
    },
    "cli": {
      "Package": "cli",
      "Version": "3.6.2",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "utils"
      ],
      "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52"
    },
    "digest": {
      "Package": "digest",
      "Version": "0.6.35",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "utils"
      ],
      "Hash": "698ece7ba5a4fa4559e3d537e7ec3d31"
    },
    "ellipsis": {
      "Package": "ellipsis",
      "Version": "0.3.2",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "rlang"
      ],
      "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077"
    },
    "evaluate": {
      "Package": "evaluate",
      "Version": "0.23",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "methods"
      ],
      "Hash": "daf4a1246be12c1fa8c7705a0935c1a0"
    },
    "fastmap": {
      "Package": "fastmap",
      "Version": "1.1.1",
      "Source": "Repository",
      "Repository": "CRAN",
      "Hash": "f7736a18de97dea803bde0a2daaafb27"
    },
    "fontawesome": {
      "Package": "fontawesome",
      "Version": "0.5.2",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "htmltools",
        "rlang"
      ],
      "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d"
    },
    "fs": {
      "Package": "fs",
      "Version": "1.6.3",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "methods"
      ],
      "Hash": "47b5f30c720c23999b913a1a635cf0bb"
    },
    "glue": {
      "Package": "glue",
      "Version": "1.7.0",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "methods"
      ],
      "Hash": "e0b3a53876554bd45879e596cdb10a52"
    },
    "highr": {
      "Package": "highr",
      "Version": "0.10",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "xfun"
      ],
      "Hash": "06230136b2d2b9ba5805e1963fa6e890"
    },
    "htmltools": {
      "Package": "htmltools",
      "Version": "0.5.7",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "base64enc",
        "digest",
        "ellipsis",
        "fastmap",
        "grDevices",
        "rlang",
        "utils"
      ],
      "Hash": "2d7b3857980e0e0d0a1fd6f11928ab0f"
    },
    "jquerylib": {
      "Package": "jquerylib",
      "Version": "0.1.4",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "htmltools"
      ],
      "Hash": "5aab57a3bd297eee1c1d862735972182"
    },
    "jsonlite": {
      "Package": "jsonlite",
      "Version": "1.8.8",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "methods"
      ],
      "Hash": "e1b9c55281c5adc4dd113652d9e26768"
    },
    "knitr": {
      "Package": "knitr",
      "Version": "1.45",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "evaluate",
        "highr",
        "methods",
        "tools",
        "xfun",
        "yaml"
      ],
      "Hash": "1ec462871063897135c1bcbe0fc8f07d"
    },
    "lifecycle": {
      "Package": "lifecycle",
      "Version": "1.0.4",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "cli",
        "glue",
        "rlang"
      ],
      "Hash": "b8552d117e1b808b09a832f589b79035"
    },
    "memoise": {
      "Package": "memoise",
      "Version": "2.0.1",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "cachem",
        "rlang"
      ],
      "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c"
    },
    "mime": {
      "Package": "mime",
      "Version": "0.12",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "tools"
      ],
      "Hash": "18e9c28c1d3ca1560ce30658b22ce104"
    },
    "rappdirs": {
      "Package": "rappdirs",
      "Version": "0.3.3",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R"
      ],
      "Hash": "5e3c5dc0b071b21fa128676560dbe94d"
    },
    "renv": {
      "Package": "renv",
      "Version": "1.0.5",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "utils"
      ],
      "Hash": "32c3f93e8360f667ca5863272ec8ba6a"
    },
    "rlang": {
      "Package": "rlang",
      "Version": "1.1.3",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "utils"
      ],
      "Hash": "42548638fae05fd9a9b5f3f437fbbbe2"
    },
    "rmarkdown": {
      "Package": "rmarkdown",
      "Version": "2.26",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "bslib",
        "evaluate",
        "fontawesome",
        "htmltools",
        "jquerylib",
        "jsonlite",
        "knitr",
        "methods",
        "tinytex",
        "tools",
        "utils",
        "xfun",
        "yaml"
      ],
      "Hash": "9b148e7f95d33aac01f31282d49e4f44"
    },
    "sass": {
      "Package": "sass",
      "Version": "0.4.9",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R6",
        "fs",
        "htmltools",
        "rappdirs",
        "rlang"
      ],
      "Hash": "d53dbfddf695303ea4ad66f86e99b95d"
    },
    "tinytex": {
      "Package": "tinytex",
      "Version": "0.50",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "xfun"
      ],
      "Hash": "be7a76845222ad20adb761f462eed3ea"
    },
    "xfun": {
      "Package": "xfun",
      "Version": "0.42",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "grDevices",
        "stats",
        "tools"
      ],
      "Hash": "fd1349170df31f7a10bd98b0189e85af"
    },
    "yaml": {
      "Package": "yaml",
      "Version": "2.3.8",
      "Source": "Repository",
      "Repository": "CRAN",
      "Hash": "29240487a071f535f5e5d5a323b7afbd"
    }
  }
}

In this case what will the best approach to solve the problem?

i. Change the way I am using tikz?
ii. Include manually magick and its dependencies in the renv.lock file?

Also I don't know how to proceed even if I will be able to include magick and its dependencies in the renv.lock file because according to https://cran.r-project.org/web/packages/magick/index.html you need the following system requirements: ImageMagick++: ImageMagick-c++-devel (rpm) or libmagick++-dev (deb). In this case what changes should I need to incorporate in .github/workflows/publish.yml?:

on:
  workflow_dispatch:
  push:
    branches: main

name: Quarto Publish

jobs:
  build-deploy:
    runs-on: ubuntu-latest
    permissions:
      contents: write
    steps:
      - name: Check out repository
        uses: actions/checkout@v4

      - name: Set up Quarto
        uses: quarto-dev/quarto-actions/setup@v2
        with:
          tinytex: true

      - name: Install R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: '4.2.0'

      - name: Install R Dependencies
        uses: r-lib/actions/setup-renv@v2
        with:
          cache-version: 1

      - name: Render and Publish
        uses: quarto-dev/quarto-actions/publish@v2
        with:
          target: gh-pages
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

[mcanouil]

Unfortunately, this is out of Quarto scope.

See system requirements: https://github.com/ropensci/magick/blob/8d22d7badda48a936db739d468c244fbc286132f/DESCRIPTION#L20

You need to add this in your workflow.

[luifrancgom]

Thank you Mickaël Canouil.

You were right, this is out of the Quarto scope. If anyone needs to solve the same or a similar problem I find a possible solution in the following way:

• Use the recommendation pointed out in https://rstudio.github.io/renv/articles/faq.html#capturing-all-dependencies by using renv::settings$snapshot.type("all")

• Add to publish.yml after installing R the different system requirements when a package fails. In my case I needed to take into account the system requirements related to magick and pdftools by installing Magick++ and Poppler C++ API:

on:
  workflow_dispatch:
  push:
    branches: main

name: Quarto Publish

jobs:
  build-deploy:
    runs-on: ubuntu-latest
    permissions:
      contents: write
    steps:
      - name: Check out repository
        uses: actions/checkout@v4

      - name: Set up Quarto
        uses: quarto-dev/quarto-actions/setup@v2
        with:
          tinytex: true

      - name: Install R
        uses: r-lib/actions/setup-r@v2

      - name: Install Magick++
        run: sudo apt-get install -y libmagick++-dev
        
      - name: Install Poppler C++ API
        run: sudo apt-get -y install libpoppler-cpp-dev

      - name: Install R Dependencies
        uses: r-lib/actions/setup-renv@v2
        with:
          cache-version: 1

      - name: Render and Publish
        uses: quarto-dev/quarto-actions/publish@v2
        with:
          target: gh-pages
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

[mcanouil]

Glad you solved your system dependency issue.

[cderv]

Some other tricks with renv I know to be useful in this type of situations.

• Using _dependencies.R file to add missed dependencies https://rstudio.github.io/renv/reference/dependencies.html#missing-dependencies
• Using explicit dependencies https://rstudio.github.io/renv/reference/dependencies.html#explicit-dependencies

For installing the dependencies, pak can be useful too. It has some helpers to query some databases to known the requirements regarding system libs. See https://pak.r-lib.org/reference/sysreqs.html and pak::pkg_sysreqs

It can be enabled with renv it seems : https://rstudio.github.io/renv/reference/config.html#renv-config-pak-enabled

Just alternative to snapshoting the whole library, which also works as you found !

[luifrancgom]

Thank you Christophe Dervieux for pointing me out the other possible options.