diff --git a/.Rprofile b/.Rprofile new file mode 100644 index 0000000..81b960f --- /dev/null +++ b/.Rprofile @@ -0,0 +1 @@ +source("renv/activate.R") diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml new file mode 100644 index 0000000..9d3cd7f --- /dev/null +++ b/.github/workflows/build.yml @@ -0,0 +1,53 @@ +name: Deploy + +on: + workflow_dispatch: + push: + branches: + - main + +permissions: + contents: write + +concurrency: + group: "pages" + cancel-in-progress: false + +jobs: + deploy: + runs-on: ubuntu-latest + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + GH_TOKEN: ${{ github.token }} + steps: + - uses: actions/checkout@v4 + + - name: Install R + uses: r-lib/actions/setup-r@v2 + with: + r-version: '4.2.0' + use-public-rspm: true + + - uses: r-lib/actions/setup-renv@v2 + with: + cache-version: 1 + + - uses: quarto-dev/quarto-actions/setup@v2 + with: + version: pre-release + tinytex: false + + - name: Render Quarto Project + shell: bash + run: | + quarto render index.qmd --output-dir _site + + - name: Deploy gh_pages + uses: JamesIves/github-pages-deploy-action@v4 + with: + BRANCH: gh-pages + FOLDER: _site + SINGLE_COMMIT: true diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..bd31527 --- /dev/null +++ b/.gitignore @@ -0,0 +1,8 @@ +.Rhistoryt +.Rhistory +/.quarto/ +/_*.local +*_cache/ +index_files +/_site/ +*.html diff --git a/README.md b/README.md new file mode 100644 index 0000000..4e42772 --- /dev/null +++ b/README.md @@ -0,0 +1,50 @@ +# Quarto presentation template + +[![Deploy](https://github.com/habitat-nature/presentation_template/actions/workflows/build.yml/badge.svg)](https://github.com/habitat-nature/presentation_template/actions/workflows/build.yml) [![html](https://img.shields.io/badge/read-html-blue)](https://habitat-nature.github.io/presentation_template/) + +Build and deploy interactive slides with a single click. + + +## Getting Started + +1. First click on the [Use this template](https://github.com/habitat-nature/presentation_template/generate) button to fork this repository, and check the option `Include all branches`. + +2. Once the fork is completed, git clone the repo to your local machine + +3. Install the R dependencies with the help of `renv` R package: + +```r +# install.packages('renv') + +# check with repo dependencies +renv::restore() +``` + +4. Edit your slides with Markdown flavor, with R, Python, and Julia integration. If you add new R packages in the slides, don't forget to run `renv::snapshot()` to update the dependencies list. + +5. Add, commit, and push your changes to the remote GitHub repo and let the GitHub Actions render and deploy the presentation for you + +6. Your presentation will be available on the `https://habitat-nature.github.io//` URL when the Action is completed. + +7. Enjoy 😎 + + +### Render the presentation locally + +To avoid pushing and waiting for the GitHub Action to render and deploy your presentation, it is recommended to keep rendering frequently as you edit your slides. This will avoid surprises (🐛) in the compilation process. To render the presentation locally, you need the [Quarto](https://quarto.org/docs/get-started/) client installed. + +Render the HTML presentation by running the following code on Terminal: + +```bash +quarto render index.qmd +``` + +Open the output `index.html` file. + + +## Getting involved + +The layout of the presentation and color theme are still open for improvement. I tried my best to use some Habitat color palettes, but they are not easy to compose with. Any suggestion as an [issue](https://github.com/habitat-nature/presentation_template/issues) is welcome! + +GitHub Actions uses Quarto to render the HTML output and send it to the `gh-pages` branch. We use [GitHub Pages](https://pages.github.com/) to host the files available on the `gh-pages` branch to the web. Because of our GitHub plan, we cannot host private websites for free, meaning that the presentation will be available to anyone with the URL link. An alternative is to use [Azure Static WebApp](https://azure.microsoft.com/en-us/products/app-service/static). + diff --git a/images/habitat_compact.png b/images/habitat_compact.png new file mode 100644 index 0000000..2dc7848 Binary files /dev/null and b/images/habitat_compact.png differ diff --git a/index.qmd b/index.qmd new file mode 100644 index 0000000..1f96dad --- /dev/null +++ b/index.qmd @@ -0,0 +1,468 @@ +--- +title: "Quarto Presentations" +subtitle: "An interactive slide **template** for Habitat
build with Quarto and Reveal.js" +authors: "" +# add emoji extension +from: markdown+emoji +format: + revealjs: + theme: [moon, styles.scss] + slide-number: false + chalkboard: + buttons: false + preview-links: auto + logo: images/habitat_compact.png + footer: Slides adapted from the [`Quarto`](https://quarto.org/docs/presentations/revealjs/) example +--- + +## :wave: Hello, There + +This presentation will show you examples of what you can do with Quarto and [Reveal.js](https://revealjs.com), including: + +- Presenting code and LaTeX equations +- Including computations in slide output +- Image, video, and iframe backgrounds +- Fancy transitions and animations + +...and much more + +## Pretty Code {auto-animate="true"} + +- Over 20 syntax highlighting themes available +- Default theme optimized for accessibility + +``` r +# Define a server for the Shiny app +function(input, output) { + + # Fill in the spot we created for a plot + output$phonePlot <- renderPlot({ + # Render a barplot + }) +} +``` + +::: footer +Learn more: [Syntax Highlighting](https://quarto.org/docs/output-formats/html-code.html#highlighting) +::: + +## Code Animations {auto-animate="true"} + +- Over 20 syntax highlighting themes available +- Default theme optimized for accessibility + +``` r +# Define a server for the Shiny app +function(input, output) { + + # Fill in the spot we created for a plot + output$phonePlot <- renderPlot({ + # Render a barplot + barplot(WorldPhones[,input$region]*1000, + main=input$region, + ylab="Number of Telephones", + xlab="Year") + }) +} +``` + +::: footer +Learn more: [Code Animations](https://quarto.org/docs/presentations/revealjs/advanced.html#code-animations) +::: + +## Line Highlighting + +- Highlight specific lines for emphasis +- Incrementally highlight additional lines + +``` {.python code-line-numbers="4-5|7|10"} +import numpy as np +import matplotlib.pyplot as plt + +r = np.arange(0, 2, 0.01) +theta = 2 * np.pi * r +fig, ax = plt.subplots(subplot_kw={'projection': 'polar'}) +ax.plot(theta, r) +ax.set_rticks([0.5, 1, 1.5, 2]) +ax.grid(True) +plt.show() +``` + +::: footer +Learn more: [Line Highlighting](https://quarto.org/docs/presentations/revealjs/#line-highlighting) +::: + +## Executable Code + +```{r} +#| echo: true +#| fig-width: 10 +#| fig-height: 4.5 +library(ggplot2) +ggplot(mtcars, aes(hp, mpg, color = am)) + + geom_point() + + geom_smooth(formula = y ~ x, method = "loess") +``` + +::: footer +Learn more: [Executable Code](https://quarto.org/docs/presentations/revealjs/#executable-code) +::: + +## LaTeX Equations + +[MathJax](https://www.mathjax.org/) rendering of equations to HTML + +::: columns +::: {.column width="40%"} +``` tex +\begin{gather*} +a_1=b_1+c_1\\ +a_2=b_2+c_2-d_2+e_2 +\end{gather*} + +\begin{align} +a_{11}& =b_{11}& + a_{12}& =b_{12}\\ +a_{21}& =b_{21}& + a_{22}& =b_{22}+c_{22} +\end{align} +``` +::: + +::: {.column width="60%"} +```{=tex} +\begin{gather*} +a_1=b_1+c_1\\ +a_2=b_2+c_2-d_2+e_2 +\end{gather*} +``` +```{=tex} +\begin{align} +a_{11}& =b_{11}& + a_{12}& =b_{12}\\ +a_{21}& =b_{21}& + a_{22}& =b_{22}+c_{22} +\end{align} +``` +::: +::: + +::: footer +Learn more: [LaTeX Equations](https://quarto.org/docs/authoring/markdown-basics.html#equations) +::: + +## Column Layout {.smaller} + +Arrange content into columns of varying widths: + +::: columns +::: {.column width="35%"} +#### Motor Trend Car Road Tests + +The data was extracted from the 1974 Motor Trend US magazine, and comprises fuel consumption and 10 aspects of automobile design and performance for 32 automobiles. +::: + +::: {.column width="3%"} +::: + +::: {.column width="62%"} +```{r} +knitr::kable(head(mtcars)[,c("mpg", "cyl", "disp", "hp", "wt")]) +``` +::: +::: + +::: footer +Learn more: [Multiple Columns](https://quarto.org/docs/presentations/revealjs/#multiple-columns) +::: + +## Incremental Lists + +Lists can optionally be displayed incrementally: + +::: incremental +- First item +- Second item +- Third item +::: + +. . . + +
Insert pauses to make other types of content display incrementally. + +::: footer +Learn more: [Incremental Lists](https://quarto.org/docs/presentations/revealjs/#incremental-lists) +::: + +## Fragments + +Incremental text display and animation with fragments: + +
+ +::: {.fragment .fade-in} +Fade in +::: + +::: {.fragment .fade-up} +Slide up while fading in +::: + +::: {.fragment .fade-left} +Slide left while fading in +::: + +::: {.fragment .fade-in-then-semi-out} +Fade in then semi out +::: + +. . . + +::: {.fragment .strike} +Strike +::: + +::: {.fragment .highlight-red} +Highlight red +::: + +::: footer +Learn more: [Fragments](https://quarto.org/docs/presentations/revealjs/advanced.html#fragments) +::: + +## Slide Backgrounds {background="#43464B"} + +Set the `background` attribute on a slide to change the background color (all CSS color formats are supported). + +Different background transitions are available via the `background-transition` option. + +::: footer +Learn more: [Slide Backgrounds](https://quarto.org/docs/presentations/revealjs/#color-backgrounds) +::: + +## Media Backgrounds {background="#43464B" background-image="https://raw.githubusercontent.com/quarto-dev/quarto-web/main/docs/presentations/revealjs/demo/images/milky-way.jpeg"} + +You can also use the following as a slide background: + +- An image: `background-image` + +- A video: `background-video` + +- An iframe: `background-iframe` + +::: footer +Learn more: [Media Backgrounds](https://quarto.org/docs/presentations/revealjs/#image-backgrounds) +::: + +## Absolute Position + +Position images or other elements at precise locations + +![](https://raw.githubusercontent.com/quarto-dev/quarto-web/main/docs/presentations/revealjs/demo/mini/images/kitten-400-350.jpeg){.absolute top="170" left="30" width="400" height="400"} + +![](https://raw.githubusercontent.com/quarto-dev/quarto-web/main/docs/presentations/revealjs/demo/mini/images/kitten-450-250.jpeg){.absolute .fragment top="150" right="80" width="450"} + +![](https://raw.githubusercontent.com/quarto-dev/quarto-web/main/docs/presentations/revealjs/demo/mini/images/kitten-300-200.jpeg){.absolute .fragment bottom="110" right="130" width="300"} + +::: footer +Learn more: [Absolute Position](https://quarto.org/docs/presentations/revealjs/advanced.html#absolute-position) +::: + +## Auto-Animate {auto-animate="true" auto-animate-easing="ease-in-out"} + +Automatically animate matching elements across slides with Auto-Animate. + +::: r-hstack +::: {data-id="box1" auto-animate-delay="0" style="background: #2780e3; width: 200px; height: 150px; margin: 10px;"} +::: + +::: {data-id="box2" auto-animate-delay="0.1" style="background: #3fb618; width: 200px; height: 150px; margin: 10px;"} +::: + +::: {data-id="box3" auto-animate-delay="0.2" style="background: #e83e8c; width: 200px; height: 150px; margin: 10px;"} +::: +::: + +::: footer +Learn more: [Auto-Animate](https://quarto.org/docs/presentations/revealjs/advanced.html#auto-animate) +::: + +## Auto-Animate {auto-animate="true" auto-animate-easing="ease-in-out"} + +Automatically animate matching elements across slides with Auto-Animate. + +::: r-stack +::: {data-id="box1" style="background: #2780e3; width: 350px; height: 350px; border-radius: 200px;"} +::: + +::: {data-id="box2" style="background: #3fb618; width: 250px; height: 250px; border-radius: 200px;"} +::: + +::: {data-id="box3" style="background: #e83e8c; width: 150px; height: 150px; border-radius: 200px;"} +::: +::: + +::: footer +Learn more: [Auto-Animate](https://quarto.org/docs/presentations/revealjs/advanced.html#auto-animate) +::: + +## Slide Transitions {.smaller} + +The next few slides will transition using the `slide` transition + +| Transition | Description | +|------------|------------------------------------------------------------------------| +| `none` | No transition (default, switch instantly) | +| `fade` | Cross fade | +| `slide` | Slide horizontally | +| `convex` | Slide at a convex angle | +| `concave` | Slide at a concave angle | +| `zoom` | Scale the incoming slide so it grows in from the center of the screen. | + +::: footer +Learn more: [Slide Transitions](https://quarto.org/docs/presentations/revealjs/advanced.html#slide-transitions) +::: + +## Tabsets {.smaller .scrollable transition="slide"} + +::: panel-tabset +### Plot + +```{r} +library(ggplot2) +ggplot(mtcars, aes(hp, mpg, color = am)) + + geom_point() + + geom_smooth(formula = y ~ x, method = "loess") +``` + +### Data + +```{r} +knitr::kable(mtcars) +``` +::: + +::: footer +Learn more: [Tabsets](https://quarto.org/docs/presentations/revealjs/#tabsets) +::: + +## Preview Links + +Navigate to hyperlinks without disrupting the flow of your presentation. + +Use the `preview-links` option to open links in an iframe on top of your slides. Try clicking the link below for a demonstration: + +::: {style="text-align: center; margin-top: 1em"} +[Matplotlib: Visualization with Python](https://matplotlib.org/){preview-link="true" style="text-align: center"} +::: + +::: footer +Learn more: [Preview Links](https://quarto.org/docs/presentations/revealjs/presenting.html#preview-links) +::: + +## Themes + +10 Built-in Themes (or [create your own](https://quarto.org/docs/presentations/revealjs/themes.html#creating-themes)) + +::: {layout-ncol="2"} +![](https://raw.githubusercontent.com/quarto-dev/quarto-web/main/docs/presentations/revealjs/demo/images/moon.png) + +![](https://raw.githubusercontent.com/quarto-dev/quarto-web/main/docs/presentations/revealjs/demo/images/sky.png) +::: + +::: footer +Learn more: [Themes](https://quarto.org/docs/presentations/revealjs/themes.html) +::: + +## Easy Navigation + +::: {style="margin-bottom: 0.9em;"} +Quickly jump to other parts of your presentation +::: + +::: {layout="[1, 20]"} +![](https://raw.githubusercontent.com/quarto-dev/quarto-web/main/docs/presentations/revealjs/demo/images/presentation-menu.png){width="41"} + +Toggle the slide menu with the menu button (bottom left of slide) to go to other slides and access presentation tools. +::: + +You can also press `m` to toggle the menu open and closed. + +::: footer +Learn more: [Navigation](https://quarto.org/docs/presentations/revealjs/presenting.html#navigation-menu) +::: + +## Chalkboard {chalkboard-buttons="true"} + +::: {style="margin-bottom: 0.9em;"} +Free form drawing and slide annotations +::: + +::: {layout="[1, 20]"} +![](https://raw.githubusercontent.com/quarto-dev/quarto-web/main/docs/presentations/revealjs/demo/images/presentation-chalkboard.png){width="41"} + +Use the chalkboard button at the bottom left of the slide to toggle the chalkboard. +::: + +::: {layout="[1, 20]"} +![](https://raw.githubusercontent.com/quarto-dev/quarto-web/main/docs/presentations/revealjs/demo/images/presentation-notes-canvas.png){width="41"} + +Use the notes canvas button at the bottom left of the slide to toggle drawing on top of the current slide. +::: + +You can also press `b` to toggle the chalkboard or `c` to toggle the notes canvas. + +::: footer +Learn more: [Chalkboard](https://quarto.org/docs/presentations/revealjs/presenting.html#chalkboard) +::: + +## Point of View + +Press `o` to toggle overview mode: + +![](https://raw.githubusercontent.com/quarto-dev/quarto-web/main/docs/presentations/revealjs/images/overview-mode.png){.border} + +Hold down the `Alt` key (or `Ctrl` in Linux) and click on any element to zoom towards it---try it now on this slide. + +::: footer +Learn more: [Overview Mode](https://quarto.org/docs/presentations/revealjs/presenting.html#overview-mode), [Slide Zoom](https://quarto.org/docs/presentations/revealjs/presenting.html#slide-zoom) +::: + +## Speaker View + +Press `s` (or use the presentation menu) to open speaker view + +![](https://raw.githubusercontent.com/quarto-dev/quarto-web/main/docs/presentations/revealjs/images/speaker-view.png){fig-align="center" style="border: 3px solid #dee2e6;" width="780"} + +::: footer +Learn more: [Speaker View](https://quarto.org/docs/presentations/revealjs/presenting.html#speaker-view) +::: + +## Authoring Tools {.smaller} + +Live side-by-side preview for any notebook or text editor including Jupyter and VS Code + +::: columns +::: {.column width="50%"} +![](https://raw.githubusercontent.com/quarto-dev/quarto-web/main/docs/presentations/revealjs/demo/images/jupyter-edit.png){.border .border-thick} +::: + +::: {.column width="50%"} +![](https://raw.githubusercontent.com/quarto-dev/quarto-web/main/docs/manuscripts/authoring/images/jupyter-preview.png){.border .border-thick} +::: +::: + +::: footer +Learn more: [Jupyter](https://quarto.org/docs/tools/jupyter-lab.html), [VS Code](https://quarto.org/docs/tools/vscode.html), [Text Editors](https://quarto.org/docs/tools/text-editors.html) +::: + +## And More... + +- [Touch](https://quarto.org/docs/presentations/revealjs/advanced.html#touch-navigation) optimized (presentations look great on mobile, swipe to navigate slides) +- [Footer & Logo](https://quarto.org/docs/presentations/revealjs/#footer-logo) (optionally specify custom footer per-slide) +- [Auto-Slide](https://quarto.org/docs/presentations/revealjs/presenting.html#auto-slide) (step through slides automatically, without any user input) +- [Multiplex](https://quarto.org/docs/presentations/revealjs/presenting.html#multiplex) (allows your audience to follow the slides of the presentation you are controlling on their own phone, tablet or laptop). + +::: footer +Learn more: [Quarto Presentations](https://quarto.org/docs/presentations/revealjs/) +::: \ No newline at end of file diff --git a/renv.lock b/renv.lock new file mode 100644 index 0000000..28e56cb --- /dev/null +++ b/renv.lock @@ -0,0 +1,650 @@ +{ + "R": { + "Version": "4.3.2", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://cran.case.edu" + } + ] + }, + "Packages": { + "MASS": { + "Package": "MASS", + "Version": "7.3-60", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics", + "methods", + "stats", + "utils" + ], + "Hash": "a56a6365b3fa73293ea8d084be0d9bb0" + }, + "Matrix": { + "Package": "Matrix", + "Version": "1.6-1.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics", + "grid", + "lattice", + "methods", + "stats", + "utils" + ], + "Hash": "1a00d4828f33a9d690806e98bd17150c" + }, + "R6": { + "Package": "R6", + "Version": "2.5.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "470851b6d5d0ac559e9d01bb352b4021" + }, + "RColorBrewer": { + "Package": "RColorBrewer", + "Version": "1.1-3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "45f0398006e83a5b10b72a90663d8d8c" + }, + "base64enc": { + "Package": "base64enc", + "Version": "0.1-3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "543776ae6848fde2f48ff3816d0628bc" + }, + "bslib": { + "Package": "bslib", + "Version": "0.7.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "base64enc", + "cachem", + "fastmap", + "grDevices", + "htmltools", + "jquerylib", + "jsonlite", + "lifecycle", + "memoise", + "mime", + "rlang", + "sass" + ], + "Hash": "8644cc53f43828f19133548195d7e59e" + }, + "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" + }, + "colorspace": { + "Package": "colorspace", + "Version": "2.1-0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics", + "methods", + "stats" + ], + "Hash": "f20c47fd52fae58b4e377c37bb8c335b" + }, + "digest": { + "Package": "digest", + "Version": "0.6.35", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "utils" + ], + "Hash": "698ece7ba5a4fa4559e3d537e7ec3d31" + }, + "evaluate": { + "Package": "evaluate", + "Version": "0.23", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "methods" + ], + "Hash": "daf4a1246be12c1fa8c7705a0935c1a0" + }, + "fansi": { + "Package": "fansi", + "Version": "1.0.6", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "utils" + ], + "Hash": "962174cf2aeb5b9eea581522286a911f" + }, + "farver": { + "Package": "farver", + "Version": "2.1.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "8106d78941f34855c440ddb946b8f7a5" + }, + "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" + }, + "ggplot2": { + "Package": "ggplot2", + "Version": "3.5.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "MASS", + "R", + "cli", + "glue", + "grDevices", + "grid", + "gtable", + "isoband", + "lifecycle", + "mgcv", + "rlang", + "scales", + "stats", + "tibble", + "vctrs", + "withr" + ], + "Hash": "52ef83f93f74833007f193b2d4c159a2" + }, + "glue": { + "Package": "glue", + "Version": "1.7.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "methods" + ], + "Hash": "e0b3a53876554bd45879e596cdb10a52" + }, + "gtable": { + "Package": "gtable", + "Version": "0.3.4", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cli", + "glue", + "grid", + "lifecycle", + "rlang" + ], + "Hash": "b29cf3031f49b04ab9c852c912547eef" + }, + "highr": { + "Package": "highr", + "Version": "0.10", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "xfun" + ], + "Hash": "06230136b2d2b9ba5805e1963fa6e890" + }, + "htmltools": { + "Package": "htmltools", + "Version": "0.5.8.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "base64enc", + "digest", + "fastmap", + "grDevices", + "rlang", + "utils" + ], + "Hash": "81d371a9cc60640e74e4ab6ac46dcedc" + }, + "isoband": { + "Package": "isoband", + "Version": "0.2.7", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "grid", + "utils" + ], + "Hash": "0080607b4a1a7b28979aecef976d8bc2" + }, + "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": "1.46", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "evaluate", + "highr", + "methods", + "tools", + "xfun", + "yaml" + ], + "Hash": "6e008ab1d696a5283c79765fa7b56b47" + }, + "labeling": { + "Package": "labeling", + "Version": "0.4.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "graphics", + "stats" + ], + "Hash": "b64ec208ac5bc1852b285f665d6368b3" + }, + "lattice": { + "Package": "lattice", + "Version": "0.21-9", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics", + "grid", + "stats", + "utils" + ], + "Hash": "5558c61e0136e247252f5f952cdaad6a" + }, + "lifecycle": { + "Package": "lifecycle", + "Version": "1.0.4", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cli", + "glue", + "rlang" + ], + "Hash": "b8552d117e1b808b09a832f589b79035" + }, + "magrittr": { + "Package": "magrittr", + "Version": "2.0.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "7ce2733a9826b3aeb1775d56fd305472" + }, + "memoise": { + "Package": "memoise", + "Version": "2.0.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "cachem", + "rlang" + ], + "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c" + }, + "mgcv": { + "Package": "mgcv", + "Version": "1.9-0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "Matrix", + "R", + "graphics", + "methods", + "nlme", + "splines", + "stats", + "utils" + ], + "Hash": "086028ca0460d0c368028d3bda58f31b" + }, + "mime": { + "Package": "mime", + "Version": "0.12", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "tools" + ], + "Hash": "18e9c28c1d3ca1560ce30658b22ce104" + }, + "munsell": { + "Package": "munsell", + "Version": "0.5.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "colorspace", + "methods" + ], + "Hash": "4fd8900853b746af55b81fda99da7695" + }, + "nlme": { + "Package": "nlme", + "Version": "3.1-163", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "graphics", + "lattice", + "stats", + "utils" + ], + "Hash": "8d1938040a05566f4f7a14af4feadd6b" + }, + "pillar": { + "Package": "pillar", + "Version": "1.9.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "cli", + "fansi", + "glue", + "lifecycle", + "rlang", + "utf8", + "utils", + "vctrs" + ], + "Hash": "15da5a8412f317beeee6175fbc76f4bb" + }, + "pkgconfig": { + "Package": "pkgconfig", + "Version": "2.0.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "utils" + ], + "Hash": "01f28d4278f15c76cddbea05899c5d6f" + }, + "rappdirs": { + "Package": "rappdirs", + "Version": "0.3.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "5e3c5dc0b071b21fa128676560dbe94d" + }, + "renv": { + "Package": "renv", + "Version": "1.0.7", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "utils" + ], + "Hash": "397b7b2a265bc5a7a06852524dabae20" + }, + "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" + }, + "scales": { + "Package": "scales", + "Version": "1.3.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "R6", + "RColorBrewer", + "cli", + "farver", + "glue", + "labeling", + "lifecycle", + "munsell", + "rlang", + "viridisLite" + ], + "Hash": "c19df082ba346b0ffa6f833e92de34d1" + }, + "tibble": { + "Package": "tibble", + "Version": "3.2.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "fansi", + "lifecycle", + "magrittr", + "methods", + "pillar", + "pkgconfig", + "rlang", + "utils", + "vctrs" + ], + "Hash": "a84e2cc86d07289b3b6f5069df7a004c" + }, + "tinytex": { + "Package": "tinytex", + "Version": "0.50", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "xfun" + ], + "Hash": "be7a76845222ad20adb761f462eed3ea" + }, + "utf8": { + "Package": "utf8", + "Version": "1.2.4", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "62b65c52671e6665f803ff02954446e9" + }, + "vctrs": { + "Package": "vctrs", + "Version": "0.6.5", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cli", + "glue", + "lifecycle", + "rlang" + ], + "Hash": "c03fa420630029418f7e6da3667aac4a" + }, + "viridisLite": { + "Package": "viridisLite", + "Version": "0.4.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "c826c7c4241b6fc89ff55aaea3fa7491" + }, + "withr": { + "Package": "withr", + "Version": "3.0.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics" + ], + "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35" + }, + "xfun": { + "Package": "xfun", + "Version": "0.43", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "grDevices", + "stats", + "tools" + ], + "Hash": "ab6371d8653ce5f2f9290f4ec7b42a8e" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.8", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "29240487a071f535f5e5d5a323b7afbd" + } + } +} diff --git a/renv/.gitignore b/renv/.gitignore new file mode 100644 index 0000000..0ec0cbb --- /dev/null +++ b/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/renv/activate.R b/renv/activate.R new file mode 100644 index 0000000..d13f993 --- /dev/null +++ b/renv/activate.R @@ -0,0 +1,1220 @@ + +local({ + + # the requested version of renv + version <- "1.0.7" + attr(version, "sha") <- NULL + + # the project directory + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() + + # use start-up diagnostics if enabled + diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") + if (diagnostics) { + start <- Sys.time() + profile <- tempfile("renv-startup-", fileext = ".Rprof") + utils::Rprof(profile) + on.exit({ + utils::Rprof(NULL) + elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) + writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) + writeLines(sprintf("- Profile: %s", profile)) + print(utils::summaryRprof(profile)) + }, add = TRUE) + } + + # figure out whether the autoloader is enabled + enabled <- local({ + + # first, check config option + override <- getOption("renv.config.autoloader.enabled") + if (!is.null(override)) + return(override) + + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + + # next, check environment variables + # TODO: prefer using the configuration one in the future + envvars <- c( + "RENV_CONFIG_AUTOLOADER_ENABLED", + "RENV_AUTOLOADER_ENABLED", + "RENV_ACTIVATE_PROJECT" + ) + + for (envvar in envvars) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(tolower(envval) %in% c("true", "t", "1")) + } + + # enable by default + TRUE + + }) + + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + + return(FALSE) + + } + + # avoid recursion + if (identical(getOption("renv.autoloader.running"), TRUE)) { + warning("ignoring recursive attempt to run renv autoloader") + return(invisible(TRUE)) + } + + # signal that we're loading renv during R startup + options(renv.autoloader.running = TRUE) + on.exit(options(renv.autoloader.running = NULL), add = TRUE) + + # signal that we've consented to use renv + options(renv.consent = TRUE) + + # load the 'utils' package eagerly -- this ensures that renv shims, which + # mask 'utils' packages, will come first on the search path + library(utils, lib.loc = .Library) + + # unload renv if it's already been loaded + if ("renv" %in% loadedNamespaces()) + unloadNamespace("renv") + + # load bootstrap tools + `%||%` <- function(x, y) { + if (is.null(x)) y else x + } + + catf <- function(fmt, ..., appendLF = TRUE) { + + quiet <- getOption("renv.bootstrap.quiet", default = FALSE) + if (quiet) + return(invisible()) + + msg <- sprintf(fmt, ...) + cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") + + invisible(msg) + + } + + header <- function(label, + ..., + prefix = "#", + suffix = "-", + n = min(getOption("width"), 78)) + { + label <- sprintf(label, ...) + n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) + if (n <= 0) + return(paste(prefix, label)) + + tail <- paste(rep.int(suffix, n), collapse = "") + paste0(prefix, " ", label, " ", tail) + + } + + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + paste(substring(lines, common), collapse = "\n") + + } + + startswith <- function(string, prefix) { + substring(string, 1, nchar(prefix)) == prefix + } + + bootstrap <- function(version, library) { + + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + + # attempt to download renv + catf("- Downloading renv ... ", appendLF = FALSE) + withCallingHandlers( + tarball <- renv_bootstrap_download(version), + error = function(err) { + catf("FAILED") + stop("failed to download:\n", conditionMessage(err)) + } + ) + catf("OK") + on.exit(unlink(tarball), add = TRUE) + + # now attempt to install + catf("- Installing renv ... ", appendLF = FALSE) + withCallingHandlers( + status <- renv_bootstrap_install(version, tarball, library), + error = function(err) { + catf("FAILED") + stop("failed to install:\n", conditionMessage(err)) + } + ) + catf("OK") + + # add empty line to break up bootstrapping from normal output + catf("") + + return(invisible()) + } + + renv_bootstrap_tests_running <- function() { + getOption("renv.tests.running", default = FALSE) + } + + renv_bootstrap_repos <- function() { + + # get CRAN repository + cran <- getOption("renv.repos.cran", "https://cloud.r-project.org") + + # check for repos override + repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) + if (!is.na(repos)) { + + # check for RSPM; if set, use a fallback repository for renv + rspm <- Sys.getenv("RSPM", unset = NA) + if (identical(rspm, repos)) + repos <- c(RSPM = rspm, CRAN = cran) + + return(repos) + + } + + # check for lockfile repositories + repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) + if (!inherits(repos, "error") && length(repos)) + return(repos) + + # retrieve current repos + repos <- getOption("repos") + + # ensure @CRAN@ entries are resolved + repos[repos == "@CRAN@"] <- cran + + # add in renv.bootstrap.repos if set + default <- c(FALLBACK = "https://cloud.r-project.org") + extra <- getOption("renv.bootstrap.repos", default = default) + repos <- c(repos, extra) + + # remove duplicates that might've snuck in + dupes <- duplicated(repos) | duplicated(names(repos)) + repos[!dupes] + + } + + renv_bootstrap_repos_lockfile <- function() { + + lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") + if (!file.exists(lockpath)) + return(NULL) + + lockfile <- tryCatch(renv_json_read(lockpath), error = identity) + if (inherits(lockfile, "error")) { + warning(lockfile) + return(NULL) + } + + repos <- lockfile$R$Repositories + if (length(repos) == 0) + return(NULL) + + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) + vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) + names(vals) <- keys + + return(vals) + + } + + renv_bootstrap_download <- function(version) { + + sha <- attr(version, "sha", exact = TRUE) + + methods <- if (!is.null(sha)) { + + # attempting to bootstrap a development version of renv + c( + function() renv_bootstrap_download_tarball(sha), + function() renv_bootstrap_download_github(sha) + ) + + } else { + + # attempting to bootstrap a release version of renv + c( + function() renv_bootstrap_download_tarball(version), + function() renv_bootstrap_download_cran_latest(version), + function() renv_bootstrap_download_cran_archive(version) + ) + + } + + for (method in methods) { + path <- tryCatch(method(), error = identity) + if (is.character(path) && file.exists(path)) + return(path) + } + + stop("All download methods failed") + + } + + renv_bootstrap_download_impl <- function(url, destfile) { + + mode <- "wb" + + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 + fixup <- + Sys.info()[["sysname"]] == "Windows" && + substring(url, 1L, 5L) == "file:" + + if (fixup) + mode <- "w+b" + + args <- list( + url = url, + destfile = destfile, + mode = mode, + quiet = TRUE + ) + + if ("headers" %in% names(formals(utils::download.file))) + args$headers <- renv_bootstrap_download_custom_headers(url) + + do.call(utils::download.file, args) + + } + + renv_bootstrap_download_custom_headers <- function(url) { + + headers <- getOption("renv.download.headers") + if (is.null(headers)) + return(character()) + + if (!is.function(headers)) + stopf("'renv.download.headers' is not a function") + + headers <- headers(url) + if (length(headers) == 0L) + return(character()) + + if (is.list(headers)) + headers <- unlist(headers, recursive = FALSE, use.names = TRUE) + + ok <- + is.character(headers) && + is.character(names(headers)) && + all(nzchar(names(headers))) + + if (!ok) + stop("invocation of 'renv.download.headers' did not return a named character vector") + + headers + + } + + renv_bootstrap_download_cran_latest <- function(version) { + + spec <- renv_bootstrap_download_cran_latest_find(version) + type <- spec$type + repos <- spec$repos + + baseurl <- utils::contrib.url(repos = repos, type = type) + ext <- if (identical(type, "source")) + ".tar.gz" + else if (Sys.info()[["sysname"]] == "Windows") + ".zip" + else + ".tgz" + name <- sprintf("renv_%s%s", version, ext) + url <- paste(baseurl, name, sep = "/") + + destfile <- file.path(tempdir(), name) + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (inherits(status, "condition")) + return(FALSE) + + # report success and return + destfile + + } + + renv_bootstrap_download_cran_latest_find <- function(version) { + + # check whether binaries are supported on this system + binary <- + getOption("renv.bootstrap.binary", default = TRUE) && + !identical(.Platform$pkgType, "source") && + !identical(getOption("pkgType"), "source") && + Sys.info()[["sysname"]] %in% c("Darwin", "Windows") + + types <- c(if (binary) "binary", "source") + + # iterate over types + repositories + for (type in types) { + for (repos in renv_bootstrap_repos()) { + + # retrieve package database + db <- tryCatch( + as.data.frame( + utils::available.packages(type = type, repos = repos), + stringsAsFactors = FALSE + ), + error = identity + ) + + if (inherits(db, "error")) + next + + # check for compatible entry + entry <- db[db$Package %in% "renv" & db$Version %in% version, ] + if (nrow(entry) == 0) + next + + # found it; return spec to caller + spec <- list(entry = entry, type = type, repos = repos) + return(spec) + + } + } + + # if we got here, we failed to find renv + fmt <- "renv %s is not available from your declared package repositories" + stop(sprintf(fmt, version)) + + } + + renv_bootstrap_download_cran_archive <- function(version) { + + name <- sprintf("renv_%s.tar.gz", version) + repos <- renv_bootstrap_repos() + urls <- file.path(repos, "src/contrib/Archive/renv", name) + destfile <- file.path(tempdir(), name) + + for (url in urls) { + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (identical(status, 0L)) + return(destfile) + + } + + return(FALSE) + + } + + renv_bootstrap_download_tarball <- function(version) { + + # if the user has provided the path to a tarball via + # an environment variable, then use it + tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) + if (is.na(tarball)) + return() + + # allow directories + if (dir.exists(tarball)) { + name <- sprintf("renv_%s.tar.gz", version) + tarball <- file.path(tarball, name) + } + + # bail if it doesn't exist + if (!file.exists(tarball)) { + + # let the user know we weren't able to honour their request + fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." + msg <- sprintf(fmt, tarball) + warning(msg) + + # bail + return() + + } + + catf("- Using local tarball '%s'.", tarball) + tarball + + } + + renv_bootstrap_download_github <- function(version) { + + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") + if (!identical(enabled, "TRUE")) + return(FALSE) + + # prepare download options + pat <- Sys.getenv("GITHUB_PAT") + if (nzchar(Sys.which("curl")) && nzchar(pat)) { + fmt <- "--location --fail --header \"Authorization: token %s\"" + extra <- sprintf(fmt, pat) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "curl", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } else if (nzchar(Sys.which("wget")) && nzchar(pat)) { + fmt <- "--header=\"Authorization: token %s\"" + extra <- sprintf(fmt, pat) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "wget", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } + + url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) + name <- sprintf("renv_%s.tar.gz", version) + destfile <- file.path(tempdir(), name) + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (!identical(status, 0L)) + return(FALSE) + + renv_bootstrap_download_augment(destfile) + + return(destfile) + + } + + # Add Sha to DESCRIPTION. This is stop gap until #890, after which we + # can use renv::install() to fully capture metadata. + renv_bootstrap_download_augment <- function(destfile) { + sha <- renv_bootstrap_git_extract_sha1_tar(destfile) + if (is.null(sha)) { + return() + } + + # Untar + tempdir <- tempfile("renv-github-") + on.exit(unlink(tempdir, recursive = TRUE), add = TRUE) + untar(destfile, exdir = tempdir) + pkgdir <- dir(tempdir, full.names = TRUE)[[1]] + + # Modify description + desc_path <- file.path(pkgdir, "DESCRIPTION") + desc_lines <- readLines(desc_path) + remotes_fields <- c( + "RemoteType: github", + "RemoteHost: api.github.com", + "RemoteRepo: renv", + "RemoteUsername: rstudio", + "RemotePkgRef: rstudio/renv", + paste("RemoteRef: ", sha), + paste("RemoteSha: ", sha) + ) + writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path) + + # Re-tar + local({ + old <- setwd(tempdir) + on.exit(setwd(old), add = TRUE) + + tar(destfile, compression = "gzip") + }) + invisible() + } + + # Extract the commit hash from a git archive. Git archives include the SHA1 + # hash as the comment field of the tarball pax extended header + # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html) + # For GitHub archives this should be the first header after the default one + # (512 byte) header. + renv_bootstrap_git_extract_sha1_tar <- function(bundle) { + + # open the bundle for reading + # We use gzcon for everything because (from ?gzcon) + # > Reading from a connection which does not supply a 'gzip' magic + # > header is equivalent to reading from the original connection + conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) + on.exit(close(conn)) + + # The default pax header is 512 bytes long and the first pax extended header + # with the comment should be 51 bytes long + # `52 comment=` (11 chars) + 40 byte SHA1 hash + len <- 0x200 + 0x33 + res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len]) + + if (grepl("^52 comment=", res)) { + sub("52 comment=", "", res) + } else { + NULL + } + } + + renv_bootstrap_install <- function(version, tarball, library) { + + # attempt to install it into project library + dir.create(library, showWarnings = FALSE, recursive = TRUE) + output <- renv_bootstrap_install_impl(library, tarball) + + # check for successful install + status <- attr(output, "status") + if (is.null(status) || identical(status, 0L)) + return(status) + + # an error occurred; report it + header <- "installation of renv failed" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- paste(c(header, lines, output), collapse = "\n") + stop(text) + + } + + renv_bootstrap_install_impl <- function(library, tarball) { + + # invoke using system2 so we can capture and report output + bin <- R.home("bin") + exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" + R <- file.path(bin, exe) + + args <- c( + "--vanilla", "CMD", "INSTALL", "--no-multiarch", + "-l", shQuote(path.expand(library)), + shQuote(path.expand(tarball)) + ) + + system2(R, args, stdout = TRUE, stderr = TRUE) + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- paste(R.version$major, R.version$minor, sep = ".") + prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") + + # include SVN revision for development versions of R + # (to avoid sharing platform-specific artefacts with released versions of R) + devel <- + identical(R.version[["status"]], "Under development (unstable)") || + identical(R.version[["nickname"]], "Unsuffered Consequences") + + if (devel) + prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") + + # build list of path components + components <- c(prefix, R.version$platform) + + # include prefix if provided by user + prefix <- renv_bootstrap_platform_prefix_impl() + if (!is.na(prefix) && nzchar(prefix)) + components <- c(prefix, components) + + # build prefix + paste(components, collapse = "/") + + } + + renv_bootstrap_platform_prefix_impl <- function() { + + # if an explicit prefix has been supplied, use it + prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) + if (!is.na(prefix)) + return(prefix) + + # if the user has requested an automatic prefix, generate it + auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + + if (auto %in% c("TRUE", "True", "true", "1")) + return(renv_bootstrap_platform_prefix_auto()) + + # empty string on failure + "" + + } + + renv_bootstrap_platform_prefix_auto <- function() { + + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) + if (inherits(prefix, "error") || prefix %in% "unknown") { + + msg <- paste( + "failed to infer current operating system", + "please file a bug report at https://github.com/rstudio/renv/issues", + sep = "; " + ) + + warning(msg) + + } + + prefix + + } + + renv_bootstrap_platform_os <- function() { + + sysinfo <- Sys.info() + sysname <- sysinfo[["sysname"]] + + # handle Windows + macOS up front + if (sysname == "Windows") + return("windows") + else if (sysname == "Darwin") + return("macos") + + # check for os-release files + for (file in c("/etc/os-release", "/usr/lib/os-release")) + if (file.exists(file)) + return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) + + # check for redhat-release files + if (file.exists("/etc/redhat-release")) + return(renv_bootstrap_platform_os_via_redhat_release()) + + "unknown" + + } + + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { + + # read /etc/os-release + release <- utils::read.table( + file = file, + sep = "=", + quote = c("\"", "'"), + col.names = c("Key", "Value"), + comment.char = "#", + stringsAsFactors = FALSE + ) + + vars <- as.list(release$Value) + names(vars) <- release$Key + + # get os name + os <- tolower(sysinfo[["sysname"]]) + + # read id + id <- "unknown" + for (field in c("ID", "ID_LIKE")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + id <- vars[[field]] + break + } + } + + # read version + version <- "unknown" + for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + version <- vars[[field]] + break + } + } + + # join together + paste(c(os, id, version), collapse = "-") + + } + + renv_bootstrap_platform_os_via_redhat_release <- function() { + + # read /etc/redhat-release + contents <- readLines("/etc/redhat-release", warn = FALSE) + + # infer id + id <- if (grepl("centos", contents, ignore.case = TRUE)) + "centos" + else if (grepl("redhat", contents, ignore.case = TRUE)) + "redhat" + else + "unknown" + + # try to find a version component (very hacky) + version <- "unknown" + + parts <- strsplit(contents, "[[:space:]]")[[1L]] + for (part in parts) { + + nv <- tryCatch(numeric_version(part), error = identity) + if (inherits(nv, "error")) + next + + version <- nv[1, 1] + break + + } + + paste(c("linux", id, version), collapse = "-") + + } + + renv_bootstrap_library_root_name <- function(project) { + + # use project name as-is if requested + asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") + if (asis) + return(basename(project)) + + # otherwise, disambiguate based on project's path + id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) + paste(basename(project), id, sep = "-") + + } + + renv_bootstrap_library_root <- function(project) { + + prefix <- renv_bootstrap_profile_prefix() + + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) + if (!is.na(path)) + return(paste(c(path, prefix), collapse = "/")) + + path <- renv_bootstrap_library_root_impl(project) + if (!is.null(path)) { + name <- renv_bootstrap_library_root_name(project) + return(paste(c(path, prefix, name), collapse = "/")) + } + + renv_bootstrap_paths_renv("library", project = project) + + } + + renv_bootstrap_library_root_impl <- function(project) { + + root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) + if (!is.na(root)) + return(root) + + type <- renv_bootstrap_project_type(project) + if (identical(type, "package")) { + userdir <- renv_bootstrap_user_dir() + return(file.path(userdir, "library")) + } + + } + + renv_bootstrap_validate_version <- function(version, description = NULL) { + + # resolve description file + # + # avoid passing lib.loc to `packageDescription()` below, since R will + # use the loaded version of the package by default anyhow. note that + # this function should only be called after 'renv' is loaded + # https://github.com/rstudio/renv/issues/1625 + description <- description %||% packageDescription("renv") + + # check whether requested version 'version' matches loaded version of renv + sha <- attr(version, "sha", exact = TRUE) + valid <- if (!is.null(sha)) + renv_bootstrap_validate_version_dev(sha, description) + else + renv_bootstrap_validate_version_release(version, description) + + if (valid) + return(TRUE) + + # the loaded version of renv doesn't match the requested version; + # give the user instructions on how to proceed + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) + paste("rstudio/renv", description[["RemoteSha"]], sep = "@") + else + paste("renv", description[["Version"]], sep = "@") + + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = if (dev) description[["RemoteSha"]] + ) + + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") + catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) + + FALSE + + } + + renv_bootstrap_validate_version_dev <- function(version, description) { + expected <- description[["RemoteSha"]] + is.character(expected) && startswith(expected, version) + } + + renv_bootstrap_validate_version_release <- function(version, description) { + expected <- description[["Version"]] + is.character(expected) && identical(expected, version) + } + + renv_bootstrap_hash_text <- function(text) { + + hashfile <- tempfile("renv-hash-") + on.exit(unlink(hashfile), add = TRUE) + + writeLines(text, con = hashfile) + tools::md5sum(hashfile) + + } + + renv_bootstrap_load <- function(project, libpath, version) { + + # try to load renv from the project library + if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) + return(FALSE) + + # warn if the version of renv loaded does not match + renv_bootstrap_validate_version(version) + + # execute renv load hooks, if any + hooks <- getHook("renv::autoload") + for (hook in hooks) + if (is.function(hook)) + tryCatch(hook(), error = warnify) + + # load the project + renv::load(project) + + TRUE + + } + + renv_bootstrap_profile_load <- function(project) { + + # if RENV_PROFILE is already set, just use that + profile <- Sys.getenv("RENV_PROFILE", unset = NA) + if (!is.na(profile) && nzchar(profile)) + return(profile) + + # check for a profile file (nothing to do if it doesn't exist) + path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) + if (!file.exists(path)) + return(NULL) + + # read the profile, and set it if it exists + contents <- readLines(path, warn = FALSE) + if (length(contents) == 0L) + return(NULL) + + # set RENV_PROFILE + profile <- contents[[1L]] + if (!profile %in% c("", "default")) + Sys.setenv(RENV_PROFILE = profile) + + profile + + } + + renv_bootstrap_profile_prefix <- function() { + profile <- renv_bootstrap_profile_get() + if (!is.null(profile)) + return(file.path("profiles", profile, "renv")) + } + + renv_bootstrap_profile_get <- function() { + profile <- Sys.getenv("RENV_PROFILE", unset = "") + renv_bootstrap_profile_normalize(profile) + } + + renv_bootstrap_profile_set <- function(profile) { + profile <- renv_bootstrap_profile_normalize(profile) + if (is.null(profile)) + Sys.unsetenv("RENV_PROFILE") + else + Sys.setenv(RENV_PROFILE = profile) + } + + renv_bootstrap_profile_normalize <- function(profile) { + + if (is.null(profile) || profile %in% c("", "default")) + return(NULL) + + profile + + } + + renv_bootstrap_path_absolute <- function(path) { + + substr(path, 1L, 1L) %in% c("~", "/", "\\") || ( + substr(path, 1L, 1L) %in% c(letters, LETTERS) && + substr(path, 2L, 3L) %in% c(":/", ":\\") + ) + + } + + renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) { + renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv") + root <- if (renv_bootstrap_path_absolute(renv)) NULL else project + prefix <- if (profile) renv_bootstrap_profile_prefix() + components <- c(root, renv, prefix, ...) + paste(components, collapse = "/") + } + + renv_bootstrap_project_type <- function(path) { + + descpath <- file.path(path, "DESCRIPTION") + if (!file.exists(descpath)) + return("unknown") + + desc <- tryCatch( + read.dcf(descpath, all = TRUE), + error = identity + ) + + if (inherits(desc, "error")) + return("unknown") + + type <- desc$Type + if (!is.null(type)) + return(tolower(type)) + + package <- desc$Package + if (!is.null(package)) + return("package") + + "unknown" + + } + + renv_bootstrap_user_dir <- function() { + dir <- renv_bootstrap_user_dir_impl() + path.expand(chartr("\\", "/", dir)) + } + + renv_bootstrap_user_dir_impl <- function() { + + # use local override if set + override <- getOption("renv.userdir.override") + if (!is.null(override)) + return(override) + + # use R_user_dir if available + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) + return(tools$R_user_dir("renv", "cache")) + + # try using our own backfill for older versions of R + envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") + for (envvar in envvars) { + root <- Sys.getenv(envvar, unset = NA) + if (!is.na(root)) + return(file.path(root, "R/renv")) + } + + # use platform-specific default fallbacks + if (Sys.info()[["sysname"]] == "Windows") + file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv") + else if (Sys.info()[["sysname"]] == "Darwin") + "~/Library/Caches/org.R-project.R/R/renv" + else + "~/.cache/R/renv" + + } + + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = "") + } + + renv_bootstrap_exec <- function(project, libpath, version) { + if (!renv_bootstrap_load(project, libpath, version)) + renv_bootstrap_run(version, libpath) + } + + renv_bootstrap_run <- function(version, libpath) { + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + return(renv::load(project = getwd())) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + + } + + renv_json_read <- function(file = NULL, text = NULL) { + + jlerr <- NULL + + # if jsonlite is loaded, use that instead + if ("jsonlite" %in% loadedNamespaces()) { + + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- tryCatch(renv_json_read_default(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + # report an error + if (!is.null(jlerr)) + stop(jlerr) + else + stop(json) + + } + + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + jsonlite::fromJSON(txt = text, simplifyVector = FALSE) + } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # find strings in the JSON + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' + locs <- gregexpr(pattern, text, perl = TRUE)[[1]] + + # if any are found, replace them with placeholders + replaced <- text + strings <- character() + replacements <- character() + + if (!identical(c(locs), -1L)) { + + # get the string values + starts <- locs + ends <- locs + attr(locs, "match.length") - 1L + strings <- substring(text, starts, ends) + + # only keep those requiring escaping + strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) + + # compute replacements + replacements <- sprintf('"\032%i\032"', seq_along(strings)) + + # replace the strings + mapply(function(string, replacement) { + replaced <<- sub(string, replacement, replaced, fixed = TRUE) + }, strings, replacements) + + } + + # transform the JSON into something the R parser understands + transformed <- replaced + transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE) + transformed <- gsub("[[{]", "list(", transformed, perl = TRUE) + transformed <- gsub("[]}]", ")", transformed, perl = TRUE) + transformed <- gsub(":", "=", transformed, fixed = TRUE) + text <- paste(transformed, collapse = "\n") + + # parse it + json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] + + # construct map between source strings, replaced strings + map <- as.character(parse(text = strings)) + names(map) <- as.character(parse(text = replacements)) + + # convert to list + map <- as.list(map) + + # remap strings in object + remapped <- renv_json_read_remap(json, map) + + # evaluate + eval(remapped, envir = baseenv()) + + } + + renv_json_read_remap <- function(json, map) { + + # fix names + if (!is.null(names(json))) { + lhs <- match(names(json), names(map), nomatch = 0L) + rhs <- match(names(map), names(json), nomatch = 0L) + names(json)[rhs] <- map[lhs] + } + + # fix values + if (is.character(json)) + return(map[[json]] %||% json) + + # handle true, false, null + if (is.name(json)) { + text <- as.character(json) + if (text == "true") + return(TRUE) + else if (text == "false") + return(FALSE) + else if (text == "null") + return(NULL) + } + + # recurse + if (is.recursive(json)) { + for (i in seq_along(json)) { + json[i] <- list(renv_json_read_remap(json[[i]], map)) + } + } + + json + + } + + # load the renv profile, if any + renv_bootstrap_profile_load(project) + + # construct path to library root + root <- renv_bootstrap_library_root(project) + + # construct library prefix for platform + prefix <- renv_bootstrap_platform_prefix() + + # construct full libpath + libpath <- file.path(root, prefix) + + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) + + invisible() + +}) diff --git a/renv/settings.json b/renv/settings.json new file mode 100644 index 0000000..ffdbb32 --- /dev/null +++ b/renv/settings.json @@ -0,0 +1,19 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.type": "implicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} diff --git a/styles.scss b/styles.scss new file mode 100644 index 0000000..5a42767 --- /dev/null +++ b/styles.scss @@ -0,0 +1,58 @@ +/*-- scss:defaults --*/ + +// Fonts +@import url('https://fonts.googleapis.com/css2?family=Work+Sans:ital,wght@0,400;0,700;1,400&display=swap'); +$work-sans: 'Work Sans', sans-serif; +$font-family-sans-serif: $work-sans !default; +$presentation-font-size-root: 36px !default; + +// Colors +$yellow: rgb(255, 200, 0); +$darkyellow: rgb(67, 64, 49); +$black: rgb(44, 50, 63); +$pastel: rgb(250, 242, 216); +$green: rgb(11, 69, 73); +$darkgreen: rgb(35, 55, 59); +$body-color: $pastel !default; +$presentation-heading-font-weight: bold !default; +$body-bg: $darkyellow !default; +$link-color: $yellow !default; +$code-block-bg: $darkgreen; +$code-color: $yellow; + +/*-- scss:rules --*/ +.reveal h1 { + color: $yellow; + font-family: $work-sans; + font-size: 115px; + text-shadow: 4px 5px 4px rgba($yellow, 0.4) !important; +} + +.quarto-title-authors { + font-size: 32px; +} + +.reveal h2 { + color: $pastel; + font-family: $work-sans; + font-size: 60px; + margin-bottom: 45px; + text-shadow: 3px 4px 3px rgba($yellow, 0.3) !important +} + +.reveal h3 { + color: $pastel; + font-family: $work-sans; +} + +.reveal .slide-logo { + max-height: 4rem !important; +} + +.right { + text-align: right !important; +} + +.center { + text-align: center !important; +}