Merge pull request #266 from pbs-assess/fix/invalid-html5

check html5 workflow

.github/workflows/R-CMD-check-HTML5.yaml

@@ -0,0 +1,44 @@
+# 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:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: HTML5 check
+
+jobs:
+  HTML5-check:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'devel'
+          http-user-agent: 'release'
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          dependencies: 'character()'
+
+      - name: Install pdflatex
+        run: sudo apt-get install texlive-latex-base texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra
+
+      - name: Install tidy
+        run: sudo apt install tidy
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: 'c("--as-cran", "--no-codoc", "--no-examples", "--no-tests", "--no-vignettes", "--no-build-vignettes", "--ignore-vignettes", "--no-install")'
+          build_args: 'c("--no-build-vignettes")'
+          error-on: '"note"'
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+          _R_CHECK_CRAN_INCOMING_: false

.github/workflows/pkgdown.yaml

@@ -38,6 +38,8 @@ jobs:
         run: |
           remotes::install_github("pbs-assess/sdmTMBextra", dependencies = TRUE)
           remotes::install_cran("cowplot")
+          remotes::install_cran("rnaturalearth")
+          remotes::install_cran("rnaturalearthdata")
         shell: Rscript {0}
 
       - name: Build site

vignettes/web_only/pretty-plots.Rmd

@@ -12,7 +12,9 @@ vignette: >
 ```{r, include = FALSE}
 sf_installed <- require("sf", quietly = TRUE)
 ggplot_installed <- require("ggplot2", quietly = TRUE)
-pkgs <- sf_installed && ggplot_installed
+rnaturalearth_installed <- require("rnaturalearth", quietly = TRUE)
+rnaturalearthdata_installed <- require("rnaturalearthdata", quietly = TRUE)
+pkgs <- sf_installed && ggplot_installed && rnaturalearth_installed && rnaturalearthdata_installed
 EVAL <- identical(Sys.getenv("NOT_CRAN"), "true") && pkgs
 knitr::opts_chunk$set(
   collapse = TRUE,
@@ -32,14 +34,14 @@ library(sdmTMB)
 First, we will download coastline data for our region. 
 We will use a medium resolution version. For applied situations on finer scales, you may want to use `scale = "large"`.
 
-```{r, eval=FALSE}
+```{r}
 map_data <- rnaturalearth::ne_countries(
   scale = "medium",
   returnclass = "sf", country = "canada")
 # Crop the polygon for plotting and efficiency:
 # st_bbox(map_data) # find the rough coordinates
 bc_coast <- suppressWarnings(suppressMessages(
-  st_crop(map_data,
+  sf::st_crop(map_data,
     c(xmin = -134, ymin = 46, xmax = -120, ymax = 57))))
 ```