[r/ci] Unbreak pkgdown CI (#2703)

* [r/ci] Unbreak `pkgdown` CI [WIP]

* feedback from paul h

.github/workflows/pkgdown.yaml

@@ -34,6 +34,23 @@ jobs:
           use-public-rspm: true
           working-directory: "apis/r"
 
+      - name: Set additional repositories (macOS)
+        if: ${{ matrix.os != 'ubuntu-latest' }}
+        run: echo 'options(repos = c("https://tiledb-inc.r-universe.dev", getOption("repos")), timeout = 300L)' | tee -a ~/.Rprofile
+
+      - name: Set additional repositories (Linux)
+        if: ${{ matrix.os == 'ubuntu-latest' }}
+        run: |
+          rversion <- paste(strsplit(as.character(getRversion()), split = '\\.')[[1L]][1:2], collapse = '.')
+          codename <-  system('. /etc/os-release; echo ${VERSION_CODENAME}', intern = TRUE)
+          repo <- "https://tiledb-inc.r-universe.dev"
+          (opt <- sprintf('options(repos = c("%s/bin/linux/%s/%s", "%s", getOption("repos")), timeout = 300L)', repo, codename, rversion, repo))
+          cat(opt, "\n", file = "~/.Rprofile", append = TRUE)
+        shell: Rscript {0}
+
+      - name: Install tiledb-r
+        run: cd apis/r && Rscript tools/install-tiledb-r.R
+
       # Run this daily to surface errors as tracked at
       # https://github.com/single-cell-data/TileDB-SOMA/issues/2052
       - name: Install dependencies

apis/r/tools/install-pkgdown-dependencies.sh

@@ -4,6 +4,8 @@ set -euo pipefail
 export R_REMOTES_NO_ERRORS_FROM_WARNINGS='true'
 Rscript -e 'install.packages(c("remotes", "pkgdown"))'
 cd apis/r
-Rscript -e 'remotes::install_deps(dependencies = TRUE)'
-Rscript -e 'remotes::install_local()'
+Rscript -e 'remotes::install_deps(dependencies = TRUE, upgrade=FALSE)'
+# Need dependencies = FALSE to avoid getting latest/sometimes-too-new r-tiledb from CRAN when we
+# really want it from our r-universe where we control the version we want:
+Rscript -e 'remotes::install_local(dependencies = FALSE)'
 cd ../..