add setup-r-dependencies (#233)

Related to insightsengineering/nestdevs-tasks#65 Switch to setup-r-dependencies. Added `hermes` for lookup-refs.
insightsengineering · Dec 12, 2024 · 5d72b38 · 5d72b38
1 parent e7eb4b4
commit 5d72b38
Show file tree

Hide file tree

Showing 13 changed files with 26 additions and 18 deletions.
diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
@@ -27,6 +27,7 @@ jobs:
     with:
       additional-env-vars: |
         NOT_CRAN=true
+      deps-installation-method: setup-r-dependencies
   bioccheck:
     name: BiocCheck 🩺
     uses: insightsengineering/r.pkg.template/.github/workflows/bioccheck.yaml@main
@@ -42,6 +43,7 @@ jobs:
     with:
       additional-env-vars: |
         NOT_CRAN=true
+      deps-installation-method: setup-r-dependencies
   linter:
     if: github.event_name != 'push'
     name: SuperLinter 🦸‍♀️
@@ -53,6 +55,7 @@ jobs:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
     with:
       auto-update: true
+      deps-installation-method: setup-r-dependencies
   gitleaks:
     name: gitleaks 💧
     uses: insightsengineering/r.pkg.template/.github/workflows/gitleaks.yaml@main

diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
@@ -41,3 +41,4 @@ jobs:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
     with:
       default-landing-page: latest-tag
+      deps-installation-method: setup-r-dependencies
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -17,6 +17,7 @@ jobs:
     with:
       skip-r-cmd-check: true
       skip-r-cmd-install: true
+      deps-installation-method: setup-r-dependencies
   docs:
     name: Pkgdown Docs 📚
     needs: release
@@ -25,12 +26,15 @@ jobs:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
     with:
       default-landing-page: latest-tag
+      deps-installation-method: setup-r-dependencies
   validation:
     name: R Package Validation report 📃
     needs: release
     uses: insightsengineering/r.pkg.template/.github/workflows/validation.yaml@main
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
+    with:
+      deps-installation-method: setup-r-dependencies
   release:
     name: Create release 🎉
     uses: insightsengineering/r.pkg.template/.github/workflows/release.yaml@main

diff --git a/man/HermesData-class.Rd b/man/HermesData-class.Rd
diff --git a/man/cbind.Rd b/man/cbind.Rd
diff --git a/man/expression_set.Rd b/man/expression_set.Rd
diff --git a/man/hermes_data.Rd b/man/hermes_data.Rd
diff --git a/man/isEmpty.Rd b/man/isEmpty.Rd
diff --git a/man/rbind.Rd b/man/rbind.Rd
diff --git a/man/rename.Rd b/man/rename.Rd
diff --git a/man/show.Rd b/man/show.Rd
diff --git a/man/summarized_experiment.Rd b/man/summarized_experiment.Rd
diff --git a/man/validate.Rd b/man/validate.Rd