From dda59c12ead412adb21ad2c2d48df70d2de0bc34 Mon Sep 17 00:00:00 2001
From: Vedha Viyash <49812166+vedhav@users.noreply.github.com>
Date: Wed, 11 Dec 2024 20:00:32 +0530
Subject: [PATCH] add setup-r-dependencies (#1297)

Related to
https://github.com/insightsengineering/nestdevs-tasks/issues/65
Switch to setup-r-dependencies.
Added `teal.modules.clinical` for lookup-refs.
---
 .github/workflows/check.yaml     | 76 +++++++++++++++++++++++++++++++
 .github/workflows/docs.yaml      | 19 ++++++++
 .github/workflows/release.yaml   | 77 ++++++++++++++++++++++++++++++++
 .github/workflows/scheduled.yaml | 23 +++++++++-
 4 files changed, 193 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index bf02a968f..ee2ebec25 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -41,6 +41,25 @@ jobs:
         checking top-level files .* NOTE
       unit-test-report-brand: >-
         https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/thumbs/teal.png
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
+        insightsengineering/nestcolor
+        insightsengineering/roxy.shinylive
   r-cmd-non-cran:
     name: R CMD Check (non-CRAN) 🧬
     uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
@@ -61,6 +80,25 @@ jobs:
         checking Rd .usage sections .* NOTE
         checking for unstated dependencies in vignettes .* NOTE
         checking top-level files .* NOTE
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
+        insightsengineering/nestcolor
+        insightsengineering/roxy.shinylive
   coverage:
     name: Coverage 📔
     uses: insightsengineering/r.pkg.template/.github/workflows/test-coverage.yaml@main
@@ -69,6 +107,25 @@ jobs:
     with:
       additional-env-vars: |
         NOT_CRAN=true
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
+        insightsengineering/nestcolor
+        insightsengineering/roxy.shinylive
   linter:
     if: github.event_name != 'push'
     name: SuperLinter 🦸‍♀️
@@ -80,6 +137,25 @@ jobs:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
     with:
       auto-update: true
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
+        insightsengineering/nestcolor
+        insightsengineering/roxy.shinylive
   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
index 57ae80042..784f18116 100644
--- a/.github/workflows/docs.yaml
+++ b/.github/workflows/docs.yaml
@@ -42,3 +42,22 @@ jobs:
     with:
       default-landing-page: latest-tag
       additional-unit-test-report-directories: unit-test-report-non-cran
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
+        insightsengineering/nestcolor
+        insightsengineering/roxy.shinylive
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
index aa3e7bb45..323ce2afd 100644
--- a/.github/workflows/release.yaml
+++ b/.github/workflows/release.yaml
@@ -16,12 +16,51 @@ jobs:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
     with:
       default-landing-page: latest-tag
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
+        insightsengineering/nestcolor
+        insightsengineering/roxy.shinylive
   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
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
+        insightsengineering/nestcolor
+        insightsengineering/roxy.shinylive
   release:
     name: Create release 🎉
     uses: insightsengineering/r.pkg.template/.github/workflows/release.yaml@main
@@ -46,6 +85,25 @@ jobs:
         checking top-level files .* NOTE
       unit-test-report-brand: >-
         https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/thumbs/teal.png
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
+        insightsengineering/nestcolor
+        insightsengineering/roxy.shinylive
   coverage:
     name: Coverage 📔
     needs: [release, docs]
@@ -55,6 +113,25 @@ jobs:
     with:
       additional-env-vars: |
         NOT_CRAN=true
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
+        insightsengineering/nestcolor
+        insightsengineering/roxy.shinylive
   wasm:
     name: Build WASM packages 🧑‍🏭
     needs: release
diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml
index fd71e5290..eb913b2ea 100644
--- a/.github/workflows/scheduled.yaml
+++ b/.github/workflows/scheduled.yaml
@@ -3,7 +3,7 @@ name: Scheduled 🕰️
 
 on:
   schedule:
-    - cron: '45 3 * * 0'
+    - cron: "45 3 * * 0"
   workflow_dispatch:
     inputs:
       chosen-workflow:
@@ -56,6 +56,23 @@ jobs:
       )
     name: revdepcheck ↩️
     uses: insightsengineering/r.pkg.template/.github/workflows/revdepcheck.yaml@main
+    with:
+      lookup-refs: |
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/tern
+        insightsengineering/rlistings
+        insightsengineering/formatters
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/teal.slice
+        insightsengineering/tern.gee
+        insightsengineering/tern.mmrm
   rhub:
     if: >
       github.event_name == 'schedule' || (
@@ -70,12 +87,14 @@ jobs:
         insightsengineering/teal.transform
         insightsengineering/tern
         insightsengineering/rlistings
+        insightsengineering/formatters
         insightsengineering/rtables
+        insightsengineering/rtables.officer
         insightsengineering/teal.code
         insightsengineering/teal.data
         insightsengineering/teal.logger
         insightsengineering/teal.reporter
-        insightsengineering/teal.slice
         insightsengineering/teal.widgets
+        insightsengineering/teal.slice
         insightsengineering/tern.gee
         insightsengineering/tern.mmrm