From a905dd3c501f6e61e80bdaee5f708e49a7d4259c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daphn=C3=A9=20Grasselly?=
 <56442075+dgrassellyb@users.noreply.github.com>
Date: Mon, 6 Nov 2023 12:44:13 +0100
Subject: [PATCH 1/2] Update common.yml

---
 .github/workflows/common.yml | 44 +++++++++++++++++++++++++-----------
 1 file changed, 31 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/common.yml b/.github/workflows/common.yml
index ed767000..7294cd56 100644
--- a/.github/workflows/common.yml
+++ b/.github/workflows/common.yml
@@ -29,41 +29,54 @@ on:
   release:
     types: [published]
 
-env:
-  # R version to use for the workflows
-  R_VERSION: "3.6"
-
 # Docs on concurrency:
 # https://docs.github.com/en/actions/using-jobs/using-concurrency
 concurrency:
   group: admiral-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
+env:
+  R_VERSION: "4.1"
+  
 jobs:
+  get_r_version:
+    name: Get R version
+    runs-on: ubuntu-latest
+    outputs:
+      r-version: ${{ steps.get_r_version.outputs.R_VERSION }}
+    steps:
+      - name: Get R Version for Downstream Container Jobs
+        id: get_r_version
+        run: echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT
+        shell: bash
   style:
     name: Code Style
     uses: pharmaverse/admiralci/.github/workflows/style.yml@main
     if: github.event_name == 'pull_request'
+    needs: get_r_version
     with:
-      r-version: $R_VERSION
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   spellcheck:
     name: Spelling
     uses: pharmaverse/admiralci/.github/workflows/spellcheck.yml@main
     if: github.event_name == 'pull_request'
+    needs: get_r_version
     with:
-      r-version: $R_VERSION
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   readme:
     name: Render README
     uses: pharmaverse/admiralci/.github/workflows/readme-render.yml@main
     if: github.event_name == 'push'
+    needs: get_r_version
     with:
-      r-version: $R_VERSION
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   validation:
     name: Validation
     uses: pharmaverse/admiralci/.github/workflows/r-pkg-validation.yml@main
     if: github.event_name == 'release'
+    needs: get_r_version
     with:
-      r-version: $R_VERSION
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   check:
     name: Check
     uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
@@ -72,8 +85,9 @@ jobs:
     name: Documentation
     uses: pharmaverse/admiralci/.github/workflows/pkgdown.yml@main
     if: github.event_name == 'push'
+    needs: get_r_version
     with:
-      r-version: $R_VERSION
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
       # Whether to skip multiversion docs
       # Note that if you have multiple versions of docs,
       # your URL links are likely to break due to path changes
@@ -82,8 +96,9 @@ jobs:
     name: Lint
     uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main
     if: github.event_name == 'pull_request'
+    needs: get_r_version
     with:
-      r-version: $R_VERSION
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   links:
     name: Links
     uses: pharmaverse/admiralci/.github/workflows/links.yml@main
@@ -94,8 +109,9 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/code-coverage.yml@main
     if: >
       github.event_name == 'push' || github.event_name == 'pull_request'
+    needs: get_r_version
     with:
-      r-version: $R_VERSION
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
       # Whether to skip code coverage badge creation
       # Setting to 'false' will require you to create
       # an orphan branch called 'badges' in your repository
@@ -105,11 +121,13 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/check-templates.yml@main
     if: >
       github.event_name == 'push' || github.event_name == 'pull_request'
+    needs: get_r_version
     with:
-      r-version: $R_VERSION
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   man-pages:
     name: Man Pages
     uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main
     if: github.event_name == 'pull_request'
+    needs: get_r_version
     with:
-      r-version: $R_VERSION
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"

From 9cfa3318272009693c5900c5441d5da80ee795bc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daphn=C3=A9=20Grasselly?=
 <56442075+dgrassellyb@users.noreply.github.com>
Date: Mon, 6 Nov 2023 14:09:47 +0100
Subject: [PATCH 2/2] Update README.Rmd

---
 README.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.Rmd b/README.Rmd
index 09f81f69..d59379c3 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -89,7 +89,7 @@ version of {admiralvaccine} was released.
 
 ## References and Documentation
 
-* Please refer to the [{admiral} References and Documentation](https://pharmaverse.github.io/admiral/main/)
+* Please refer to the [{admiral} References and Documentation](https://pharmaverse.github.io/admiral/)
 
 ## R Versions