setup-r-deps: replace github-token param with GITHUB_PAT env var (#262)

Fix the issue when private repos cannot be accessed:
https://github.com/insightsengineering/citril/actions/runs/11717635984/job/32642879518?pr=464

- `github-token` was not used and removed in a companion PR:
insightsengineering/setup-r-dependencies#17
- set up `GITHUB_ENV` on setup-r-deps use

---------

Signed-off-by: Pawel Rucki <[email protected]>

Author: pawelru

.github/workflows/bioccheck.yaml

@@ -159,9 +159,10 @@ jobs:
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
         uses: insightsengineering/setup-r-dependencies@v1
+        env:
+          GITHUB_PAT: ${{ steps.github-token.outputs.token }}
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
-          github-token: ${{ steps.github-token.outputs.token }}
           repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
       - name: Run BiocCheck ☣️

.github/workflows/build-check-install.yaml

@@ -437,9 +437,10 @@ jobs:
           env.deps_installation_method == 'setup-r-dependencies'
           && inputs.install-deps-from-package-repositories == ''
         uses: insightsengineering/setup-r-dependencies@v1
+        env:
+          GITHUB_PAT: ${{ steps.github-token.outputs.token }}
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
-          github-token: ${{ steps.github-token.outputs.token }}
           repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
           skip-desc-branch: ${{ inputs.skip-desc-branch }}
           skip-desc-dev: ${{ inputs.skip-desc-dev }}

.github/workflows/pkgdown.yaml

@@ -231,9 +231,10 @@ jobs:
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
         uses: insightsengineering/setup-r-dependencies@v1
+        env:
+          GITHUB_PAT: ${{ steps.github-token.outputs.token }}
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
-          github-token: ${{ steps.github-token.outputs.token }}
           repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
       - name: Install R package 🚧

.github/workflows/revdepcheck.yaml

@@ -92,10 +92,11 @@ jobs:
 
       - name: Install dependencies
         uses: insightsengineering/setup-r-dependencies@v1
+        env:
+          GITHUB_PAT: ${{ steps.github-token.outputs.token }}
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           skip-desc-branch: true
-          github-token: ${{ steps.github-token.outputs.token }}
 
       - name: revdepcheck 🔄
         id: revdepcheck

.github/workflows/rhub.yaml

@@ -97,10 +97,11 @@ jobs:
           job-config: ${{ matrix.config.job-config }}
 
       - uses: insightsengineering/setup-r-dependencies@v1
+        env:
+          GITHUB_PAT: ${{ steps.github-token.outputs.token }}
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           skip-install: true
-          github-token: ${{ steps.github-token.outputs.token }}
           restore-description: false
           install-quarto: "false"
 
@@ -149,10 +150,11 @@ jobs:
           job-config: ${{ matrix.config.job-config }}
 
       - uses: insightsengineering/setup-r-dependencies@v1
+        env:
+          GITHUB_PAT: ${{ steps.github-token.outputs.token }}
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           skip-install: true
-          github-token: ${{ steps.github-token.outputs.token }}
           restore-description: false
           install-quarto: "false"
 

.github/workflows/roxygen.yaml

@@ -153,9 +153,10 @@ jobs:
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
         uses: insightsengineering/setup-r-dependencies@v1
+        env:
+          GITHUB_PAT: ${{ steps.github-token.outputs.token }}
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
-          github-token: ${{ steps.github-token.outputs.token }}
           repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
       - name: Generate man pages 📄

.github/workflows/test-coverage.yaml

@@ -244,9 +244,10 @@ jobs:
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
         uses: insightsengineering/setup-r-dependencies@v1
+        env:
+          GITHUB_PAT: ${{ steps.github-token.outputs.token }}
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
-          github-token: ${{ steps.github-token.outputs.token }}
           repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
       - name: Install R package 🚧

.github/workflows/validation.yaml

@@ -148,9 +148,10 @@ jobs:
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
         uses: insightsengineering/setup-r-dependencies@v1
+        env:
+          GITHUB_PAT: ${{ steps.github-token.outputs.token }}
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
-          github-token: ${{ steps.github-token.outputs.token }}
           repository-path: ${{ env.package_subdirectory }}
 
       - name: Build report 🏗