From 1aad0ff845aaf52c3fc2dea37b1a3343bcec51fb Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Mon, 9 Sep 2024 12:14:20 +0200
Subject: [PATCH 01/31] feat: add an option to choose between
 staged-dependencies and setup-r-dependencies

---
 .github/workflows/bioccheck.yaml           | 25 +++++++++++++++++++++
 .github/workflows/build-check-install.yaml | 26 ++++++++++++++++++++++
 .github/workflows/pkgdown.yaml             | 25 +++++++++++++++++++++
 .github/workflows/roxygen.yaml             | 25 +++++++++++++++++++++
 .github/workflows/test-coverage.yaml       | 25 +++++++++++++++++++++
 .github/workflows/validation.yaml          | 25 +++++++++++++++++++++
 6 files changed, 151 insertions(+)

diff --git a/.github/workflows/bioccheck.yaml b/.github/workflows/bioccheck.yaml
index e86dd6967..d49f68d0e 100644
--- a/.github/workflows/bioccheck.yaml
+++ b/.github/workflows/bioccheck.yaml
@@ -53,6 +53,19 @@ on:
         required: false
         type: string
         default: "."
+      deps-installation-method:
+        description: Which method for installing R package dependencies to use?
+        required: true
+        type: choice
+        default: staged-dependencies
+        options:
+          - staged-dependencies
+          - setup-r-dependencies
+      lookup-refs:
+        description: |
+          List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
+        required: false
+        default: ""
 
 concurrency:
   group: bioccheck-${{ github.event.pull_request.number || github.ref }}
@@ -122,12 +135,16 @@ jobs:
           SKIP_INSTRUCTION: "[skip bioccheck]"
 
       - name: Restore SD cache 💰
+        if: >-
+          inputs.deps-installation-method == 'staged-dependencies'
         uses: actions/cache@v4
         with:
           key: sd-${{ runner.os }}-${{ github.event.repository.name }}
           path: ~/.staged.dependencies
 
       - name: Run Staged dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'staged-dependencies'
         uses: insightsengineering/staged-dependencies-action@v2
         env:
           GITHUB_PAT: ${{ steps.github-token.outputs.token }}
@@ -137,6 +154,14 @@ jobs:
           run-system-dependencies: ${{ inputs.install-system-dependencies }}
           direction: ${{ inputs.sd-direction }}
 
+      - name: Setup R dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'setup-r-dependencies'
+        uses: insightsengineering/setup-r-dependencies@v1
+        with:
+          lookup-refs: ${{ inputs.lookup-refs }}
+          github-token: ${{ steps.github-token.outputs.token }}
+
       - name: Run BiocCheck ☣️
         uses: insightsengineering/bioc-check-action@v1
         with:
diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index edab16731..f30372413 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -126,9 +126,23 @@ on:
         description: |
           Set this to a comma-separated named list of R packages repositories to use for installing dependencies.
           Example: "R-universe=https://insightsengineering.r-universe.dev/,CRAN=https://cloud.r-project.org/"
+          If the value is non-empty, it takes precedence over deps-installation-method.
         required: false
         type: string
         default: ""
+      deps-installation-method:
+        description: Which method for installing R package dependencies to use?
+        required: true
+        type: choice
+        default: staged-dependencies
+        options:
+          - staged-dependencies
+          - setup-r-dependencies
+      lookup-refs:
+        description: |
+          List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
+        required: false
+        default: ""
       unit-test-report-brand:
         description: Image URL to use in unit test report for branding. If empty, the default xunit-viewer brand will be used.
         required: false
@@ -177,6 +191,8 @@ on:
       enable-sd:
         description: |
           Whether the installation of package dependencies via staged.dependencies should be enabled.
+          Has no effect if deps-installation-method == 'setup-r-dependencies' or
+          install-deps-from-package-repositories is set to non-empty value.
         required: false
         type: boolean
         default: true
@@ -373,6 +389,7 @@ jobs:
         if: >-
           env.enable_sd == 'true'
             && inputs.install-deps-from-package-repositories == ''
+            && inputs.deps-installation-method == 'staged-dependencies'
         uses: insightsengineering/staged-dependencies-action@v2
         env:
           GITHUB_PAT: ${{ steps.github-token.outputs.token }}
@@ -382,6 +399,15 @@ jobs:
           run-system-dependencies: ${{ inputs.install-system-dependencies }}
           direction: ${{ inputs.sd-direction }}
 
+      - name: Setup R dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'setup-r-dependencies'
+          inputs.install-deps-from-package-repositories == ''
+        uses: insightsengineering/setup-r-dependencies@v1
+        with:
+          lookup-refs: ${{ inputs.lookup-refs }}
+          github-token: ${{ steps.github-token.outputs.token }}
+
       - name: Install dependencies from package repositories 🗄️
         if: inputs.install-deps-from-package-repositories != ''
         run: |
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index e1b20ab9f..16ec2d94b 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -120,6 +120,19 @@ on:
         required: false
         type: string
         default: ""
+      deps-installation-method:
+        description: Which method for installing R package dependencies to use?
+        required: true
+        type: choice
+        default: staged-dependencies
+        options:
+          - staged-dependencies
+          - setup-r-dependencies
+      lookup-refs:
+        description: |
+          List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
+        required: false
+        default: ""
 
 concurrency:
   group: docs-${{ github.event.pull_request.number || github.ref }}
@@ -194,12 +207,16 @@ jobs:
           SKIP_INSTRUCTION: "[skip docs]"
 
       - name: Restore SD cache 💰
+        if: >-
+          inputs.deps-installation-method == 'staged-dependencies'
         uses: actions/cache@v4
         with:
           key: sd-${{ runner.os }}-${{ github.event.repository.name }}
           path: ~/.staged.dependencies
 
       - name: Run Staged dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'staged-dependencies'
         uses: insightsengineering/staged-dependencies-action@v2
         env:
           GITHUB_PAT: ${{ steps.github-token.outputs.token }}
@@ -209,6 +226,14 @@ jobs:
           run-system-dependencies: ${{ inputs.install-system-dependencies }}
           direction: ${{ inputs.sd-direction }}
 
+      - name: Setup R dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'setup-r-dependencies'
+        uses: insightsengineering/setup-r-dependencies@v1
+        with:
+          lookup-refs: ${{ inputs.lookup-refs }}
+          github-token: ${{ steps.github-token.outputs.token }}
+
       - name: Install R package 🚧
         run: |
           if (file.exists("renv.lock")) renv::restore()
diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index e79d4c44c..478e9470e 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -41,6 +41,19 @@ on:
         required: false
         type: string
         default: "."
+      deps-installation-method:
+        description: Which method for installing R package dependencies to use?
+        required: true
+        type: choice
+        default: staged-dependencies
+        options:
+          - staged-dependencies
+          - setup-r-dependencies
+      lookup-refs:
+        description: |
+          List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
+        required: false
+        default: ""
     secrets:
       REPO_GITHUB_TOKEN:
         description: |
@@ -109,12 +122,16 @@ jobs:
           SKIP_INSTRUCTION: "[skip roxygen]"
 
       - name: Restore SD cache 💰
+        if: >-
+          inputs.deps-installation-method == 'staged-dependencies'
         uses: actions/cache@v4
         with:
           key: sd-${{ runner.os }}-${{ github.event.repository.name }}
           path: ~/.staged.dependencies
 
       - name: Run Staged dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'staged-dependencies'
         uses: insightsengineering/staged-dependencies-action@v2
         env:
           GITHUB_PAT: ${{ steps.github-token.outputs.token }}
@@ -124,6 +141,14 @@ jobs:
           run-system-dependencies: ${{ inputs.install-system-dependencies }}
           direction: ${{ inputs.sd-direction }}
 
+      - name: Setup R dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'setup-r-dependencies'
+        uses: insightsengineering/setup-r-dependencies@v1
+        with:
+          lookup-refs: ${{ inputs.lookup-refs }}
+          github-token: ${{ steps.github-token.outputs.token }}
+
       - name: Generate man pages 📄
         run: |
           logfile <- "roxygen_${{ github.event.repository.name }}.log"
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 1a7eda3f1..3676335da 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -82,6 +82,19 @@ on:
         required: false
         type: string
         default: ""
+      deps-installation-method:
+        description: Which method for installing R package dependencies to use?
+        required: true
+        type: choice
+        default: staged-dependencies
+        options:
+          - staged-dependencies
+          - setup-r-dependencies
+      lookup-refs:
+        description: |
+          List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
+        required: false
+        default: ""
     secrets:
       REPO_GITHUB_TOKEN:
         description: |
@@ -207,12 +220,16 @@ jobs:
           fi
 
       - name: Restore SD cache 💰
+        if: >-
+          inputs.deps-installation-method == 'staged-dependencies'
         uses: actions/cache@v4
         with:
           key: sd-${{ runner.os }}-${{ github.event.repository.name }}
           path: ~/.staged.dependencies
 
       - name: Run Staged dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'staged-dependencies'
         uses: insightsengineering/staged-dependencies-action@v2
         env:
           GITHUB_PAT: ${{ secrets.REPO_GITHUB_TOKEN }}
@@ -222,6 +239,14 @@ jobs:
           run-system-dependencies: ${{ inputs.install-system-dependencies }}
           direction: ${{ inputs.sd-direction }}
 
+      - name: Setup R dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'setup-r-dependencies'
+        uses: insightsengineering/setup-r-dependencies@v1
+        with:
+          lookup-refs: ${{ inputs.lookup-refs }}
+          github-token: ${{ steps.github-token.outputs.token }}
+
       - name: Install R package 🚧
         run: |
           if (file.exists("renv.lock")) renv::restore()
diff --git a/.github/workflows/validation.yaml b/.github/workflows/validation.yaml
index 655a5fb5b..55292e099 100644
--- a/.github/workflows/validation.yaml
+++ b/.github/workflows/validation.yaml
@@ -38,6 +38,19 @@ on:
         required: false
         type: string
         default: "."
+      deps-installation-method:
+        description: Which method for installing R package dependencies to use?
+        required: true
+        type: choice
+        default: staged-dependencies
+        options:
+          - staged-dependencies
+          - setup-r-dependencies
+      lookup-refs:
+        description: |
+          List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
+        required: false
+        default: ""
     secrets:
       REPO_GITHUB_TOKEN:
         description: |
@@ -111,12 +124,16 @@ jobs:
         shell: bash
 
       - name: Restore SD cache 💰
+        if: >-
+          inputs.deps-installation-method == 'staged-dependencies'
         uses: actions/cache@v4
         with:
           key: sd-${{ runner.os }}-${{ github.event.repository.name }}
           path: ~/.staged.dependencies
 
       - name: Run Staged dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'staged-dependencies'
         uses: insightsengineering/staged-dependencies-action@v2
         env:
           GITHUB_PAT: ${{ steps.github-token.outputs.token }}
@@ -126,6 +143,14 @@ jobs:
           run-system-dependencies: ${{ inputs.install-system-dependencies }}
           direction: ${{ inputs.sd-direction }}
 
+      - name: Setup R dependencies 🎦
+        if: >-
+          inputs.deps-installation-method == 'setup-r-dependencies'
+        uses: insightsengineering/setup-r-dependencies@v1
+        with:
+          lookup-refs: ${{ inputs.lookup-refs }}
+          github-token: ${{ steps.github-token.outputs.token }}
+
       - name: Build report 🏗
         uses: insightsengineering/thevalidatoR@v2
         env:

From 04ad6fc9ccfda69a3f31a8601766c89d9e5264e0 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Mon, 9 Sep 2024 12:19:28 +0200
Subject: [PATCH 02/31] fix: deps-installation-method input

---
 .github/workflows/bioccheck.yaml           | 12 ++++++------
 .github/workflows/build-check-install.yaml | 12 ++++++------
 .github/workflows/pkgdown.yaml             | 12 ++++++------
 .github/workflows/roxygen.yaml             | 12 ++++++------
 .github/workflows/test-coverage.yaml       | 12 ++++++------
 .github/workflows/validation.yaml          | 12 ++++++------
 6 files changed, 36 insertions(+), 36 deletions(-)

diff --git a/.github/workflows/bioccheck.yaml b/.github/workflows/bioccheck.yaml
index d49f68d0e..d7247bd94 100644
--- a/.github/workflows/bioccheck.yaml
+++ b/.github/workflows/bioccheck.yaml
@@ -54,13 +54,13 @@ on:
         type: string
         default: "."
       deps-installation-method:
-        description: Which method for installing R package dependencies to use?
-        required: true
-        type: choice
+        description: |
+          Which method for installing R package dependencies to use? Supported values are:
+          staged-dependencies
+          setup-r-dependencies
+        required: false
+        type: string
         default: staged-dependencies
-        options:
-          - staged-dependencies
-          - setup-r-dependencies
       lookup-refs:
         description: |
           List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index f30372413..1eaa2d8cc 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -131,13 +131,13 @@ on:
         type: string
         default: ""
       deps-installation-method:
-        description: Which method for installing R package dependencies to use?
-        required: true
-        type: choice
+        description: |
+          Which method for installing R package dependencies to use? Supported values are:
+          staged-dependencies
+          setup-r-dependencies
+        required: false
+        type: string
         default: staged-dependencies
-        options:
-          - staged-dependencies
-          - setup-r-dependencies
       lookup-refs:
         description: |
           List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 16ec2d94b..391afa1ad 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -121,13 +121,13 @@ on:
         type: string
         default: ""
       deps-installation-method:
-        description: Which method for installing R package dependencies to use?
-        required: true
-        type: choice
+        description: |
+          Which method for installing R package dependencies to use? Supported values are:
+          staged-dependencies
+          setup-r-dependencies
+        required: false
+        type: string
         default: staged-dependencies
-        options:
-          - staged-dependencies
-          - setup-r-dependencies
       lookup-refs:
         description: |
           List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index 478e9470e..08cab4032 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -42,13 +42,13 @@ on:
         type: string
         default: "."
       deps-installation-method:
-        description: Which method for installing R package dependencies to use?
-        required: true
-        type: choice
+        description: |
+          Which method for installing R package dependencies to use? Supported values are:
+          staged-dependencies
+          setup-r-dependencies
+        required: false
+        type: string
         default: staged-dependencies
-        options:
-          - staged-dependencies
-          - setup-r-dependencies
       lookup-refs:
         description: |
           List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 3676335da..594b01c7b 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -83,13 +83,13 @@ on:
         type: string
         default: ""
       deps-installation-method:
-        description: Which method for installing R package dependencies to use?
-        required: true
-        type: choice
+        description: |
+          Which method for installing R package dependencies to use? Supported values are:
+          staged-dependencies
+          setup-r-dependencies
+        required: false
+        type: string
         default: staged-dependencies
-        options:
-          - staged-dependencies
-          - setup-r-dependencies
       lookup-refs:
         description: |
           List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
diff --git a/.github/workflows/validation.yaml b/.github/workflows/validation.yaml
index 55292e099..65388a34e 100644
--- a/.github/workflows/validation.yaml
+++ b/.github/workflows/validation.yaml
@@ -39,13 +39,13 @@ on:
         type: string
         default: "."
       deps-installation-method:
-        description: Which method for installing R package dependencies to use?
-        required: true
-        type: choice
+        description: |
+          Which method for installing R package dependencies to use? Supported values are:
+          staged-dependencies
+          setup-r-dependencies
+        required: false
+        type: string
         default: staged-dependencies
-        options:
-          - staged-dependencies
-          - setup-r-dependencies
       lookup-refs:
         description: |
           List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.

From 84bb90b9aa051e5e068e6af561081391de5d28c5 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Mon, 9 Sep 2024 12:21:22 +0200
Subject: [PATCH 03/31] fix: add type to lookup-refs input

---
 .github/workflows/bioccheck.yaml           | 1 +
 .github/workflows/build-check-install.yaml | 1 +
 .github/workflows/pkgdown.yaml             | 1 +
 .github/workflows/roxygen.yaml             | 1 +
 .github/workflows/test-coverage.yaml       | 1 +
 .github/workflows/validation.yaml          | 1 +
 6 files changed, 6 insertions(+)

diff --git a/.github/workflows/bioccheck.yaml b/.github/workflows/bioccheck.yaml
index d7247bd94..5ba12ac35 100644
--- a/.github/workflows/bioccheck.yaml
+++ b/.github/workflows/bioccheck.yaml
@@ -65,6 +65,7 @@ on:
         description: |
           List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
         required: false
+        type: string
         default: ""
 
 concurrency:
diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 1eaa2d8cc..b8cc5a2aa 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -142,6 +142,7 @@ on:
         description: |
           List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
         required: false
+        type: string
         default: ""
       unit-test-report-brand:
         description: Image URL to use in unit test report for branding. If empty, the default xunit-viewer brand will be used.
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 391afa1ad..eb12bdf03 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -132,6 +132,7 @@ on:
         description: |
           List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
         required: false
+        type: string
         default: ""
 
 concurrency:
diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index 08cab4032..62658c4a3 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -53,6 +53,7 @@ on:
         description: |
           List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
         required: false
+        type: string
         default: ""
     secrets:
       REPO_GITHUB_TOKEN:
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 594b01c7b..fa85e1812 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -94,6 +94,7 @@ on:
         description: |
           List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
         required: false
+        type: string
         default: ""
     secrets:
       REPO_GITHUB_TOKEN:
diff --git a/.github/workflows/validation.yaml b/.github/workflows/validation.yaml
index 65388a34e..9235d1dbb 100644
--- a/.github/workflows/validation.yaml
+++ b/.github/workflows/validation.yaml
@@ -50,6 +50,7 @@ on:
         description: |
           List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
         required: false
+        type: string
         default: ""
     secrets:
       REPO_GITHUB_TOKEN:

From 5a9b4b0d7159e1f2113b2b34973b04b8134d03a9 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Mon, 9 Sep 2024 12:23:02 +0200
Subject: [PATCH 04/31] fix: step condition

---
 .github/workflows/build-check-install.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index b8cc5a2aa..65b14b290 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -403,7 +403,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-          inputs.install-deps-from-package-repositories == ''
+          && inputs.install-deps-from-package-repositories == ''
         uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}

From 66aae703b0fd7018dabde6a8f3c2d7689a471166 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Mon, 9 Sep 2024 12:55:45 +0200
Subject: [PATCH 05/31] fix: set repository-path for setup-r-dependencies

---
 .github/workflows/bioccheck.yaml           | 1 +
 .github/workflows/build-check-install.yaml | 1 +
 .github/workflows/pkgdown.yaml             | 1 +
 .github/workflows/roxygen.yaml             | 1 +
 .github/workflows/test-coverage.yaml       | 1 +
 .github/workflows/validation.yaml          | 1 +
 6 files changed, 6 insertions(+)

diff --git a/.github/workflows/bioccheck.yaml b/.github/workflows/bioccheck.yaml
index 5ba12ac35..0a59282a5 100644
--- a/.github/workflows/bioccheck.yaml
+++ b/.github/workflows/bioccheck.yaml
@@ -162,6 +162,7 @@ jobs:
         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 ☣️
         uses: insightsengineering/bioc-check-action@v1
diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 65b14b290..e309c6313 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -408,6 +408,7 @@ jobs:
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
+          repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
       - name: Install dependencies from package repositories 🗄️
         if: inputs.install-deps-from-package-repositories != ''
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index eb12bdf03..3e4fab34c 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -234,6 +234,7 @@ jobs:
         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 🚧
         run: |
diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index 62658c4a3..7d1d933cb 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -149,6 +149,7 @@ jobs:
         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 📄
         run: |
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index fa85e1812..240582690 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -247,6 +247,7 @@ jobs:
         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 🚧
         run: |
diff --git a/.github/workflows/validation.yaml b/.github/workflows/validation.yaml
index 9235d1dbb..f33b21a24 100644
--- a/.github/workflows/validation.yaml
+++ b/.github/workflows/validation.yaml
@@ -151,6 +151,7 @@ jobs:
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
+          repository-path: ${{ env.package_subdirectory }}
 
       - name: Build report 🏗
         uses: insightsengineering/thevalidatoR@v2

From 72d80197f5f58e4efdca0013e0fc8a08cd9317b0 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Mon, 9 Sep 2024 13:29:59 +0200
Subject: [PATCH 06/31] fix: update repository-path input

---
 .github/workflows/bioccheck.yaml           |  2 +-
 .github/workflows/build-check-install.yaml | 12 ++++++++++--
 .github/workflows/pkgdown.yaml             |  8 +++++++-
 .github/workflows/roxygen.yaml             |  8 +++++++-
 .github/workflows/test-coverage.yaml       |  8 +++++++-
 5 files changed, 32 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/bioccheck.yaml b/.github/workflows/bioccheck.yaml
index 0a59282a5..345226c0a 100644
--- a/.github/workflows/bioccheck.yaml
+++ b/.github/workflows/bioccheck.yaml
@@ -162,7 +162,7 @@ jobs:
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
-          repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+          repository-path: ${{ github.event.repository.name }}
 
       - name: Run BiocCheck ☣️
         uses: insightsengineering/bioc-check-action@v1
diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index e309c6313..2cd0320d0 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -373,7 +373,9 @@ jobs:
         shell: bash
 
       - name: Restore SD cache 💰
-        if: inputs.install-deps-from-package-repositories == ''
+        if: >-
+          inputs.install-deps-from-package-repositories == ''
+            && inputs.deps-installation-method == 'staged-dependencies'
         uses: actions/cache@v4
         with:
           key: sd-${{ runner.os }}-${{ github.event.repository.name }}
@@ -408,7 +410,13 @@ jobs:
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
-          repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+          # Setting repository path to
+          # ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+          # causes the following error:
+          # Error in `get_remote_types(refs)`:
+          # ! Cannot parse package: teal/.
+          # ℹ See `?pkgdepends::pkg_refs()` for supported package sources.
+          repository-path: ${{ github.event.repository.name }}
 
       - name: Install dependencies from package repositories 🗄️
         if: inputs.install-deps-from-package-repositories != ''
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 3e4fab34c..a5351a48a 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -234,7 +234,13 @@ jobs:
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
-          repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+          # Setting repository path to
+          # ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+          # causes the following error:
+          # Error in `get_remote_types(refs)`:
+          # ! Cannot parse package: teal/.
+          # ℹ See `?pkgdepends::pkg_refs()` for supported package sources.
+          repository-path: ${{ github.event.repository.name }}
 
       - name: Install R package 🚧
         run: |
diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index 7d1d933cb..c759e8c22 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -149,7 +149,13 @@ jobs:
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
-          repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+          # Setting repository path to
+          # ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+          # causes the following error:
+          # Error in `get_remote_types(refs)`:
+          # ! Cannot parse package: teal/.
+          # ℹ See `?pkgdepends::pkg_refs()` for supported package sources.
+          repository-path: ${{ github.event.repository.name }}
 
       - name: Generate man pages 📄
         run: |
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 240582690..bc479b776 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -247,7 +247,13 @@ jobs:
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
-          repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+          # Setting repository path to
+          # ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+          # causes the following error:
+          # Error in `get_remote_types(refs)`:
+          # ! Cannot parse package: teal/.
+          # ℹ See `?pkgdepends::pkg_refs()` for supported package sources.
+          repository-path: ${{ github.event.repository.name }}
 
       - name: Install R package 🚧
         run: |

From df1961e5a9545868f9843e9691c8565260469072 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Mon, 9 Sep 2024 17:18:25 +0200
Subject: [PATCH 07/31] chore: test fix_paths branch of setup-r-dependencies

---
 .github/workflows/bioccheck.yaml           | 2 +-
 .github/workflows/build-check-install.yaml | 2 +-
 .github/workflows/pkgdown.yaml             | 2 +-
 .github/workflows/roxygen.yaml             | 2 +-
 .github/workflows/test-coverage.yaml       | 2 +-
 .github/workflows/validation.yaml          | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/bioccheck.yaml b/.github/workflows/bioccheck.yaml
index 345226c0a..aced7ebcf 100644
--- a/.github/workflows/bioccheck.yaml
+++ b/.github/workflows/bioccheck.yaml
@@ -158,7 +158,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@fix_paths
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 2cd0320d0..8a1ce3d28 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -406,7 +406,7 @@ jobs:
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
           && inputs.install-deps-from-package-repositories == ''
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@fix_paths
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index a5351a48a..d25016891 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -230,7 +230,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@fix_paths
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index c759e8c22..ef331ffc8 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -145,7 +145,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@fix_paths
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index bc479b776..91763a561 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -243,7 +243,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@fix_paths
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/validation.yaml b/.github/workflows/validation.yaml
index f33b21a24..9e391be7b 100644
--- a/.github/workflows/validation.yaml
+++ b/.github/workflows/validation.yaml
@@ -147,7 +147,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@fix_paths
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}

From 2d467d7419940f2243153a47018e4fb5c61369b3 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Mon, 9 Sep 2024 17:51:01 +0200
Subject: [PATCH 08/31] fix: restore DESCRIPTION modified by Roxygen

---
 .github/workflows/roxygen.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index ef331ffc8..c35b20143 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -157,6 +157,9 @@ jobs:
           # ℹ See `?pkgdepends::pkg_refs()` for supported package sources.
           repository-path: ${{ github.event.repository.name }}
 
+      - name: Restore DESCRIPTION ⚙️
+        run: git restore DESCRIPTION
+
       - name: Generate man pages 📄
         run: |
           logfile <- "roxygen_${{ github.event.repository.name }}.log"

From e5b303c58823b2603e737f1ba4463714b3f03234 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Mon, 9 Sep 2024 18:00:18 +0200
Subject: [PATCH 09/31] fix: set working directory in Roxygen workflow

---
 .github/workflows/roxygen.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index c35b20143..8ec7906c7 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -159,6 +159,8 @@ jobs:
 
       - name: Restore DESCRIPTION ⚙️
         run: git restore DESCRIPTION
+        working-directory: ${{ github.event.repository.name }}
+        shell: bash
 
       - name: Generate man pages 📄
         run: |

From 7523215bdb120f3918c768a0097de3d532b0c2fe Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 10 Sep 2024 14:09:04 +0200
Subject: [PATCH 10/31] fix: normalize variables

---
 .github/workflows/build-check-install.yaml |  8 +++++---
 .github/workflows/roxygen.yaml             | 12 +++++++++---
 2 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 8a1ce3d28..29e0173dd 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -336,12 +336,14 @@ jobs:
           junit_xml_positive_threshold="${{ inputs.junit-xml-positive-threshold }}"
           junit_xml_negative_threshold="${{ inputs.junit-xml-negative-threshold }}"
           enable_sd="${{ inputs.enable-sd }}"
+          deps_installation_method="${{ inputs.deps-installation-method }}"
           echo "junit_xml_storage=${junit_xml_storage_input:-_junit_xml_reports}" >> $GITHUB_ENV
           echo "junit_xml_diff_branch=${junit_xml_diff_branch_input:-main}" >> $GITHUB_ENV
           echo "junit_xml_comparison=${junit_xml_comparison_input:-true}" >> $GITHUB_ENV
           echo "junit_xml_positive_threshold=${junit_xml_positive_threshold:-1.0}" >> $GITHUB_ENV
           echo "junit_xml_negative_threshold=${junit_xml_negative_threshold:-1.0}" >> $GITHUB_ENV
           echo "enable_sd=${enable_sd:-true}" >> $GITHUB_ENV
+          echo "deps_installation_method=${deps_installation_method:-staged-dependencies}" >> $GITHUB_ENV
         shell: bash
 
       - name: Restore npm cache 💰
@@ -375,7 +377,7 @@ jobs:
       - name: Restore SD cache 💰
         if: >-
           inputs.install-deps-from-package-repositories == ''
-            && inputs.deps-installation-method == 'staged-dependencies'
+            && env.deps_installation_method == 'staged-dependencies'
         uses: actions/cache@v4
         with:
           key: sd-${{ runner.os }}-${{ github.event.repository.name }}
@@ -392,7 +394,7 @@ jobs:
         if: >-
           env.enable_sd == 'true'
             && inputs.install-deps-from-package-repositories == ''
-            && inputs.deps-installation-method == 'staged-dependencies'
+            && env.deps_installation_method == 'staged-dependencies'
         uses: insightsengineering/staged-dependencies-action@v2
         env:
           GITHUB_PAT: ${{ steps.github-token.outputs.token }}
@@ -404,7 +406,7 @@ jobs:
 
       - name: Setup R dependencies 🎦
         if: >-
-          inputs.deps-installation-method == 'setup-r-dependencies'
+          env.deps_installation_method == 'setup-r-dependencies'
           && inputs.install-deps-from-package-repositories == ''
         uses: insightsengineering/setup-r-dependencies@fix_paths
         with:
diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index 8ec7906c7..c7364d6d5 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -122,9 +122,15 @@ jobs:
         env:
           SKIP_INSTRUCTION: "[skip roxygen]"
 
+      - name: Normalize variables 📏
+        run: |
+          deps_installation_method="${{ inputs.deps-installation-method }}"
+          echo "deps_installation_method=${deps_installation_method:-staged-dependencies}" >> $GITHUB_ENV
+        shell: bash
+
       - name: Restore SD cache 💰
         if: >-
-          inputs.deps-installation-method == 'staged-dependencies'
+          env.deps_installation_method == 'staged-dependencies'
         uses: actions/cache@v4
         with:
           key: sd-${{ runner.os }}-${{ github.event.repository.name }}
@@ -132,7 +138,7 @@ jobs:
 
       - name: Run Staged dependencies 🎦
         if: >-
-          inputs.deps-installation-method == 'staged-dependencies'
+          env.deps_installation_method == 'staged-dependencies'
         uses: insightsengineering/staged-dependencies-action@v2
         env:
           GITHUB_PAT: ${{ steps.github-token.outputs.token }}
@@ -144,7 +150,7 @@ jobs:
 
       - name: Setup R dependencies 🎦
         if: >-
-          inputs.deps-installation-method == 'setup-r-dependencies'
+          env.deps_installation_method == 'setup-r-dependencies'
         uses: insightsengineering/setup-r-dependencies@fix_paths
         with:
           lookup-refs: ${{ inputs.lookup-refs }}

From d83970012fbefa639267f8f0dd98338e02837c29 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 10 Sep 2024 14:19:50 +0200
Subject: [PATCH 11/31] fix: add package subdirectory to repository-path input

---
 .github/workflows/build-check-install.yaml | 2 +-
 .github/workflows/pkgdown.yaml             | 2 +-
 .github/workflows/roxygen.yaml             | 4 +++-
 .github/workflows/test-coverage.yaml       | 2 +-
 4 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 29e0173dd..a7e19a81a 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -418,7 +418,7 @@ jobs:
           # Error in `get_remote_types(refs)`:
           # ! Cannot parse package: teal/.
           # ℹ See `?pkgdepends::pkg_refs()` for supported package sources.
-          repository-path: ${{ github.event.repository.name }}
+          repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
       - name: Install dependencies from package repositories 🗄️
         if: inputs.install-deps-from-package-repositories != ''
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index d25016891..15506fa14 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -240,7 +240,7 @@ jobs:
           # Error in `get_remote_types(refs)`:
           # ! Cannot parse package: teal/.
           # ℹ See `?pkgdepends::pkg_refs()` for supported package sources.
-          repository-path: ${{ github.event.repository.name }}
+          repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
       - name: Install R package 🚧
         run: |
diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index c7364d6d5..50c99cc39 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -161,8 +161,10 @@ jobs:
           # Error in `get_remote_types(refs)`:
           # ! Cannot parse package: teal/.
           # ℹ See `?pkgdepends::pkg_refs()` for supported package sources.
-          repository-path: ${{ github.event.repository.name }}
+          repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
+      # setup-r-dependencies makes modifications to DESCRIPTION which
+      # should not be committed during Roxygen auto-update.
       - name: Restore DESCRIPTION ⚙️
         run: git restore DESCRIPTION
         working-directory: ${{ github.event.repository.name }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 91763a561..d52707c75 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -253,7 +253,7 @@ jobs:
           # Error in `get_remote_types(refs)`:
           # ! Cannot parse package: teal/.
           # ℹ See `?pkgdepends::pkg_refs()` for supported package sources.
-          repository-path: ${{ github.event.repository.name }}
+          repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
       - name: Install R package 🚧
         run: |

From a881fa75166655d92a3b533c80fe340ff3887d13 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 10 Sep 2024 14:25:19 +0200
Subject: [PATCH 12/31] fix: restore repository-path

---
 .github/workflows/build-check-install.yaml | 2 +-
 .github/workflows/pkgdown.yaml             | 2 +-
 .github/workflows/roxygen.yaml             | 2 +-
 .github/workflows/test-coverage.yaml       | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index a7e19a81a..29e0173dd 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -418,7 +418,7 @@ jobs:
           # Error in `get_remote_types(refs)`:
           # ! Cannot parse package: teal/.
           # ℹ See `?pkgdepends::pkg_refs()` for supported package sources.
-          repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+          repository-path: ${{ github.event.repository.name }}
 
       - name: Install dependencies from package repositories 🗄️
         if: inputs.install-deps-from-package-repositories != ''
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 15506fa14..d25016891 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -240,7 +240,7 @@ jobs:
           # Error in `get_remote_types(refs)`:
           # ! Cannot parse package: teal/.
           # ℹ See `?pkgdepends::pkg_refs()` for supported package sources.
-          repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+          repository-path: ${{ github.event.repository.name }}
 
       - name: Install R package 🚧
         run: |
diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index 50c99cc39..fc222747a 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -161,7 +161,7 @@ jobs:
           # Error in `get_remote_types(refs)`:
           # ! Cannot parse package: teal/.
           # ℹ See `?pkgdepends::pkg_refs()` for supported package sources.
-          repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+          repository-path: ${{ github.event.repository.name }}
 
       # setup-r-dependencies makes modifications to DESCRIPTION which
       # should not be committed during Roxygen auto-update.
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index d52707c75..91763a561 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -253,7 +253,7 @@ jobs:
           # Error in `get_remote_types(refs)`:
           # ! Cannot parse package: teal/.
           # ℹ See `?pkgdepends::pkg_refs()` for supported package sources.
-          repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+          repository-path: ${{ github.event.repository.name }}
 
       - name: Install R package 🚧
         run: |

From 04a5cc119a0f9880c8ad32b65dc207d48e3dbb53 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 10 Sep 2024 14:34:02 +0200
Subject: [PATCH 13/31] chore: set setup-r-dependencies to v1

---
 .github/workflows/bioccheck.yaml           | 2 +-
 .github/workflows/build-check-install.yaml | 8 +-------
 .github/workflows/pkgdown.yaml             | 8 +-------
 .github/workflows/roxygen.yaml             | 8 +-------
 .github/workflows/test-coverage.yaml       | 8 +-------
 .github/workflows/validation.yaml          | 2 +-
 6 files changed, 6 insertions(+), 30 deletions(-)

diff --git a/.github/workflows/bioccheck.yaml b/.github/workflows/bioccheck.yaml
index aced7ebcf..345226c0a 100644
--- a/.github/workflows/bioccheck.yaml
+++ b/.github/workflows/bioccheck.yaml
@@ -158,7 +158,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@fix_paths
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 29e0173dd..035e3b64b 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -408,16 +408,10 @@ jobs:
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
           && inputs.install-deps-from-package-repositories == ''
-        uses: insightsengineering/setup-r-dependencies@fix_paths
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
-          # Setting repository path to
-          # ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
-          # causes the following error:
-          # Error in `get_remote_types(refs)`:
-          # ! Cannot parse package: teal/.
-          # ℹ See `?pkgdepends::pkg_refs()` for supported package sources.
           repository-path: ${{ github.event.repository.name }}
 
       - name: Install dependencies from package repositories 🗄️
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index d25016891..b2865c236 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -230,16 +230,10 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@fix_paths
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
-          # Setting repository path to
-          # ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
-          # causes the following error:
-          # Error in `get_remote_types(refs)`:
-          # ! Cannot parse package: teal/.
-          # ℹ See `?pkgdepends::pkg_refs()` for supported package sources.
           repository-path: ${{ github.event.repository.name }}
 
       - name: Install R package 🚧
diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index fc222747a..2e54b44ae 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -151,16 +151,10 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@fix_paths
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
-          # Setting repository path to
-          # ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
-          # causes the following error:
-          # Error in `get_remote_types(refs)`:
-          # ! Cannot parse package: teal/.
-          # ℹ See `?pkgdepends::pkg_refs()` for supported package sources.
           repository-path: ${{ github.event.repository.name }}
 
       # setup-r-dependencies makes modifications to DESCRIPTION which
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 91763a561..8406b052c 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -243,16 +243,10 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@fix_paths
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
-          # Setting repository path to
-          # ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
-          # causes the following error:
-          # Error in `get_remote_types(refs)`:
-          # ! Cannot parse package: teal/.
-          # ℹ See `?pkgdepends::pkg_refs()` for supported package sources.
           repository-path: ${{ github.event.repository.name }}
 
       - name: Install R package 🚧
diff --git a/.github/workflows/validation.yaml b/.github/workflows/validation.yaml
index 9e391be7b..f33b21a24 100644
--- a/.github/workflows/validation.yaml
+++ b/.github/workflows/validation.yaml
@@ -147,7 +147,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@fix_paths
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}

From b6b66497359bb91f6451a500355eb15ef9e2486a Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 12 Sep 2024 11:38:33 +0200
Subject: [PATCH 14/31] chore: test with rocker image

---
 .github/workflows/build-check-install.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 035e3b64b..c77744eba 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -224,7 +224,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - image: ghcr.io/insightsengineering/rstudio
+          - image: rocker/verse
             tag: latest
     name: ${{ matrix.config.image }}, version ${{ matrix.config.tag }}
     runs-on: ubuntu-latest

From eaaa1fecfe7a14ceef525f6fbddf329e4d661790 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 12 Sep 2024 12:12:29 +0200
Subject: [PATCH 15/31] chore: set custom binary repositories

---
 .github/workflows/build-check-install.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index c77744eba..b35d5a57a 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -224,7 +224,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - image: rocker/verse
+          - image: ghcr.io/insightsengineering/rstudio
             tag: latest
     name: ${{ matrix.config.image }}, version ${{ matrix.config.tag }}
     runs-on: ubuntu-latest
@@ -408,7 +408,7 @@ jobs:
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
           && inputs.install-deps-from-package-repositories == ''
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@set-custom-repositories
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}

From 26fd3ef244f9bd5e8803a7881c6300abe5fa9cdc Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 12 Sep 2024 12:26:53 +0200
Subject: [PATCH 16/31] chore: test without custom repos

---
 .github/workflows/build-check-install.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index b35d5a57a..9239e5c9c 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -408,7 +408,8 @@ jobs:
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
           && inputs.install-deps-from-package-repositories == ''
-        uses: insightsengineering/setup-r-dependencies@set-custom-repositories
+        # uses: insightsengineering/setup-r-dependencies@set-custom-repositories
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}

From e75aee544a84172edfc40eb070241d321bbee913 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 12 Sep 2024 12:45:26 +0200
Subject: [PATCH 17/31] chore: switch to set-custom-repositories branch

---
 .github/workflows/build-check-install.yaml | 4 ++--
 .github/workflows/roxygen.yaml             | 3 ++-
 .github/workflows/test-coverage.yaml       | 3 ++-
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 9239e5c9c..334f45aed 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -408,8 +408,8 @@ jobs:
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
           && inputs.install-deps-from-package-repositories == ''
-        # uses: insightsengineering/setup-r-dependencies@set-custom-repositories
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@set-custom-repositories
+        # uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index 2e54b44ae..001e2554a 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -151,7 +151,8 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@set-custom-repositories
+        # uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 8406b052c..742b0625d 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -243,7 +243,8 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@set-custom-repositories
+        # uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}

From 4b8abdf98d1a8249d741eead0192bd0c62aa292c Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 12 Sep 2024 15:31:36 +0200
Subject: [PATCH 18/31] chore: restore setup-r-dependencies version after
 testing

---
 .github/workflows/build-check-install.yaml | 3 +--
 .github/workflows/roxygen.yaml             | 3 +--
 .github/workflows/test-coverage.yaml       | 3 +--
 3 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 334f45aed..035e3b64b 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -408,8 +408,7 @@ jobs:
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
           && inputs.install-deps-from-package-repositories == ''
-        uses: insightsengineering/setup-r-dependencies@set-custom-repositories
-        # uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index 001e2554a..2e54b44ae 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -151,8 +151,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@set-custom-repositories
-        # uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 742b0625d..8406b052c 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -243,8 +243,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@set-custom-repositories
-        # uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}

From 2098b524a96a67a8a2674ee803c0e1d8acd0d7d6 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 12 Sep 2024 15:36:11 +0200
Subject: [PATCH 19/31] Revert "chore: restore setup-r-dependencies version
 after testing"

This reverts commit 4b8abdf98d1a8249d741eead0192bd0c62aa292c.
---
 .github/workflows/build-check-install.yaml | 3 ++-
 .github/workflows/roxygen.yaml             | 3 ++-
 .github/workflows/test-coverage.yaml       | 3 ++-
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 035e3b64b..334f45aed 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -408,7 +408,8 @@ jobs:
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
           && inputs.install-deps-from-package-repositories == ''
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@set-custom-repositories
+        # uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index 2e54b44ae..001e2554a 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -151,7 +151,8 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@set-custom-repositories
+        # uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 8406b052c..742b0625d 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -243,7 +243,8 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@set-custom-repositories
+        # uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}

From 667134dacccf24248c7d1a5b02229143caeb0068 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 12 Sep 2024 16:32:33 +0200
Subject: [PATCH 20/31] Revert "Revert "chore: restore setup-r-dependencies
 version after testing""

This reverts commit 2098b524a96a67a8a2674ee803c0e1d8acd0d7d6.
---
 .github/workflows/build-check-install.yaml | 3 +--
 .github/workflows/roxygen.yaml             | 3 +--
 .github/workflows/test-coverage.yaml       | 3 +--
 3 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 334f45aed..035e3b64b 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -408,8 +408,7 @@ jobs:
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
           && inputs.install-deps-from-package-repositories == ''
-        uses: insightsengineering/setup-r-dependencies@set-custom-repositories
-        # uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index 001e2554a..2e54b44ae 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -151,8 +151,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@set-custom-repositories
-        # uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 742b0625d..8406b052c 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -243,8 +243,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@set-custom-repositories
-        # uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}

From 4657c32c17a46e27896f3bf8282c7fa88020596b Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Mon, 23 Sep 2024 11:43:54 +0200
Subject: [PATCH 21/31] chore: test binary dependencies

---
 .github/workflows/build-check-install.yaml | 2 +-
 .github/workflows/test-coverage.yaml       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 035e3b64b..c51a3db1b 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -408,7 +408,7 @@ jobs:
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
           && inputs.install-deps-from-package-repositories == ''
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@setup-binary-package-repository-for-different-platforms
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 8406b052c..da9945543 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -243,7 +243,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@setup-binary-package-repository-for-different-platforms
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}

From 56ed6404cb5616a269f20ae7f31f18f3d27c7add Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Mon, 23 Sep 2024 11:52:59 +0200
Subject: [PATCH 22/31] Revert "chore: test binary dependencies"

This reverts commit 4657c32c17a46e27896f3bf8282c7fa88020596b.
---
 .github/workflows/build-check-install.yaml | 2 +-
 .github/workflows/test-coverage.yaml       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index c51a3db1b..035e3b64b 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -408,7 +408,7 @@ jobs:
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
           && inputs.install-deps-from-package-repositories == ''
-        uses: insightsengineering/setup-r-dependencies@setup-binary-package-repository-for-different-platforms
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index da9945543..8406b052c 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -243,7 +243,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@setup-binary-package-repository-for-different-platforms
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}

From 171e39cc07ec0cba2f38a3b8a0f8c8759c75cd58 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Mon, 23 Sep 2024 16:37:17 +0200
Subject: [PATCH 23/31] Revert "Revert "chore: test binary dependencies""

This reverts commit 56ed6404cb5616a269f20ae7f31f18f3d27c7add.
---
 .github/workflows/build-check-install.yaml | 2 +-
 .github/workflows/test-coverage.yaml       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 035e3b64b..c51a3db1b 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -408,7 +408,7 @@ jobs:
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
           && inputs.install-deps-from-package-repositories == ''
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@setup-binary-package-repository-for-different-platforms
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 8406b052c..da9945543 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -243,7 +243,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@setup-binary-package-repository-for-different-platforms
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}

From 55685758bcfce8c341540f49d580e140583b97f1 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Mon, 23 Sep 2024 16:59:06 +0200
Subject: [PATCH 24/31] Revert "Revert "Revert "chore: test binary
 dependencies"""

This reverts commit 171e39cc07ec0cba2f38a3b8a0f8c8759c75cd58.
---
 .github/workflows/build-check-install.yaml | 2 +-
 .github/workflows/test-coverage.yaml       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index c51a3db1b..035e3b64b 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -408,7 +408,7 @@ jobs:
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
           && inputs.install-deps-from-package-repositories == ''
-        uses: insightsengineering/setup-r-dependencies@setup-binary-package-repository-for-different-platforms
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index da9945543..8406b052c 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -243,7 +243,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@setup-binary-package-repository-for-different-platforms
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}

From 67f88715aa911b1011da1d707081dc1daa7ee46a Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 24 Sep 2024 11:11:58 +0200
Subject: [PATCH 25/31] chore: use
 setup-r-dependencies@setup-binary-package-repository-for-different-platforms

---
 .github/workflows/build-check-install.yaml | 2 +-
 .github/workflows/roxygen.yaml             | 2 +-
 .github/workflows/test-coverage.yaml       | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 035e3b64b..c51a3db1b 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -408,7 +408,7 @@ jobs:
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
           && inputs.install-deps-from-package-repositories == ''
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@setup-binary-package-repository-for-different-platforms
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index 2e54b44ae..de416f82a 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -151,7 +151,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@setup-binary-package-repository-for-different-platforms
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 8406b052c..da9945543 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -243,7 +243,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@setup-binary-package-repository-for-different-platforms
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}

From e178a40a4d5b927b11a96c0dad752e10c48a0f0e Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 26 Sep 2024 10:14:07 +0200
Subject: [PATCH 26/31] Revert "chore: use
 setup-r-dependencies@setup-binary-package-repository-for-different-platforms"

This reverts commit 67f88715aa911b1011da1d707081dc1daa7ee46a.
---
 .github/workflows/build-check-install.yaml | 2 +-
 .github/workflows/roxygen.yaml             | 2 +-
 .github/workflows/test-coverage.yaml       | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index c51a3db1b..035e3b64b 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -408,7 +408,7 @@ jobs:
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
           && inputs.install-deps-from-package-repositories == ''
-        uses: insightsengineering/setup-r-dependencies@setup-binary-package-repository-for-different-platforms
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index de416f82a..2e54b44ae 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -151,7 +151,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@setup-binary-package-repository-for-different-platforms
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index da9945543..8406b052c 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -243,7 +243,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@setup-binary-package-repository-for-different-platforms
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}

From 6d6d8f7c60fa043d992e2666486434ac00c55afc Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 26 Sep 2024 12:19:53 +0200
Subject: [PATCH 27/31] docs: update lookup-refs input description

---
 .github/workflows/roxygen.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index 2e54b44ae..ad7c02b52 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -51,7 +51,8 @@ on:
         default: staged-dependencies
       lookup-refs:
         description: |
-          List of package references to be used by setup-r-dependencies action if deps-installation-method == 'setup-r-dependencies'.
+          Passed to insightsengineering/setup-r-dependencies. See its documentation.
+          Used only if deps-installation-method == 'setup-r-dependencies'.
         required: false
         type: string
         default: ""

From f5bf0cfdaef949512b095ee840bf888da7ac7a06 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 26 Sep 2024 12:57:09 +0200
Subject: [PATCH 28/31] fix: don't restore DESCRIPTION in roxygen workflow

---
 .github/workflows/roxygen.yaml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index ad7c02b52..f8295f090 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -158,13 +158,6 @@ jobs:
           github-token: ${{ steps.github-token.outputs.token }}
           repository-path: ${{ github.event.repository.name }}
 
-      # setup-r-dependencies makes modifications to DESCRIPTION which
-      # should not be committed during Roxygen auto-update.
-      - name: Restore DESCRIPTION ⚙️
-        run: git restore DESCRIPTION
-        working-directory: ${{ github.event.repository.name }}
-        shell: bash
-
       - name: Generate man pages 📄
         run: |
           logfile <- "roxygen_${{ github.event.repository.name }}.log"

From be437d54f87a0f8689ef957c76ceff88659703fe Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 26 Sep 2024 13:49:48 +0200
Subject: [PATCH 29/31] chore: use
 insightsengineering/setup-r-dependencies@fix/copy-and-restore-description

---
 .github/workflows/build-check-install.yaml | 2 +-
 .github/workflows/roxygen.yaml             | 2 +-
 .github/workflows/test-coverage.yaml       | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 035e3b64b..e0f00c864 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -408,7 +408,7 @@ jobs:
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
           && inputs.install-deps-from-package-repositories == ''
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@fix/copy-and-restore-description
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index f8295f090..4e4e6698b 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -152,7 +152,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@fix/copy-and-restore-description
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 8406b052c..66475e631 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -243,7 +243,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@fix/copy-and-restore-description
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}

From 49c69c09b6222caf45d33f2e2d6101a7ddbfc1f7 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 26 Sep 2024 14:39:49 +0200
Subject: [PATCH 30/31] chore: use
 insightsengineering/setup-r-dependencies@fix/copy-and-restore-description in
 rhub.yaml

---
 .github/workflows/rhub.yaml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml
index 528200987..b475577ca 100644
--- a/.github/workflows/rhub.yaml
+++ b/.github/workflows/rhub.yaml
@@ -95,11 +95,12 @@ jobs:
           job-config: ${{ matrix.config.job-config }}
 
       - name: Prepare DESCRIPTION file
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@fix/copy-and-restore-description
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           skip-install: true
           github-token: ${{ steps.github-token.outputs.token }}
+          restore-description: false
 
       - uses: r-hub/actions/setup-deps@v1
         with:
@@ -146,11 +147,12 @@ jobs:
           job-config: ${{ matrix.config.job-config }}
 
       - name: Setup R dependencies
-        uses: insightsengineering/setup-r-dependencies@v1
+        uses: insightsengineering/setup-r-dependencies@fix/copy-and-restore-description
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           skip-install: true
           github-token: ${{ steps.github-token.outputs.token }}
+          restore-description: false
 
       - uses: r-hub/actions/setup-deps@v1
         with:

From bbaf1eb6c954c1c58ec928269ec09454d83664b1 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 26 Sep 2024 16:22:27 +0200
Subject: [PATCH 31/31] chore: restore
 insightsengineering/setup-r-dependencies@v1

---
 .github/workflows/build-check-install.yaml | 2 +-
 .github/workflows/rhub.yaml                | 4 ++--
 .github/workflows/roxygen.yaml             | 2 +-
 .github/workflows/test-coverage.yaml       | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index e0f00c864..035e3b64b 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -408,7 +408,7 @@ jobs:
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
           && inputs.install-deps-from-package-repositories == ''
-        uses: insightsengineering/setup-r-dependencies@fix/copy-and-restore-description
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml
index b475577ca..7fdcb07fc 100644
--- a/.github/workflows/rhub.yaml
+++ b/.github/workflows/rhub.yaml
@@ -95,7 +95,7 @@ jobs:
           job-config: ${{ matrix.config.job-config }}
 
       - name: Prepare DESCRIPTION file
-        uses: insightsengineering/setup-r-dependencies@fix/copy-and-restore-description
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           skip-install: true
@@ -147,7 +147,7 @@ jobs:
           job-config: ${{ matrix.config.job-config }}
 
       - name: Setup R dependencies
-        uses: insightsengineering/setup-r-dependencies@fix/copy-and-restore-description
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           skip-install: true
diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
index 4e4e6698b..f8295f090 100644
--- a/.github/workflows/roxygen.yaml
+++ b/.github/workflows/roxygen.yaml
@@ -152,7 +152,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@fix/copy-and-restore-description
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 66475e631..8406b052c 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -243,7 +243,7 @@ jobs:
       - name: Setup R dependencies 🎦
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
-        uses: insightsengineering/setup-r-dependencies@fix/copy-and-restore-description
+        uses: insightsengineering/setup-r-dependencies@v1
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           github-token: ${{ steps.github-token.outputs.token }}