From 9ffe90ee82351f75b63c6a2277054c414de1b113 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Fri, 3 Jan 2025 08:52:50 +0100
Subject: [PATCH 01/14] chore: restored spellcheck

---
 .github/workflows/main.yml | 73 ++++++++++++++++++--------------------
 1 file changed, 35 insertions(+), 38 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 6e9e7404..b2e48b2c 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -3,7 +3,7 @@
 # the developement process. When package is ready to
 # be published, revisit and add release-related
 # workflows.
-name: admiral CI/CD Workflows
+name: admiral CI/CD Wortkflows
 
 on:
   workflow_dispatch:
@@ -32,49 +32,46 @@ jobs:
         id: get_r_version
         run: echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT
         shell: bash
+
   spellcheck:
     name: Spelling
-    uses: pharmaverse/admiralci/.github/workflows/spellcheck.yml@main
-    if: github.event_name == 'pull_request'
-    needs: get_r_version
-    with:
-      r-version: "${{ needs.get_r_version.outputs.r-version }}"
-  linter:
-    name: Lint
-    uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main
-    needs: get_r_version
-    if: github.event_name == 'pull_request'
-    with:
-      r-version: "${{ needs.get_r_version.outputs.r-version }}"
-  man-pages:
-    name: Man Pages
-    uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main
-    if: github.event_name == 'pull_request'
-    needs: get_r_version
-    with:
-      r-version: "${{ needs.get_r_version.outputs.r-version }}"
-  tests:
-    name: Tests
     runs-on: ubuntu-latest
     needs: get_r_version
     container:
       image: "ghcr.io/pharmaverse/admiralci-${{ needs.get_r_version.outputs.r-version }}:latest"
     steps:
-        - name: Checkout code
-          uses: actions/checkout@v2
+      - name: Get branch names
+        id: branch-name
+        uses: tj-actions/branch-names@v8
+
+      - name: Checkout repo
+        uses: actions/checkout@v4.2.2
+        if: github.event_name == 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+
+      - name: Checkout repository
+        uses: actions/checkout@v4.2.2
+        if: github.event_name != 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+
+      - name: Restore cache
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.staged.dependencies
+          key: staged-deps
 
-        - name: Install dependencies
-          run: |
-            Rscript -e 'remotes::install_deps(dependencies = TRUE)'
+      - name: Run Staged dependencies
+        uses: insightsengineering/staged-dependencies-action@v1
+        with:
+          run-system-dependencies: true
+          renv-restore: false
+          enable-check: false
+          direction: upstream
+          git-ref: ${{ steps.branch-name.outputs.current_branch }}
 
-        - name: Run tests
-          shell: Rscript {0}
-          run: |
-            devtools::load_all(".")
-            devtools::test()
-  check:
-    name: Check
-    uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
-    if: github.event_name == 'pull_request'
-    with:
-        error-on: error
+      - name: Run Spellcheck
+        uses: insightsengineering/r-spellcheck-action@v3
\ No newline at end of file

From e149ec6687e89b858894cf1154f4b92bd2c87f67 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Fri, 3 Jan 2025 09:08:39 +0100
Subject: [PATCH 02/14] chore: restored linting

---
 .github/workflows/main.yml | 58 +++++++++++++++++++++++++++++++++++++-
 1 file changed, 57 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index b2e48b2c..b3d672e1 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -74,4 +74,60 @@ jobs:
           git-ref: ${{ steps.branch-name.outputs.current_branch }}
 
       - name: Run Spellcheck
-        uses: insightsengineering/r-spellcheck-action@v3
\ No newline at end of file
+        uses: insightsengineering/r-spellcheck-action@v3
+
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    needs: get_r_version
+    container:
+      image: "ghcr.io/pharmaverse/admiralci-${{ needs.get_r_version.outputs.r-version }}:latest"
+    steps:
+      - name: Get branch names
+        id: branch-name
+        uses: tj-actions/branch-names@v8
+
+      - name: Checkout repo
+        uses: actions/checkout@v4.2.2
+        if: github.event_name == 'pull_request'
+        with:
+            ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+            repository: ${{ github.event.pull_request.head.repo.full_name }}
+
+      - name: Checkout repository
+        uses: actions/checkout@v4.2.2
+        if: github.event_name != 'pull_request'
+        with:
+            ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+
+      - name: Restore cache
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.staged.dependencies
+          key: staged-deps
+
+      - name: Run Staged dependencies
+        uses: insightsengineering/staged-dependencies-action@v1
+        with:
+            run-system-dependencies: true
+            renv-restore: false
+            enable-check: false
+            direction: upstream
+            git-ref: ${{ steps.branch-name.outputs.current_branch }}
+        env:
+            GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Install latest release of lintr
+        run: |
+            install.packages("lintr", repos = "https://packagemanager.posit.co/cran/latest/")
+        shell: Rscript {0}
+
+      - name: Lint
+        run: |
+          lints <- lintr::lint_package()
+          if (length(lints) > 0L) {
+              print(lints)
+              stop("Lints detected. Please review and adjust code according to the comments provided.", call. = FALSE)
+          }
+        shell: Rscript {0}
\ No newline at end of file

From e52220808ed4b8e7a7df21d8f4539d0f4ec6b4d7 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Fri, 3 Jan 2025 09:25:09 +0100
Subject: [PATCH 03/14] chore: restore man-pages

---
 .github/workflows/main.yml | 75 +++++++++++++++++++++++++++++++++++++-
 1 file changed, 74 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index b3d672e1..734a72b3 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -130,4 +130,77 @@ jobs:
               print(lints)
               stop("Lints detected. Please review and adjust code according to the comments provided.", call. = FALSE)
           }
-        shell: Rscript {0}
\ No newline at end of file
+        shell: Rscript {0}
+
+  man-pages:
+    name: Man Pages
+    runs-on: ubuntu-latest
+    needs: get_r_version
+    container:
+      image: "ghcr.io/pharmaverse/admiralci-${{ needs.get_r_version.outputs.r-version }}:latest"
+    steps:
+      - name: Get branch names
+        id: branch-name
+        uses: tj-actions/branch-names@v8
+
+      - name: Checkout repo
+        uses: actions/checkout@v4.2.2
+        if: github.event_name == 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+
+      - name: Restore cache
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.staged.dependencies
+          key: staged-deps
+
+      - name: Run Staged dependencies
+        uses: insightsengineering/staged-dependencies-action@v1
+        with:
+          run-system-dependencies: false
+          renv-restore: false
+          enable-check: false
+          direction: upstream
+          git-ref: ${{ steps.branch-name.outputs.current_branch }}
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Install dependencies from DESCRIPTION
+        run: |
+          remotes::install_local(force = TRUE, dependencies = TRUE)
+        shell: Rscript {0}
+        env:
+          R_REMOTES_STANDALONE: "true"
+
+      - name: Generate man pages
+        run: roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))
+        shell: Rscript {0}
+
+      - name: Set-up safe dir
+        run: git config --global --add safe.directory "${GITHUB_WORKSPACE}"
+        shell: bash
+
+      - name: Roxygen check
+        run: |
+          git status -s
+          if [[ -n `git status -s | grep -E "man|DESCRIPTION"` ]]
+          then {
+            ROXYGEN_VERSION="$(Rscript -e 'packageVersion("roxygen2")' | awk '{print $NF}')"
+            echo "🙈 Manuals are not up-to-date with roxygen comments!"
+            echo "🔀 The following differences were noted:"
+            git diff man/* DESCRIPTION
+            echo -e "\n💻 Please rerun the following command on your workstation and push your changes"
+            echo "--------------------------------------------------------------------"
+            echo "roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))"
+            echo "--------------------------------------------------------------------"
+            echo "ℹ roxygen2 version that was used in this workflow: $ROXYGEN_VERSION"
+            echo "🙏 Please ensure that the 'RoxygenNote' field in the DESCRIPTION file matches this version"
+            exit 1
+          } else {
+            echo "💚 Manuals are up-to-date with roxygen comments"
+          }
+          fi
+        shell: bash
+      

From 3b24b8b10e2e5a02afd2163d4e4067aaef51e798 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Fri, 3 Jan 2025 09:25:48 +0100
Subject: [PATCH 04/14] chore: restore tests

---
 .github/workflows/main.yml | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 734a72b3..31465046 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -203,4 +203,28 @@ jobs:
           }
           fi
         shell: bash
+  tests:
+    name: Tests
+    runs-on: ubuntu-latest
+    needs: get_r_version
+    container:
+      image: "ghcr.io/pharmaverse/admiralci-${{ needs.get_r_version.outputs.r-version }}:latest"
+    steps:
+        - name: Checkout code
+          uses: actions/checkout@v2
+
+        - name: Install system dependencies
+          run: |
+            apt-get install -y --no-install-recommends \
+                libudunits2-dev
+
+        - name: Install dependencies
+          run: |
+            Rscript -e 'remotes::install_deps(dependencies = TRUE)'
+
+        - name: Run tests
+          shell: Rscript {0}
+          run: |
+            devtools::load_all(".")
+            devtools::test()
       

From 94c80f4d3cd5fc16796179f55700bc0e6788ca71 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Tue, 7 Jan 2025 07:09:16 +0100
Subject: [PATCH 05/14] feat: restored R CMD Check, as-is in admiralci package

---
 .github/workflows/main.yml | 202 +++++++++++++++++++++++++++++++++++++
 1 file changed, 202 insertions(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 31465046..382bbd21 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -227,4 +227,206 @@ jobs:
           run: |
             devtools::load_all(".")
             devtools::test()
+  
+  check:
+    runs-on: ubuntu-latest
+    needs: get_r_version
+    container:
+      image: "ghcr.io/pharmaverse/admiralci-${{ matrix.r_version }}:latest"
+    name: (${{ matrix.r_version }})
+    strategy:
+      fail-fast: false
+      matrix:
+        r_version: ["release", "devel", "oldrel"]
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: true
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      R_REPOS: "https://cran.r-project.org"
+      DEPS_IGNORE: >-
+        pharmaversesdtm,
+        pharmaverseadam,
+        admiral,
+        admiraldev,
+        admiralophtha,
+        admiralonco,
+        admiralvaccine,
+        staged.dependencies
+    steps:
+      - name: Get branch names
+        id: branch-name
+        uses: tj-actions/branch-names@v8
+
+      - name: Checkout repo (PR) 🛎
+        uses: actions/checkout@v4.2.2
+        if: |
+          github.event_name == 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+
+      - name: Checkout repository
+        uses: actions/checkout@v4.2.2
+        if: |
+          github.event_name != 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+
+      - name: Restore cache
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.staged.dependencies
+          key: staged-deps
+
+      - name: Run Staged dependencies
+        uses: insightsengineering/staged-dependencies-action@v1
+        if: |
+          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
+          matrix.r_version != 'devel'
+        with:
+          git-ref: ${{ steps.branch-name.outputs.current_branch }}
+          run-system-dependencies: false
+          renv-restore: false
+          enable-check: false
+          cran-repos: "https://cloud.r-project.org"
+          direction: upstream
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Install dependencies from DESCRIPTION
+        if: |
+          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
+          matrix.r_version != 'devel'
+        run: |
+          remotes::install_local(force = TRUE, dependencies = TRUE)
+        shell: Rscript {0}
+
+      - name: Upload dependencies artifact
+        if: |
+          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
+          matrix.r_version != 'devel'
+        run: |
+          dir.create("/workspace/tmp")
+          library(dplyr)
+          installed_packages <- as.data.frame(installed.packages())
+          packages_to_remove <- Sys.getenv("DEPS_IGNORE", "")
+          packages_to_remove <- unlist(strsplit(packages_to_remove, ","))
+          installed_packages <- installed_packages %>% filter(LibPath != "/usr/local/lib/R/library") %>%  # remove pre-built deps
+          filter(!Package %in% packages_to_remove)
+          # save deps as csv file
+          write.csv(installed_packages, "/workspace/tmp/deps-${{ matrix.r_version }}.csv", row.names = FALSE)
+          # create also renv.lock file
+          setwd("/workspace/tmp")
+
+          renv_lock <- list(
+            "R" = list(
+              "Version" = paste(R.version$major, R.version$minor, sep=".")
+            ),
+            "Repositories" = list(
+                list(Name = "CRAN", URL = Sys.getenv("R_REPOS"))
+              ),
+            "Packages" = list()
+          )
+
+          # Populate with information about each package
+          for (package in installed_packages$Package) {
+            dep_name <- package
+            dep_version <- installed_packages[installed_packages$Package == package, "Version"]
+
+            version_parts <- strsplit(dep_version, "\\.")[[1]]
+            if (length(version_parts) == 4) {
+              print(sprintf("skipping installation of dep %s", dep_name))
+            } else {
+              print(sprintf("append dependency %s - version %s", dep_name, dep_version))
+              requirements <- tools::package_dependencies(dep_name, recursive = TRUE)
+              have_requirements <- length(requirements[[1]]) > 0
+              if (have_requirements) {
+                  renv_lock[["Packages"]][[dep_name]] <- list(
+                      "Package" = dep_name,
+                      "Version" = dep_version,
+                      "Source" = "Repository",
+                      "Repository" = "CRAN",
+                      "Requirements" = requirements[[dep_name]]
+                  )
+              } else {
+                  renv_lock[["Packages"]][[dep_name]] <- list(
+                      "Package" = dep_name,
+                      "Version" = dep_version,
+                      "Source" = "Repository",
+                      "Repository" = "CRAN"
+                  )
+              }
+            }
+          }
+
+          # Write the list to a JSON file (renv.lock)
+          writeLines(jsonlite::toJSON(renv_lock, pretty = TRUE, auto_unbox = TRUE), "renv-${{ matrix.r_version }}.lock")
+          print("generated renv.lock content")
+          system("cat renv-${{ matrix.r_version }}.lock")
+        shell: Rscript {0}
+
+      - name: Upload deps.csv and renv.lock artifacts
+        uses: actions/upload-artifact@v4
+        if: |
+          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
+          matrix.r_version != 'devel'
+        with:
+          name: deps-${{ matrix.r_version }}
+          path: |
+            /workspace/tmp/
+
+      - name: Check Version
+        id: check_version
+        if: |
+          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
+          matrix.r_version != 'devel'
+        run: |
+          maintenance_version="F"
+          description_dat <- readLines("DESCRIPTION")
+          for (i in seq_along(description_dat)) {
+            if (grepl("^Version:", description_dat[i])) {
+              current_version <- sub("^Version: ", "", description_dat[i])
+              version_parts <- strsplit(current_version, "\\.")[[1]]
+              # check if maintenance version
+              if (length(version_parts) == 4) {
+                print("Maintenance version detected (format X.Y.Z.M with M >= 9000)")
+                maintenance_version="T"
+              }
+            }
+          }
+          cat(sprintf("maintenance_version=%s", maintenance_version), file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        if: |
+          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
+          matrix.r_version != 'devel'
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+          _R_CHECK_FORCE_SUGGESTS_: false
+        run: |
+          unlink("tmp",recursive=TRUE)
+          if ("${{ steps.check_version.outputs.maintenance_version }}" == "T"){
+            Sys.setenv("_R_CHECK_CRAN_INCOMING_SKIP_LARGE_VERSION_" = TRUE)
+          }
+          if (!requireNamespace("rcmdcheck", quietly = TRUE)) install.packages("rcmdcheck")
+          options(crayon.enabled = TRUE)
+          check_error_on <- "error"
+          if (check_error_on == "") {
+            check_error_on <- "note"
+          }
+          rcmdcheck::rcmdcheck(
+            args = c("--no-manual", "--as-cran"),
+            error_on = check_error_on,
+            check_dir = "check"
+          )
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: r${{ matrix.r_version }}-results
+          path: check
       

From a99da4cc3fb2e60c70f7d6378d5820c4993f8e97 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Tue, 7 Jan 2025 14:17:49 +0100
Subject: [PATCH 06/14] chore: installing deps using pak

---
 .github/workflows/main.yml | 17 ++++++-----------
 DESCRIPTION                |  1 +
 2 files changed, 7 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 382bbd21..2fd9cacf 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -169,7 +169,7 @@ jobs:
 
       - name: Install dependencies from DESCRIPTION
         run: |
-          remotes::install_local(force = TRUE, dependencies = TRUE)
+          pak::local_install_deps(dependencies = TRUE)
         shell: Rscript {0}
         env:
           R_REMOTES_STANDALONE: "true"
@@ -213,14 +213,9 @@ jobs:
         - name: Checkout code
           uses: actions/checkout@v2
 
-        - name: Install system dependencies
-          run: |
-            apt-get install -y --no-install-recommends \
-                libudunits2-dev
-
         - name: Install dependencies
           run: |
-            Rscript -e 'remotes::install_deps(dependencies = TRUE)'
+            pak::local_install_deps(dependencies = TRUE)
 
         - name: Run tests
           shell: Rscript {0}
@@ -230,10 +225,10 @@ jobs:
   
   check:
     runs-on: ubuntu-latest
-    needs: get_r_version
+    needs: tests
     container:
       image: "ghcr.io/pharmaverse/admiralci-${{ matrix.r_version }}:latest"
-    name: (${{ matrix.r_version }})
+    name: Check (${{ matrix.r_version }})
     strategy:
       fail-fast: false
       matrix:
@@ -257,7 +252,7 @@ jobs:
         id: branch-name
         uses: tj-actions/branch-names@v8
 
-      - name: Checkout repo (PR) 🛎
+      - name: Checkout repo
         uses: actions/checkout@v4.2.2
         if: |
           github.event_name == 'pull_request'
@@ -299,7 +294,7 @@ jobs:
           (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
           matrix.r_version != 'devel'
         run: |
-          remotes::install_local(force = TRUE, dependencies = TRUE)
+          pak::local_install_deps(dependencies = TRUE)
         shell: Rscript {0}
 
       - name: Upload dependencies artifact
diff --git a/DESCRIPTION b/DESCRIPTION
index 2466aac4..ddc33acf 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -55,6 +55,7 @@ Imports:
     tidyr,
     tools,
     utils,
+    units,
     zip
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

From 2436ea9041f8646219965edc035b650bbd7914a3 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Tue, 7 Jan 2025 14:33:42 +0100
Subject: [PATCH 07/14] chore: added docstrings, minor readability improvements

---
 .github/workflows/main.yml | 52 ++++++++++++--------------------------
 1 file changed, 16 insertions(+), 36 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 2fd9cacf..d68341c4 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -3,7 +3,14 @@
 # the developement process. When package is ready to
 # be published, revisit and add release-related
 # workflows.
-name: admiral CI/CD Wortkflows
+# Instead of using reusable actions provided by admiralci,
+# the actions are inlined in the workflow file. This is
+# because some of the R dependencies required system packages
+# not available/installable using reusable actions.
+# If any updates are available, the workflow should be
+# updated manually.
+# Last update: 2025-01-07
+name: Modfified Admiral CI/CD Wortkflows
 
 on:
   workflow_dispatch:
@@ -51,12 +58,6 @@ jobs:
           ref: ${{ steps.branch-name.outputs.head_ref_branch }}
           repository: ${{ github.event.pull_request.head.repo.full_name }}
 
-      - name: Checkout repository
-        uses: actions/checkout@v4.2.2
-        if: github.event_name != 'pull_request'
-        with:
-          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
-
       - name: Restore cache
         uses: actions/cache@v4
         with:
@@ -94,12 +95,6 @@ jobs:
             ref: ${{ steps.branch-name.outputs.head_ref_branch }}
             repository: ${{ github.event.pull_request.head.repo.full_name }}
 
-      - name: Checkout repository
-        uses: actions/checkout@v4.2.2
-        if: github.event_name != 'pull_request'
-        with:
-            ref: ${{ steps.branch-name.outputs.head_ref_branch }}
-
       - name: Restore cache
         uses: actions/cache@v4
         with:
@@ -115,22 +110,21 @@ jobs:
             enable-check: false
             direction: upstream
             git-ref: ${{ steps.branch-name.outputs.current_branch }}
-        env:
-            GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Install latest release of lintr
+        shell: Rscript {0}
         run: |
             install.packages("lintr", repos = "https://packagemanager.posit.co/cran/latest/")
-        shell: Rscript {0}
+        
 
       - name: Lint
+        shell: Rscript {0}
         run: |
           lints <- lintr::lint_package()
           if (length(lints) > 0L) {
               print(lints)
               stop("Lints detected. Please review and adjust code according to the comments provided.", call. = FALSE)
           }
-        shell: Rscript {0}
 
   man-pages:
     name: Man Pages
@@ -164,15 +158,10 @@ jobs:
           enable-check: false
           direction: upstream
           git-ref: ${{ steps.branch-name.outputs.current_branch }}
-        env:
-          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Install dependencies from DESCRIPTION
+      - name: Install dependencies
         run: |
-          pak::local_install_deps(dependencies = TRUE)
-        shell: Rscript {0}
-        env:
-          R_REMOTES_STANDALONE: "true"
+          Rscript -e 'pak::local_install_deps(dependencies = TRUE)'
 
       - name: Generate man pages
         run: roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))
@@ -203,6 +192,7 @@ jobs:
           }
           fi
         shell: bash
+
   tests:
     name: Tests
     runs-on: ubuntu-latest
@@ -215,7 +205,7 @@ jobs:
 
         - name: Install dependencies
           run: |
-            pak::local_install_deps(dependencies = TRUE)
+            Rscript -e 'pak::local_install_deps(dependencies = TRUE)'
 
         - name: Run tests
           shell: Rscript {0}
@@ -260,13 +250,6 @@ jobs:
           ref: ${{ steps.branch-name.outputs.head_ref_branch }}
           repository: ${{ github.event.pull_request.head.repo.full_name }}
 
-      - name: Checkout repository
-        uses: actions/checkout@v4.2.2
-        if: |
-          github.event_name != 'pull_request'
-        with:
-          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
-
       - name: Restore cache
         uses: actions/cache@v4
         with:
@@ -286,16 +269,13 @@ jobs:
           enable-check: false
           cran-repos: "https://cloud.r-project.org"
           direction: upstream
-        env:
-          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Install dependencies from DESCRIPTION
         if: |
           (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
           matrix.r_version != 'devel'
         run: |
-          pak::local_install_deps(dependencies = TRUE)
-        shell: Rscript {0}
+          Rscript -e 'pak::local_install_deps(dependencies = TRUE)'
 
       - name: Upload dependencies artifact
         if: |

From 0b06b6e2b83ec17c24600a804bce29215de1db15 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Tue, 7 Jan 2025 14:36:22 +0100
Subject: [PATCH 08/14] chore: other workflows are required before running
 check

---
 .github/workflows/main.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index d68341c4..d36165f5 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -10,7 +10,7 @@
 # If any updates are available, the workflow should be
 # updated manually.
 # Last update: 2025-01-07
-name: Modfified Admiral CI/CD Wortkflows
+name: Modified Admiral CI/CD Wortkflows
 
 on:
   workflow_dispatch:
@@ -215,7 +215,11 @@ jobs:
   
   check:
     runs-on: ubuntu-latest
-    needs: tests
+    needs: 
+      - spellcheck
+      - tests
+      - lint
+      - man-pages
     container:
       image: "ghcr.io/pharmaverse/admiralci-${{ matrix.r_version }}:latest"
     name: Check (${{ matrix.r_version }})

From 2f07da8fbe2aa7a7de2d5608516ff2728d18cd23 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Tue, 7 Jan 2025 14:49:34 +0100
Subject: [PATCH 09/14] chore: more docs

---
 .github/workflows/main.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index d36165f5..d820e916 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -3,6 +3,8 @@
 # the developement process. When package is ready to
 # be published, revisit and add release-related
 # workflows.
+# The below workflows are based on those provided by admiralci.
+# The testing workflow is custom.
 # Instead of using reusable actions provided by admiralci,
 # the actions are inlined in the workflow file. This is
 # because some of the R dependencies required system packages

From c52bbec435322c3238555f1b9c4ba503a9abe5f4 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Thu, 9 Jan 2025 08:57:28 +0100
Subject: [PATCH 10/14] chore: copy over admiralci workflows with minimal
 changes

---
 .github/workflows/lintr.yml       | 145 ++++++++++++
 .github/workflows/main.yml        | 379 ++----------------------------
 .github/workflows/man-pages.yml   | 111 +++++++++
 .github/workflows/r-cmd-check.yml | 227 ++++++++++++++++++
 .github/workflows/spellcheck.yml  |  88 +++++++
 5 files changed, 597 insertions(+), 353 deletions(-)
 create mode 100644 .github/workflows/lintr.yml
 create mode 100644 .github/workflows/man-pages.yml
 create mode 100644 .github/workflows/r-cmd-check.yml
 create mode 100644 .github/workflows/spellcheck.yml

diff --git a/.github/workflows/lintr.yml b/.github/workflows/lintr.yml
new file mode 100644
index 00000000..2f855d93
--- /dev/null
+++ b/.github/workflows/lintr.yml
@@ -0,0 +1,145 @@
+on:
+  workflow_dispatch:
+    inputs:
+      r-version:
+        description: "The version of R to use"
+        default: "release"
+        required: false
+        type: choice
+        options:
+          - devel
+          - latest
+      lint-all-files:
+        description: "Lint all files every time"
+        default: "false"
+        required: false
+        type: string
+      latest-lintr:
+        description: "Latest lintr CRAN release"
+        default: "false"
+        required: false
+        type: string
+      install-package:
+        description: "Install package locally."
+        default: "false"
+        required: false
+        type: string
+  workflow_call:
+    inputs:
+      r-version:
+        description: "The version of R to use"
+        default: "release"
+        required: false
+        type: string
+      lint-all-files:
+        description: "Lint all files every time"
+        default: "false"
+        required: false
+        type: string
+      latest-lintr:
+        description: "Latest lintr CRAN release"
+        default: "false"
+        required: false
+        type: string
+      install-package:
+        description: "Install package locally."
+        default: "false"
+        required: false
+        type: string
+
+name: Lint
+
+concurrency:
+  group: lint-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    container:
+      image: "ghcr.io/pharmaverse/admiralci-${{ inputs.r-version }}:latest"
+    if: >
+      !contains(github.event.commits[0].message, '[skip lint]')
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      ##################### BEGIN boilerplate steps #####################
+      - name: Get branch names
+        id: branch-name
+        uses: tj-actions/branch-names@v8
+
+      - name: Checkout repo (PR) 🛎
+        uses: actions/checkout@v4.2.2
+        if: github.event_name == 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+
+      - name: Checkout repository
+        uses: actions/checkout@v4.2.2
+        if: github.event_name != 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+
+      - name: Restore cache
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.staged.dependencies
+          key: staged-deps
+
+      - name: Run Staged dependencies
+        uses: insightsengineering/staged-dependencies-action@v1
+        with:
+          run-system-dependencies: true
+          renv-restore: false
+          enable-check: false
+          direction: upstream
+          git-ref: ${{ steps.branch-name.outputs.current_branch }}
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Install latest release of lintr
+        run: |
+          install.packages("lintr", repos = "https://packagemanager.posit.co/cran/latest/")
+        shell: Rscript {0}
+        if: ${{ inputs.latest-lintr == 'true' }}
+
+      - name: Install package
+        run: renv::install(".", dependencies = "no-deps")
+        shell: Rscript {0}
+        if: ${{ inputs.install-package == 'true' }}
+      ##################### END boilerplate steps #####################
+
+      - name: Changed files
+        id: files
+        uses: Ana06/get-changed-files@v2.2.0
+        with:
+          format: "json"
+          filter: "*"
+
+      - name: Lint
+        run: |
+          exclusions_list <- NULL
+          if (!identical("${{ inputs.lint-all-files }}", "true")) {
+            changed_files <- jsonlite::fromJSON('${{ steps.files.outputs.added_modified }}')
+            all_files <- list.files(recursive = TRUE)
+            exclusions_list <- if (any(changed_files %in% c(".lintr", "renv.lock"))) {
+              as.list(setdiff(all_files, changed_files))
+            } else {
+              NULL
+            }
+          }
+          lints <- lintr::lint_package(exclusions = exclusions_list)
+          saveRDS(lints, file = "lints.rds")
+        shell: Rscript {0}
+
+      - name: Error if lints are detected
+        run: |
+          lints <- readRDS("lints.rds")
+          if (length(lints) > 0L) {
+            print(lints)
+            stop("Lints detected. Please review and adjust code according to the comments provided.", call. = FALSE)
+          }
+        shell: Rscript {0}
\ No newline at end of file
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index d820e916..468da33f 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -3,16 +3,7 @@
 # the developement process. When package is ready to
 # be published, revisit and add release-related
 # workflows.
-# The below workflows are based on those provided by admiralci.
-# The testing workflow is custom.
-# Instead of using reusable actions provided by admiralci,
-# the actions are inlined in the workflow file. This is
-# because some of the R dependencies required system packages
-# not available/installable using reusable actions.
-# If any updates are available, the workflow should be
-# updated manually.
-# Last update: 2025-01-07
-name: Modified Admiral CI/CD Wortkflows
+name: admiral CI/CD Workflows
 
 on:
   workflow_dispatch:
@@ -41,160 +32,28 @@ jobs:
         id: get_r_version
         run: echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT
         shell: bash
-
   spellcheck:
     name: Spelling
-    runs-on: ubuntu-latest
+    uses: ./.github/workflows/spellcheck.yml
+    if: github.event_name == 'pull_request'
     needs: get_r_version
-    container:
-      image: "ghcr.io/pharmaverse/admiralci-${{ needs.get_r_version.outputs.r-version }}:latest"
-    steps:
-      - name: Get branch names
-        id: branch-name
-        uses: tj-actions/branch-names@v8
-
-      - name: Checkout repo
-        uses: actions/checkout@v4.2.2
-        if: github.event_name == 'pull_request'
-        with:
-          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
-          repository: ${{ github.event.pull_request.head.repo.full_name }}
-
-      - name: Restore cache
-        uses: actions/cache@v4
-        with:
-          path: |
-            ~/.staged.dependencies
-          key: staged-deps
-
-      - name: Run Staged dependencies
-        uses: insightsengineering/staged-dependencies-action@v1
-        with:
-          run-system-dependencies: true
-          renv-restore: false
-          enable-check: false
-          direction: upstream
-          git-ref: ${{ steps.branch-name.outputs.current_branch }}
-
-      - name: Run Spellcheck
-        uses: insightsengineering/r-spellcheck-action@v3
-
-  lint:
+    with:
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
+  linter:
     name: Lint
-    runs-on: ubuntu-latest
+    uses: ./.github/workflows/lintr.yml
     needs: get_r_version
-    container:
-      image: "ghcr.io/pharmaverse/admiralci-${{ needs.get_r_version.outputs.r-version }}:latest"
-    steps:
-      - name: Get branch names
-        id: branch-name
-        uses: tj-actions/branch-names@v8
-
-      - name: Checkout repo
-        uses: actions/checkout@v4.2.2
-        if: github.event_name == 'pull_request'
-        with:
-            ref: ${{ steps.branch-name.outputs.head_ref_branch }}
-            repository: ${{ github.event.pull_request.head.repo.full_name }}
-
-      - name: Restore cache
-        uses: actions/cache@v4
-        with:
-          path: |
-            ~/.staged.dependencies
-          key: staged-deps
-
-      - name: Run Staged dependencies
-        uses: insightsengineering/staged-dependencies-action@v1
-        with:
-            run-system-dependencies: true
-            renv-restore: false
-            enable-check: false
-            direction: upstream
-            git-ref: ${{ steps.branch-name.outputs.current_branch }}
-
-      - name: Install latest release of lintr
-        shell: Rscript {0}
-        run: |
-            install.packages("lintr", repos = "https://packagemanager.posit.co/cran/latest/")
-        
-
-      - name: Lint
-        shell: Rscript {0}
-        run: |
-          lints <- lintr::lint_package()
-          if (length(lints) > 0L) {
-              print(lints)
-              stop("Lints detected. Please review and adjust code according to the comments provided.", call. = FALSE)
-          }
-
+    if: github.event_name == 'pull_request'
+    with:
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
   man-pages:
     name: Man Pages
-    runs-on: ubuntu-latest
+    uses: ./.github/workflows/man-pages.yml
     needs: get_r_version
-    container:
-      image: "ghcr.io/pharmaverse/admiralci-${{ needs.get_r_version.outputs.r-version }}:latest"
-    steps:
-      - name: Get branch names
-        id: branch-name
-        uses: tj-actions/branch-names@v8
-
-      - name: Checkout repo
-        uses: actions/checkout@v4.2.2
-        if: github.event_name == 'pull_request'
-        with:
-          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
-
-      - name: Restore cache
-        uses: actions/cache@v4
-        with:
-          path: |
-            ~/.staged.dependencies
-          key: staged-deps
-
-      - name: Run Staged dependencies
-        uses: insightsengineering/staged-dependencies-action@v1
-        with:
-          run-system-dependencies: false
-          renv-restore: false
-          enable-check: false
-          direction: upstream
-          git-ref: ${{ steps.branch-name.outputs.current_branch }}
-
-      - name: Install dependencies
-        run: |
-          Rscript -e 'pak::local_install_deps(dependencies = TRUE)'
-
-      - name: Generate man pages
-        run: roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))
-        shell: Rscript {0}
-
-      - name: Set-up safe dir
-        run: git config --global --add safe.directory "${GITHUB_WORKSPACE}"
-        shell: bash
-
-      - name: Roxygen check
-        run: |
-          git status -s
-          if [[ -n `git status -s | grep -E "man|DESCRIPTION"` ]]
-          then {
-            ROXYGEN_VERSION="$(Rscript -e 'packageVersion("roxygen2")' | awk '{print $NF}')"
-            echo "🙈 Manuals are not up-to-date with roxygen comments!"
-            echo "🔀 The following differences were noted:"
-            git diff man/* DESCRIPTION
-            echo -e "\n💻 Please rerun the following command on your workstation and push your changes"
-            echo "--------------------------------------------------------------------"
-            echo "roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))"
-            echo "--------------------------------------------------------------------"
-            echo "ℹ roxygen2 version that was used in this workflow: $ROXYGEN_VERSION"
-            echo "🙏 Please ensure that the 'RoxygenNote' field in the DESCRIPTION file matches this version"
-            exit 1
-          } else {
-            echo "💚 Manuals are up-to-date with roxygen comments"
-          }
-          fi
-        shell: bash
-
+    if: github.event_name == 'pull_request'
+    with:
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
+    
   tests:
     name: Tests
     runs-on: ubuntu-latest
@@ -205,209 +64,23 @@ jobs:
         - name: Checkout code
           uses: actions/checkout@v2
 
+        - name: Install system dependencies
+          run: |
+            apt-get install -y --no-install-recommends \
+                libudunits2-dev
+
         - name: Install dependencies
           run: |
-            Rscript -e 'pak::local_install_deps(dependencies = TRUE)'
+            Rscript -e 'remotes::install_deps(dependencies = TRUE)'
 
         - name: Run tests
           shell: Rscript {0}
           run: |
             devtools::load_all(".")
             devtools::test()
-  
   check:
-    runs-on: ubuntu-latest
-    needs: 
-      - spellcheck
-      - tests
-      - lint
-      - man-pages
-    container:
-      image: "ghcr.io/pharmaverse/admiralci-${{ matrix.r_version }}:latest"
-    name: Check (${{ matrix.r_version }})
-    strategy:
-      fail-fast: false
-      matrix:
-        r_version: ["release", "devel", "oldrel"]
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      R_KEEP_PKG_SOURCE: true
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      R_REPOS: "https://cran.r-project.org"
-      DEPS_IGNORE: >-
-        pharmaversesdtm,
-        pharmaverseadam,
-        admiral,
-        admiraldev,
-        admiralophtha,
-        admiralonco,
-        admiralvaccine,
-        staged.dependencies
-    steps:
-      - name: Get branch names
-        id: branch-name
-        uses: tj-actions/branch-names@v8
-
-      - name: Checkout repo
-        uses: actions/checkout@v4.2.2
-        if: |
-          github.event_name == 'pull_request'
-        with:
-          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
-          repository: ${{ github.event.pull_request.head.repo.full_name }}
-
-      - name: Restore cache
-        uses: actions/cache@v4
-        with:
-          path: |
-            ~/.staged.dependencies
-          key: staged-deps
-
-      - name: Run Staged dependencies
-        uses: insightsengineering/staged-dependencies-action@v1
-        if: |
-          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
-          matrix.r_version != 'devel'
-        with:
-          git-ref: ${{ steps.branch-name.outputs.current_branch }}
-          run-system-dependencies: false
-          renv-restore: false
-          enable-check: false
-          cran-repos: "https://cloud.r-project.org"
-          direction: upstream
-
-      - name: Install dependencies from DESCRIPTION
-        if: |
-          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
-          matrix.r_version != 'devel'
-        run: |
-          Rscript -e 'pak::local_install_deps(dependencies = TRUE)'
-
-      - name: Upload dependencies artifact
-        if: |
-          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
-          matrix.r_version != 'devel'
-        run: |
-          dir.create("/workspace/tmp")
-          library(dplyr)
-          installed_packages <- as.data.frame(installed.packages())
-          packages_to_remove <- Sys.getenv("DEPS_IGNORE", "")
-          packages_to_remove <- unlist(strsplit(packages_to_remove, ","))
-          installed_packages <- installed_packages %>% filter(LibPath != "/usr/local/lib/R/library") %>%  # remove pre-built deps
-          filter(!Package %in% packages_to_remove)
-          # save deps as csv file
-          write.csv(installed_packages, "/workspace/tmp/deps-${{ matrix.r_version }}.csv", row.names = FALSE)
-          # create also renv.lock file
-          setwd("/workspace/tmp")
-
-          renv_lock <- list(
-            "R" = list(
-              "Version" = paste(R.version$major, R.version$minor, sep=".")
-            ),
-            "Repositories" = list(
-                list(Name = "CRAN", URL = Sys.getenv("R_REPOS"))
-              ),
-            "Packages" = list()
-          )
-
-          # Populate with information about each package
-          for (package in installed_packages$Package) {
-            dep_name <- package
-            dep_version <- installed_packages[installed_packages$Package == package, "Version"]
-
-            version_parts <- strsplit(dep_version, "\\.")[[1]]
-            if (length(version_parts) == 4) {
-              print(sprintf("skipping installation of dep %s", dep_name))
-            } else {
-              print(sprintf("append dependency %s - version %s", dep_name, dep_version))
-              requirements <- tools::package_dependencies(dep_name, recursive = TRUE)
-              have_requirements <- length(requirements[[1]]) > 0
-              if (have_requirements) {
-                  renv_lock[["Packages"]][[dep_name]] <- list(
-                      "Package" = dep_name,
-                      "Version" = dep_version,
-                      "Source" = "Repository",
-                      "Repository" = "CRAN",
-                      "Requirements" = requirements[[dep_name]]
-                  )
-              } else {
-                  renv_lock[["Packages"]][[dep_name]] <- list(
-                      "Package" = dep_name,
-                      "Version" = dep_version,
-                      "Source" = "Repository",
-                      "Repository" = "CRAN"
-                  )
-              }
-            }
-          }
-
-          # Write the list to a JSON file (renv.lock)
-          writeLines(jsonlite::toJSON(renv_lock, pretty = TRUE, auto_unbox = TRUE), "renv-${{ matrix.r_version }}.lock")
-          print("generated renv.lock content")
-          system("cat renv-${{ matrix.r_version }}.lock")
-        shell: Rscript {0}
-
-      - name: Upload deps.csv and renv.lock artifacts
-        uses: actions/upload-artifact@v4
-        if: |
-          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
-          matrix.r_version != 'devel'
-        with:
-          name: deps-${{ matrix.r_version }}
-          path: |
-            /workspace/tmp/
-
-      - name: Check Version
-        id: check_version
-        if: |
-          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
-          matrix.r_version != 'devel'
-        run: |
-          maintenance_version="F"
-          description_dat <- readLines("DESCRIPTION")
-          for (i in seq_along(description_dat)) {
-            if (grepl("^Version:", description_dat[i])) {
-              current_version <- sub("^Version: ", "", description_dat[i])
-              version_parts <- strsplit(current_version, "\\.")[[1]]
-              # check if maintenance version
-              if (length(version_parts) == 4) {
-                print("Maintenance version detected (format X.Y.Z.M with M >= 9000)")
-                maintenance_version="T"
-              }
-            }
-          }
-          cat(sprintf("maintenance_version=%s", maintenance_version), file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
-        shell: Rscript {0}
-
-      - name: Check
-        if: |
-          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
-          matrix.r_version != 'devel'
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-          _R_CHECK_FORCE_SUGGESTS_: false
-        run: |
-          unlink("tmp",recursive=TRUE)
-          if ("${{ steps.check_version.outputs.maintenance_version }}" == "T"){
-            Sys.setenv("_R_CHECK_CRAN_INCOMING_SKIP_LARGE_VERSION_" = TRUE)
-          }
-          if (!requireNamespace("rcmdcheck", quietly = TRUE)) install.packages("rcmdcheck")
-          options(crayon.enabled = TRUE)
-          check_error_on <- "error"
-          if (check_error_on == "") {
-            check_error_on <- "note"
-          }
-          rcmdcheck::rcmdcheck(
-            args = c("--no-manual", "--as-cran"),
-            error_on = check_error_on,
-            check_dir = "check"
-          )
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@v4
-        with:
-          name: r${{ matrix.r_version }}-results
-          path: check
-      
+    name: Check
+    uses: ./.github/workflows/r-cmd-check.yml
+    if: github.event_name == 'pull_request'
+    with:
+        error-on: error
diff --git a/.github/workflows/man-pages.yml b/.github/workflows/man-pages.yml
new file mode 100644
index 00000000..332b13e6
--- /dev/null
+++ b/.github/workflows/man-pages.yml
@@ -0,0 +1,111 @@
+on:
+  workflow_dispatch:
+    inputs:
+      r-version:
+        description: "The version of R to use"
+        default: "release"
+        required: false
+        type: choice
+        options:
+          - devel
+          - latest
+  workflow_call:
+    inputs:
+      r-version:
+        description: "The version of R to use"
+        default: "release"
+        required: false
+        type: string
+
+name: Man Pages
+
+concurrency:
+  group: roxygen-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    name: Roxygen
+    runs-on: ubuntu-latest
+    container:
+      image: "ghcr.io/pharmaverse/admiralci-${{ inputs.r-version }}:latest"
+    if: >
+      !contains(github.event.commits[0].message, '[skip lint]')
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      ##################### BEGIN boilerplate steps #####################
+      - name: Get branch names
+        id: branch-name
+        uses: tj-actions/branch-names@v8
+
+      - name: Checkout repo (PR) 🛎
+        uses: actions/checkout@v4.2.2
+        if: github.event_name == 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+
+      - name: Checkout repository
+        uses: actions/checkout@v4.2.2
+        if: github.event_name != 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+
+      - name: Restore cache
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.staged.dependencies
+          key: staged-deps
+
+      - name: Run Staged dependencies
+        uses: insightsengineering/staged-dependencies-action@v1
+        with:
+          run-system-dependencies: true
+          renv-restore: false
+          enable-check: false
+          direction: upstream
+          git-ref: ${{ steps.branch-name.outputs.current_branch }}
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Install dependencies from DESCRIPTION
+        run: |
+          remotes::install_local(force = TRUE, dependencies = TRUE)
+        shell: Rscript {0}
+        env:
+          R_REMOTES_STANDALONE: "true"
+
+      ##################### END boilerplate steps #####################
+
+      - name: Generate man pages
+        run: roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))
+        shell: Rscript {0}
+
+      - name: Set-up safe dir
+        run: git config --global --add safe.directory "${GITHUB_WORKSPACE}"
+        shell: bash
+
+      - name: Roxygen check
+        if: "!startsWith(github.event.comment.body, '/roxygenize')"
+        run: |
+          git status -s
+          if [[ -n `git status -s | grep -E "man|DESCRIPTION"` ]]
+          then {
+            ROXYGEN_VERSION="$(Rscript -e 'packageVersion("roxygen2")' | awk '{print $NF}')"
+            echo "🙈 Manuals are not up-to-date with roxygen comments!"
+            echo "🔀 The following differences were noted:"
+            git diff man/* DESCRIPTION
+            echo -e "\n💻 Please rerun the following command on your workstation and push your changes"
+            echo "--------------------------------------------------------------------"
+            echo "roxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace'))"
+            echo "--------------------------------------------------------------------"
+            echo "ℹ roxygen2 version that was used in this workflow: $ROXYGEN_VERSION"
+            echo "🙏 Please ensure that the 'RoxygenNote' field in the DESCRIPTION file matches this version"
+            exit 1
+          } else {
+            echo "💚 Manuals are up-to-date with roxygen comments"
+          }
+          fi
+        shell: bash
\ No newline at end of file
diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
new file mode 100644
index 00000000..7d91adab
--- /dev/null
+++ b/.github/workflows/r-cmd-check.yml
@@ -0,0 +1,227 @@
+on:
+  workflow_dispatch:
+  workflow_call:
+    inputs:
+      error-on:
+        description: Input for the 'error_on' parameter in rcmdcheck::rcmdcheck()
+        required: false
+        default: note
+        type: string
+
+name: R CMD Check
+
+concurrency:
+  group: r-cmd-check-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+    container:
+      image: "ghcr.io/pharmaverse/admiralci-${{ matrix.r_version }}:latest"
+    name: (${{ matrix.r_version }})
+    if: >
+      !contains(github.event.commits[0].message, '[skip r-cmd-check]')
+    strategy:
+      fail-fast: false
+      matrix:
+        r_version: ["release", "devel", "oldrel"]
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: true
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      R_REPOS: "https://cran.r-project.org"
+      DEPS_IGNORE: >-
+        pharmaversesdtm,
+        pharmaverseadam,
+        admiral,
+        admiraldev,
+        admiralophtha,
+        admiralonco,
+        admiralvaccine,
+        staged.dependencies
+
+      # DEPS_IGNORE: env variable to ignore package when building renv.lock (step Upload dependencies artifact)
+      # (improvments ideas : get this list of deps to ignore from staged.dependencies yml file)
+
+    steps:
+      ##################### BEGIN boilerplate steps #####################
+      - name: Get branch names
+        id: branch-name
+        uses: tj-actions/branch-names@v8
+
+      - name: Checkout repo (PR) 🛎
+        uses: actions/checkout@v4.2.2
+        if: |
+          github.event_name == 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+
+      - name: Checkout repository
+        uses: actions/checkout@v4.2.2
+        if: |
+          github.event_name != 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+
+      - name: Restore cache
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.staged.dependencies
+          key: staged-deps
+
+      - name: Run Staged dependencies
+        uses: insightsengineering/staged-dependencies-action@v1
+        if: |
+          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
+          matrix.r_version != 'devel'
+        with:
+          git-ref: ${{ steps.branch-name.outputs.current_branch }}
+          run-system-dependencies: true
+          renv-restore: false
+          enable-check: false
+          cran-repos: "https://cloud.r-project.org"
+          direction: upstream
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Install dependencies from DESCRIPTION
+        if: |
+          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
+          matrix.r_version != 'devel'
+        run: |
+          remotes::install_local(force = TRUE, dependencies = TRUE)
+        shell: Rscript {0}
+
+      ##################### END boilerplate steps #####################
+
+      - name: Upload dependencies artifact
+        if: |
+          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
+          matrix.r_version != 'devel'
+        run: |
+          dir.create("/workspace/tmp")
+          library(dplyr)
+          installed_packages <- as.data.frame(installed.packages())
+          packages_to_remove <- Sys.getenv("DEPS_IGNORE", "")
+          packages_to_remove <- unlist(strsplit(packages_to_remove, ","))
+          installed_packages <- installed_packages %>% filter(LibPath != "/usr/local/lib/R/library") %>%  # remove pre-built deps
+          filter(!Package %in% packages_to_remove)
+          # save deps as csv file
+          write.csv(installed_packages, "/workspace/tmp/deps-${{ matrix.r_version }}.csv", row.names = FALSE)
+          # create also renv.lock file
+          setwd("/workspace/tmp")
+
+          renv_lock <- list(
+            "R" = list(
+              "Version" = paste(R.version$major, R.version$minor, sep=".")
+            ),
+            "Repositories" = list(
+                list(Name = "CRAN", URL = Sys.getenv("R_REPOS"))
+              ),
+            "Packages" = list()
+          )
+
+          # Populate with information about each package
+          for (package in installed_packages$Package) {
+            dep_name <- package
+            dep_version <- installed_packages[installed_packages$Package == package, "Version"]
+
+            version_parts <- strsplit(dep_version, "\\.")[[1]]
+            if (length(version_parts) == 4) {
+              print(sprintf("skipping installation of dep %s", dep_name))
+            } else {
+              print(sprintf("append dependency %s - version %s", dep_name, dep_version))
+              requirements <- tools::package_dependencies(dep_name, recursive = TRUE)
+              have_requirements <- length(requirements[[1]]) > 0
+              if (have_requirements) {
+                  renv_lock[["Packages"]][[dep_name]] <- list(
+                      "Package" = dep_name,
+                      "Version" = dep_version,
+                      "Source" = "Repository",
+                      "Repository" = "CRAN",
+                      "Requirements" = requirements[[dep_name]]
+                  )
+              } else {
+                  renv_lock[["Packages"]][[dep_name]] <- list(
+                      "Package" = dep_name,
+                      "Version" = dep_version,
+                      "Source" = "Repository",
+                      "Repository" = "CRAN"
+                  )
+              }
+            }
+          }
+
+          # Write the list to a JSON file (renv.lock)
+          writeLines(jsonlite::toJSON(renv_lock, pretty = TRUE, auto_unbox = TRUE), "renv-${{ matrix.r_version }}.lock")
+          print("generated renv.lock content")
+          system("cat renv-${{ matrix.r_version }}.lock")
+        shell: Rscript {0}
+
+      - name: Upload deps.csv and renv.lock artifacts
+        uses: actions/upload-artifact@v4
+        if: |
+          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
+          matrix.r_version != 'devel'
+        with:
+          name: deps-${{ matrix.r_version }}
+          path: |
+            /workspace/tmp/
+
+      - name: Check Version
+        id: check_version
+        if: |
+          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
+          matrix.r_version != 'devel'
+        run: |
+          maintenance_version="F"
+          description_dat <- readLines("DESCRIPTION")
+          for (i in seq_along(description_dat)) {
+            if (grepl("^Version:", description_dat[i])) {
+              current_version <- sub("^Version: ", "", description_dat[i])
+              version_parts <- strsplit(current_version, "\\.")[[1]]
+              # check if maintenance version
+              if (length(version_parts) == 4) {
+                print("Maintenance version detected (format X.Y.Z.M with M >= 9000)")
+                maintenance_version="T"
+              }
+            }
+          }
+          cat(sprintf("maintenance_version=%s", maintenance_version), file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        if: |
+          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
+          matrix.r_version != 'devel'
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+          _R_CHECK_FORCE_SUGGESTS_: false
+        run: |
+          unlink("tmp",recursive=TRUE)
+          if ("${{steps.check_version.outputs.maintenance_version}}" == "T"){
+            Sys.setenv("_R_CHECK_CRAN_INCOMING_SKIP_LARGE_VERSION_" = TRUE)
+          }
+          if (!requireNamespace("rcmdcheck", quietly = TRUE)) install.packages("rcmdcheck")
+          options(crayon.enabled = TRUE)
+          check_error_on <- "${{ inputs.error-on }}"
+          if (check_error_on == "") {
+            check_error_on <- "note"
+          }
+          rcmdcheck::rcmdcheck(
+            args = c("--no-manual", "--as-cran"),
+            error_on = check_error_on,
+            check_dir = "check"
+          )
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: r${{ matrix.r_version }}-results
+          path: check
\ No newline at end of file
diff --git a/.github/workflows/spellcheck.yml b/.github/workflows/spellcheck.yml
new file mode 100644
index 00000000..d3f0b200
--- /dev/null
+++ b/.github/workflows/spellcheck.yml
@@ -0,0 +1,88 @@
+name: Spelling
+
+on:
+  workflow_dispatch:
+    inputs:
+      r-version:
+        description: "The version of R to use"
+        default: "release"
+        required: false
+        type: choice
+        options:
+          - devel
+          - latest
+      exclude:
+        description: "List of paths to exclude (comma seperated list)"
+        default: ""
+        required: false
+        type: string
+  workflow_call:
+    inputs:
+      r-version:
+        description: "The version of R to use"
+        default: "release"
+        required: false
+        type: string
+      exclude:
+        description: "List of paths to exclude (comma seperated list)"
+        default: ""
+        required: false
+        type: string
+
+concurrency:
+  group: spelling-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  spellcheck:
+    name: Spellcheck
+    runs-on: ubuntu-latest
+    container:
+      image: "ghcr.io/pharmaverse/admiralci-${{ inputs.r-version }}:latest"
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    if: >
+      !contains(github.event.commits[0].message, '[skip spellcheck]')
+    steps:
+      ##################### BEGIN boilerplate steps #####################
+      - name: Get branch names
+        id: branch-name
+        uses: tj-actions/branch-names@v8
+
+      - name: Checkout repo (PR) 🛎
+        uses: actions/checkout@v4.2.2
+        if: github.event_name == 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+
+      - name: Checkout repository
+        uses: actions/checkout@v4.2.2
+        if: github.event_name != 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+
+      - name: Restore cache
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.staged.dependencies
+          key: staged-deps
+
+      - name: Run Staged dependencies
+        uses: insightsengineering/staged-dependencies-action@v1
+        with:
+          run-system-dependencies: true
+          renv-restore: false
+          enable-check: false
+          direction: upstream
+          git-ref: ${{ steps.branch-name.outputs.current_branch }}
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      ##################### END boilerplate steps #####################
+
+      - name: Run Spellcheck
+        uses: insightsengineering/r-spellcheck-action@v3
+        with:
+          additional_options: ""
+          exclude: "${{ inputs.exclude }}"
\ No newline at end of file

From ec4dec7ced1b06df23999264a46a7d953060aeb4 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Thu, 9 Jan 2025 09:16:28 +0100
Subject: [PATCH 11/14] chore: migrated tests to separate file

---
 .github/workflows/main.yml | 27 ++++---------
 .github/workflows/test.yml | 79 ++++++++++++++++++++++++++++++++++++++
 2 files changed, 86 insertions(+), 20 deletions(-)
 create mode 100644 .github/workflows/test.yml

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 468da33f..e99598ac 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -32,6 +32,7 @@ jobs:
         id: get_r_version
         run: echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT
         shell: bash
+
   spellcheck:
     name: Spelling
     uses: ./.github/workflows/spellcheck.yml
@@ -39,6 +40,7 @@ jobs:
     needs: get_r_version
     with:
       r-version: "${{ needs.get_r_version.outputs.r-version }}"
+
   linter:
     name: Lint
     uses: ./.github/workflows/lintr.yml
@@ -46,6 +48,7 @@ jobs:
     if: github.event_name == 'pull_request'
     with:
       r-version: "${{ needs.get_r_version.outputs.r-version }}"
+
   man-pages:
     name: Man Pages
     uses: ./.github/workflows/man-pages.yml
@@ -56,28 +59,12 @@ jobs:
     
   tests:
     name: Tests
-    runs-on: ubuntu-latest
+    uses: ./.github/workflows/test.yml
     needs: get_r_version
-    container:
-      image: "ghcr.io/pharmaverse/admiralci-${{ needs.get_r_version.outputs.r-version }}:latest"
-    steps:
-        - name: Checkout code
-          uses: actions/checkout@v2
-
-        - name: Install system dependencies
-          run: |
-            apt-get install -y --no-install-recommends \
-                libudunits2-dev
-
-        - name: Install dependencies
-          run: |
-            Rscript -e 'remotes::install_deps(dependencies = TRUE)'
+    if: github.event_name == 'pull_request'
+    with:
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
 
-        - name: Run tests
-          shell: Rscript {0}
-          run: |
-            devtools::load_all(".")
-            devtools::test()
   check:
     name: Check
     uses: ./.github/workflows/r-cmd-check.yml
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 00000000..32a7e84e
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,79 @@
+name: Spelling
+
+on:
+  workflow_dispatch:
+    inputs:
+      r-version:
+        description: "The version of R to use"
+        default: "release"
+        required: false
+        type: choice
+        options:
+          - devel
+          - latest
+  workflow_call:
+    inputs:
+      r-version:
+        description: "The version of R to use"
+        default: "release"
+        required: false
+        type: string
+
+concurrency:
+  group: tests-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  tests:
+    name: Tests
+    runs-on: ubuntu-latest
+    container:
+      image: "ghcr.io/pharmaverse/admiralci-${{ inputs.r-version }}:latest"
+    steps:
+      - name: Get branch names
+        id: branch-name
+        uses: tj-actions/branch-names@v8
+
+      - name: Checkout repo (PR) 🛎
+        uses: actions/checkout@v4.2.2
+        if: github.event_name == 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+
+      - name: Checkout repository
+        uses: actions/checkout@v4.2.2
+        if: github.event_name != 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+
+      - name: Restore cache
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.staged.dependencies
+          key: staged-deps
+
+      - name: Run Staged dependencies
+        uses: insightsengineering/staged-dependencies-action@v1
+        with:
+          run-system-dependencies: true
+          renv-restore: false
+          enable-check: false
+          direction: upstream
+          git-ref: ${{ steps.branch-name.outputs.current_branch }}
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Install dependencies from DESCRIPTION
+        run: |
+          remotes::install_local(force = TRUE, dependencies = TRUE)
+        shell: Rscript {0}
+        env:
+          R_REMOTES_STANDALONE: "true"
+
+      - name: Run tests
+        shell: Rscript {0}
+        run: |
+          devtools::load_all(".")
+          devtools::test()
\ No newline at end of file

From 366d86a76fb2e94500918eac9c25f2e5a2b698f1 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Thu, 9 Jan 2025 09:40:36 +0100
Subject: [PATCH 12/14] chore: added docs

---
 .github/workflows/lintr.yml       | 8 ++++++--
 .github/workflows/main.yml        | 7 +++++++
 .github/workflows/man-pages.yml   | 8 ++++++--
 .github/workflows/r-cmd-check.yml | 8 ++++++--
 .github/workflows/spellcheck.yml  | 4 ++++
 5 files changed, 29 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/lintr.yml b/.github/workflows/lintr.yml
index 2f855d93..dd920c5b 100644
--- a/.github/workflows/lintr.yml
+++ b/.github/workflows/lintr.yml
@@ -1,3 +1,9 @@
+# Source:
+# https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/lintr.yml
+# Modified to install system dependencies.
+
+name: Lint
+
 on:
   workflow_dispatch:
     inputs:
@@ -47,8 +53,6 @@ on:
         required: false
         type: string
 
-name: Lint
-
 concurrency:
   group: lint-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index e99598ac..bdd3d051 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -3,6 +3,13 @@
 # the developement process. When package is ready to
 # be published, revisit and add release-related
 # workflows.
+# Due to the need of some customization, instead of
+# referencing the workflows directly, they are copied
+# over and modified to install needed system dependencies.
+# This means that in case of an update, the changes
+# will need to be applied manually.
+#
+# Last workflow update: 2025-09-01
 name: admiral CI/CD Workflows
 
 on:
diff --git a/.github/workflows/man-pages.yml b/.github/workflows/man-pages.yml
index 332b13e6..4ad1204e 100644
--- a/.github/workflows/man-pages.yml
+++ b/.github/workflows/man-pages.yml
@@ -1,3 +1,9 @@
+# Source:
+# https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/man-pages.yml
+# Modified to install system dependencies.
+
+name: Man Pages
+
 on:
   workflow_dispatch:
     inputs:
@@ -17,8 +23,6 @@ on:
         required: false
         type: string
 
-name: Man Pages
-
 concurrency:
   group: roxygen-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
index 7d91adab..4d168d91 100644
--- a/.github/workflows/r-cmd-check.yml
+++ b/.github/workflows/r-cmd-check.yml
@@ -1,3 +1,9 @@
+# Source:
+# https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/r-cmd-check.yml
+# Modified to install system dependencies.
+
+name: R CMD Check
+
 on:
   workflow_dispatch:
   workflow_call:
@@ -8,8 +14,6 @@ on:
         default: note
         type: string
 
-name: R CMD Check
-
 concurrency:
   group: r-cmd-check-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
diff --git a/.github/workflows/spellcheck.yml b/.github/workflows/spellcheck.yml
index d3f0b200..49204447 100644
--- a/.github/workflows/spellcheck.yml
+++ b/.github/workflows/spellcheck.yml
@@ -1,3 +1,7 @@
+# Source:
+# https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/spellcheck.yml
+# Modified to install system dependencies.
+
 name: Spelling
 
 on:

From 4a38b1cf019c35641f0c57874ceee2975923487c Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Thu, 9 Jan 2025 09:42:33 +0100
Subject: [PATCH 13/14] chore: remove units from DESCRIPTION

---
 DESCRIPTION | 1 -
 1 file changed, 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ddc33acf..2466aac4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -55,7 +55,6 @@ Imports:
     tidyr,
     tools,
     utils,
-    units,
     zip
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

From b4861a8185975393d69dad773d193d3680605305 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Thu, 9 Jan 2025 09:48:20 +0100
Subject: [PATCH 14/14] chore: added docs for test

---
 .github/workflows/test.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 32a7e84e..e579e41b 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -1,4 +1,6 @@
-name: Spelling
+# Custom workflow created based on jobs available in `admiralci` package.
+
+name: Tests
 
 on:
   workflow_dispatch: