From 3918b324fdc1a11122f5f14c6c23027d1036e1b2 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 15 May 2024 10:39:38 +0200
Subject: [PATCH 01/62] Update

---
 .github/workflows/check.yaml | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 .github/workflows/check.yaml

diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
new file mode 100644
index 00000000..e704d733
--- /dev/null
+++ b/.github/workflows/check.yaml
@@ -0,0 +1,24 @@
+---
+name: Check 🛠
+
+on:
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
+    branches:
+      - main
+  push:
+    branches:
+      - main
+      - setup-workflows
+  workflow_dispatch:
+
+
+# This reusable workflow from insightsengineering/r.pkg.template will run once a PR to main branch is created.
+jobs:
+  r-cmd:
+    name: R CMD Check 🧬
+    uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main

From 7603c7d01f44fa4a53d28852f6cc019699e49226 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 15 May 2024 10:51:15 +0200
Subject: [PATCH 02/62] Update

---
 .github/workflows/check.yaml  |  2 +-
 .github/workflows/simple.yaml | 62 +++++++++++++++++++++++++++++++++++
 2 files changed, 63 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/simple.yaml

diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index e704d733..f80cc80b 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -13,7 +13,7 @@ on:
   push:
     branches:
       - main
-      - setup-workflows
+      # - setup-workflows
   workflow_dispatch:
 
 
diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
new file mode 100644
index 00000000..a2da48c4
--- /dev/null
+++ b/.github/workflows/simple.yaml
@@ -0,0 +1,62 @@
+---
+name: Simple workflow
+
+on:
+  push:
+    branches:
+      - main
+      # TODO update this
+      - setup-workflows
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
+    branches:
+      - main
+
+env:
+  ENABLED_STEPS: "checkout_repository,get_package_name,build_r_package"
+
+jobs:
+  hello-world:
+    runs-on: ubuntu-latest
+    container:
+      image: rocker/verse:latest
+
+    steps:
+      - name: Checkout repo 🛎
+        uses: actions/checkout@v4.1.1
+        if: >
+          contains(env.ENABLED_STEPS, 'checkout_repository')
+        with:
+          path: ${{ github.event.repository.name }}
+
+      - name: Get package name 📦
+        if: >
+          contains(env.ENABLED_STEPS, 'get_package_name')
+        run: |
+          PKGBUILD="$(echo $(awk -F: '/Package:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION)_"\
+          "$(awk -F: '/Version:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION).tar.gz)"
+          echo "PKGBUILD=$PKGBUILD"
+          echo "PKGBUILD=$PKGBUILD" >> $GITHUB_ENV
+        shell: bash
+        working-directory: ${{ github.event.repository.name }}
+
+      - name: Build R package 🏗
+        if: >
+          contains(env.ENABLED_STEPS, 'build_r_package')
+        run: |
+          R CMD build ${{ github.event.repository.name }}
+        shell: bash
+
+      - name: Run R CMD check 🏁
+        if: >
+          contains(env.ENABLED_STEPS, 'run_r_cmd_check')
+        run: |
+          R CMD check  ${{ env.PKGBUILD }}
+        shell: bash
+        env:
+          _R_CHECK_TESTS_NLINES_: 0
+          _R_CHECK_VIGNETTES_NLINES_: 0

From 01c7ddd71caddb1938561506dd12bfe7963c3dbd Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 15 May 2024 10:56:00 +0200
Subject: [PATCH 03/62] Update

---
 .github/workflows/simple.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index a2da48c4..d400d4d7 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -17,13 +17,13 @@ on:
       - main
 
 env:
-  ENABLED_STEPS: "checkout_repository,get_package_name,build_r_package"
+  ENABLED_STEPS: "checkout_repository,get_package_name,build_r_package,run_r_cmd_check"
 
 jobs:
   hello-world:
     runs-on: ubuntu-latest
     container:
-      image: rocker/verse:latest
+      image: rocker/r-ubuntu:latest
 
     steps:
       - name: Checkout repo 🛎
@@ -39,7 +39,7 @@ jobs:
         run: |
           PKGBUILD="$(echo $(awk -F: '/Package:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION)_"\
           "$(awk -F: '/Version:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION).tar.gz)"
-          echo "PKGBUILD=$PKGBUILD"
+          echo "PKGBUILD = $PKGBUILD"
           echo "PKGBUILD=$PKGBUILD" >> $GITHUB_ENV
         shell: bash
         working-directory: ${{ github.event.repository.name }}

From 5a55bbcea2b27739b9df63bdb8896b4ca5632eb8 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 15 May 2024 10:58:27 +0200
Subject: [PATCH 04/62] Update

---
 .github/workflows/check.yaml  | 16 ++++++++--------
 .github/workflows/simple.yaml | 17 +++++++++++------
 2 files changed, 19 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index f80cc80b..8b62ae2f 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -2,14 +2,14 @@
 name: Check 🛠
 
 on:
-  pull_request:
-    types:
-      - opened
-      - synchronize
-      - reopened
-      - ready_for_review
-    branches:
-      - main
+  # pull_request:
+  #   types:
+  #     - opened
+  #     - synchronize
+  #     - reopened
+  #     - ready_for_review
+  #   branches:
+  #     - main
   push:
     branches:
       - main
diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index d400d4d7..4c24b66f 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -7,12 +7,12 @@ on:
       - main
       # TODO update this
       - setup-workflows
-  pull_request:
-    types:
-      - opened
-      - synchronize
-      - reopened
-      - ready_for_review
+  # pull_request:
+  #   types:
+  #     - opened
+  #     - synchronize
+  #     - reopened
+  #     - ready_for_review
     branches:
       - main
 
@@ -51,6 +51,11 @@ jobs:
           R CMD build ${{ github.event.repository.name }}
         shell: bash
 
+      - name: Install packages
+        run:
+          install.packages(c("cli", "testthat"))
+        shell: Rscript {0}
+
       - name: Run R CMD check 🏁
         if: >
           contains(env.ENABLED_STEPS, 'run_r_cmd_check')

From caf7a357497218aef7ffcb68b171727b40a73ea8 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 15 May 2024 10:59:35 +0200
Subject: [PATCH 05/62] Update

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

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 4c24b66f..c2f9e211 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -13,8 +13,8 @@ on:
   #     - synchronize
   #     - reopened
   #     - ready_for_review
-    branches:
-      - main
+  #   branches:
+  #     - main
 
 env:
   ENABLED_STEPS: "checkout_repository,get_package_name,build_r_package,run_r_cmd_check"

From 357b2972438f81f9be94e07ed5ebe4f0860a2e9e Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 15 May 2024 11:08:49 +0200
Subject: [PATCH 06/62] Update

---
 .github/workflows/simple.yaml | 51 +++++++++++++++++++++++++----------
 1 file changed, 37 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index c2f9e211..d74d912e 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -16,26 +16,42 @@ on:
   #   branches:
   #     - main
 
+# For reference, this is how the full list of steps will look like:
+#
+#env:
+#  ENABLED_STEPS: |
+#    checkout_repository
+#    get_package_name
+#    build_r_package
+#    run_r_cmd_check
+#    upload_artifact
+
+# Please set this variable to include proper steps.
 env:
-  ENABLED_STEPS: "checkout_repository,get_package_name,build_r_package,run_r_cmd_check"
+  ENABLED_STEPS: |
+    checkout_repository
+    get_package_name
+    build_r_package
+    run_r_cmd_check
+    upload_artifact
 
 jobs:
   hello-world:
     runs-on: ubuntu-latest
     container:
-      image: rocker/r-ubuntu:latest
+      # image: rocker/r-ubuntu:latest
+      image: rocker/tidyverse:4.4.0
 
     steps:
       - name: Checkout repo 🛎
+        # This means we're actually using a GitHub Action.
         uses: actions/checkout@v4.1.1
-        if: >
-          contains(env.ENABLED_STEPS, 'checkout_repository')
+        if: contains(env.ENABLED_STEPS, 'checkout_repository')
         with:
           path: ${{ github.event.repository.name }}
 
       - name: Get package name 📦
-        if: >
-          contains(env.ENABLED_STEPS, 'get_package_name')
+        if: contains(env.ENABLED_STEPS, 'get_package_name')
         run: |
           PKGBUILD="$(echo $(awk -F: '/Package:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION)_"\
           "$(awk -F: '/Version:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION).tar.gz)"
@@ -45,23 +61,30 @@ jobs:
         working-directory: ${{ github.event.repository.name }}
 
       - name: Build R package 🏗
-        if: >
-          contains(env.ENABLED_STEPS, 'build_r_package')
+        if: contains(env.ENABLED_STEPS, 'build_r_package')
         run: |
           R CMD build ${{ github.event.repository.name }}
         shell: bash
 
-      - name: Install packages
-        run:
-          install.packages(c("cli", "testthat"))
-        shell: Rscript {0}
+      # TODO Decide if we use an image with these packages installed,
+      # or we want to show how to install them (takes 2-3 minutes).
+      # - name: Install packages
+      #   run:
+      #     install.packages(c("cli", "testthat"))
+      #   shell: Rscript {0}
 
       - name: Run R CMD check 🏁
-        if: >
-          contains(env.ENABLED_STEPS, 'run_r_cmd_check')
+        if: contains(env.ENABLED_STEPS, 'run_r_cmd_check')
         run: |
           R CMD check  ${{ env.PKGBUILD }}
         shell: bash
         env:
           _R_CHECK_TESTS_NLINES_: 0
           _R_CHECK_VIGNETTES_NLINES_: 0
+
+      - name: Upload package build ⤴
+        if: contains(env.ENABLED_STEPS, 'upload_artifact')
+        uses: actions/upload-artifact@v4
+        with:
+          path: ${{ github.event.repository.name }}/${{ env.PKGBUILD }}
+          name: ${{ env.PKGBUILD }}

From 9a75faef332f3f39f64a24f5a155dab80cf8c593 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 15 May 2024 11:10:33 +0200
Subject: [PATCH 07/62] Update

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

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index d74d912e..2d87303d 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -40,7 +40,7 @@ jobs:
     runs-on: ubuntu-latest
     container:
       # image: rocker/r-ubuntu:latest
-      image: rocker/tidyverse:4.4.0
+      image: rocker/verse:4.4.0
 
     steps:
       - name: Checkout repo 🛎
@@ -68,6 +68,7 @@ jobs:
 
       # TODO Decide if we use an image with these packages installed,
       # or we want to show how to install them (takes 2-3 minutes).
+      # Additionally, LaTeX is needed to create manual.
       # - name: Install packages
       #   run:
       #     install.packages(c("cli", "testthat"))

From 2afaa9ef23302ee0317b49ff23e793a79001bbdf Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 15 May 2024 11:12:13 +0200
Subject: [PATCH 08/62] Update

---
 .Rbuildignore                 | 1 +
 .github/workflows/simple.yaml | 3 +++
 2 files changed, 4 insertions(+)

diff --git a/.Rbuildignore b/.Rbuildignore
index 6627b846..6c47ed1e 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,3 +1,4 @@
 ^r\.package\.example\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
+^.github$
diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 2d87303d..cf14453c 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -16,6 +16,9 @@ on:
   #   branches:
   #     - main
 
+# To make sure you can run this workflow in your forked repository, please go to:
+# Actions and click I understand my workflows...
+
 # For reference, this is how the full list of steps will look like:
 #
 #env:

From 7cf90b6f3107cf6b65579e3b17a1cdcd88d95b64 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 15 May 2024 11:13:33 +0200
Subject: [PATCH 09/62] Update

---
 .github/workflows/simple.yaml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index cf14453c..28e4e90a 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -35,8 +35,6 @@ env:
     checkout_repository
     get_package_name
     build_r_package
-    run_r_cmd_check
-    upload_artifact
 
 jobs:
   hello-world:

From 4f97b7c5db70f72bbd24b88b8d108015a2eb3192 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 15 May 2024 12:27:11 +0200
Subject: [PATCH 10/62] Update

---
 .github/workflows/simple.yaml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 28e4e90a..692ed209 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -20,6 +20,7 @@ on:
 # Actions and click I understand my workflows...
 
 # For reference, this is how the full list of steps will look like:
+# Remove just a single # character at the beginning of line to uncomment.
 #
 #env:
 #  ENABLED_STEPS: |
@@ -45,7 +46,7 @@ jobs:
 
     steps:
       - name: Checkout repo 🛎
-        # This means we're actually using a GitHub Action.
+        # This means we're actually using an official GitHub Action.
         uses: actions/checkout@v4.1.1
         if: contains(env.ENABLED_STEPS, 'checkout_repository')
         with:
@@ -54,8 +55,7 @@ jobs:
       - name: Get package name 📦
         if: contains(env.ENABLED_STEPS, 'get_package_name')
         run: |
-          PKGBUILD="$(echo $(awk -F: '/Package:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION)_"\
-          "$(awk -F: '/Version:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION).tar.gz)"
+          PKGBUILD="$(Rscript -e 'cat(sprintf("%s_%s.tar.gz",(dcf <- read.dcf("DESCRIPTION"))[,"Package"], dcf[,"Version"]))')"
           echo "PKGBUILD = $PKGBUILD"
           echo "PKGBUILD=$PKGBUILD" >> $GITHUB_ENV
         shell: bash
@@ -69,7 +69,8 @@ jobs:
 
       # TODO Decide if we use an image with these packages installed,
       # or we want to show how to install them (takes 2-3 minutes).
-      # Additionally, LaTeX is needed to create manual.
+      # Additionally, LaTeX is needed to create manual,
+      # so rocker/verse is working well for this purpose.
       # - name: Install packages
       #   run:
       #     install.packages(c("cli", "testthat"))
@@ -78,7 +79,7 @@ jobs:
       - name: Run R CMD check 🏁
         if: contains(env.ENABLED_STEPS, 'run_r_cmd_check')
         run: |
-          R CMD check  ${{ env.PKGBUILD }}
+          R CMD check ${{ env.PKGBUILD }}
         shell: bash
         env:
           _R_CHECK_TESTS_NLINES_: 0

From 0130477986de9b0765ef6ae2cab79842ae7a8cd0 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 15 May 2024 12:54:38 +0200
Subject: [PATCH 11/62] Update

---
 .github/workflows/simple.yaml | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 692ed209..e6ed9792 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -38,7 +38,17 @@ env:
     build_r_package
 
 jobs:
-  hello-world:
+  hello-world-from-r:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup R 🔧
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Hello world! 💬
+        run: cat("Hello world from R! 👋")
+        shell: Rscript {0}
+
+  build-r-package:
     runs-on: ubuntu-latest
     container:
       # image: rocker/r-ubuntu:latest

From d98567b3fd8fdc4e82390ae3b1c4e2babfd7eaba Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 15 May 2024 12:59:38 +0200
Subject: [PATCH 12/62] Update

---
 .github/workflows/simple.yaml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index e6ed9792..5f72899f 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -33,9 +33,8 @@ on:
 # Please set this variable to include proper steps.
 env:
   ENABLED_STEPS: |
-    checkout_repository
-    get_package_name
-    build_r_package
+    None for now, when asked to, please add the steps from above, like this:
+    step_name_from_above (four spaces before the step name are important!)
 
 jobs:
   hello-world-from-r:
@@ -45,8 +44,10 @@ jobs:
         uses: r-lib/actions/setup-r@v2
 
       - name: Hello world! 💬
-        run: cat("Hello world from R! 👋")
+        run: cat(paste0("Hello ", Sys.getenv("NAME"), "! 👋"))
         shell: Rscript {0}
+        env:
+          NAME: "Your name"
 
   build-r-package:
     runs-on: ubuntu-latest

From b93d996aec7cd5066037641b4c9aca3d0ff83565 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 15 May 2024 13:02:00 +0200
Subject: [PATCH 13/62] Update

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

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 5f72899f..46c49354 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -35,6 +35,9 @@ env:
   ENABLED_STEPS: |
     None for now, when asked to, please add the steps from above, like this:
     step_name_from_above (four spaces before the step name are important!)
+    checkout_repository
+    get_package_name
+    build_r_package
 
 jobs:
   hello-world-from-r:

From d13fb242eed0f1c6523687912858d9d6c6249e29 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 15 May 2024 13:03:36 +0200
Subject: [PATCH 14/62] Update

---
 .github/workflows/simple.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 46c49354..147d229a 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -38,6 +38,7 @@ env:
     checkout_repository
     get_package_name
     build_r_package
+    upload_artifact
 
 jobs:
   hello-world-from-r:

From bb038405f207e86f6573a762fc1d35acbb74d88c Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 15 May 2024 13:05:22 +0200
Subject: [PATCH 15/62] Update

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

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 147d229a..f4c830b0 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -80,6 +80,7 @@ jobs:
         if: contains(env.ENABLED_STEPS, 'build_r_package')
         run: |
           R CMD build ${{ github.event.repository.name }}
+          ls -l
         shell: bash
 
       # TODO Decide if we use an image with these packages installed,
@@ -104,5 +105,5 @@ jobs:
         if: contains(env.ENABLED_STEPS, 'upload_artifact')
         uses: actions/upload-artifact@v4
         with:
-          path: ${{ github.event.repository.name }}/${{ env.PKGBUILD }}
+          path: ${{ env.PKGBUILD }}
           name: ${{ env.PKGBUILD }}

From e697b68f401246b032477f893407d65cbf015879 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 15 May 2024 13:07:36 +0200
Subject: [PATCH 16/62] Update

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

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index f4c830b0..a8e4508e 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -42,6 +42,7 @@ env:
 
 jobs:
   hello-world-from-r:
+    name: Hello, world!
     runs-on: ubuntu-latest
     steps:
       - name: Setup R 🔧
@@ -54,6 +55,7 @@ jobs:
           NAME: "Your name"
 
   build-r-package:
+    name: Build R package
     runs-on: ubuntu-latest
     container:
       # image: rocker/r-ubuntu:latest

From 93d8cecebe0ec0122cd1c6a7b705506313710d61 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 21 May 2024 10:58:47 +0200
Subject: [PATCH 17/62] Update

---
 .github/workflows/check.yaml  |  5 ++++-
 .github/workflows/simple.yaml | 26 +++++++++++---------------
 2 files changed, 15 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index 8b62ae2f..9cb7756a 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -13,7 +13,7 @@ on:
   push:
     branches:
       - main
-      # - setup-workflows
+      - setup-workflows
   workflow_dispatch:
 
 
@@ -22,3 +22,6 @@ jobs:
   r-cmd:
     name: R CMD Check 🧬
     uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
+  validation:
+    name: R Package Validation report 📃
+    uses: insightsengineering/r.pkg.template/.github/workflows/validation.yaml@main
diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index a8e4508e..56dd61c6 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -19,26 +19,22 @@ on:
 # To make sure you can run this workflow in your forked repository, please go to:
 # Actions and click I understand my workflows...
 
-# For reference, this is how the full list of steps will look like:
-# Remove just a single # character at the beginning of line to uncomment.
-#
-#env:
-#  ENABLED_STEPS: |
-#    checkout_repository
-#    get_package_name
-#    build_r_package
-#    run_r_cmd_check
-#    upload_artifact
+# env:
+#   ENABLED_STEPS: |
+#     checkout_repository
+#     get_package_name
+#     build_r_package
+#     run_r_cmd_check
+#     upload_artifact
 
-# Please set this variable to include proper steps.
+# When asked to, please add the steps from the list above:
 env:
   ENABLED_STEPS: |
-    None for now, when asked to, please add the steps from above, like this:
-    step_name_from_above (four spaces before the step name are important!)
     checkout_repository
     get_package_name
-    build_r_package
-    upload_artifact
+    build_r_...
+    run_r_...
+    upload_...
 
 jobs:
   hello-world-from-r:

From fdcf33b01440132930613cb26a40a3df042631f3 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 21 May 2024 11:01:29 +0200
Subject: [PATCH 18/62] Update

---
 .github/workflows/simple.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 56dd61c6..240cf74b 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -18,6 +18,7 @@ on:
 
 # To make sure you can run this workflow in your forked repository, please go to:
 # Actions and click I understand my workflows...
+# Settings -> Actions -> General -> Workflow permissions -> Read and write permissions
 
 # env:
 #   ENABLED_STEPS: |

From 07f0815358417ada9d0b96561eb5da8072fa99a9 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 21 May 2024 11:02:00 +0200
Subject: [PATCH 19/62] Update

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

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 240cf74b..fe8280c5 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -16,8 +16,8 @@ on:
   #   branches:
   #     - main
 
-# To make sure you can run this workflow in your forked repository, please go to:
-# Actions and click I understand my workflows...
+# Prerequisites to run workflows:
+# Actions -> I understand my workflows...
 # Settings -> Actions -> General -> Workflow permissions -> Read and write permissions
 
 # env:

From 9e6a0d486a064f9faaa8aa177b3ec2ad28ce9128 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 21 May 2024 12:26:09 +0200
Subject: [PATCH 20/62] Update

---
 .github/workflows/check.yaml  | 3 ---
 .github/workflows/simple.yaml | 8 +++++---
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index 9cb7756a..108f8917 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -22,6 +22,3 @@ jobs:
   r-cmd:
     name: R CMD Check 🧬
     uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
-  validation:
-    name: R Package Validation report 📃
-    uses: insightsengineering/r.pkg.template/.github/workflows/validation.yaml@main
diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index fe8280c5..d2fb058b 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -31,8 +31,9 @@ on:
 # When asked to, please add the steps from the list above:
 env:
   ENABLED_STEPS: |
-    checkout_repository
-    get_package_name
+    build_and_check
+    checkout_...
+    get_package_...
     build_r_...
     run_r_...
     upload_...
@@ -51,9 +52,10 @@ jobs:
         env:
           NAME: "Your name"
 
-  build-r-package:
+  build-and-check:
     name: Build R package
     runs-on: ubuntu-latest
+    if: contains(env.ENABLED_STEPS, 'build_and_check')
     container:
       # image: rocker/r-ubuntu:latest
       image: rocker/verse:4.4.0

From e7336660ba0322da4ec47ebd0a9e087a199c974c Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 21 May 2024 12:29:17 +0200
Subject: [PATCH 21/62] Update

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

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index d2fb058b..82954765 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -55,7 +55,8 @@ jobs:
   build-and-check:
     name: Build R package
     runs-on: ubuntu-latest
-    if: contains(env.ENABLED_STEPS, 'build_and_check')
+    if: >
+      contains(env.ENABLED_STEPS, 'build_and_check')
     container:
       # image: rocker/r-ubuntu:latest
       image: rocker/verse:4.4.0

From fbb5757c3dd2656cb4c240b00558fce6870d98d5 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 21 May 2024 12:33:34 +0200
Subject: [PATCH 22/62] Update

---
 .github/workflows/simple.yaml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 82954765..617ef561 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -31,7 +31,6 @@ on:
 # When asked to, please add the steps from the list above:
 env:
   ENABLED_STEPS: |
-    build_and_check
     checkout_...
     get_package_...
     build_r_...
@@ -55,8 +54,6 @@ jobs:
   build-and-check:
     name: Build R package
     runs-on: ubuntu-latest
-    if: >
-      contains(env.ENABLED_STEPS, 'build_and_check')
     container:
       # image: rocker/r-ubuntu:latest
       image: rocker/verse:4.4.0

From a2dd35f812e883c92411dabc7fe075ecc535062a Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 21 May 2024 12:58:28 +0200
Subject: [PATCH 23/62] Update

---
 .github/workflows/simple.yaml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 617ef561..007f916a 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -106,3 +106,7 @@ jobs:
         with:
           path: ${{ env.PKGBUILD }}
           name: ${{ env.PKGBUILD }}
+
+  call-reusable-workflow:
+    name: Reusable workflow ♻️
+    uses: user-workshop-cicd/r.pkg.template/.github/workflows/sample-reusable-workflow.yaml@example-reusable-workflow

From 09e5dd492847a6e0984502801dadedecff041e58 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 21 May 2024 12:59:16 +0200
Subject: [PATCH 24/62] Update

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

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 007f916a..26c94b92 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -109,4 +109,4 @@ jobs:
 
   call-reusable-workflow:
     name: Reusable workflow ♻️
-    uses: user-workshop-cicd/r.pkg.template/.github/workflows/sample-reusable-workflow.yaml@example-reusable-workflow
+    uses: user-workshop-cicd/r.pkg.template/.github/workflows/sample-reusable-workflow.yaml@sample-reusable-workflow

From cae6d4307b233afa7c191331821e971ad52670a0 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 21 May 2024 13:00:21 +0200
Subject: [PATCH 25/62] Empty


From 45817d23b61ebda4bdb577b996ade08f60d6dfb4 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 21 May 2024 13:07:40 +0200
Subject: [PATCH 26/62] Update

---
 .github/workflows/check.yaml  | 2 +-
 .github/workflows/simple.yaml | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index 108f8917..8b62ae2f 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -13,7 +13,7 @@ on:
   push:
     branches:
       - main
-      - setup-workflows
+      # - setup-workflows
   workflow_dispatch:
 
 
diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 26c94b92..626ed18b 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -110,3 +110,5 @@ jobs:
   call-reusable-workflow:
     name: Reusable workflow ♻️
     uses: user-workshop-cicd/r.pkg.template/.github/workflows/sample-reusable-workflow.yaml@sample-reusable-workflow
+    with:
+      name: Octocat

From 47b6b1fdfeb362ae0cfc6e33efc79c75010c3a7c Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 21 May 2024 13:09:48 +0200
Subject: [PATCH 27/62] Update

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

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 626ed18b..a005c6dc 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -111,4 +111,4 @@ jobs:
     name: Reusable workflow ♻️
     uses: user-workshop-cicd/r.pkg.template/.github/workflows/sample-reusable-workflow.yaml@sample-reusable-workflow
     with:
-      name: Octocat
+      name: Not an Octocat

From aa670c9a4a190682bff6b7fb159a9f68e7445110 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 21 May 2024 13:11:10 +0200
Subject: [PATCH 28/62] Empty


From 7065f54d19484ac563a98415300b42f2ad23b8cd Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 21 May 2024 13:11:59 +0200
Subject: [PATCH 29/62] Empty


From 4d83660d6c20dac9993e8a5469c0b1837f6a31f1 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 21 May 2024 16:34:04 +0200
Subject: [PATCH 30/62] Update

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

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index a005c6dc..626ed18b 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -111,4 +111,4 @@ jobs:
     name: Reusable workflow ♻️
     uses: user-workshop-cicd/r.pkg.template/.github/workflows/sample-reusable-workflow.yaml@sample-reusable-workflow
     with:
-      name: Not an Octocat
+      name: Octocat

From 763b2c97bfc52134bbe4991d1ef1995eb7a95fa8 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 22 May 2024 10:11:00 +0200
Subject: [PATCH 31/62] Update

---
 .github/workflows/check.yaml | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index 8b62ae2f..23528d88 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -19,6 +19,20 @@ on:
 
 # This reusable workflow from insightsengineering/r.pkg.template will run once a PR to main branch is created.
 jobs:
+  job-setup:
+    name: Should we run R CMD check?
+    runs-on: ubuntu-latest
+    outputs:
+      check_out: ${{ steps.check.outputs.run_r_cmd_check }}
+    steps:
+      - name: To check or not to check?
+        id: check
+        run: |
+          echo "run_r_cmd_check=true" >> $GITHUB_OUTPUT
+
   r-cmd:
     name: R CMD Check 🧬
+    needs: job-setup
     uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
+    if: >
+      needs.job-setup.outputs.check_out == 'true'

From 36f89c45546d976ff05bb4670459da6ec8d28063 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 22 May 2024 10:12:02 +0200
Subject: [PATCH 32/62] Update

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

diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index 23528d88..aca39ef5 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -13,7 +13,7 @@ on:
   push:
     branches:
       - main
-      # - setup-workflows
+      - setup-workflows
   workflow_dispatch:
 
 

From 04fc181ad70b5deafa1aa466b7f87f4bc5642e65 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 22 May 2024 10:13:23 +0200
Subject: [PATCH 33/62] Update

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

diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index aca39ef5..0a6743f3 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -28,7 +28,7 @@ jobs:
       - name: To check or not to check?
         id: check
         run: |
-          echo "run_r_cmd_check=true" >> $GITHUB_OUTPUT
+          echo "run_r_cmd_check=false" >> $GITHUB_OUTPUT
 
   r-cmd:
     name: R CMD Check 🧬

From fc85dac12e793031a81318459d71d8089eebb950 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 23 May 2024 11:23:58 +0200
Subject: [PATCH 34/62] Update

---
 .github/workflows/simple.yaml | 15 +--------------
 1 file changed, 1 insertion(+), 14 deletions(-)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 626ed18b..9cd46443 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -54,13 +54,9 @@ jobs:
   build-and-check:
     name: Build R package
     runs-on: ubuntu-latest
-    container:
-      # image: rocker/r-ubuntu:latest
-      image: rocker/verse:4.4.0
-
     steps:
       - name: Checkout repo 🛎
-        # This means we're actually using an official GitHub Action.
+        # We're using an official GitHub Action.
         uses: actions/checkout@v4.1.1
         if: contains(env.ENABLED_STEPS, 'checkout_repository')
         with:
@@ -82,15 +78,6 @@ jobs:
           ls -l
         shell: bash
 
-      # TODO Decide if we use an image with these packages installed,
-      # or we want to show how to install them (takes 2-3 minutes).
-      # Additionally, LaTeX is needed to create manual,
-      # so rocker/verse is working well for this purpose.
-      # - name: Install packages
-      #   run:
-      #     install.packages(c("cli", "testthat"))
-      #   shell: Rscript {0}
-
       - name: Run R CMD check 🏁
         if: contains(env.ENABLED_STEPS, 'run_r_cmd_check')
         run: |

From 91f2c0537cfb9a6089bb2cec9fb2a101f32b76cc Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 23 May 2024 11:26:35 +0200
Subject: [PATCH 35/62] Update

---
 .github/workflows/simple.yaml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 9cd46443..1d8cc87f 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -62,6 +62,14 @@ jobs:
         with:
           path: ${{ github.event.repository.name }}
 
+      - name: Setup R 🔧
+        if: contains(env.ENABLED_STEPS, 'setup_r')
+        uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+
       - name: Get package name 📦
         if: contains(env.ENABLED_STEPS, 'get_package_name')
         run: |

From 3beb5f9619406b6c85a19e92c0dfe54145e9f7c5 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 23 May 2024 11:28:03 +0200
Subject: [PATCH 36/62] Update

---
 .github/workflows/simple.yaml | 36 ++++++++++++++++++++---------------
 1 file changed, 21 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 1d8cc87f..49c423e6 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -20,22 +20,26 @@ on:
 # Actions -> I understand my workflows...
 # Settings -> Actions -> General -> Workflow permissions -> Read and write permissions
 
-# env:
-#   ENABLED_STEPS: |
-#     checkout_repository
-#     get_package_name
-#     build_r_package
-#     run_r_cmd_check
-#     upload_artifact
-
-# When asked to, please add the steps from the list above:
 env:
   ENABLED_STEPS: |
-    checkout_...
-    get_package_...
-    build_r_...
-    run_r_...
-    upload_...
+    checkout_repository
+    setup_r
+    setup_dependencies
+    get_package_name
+    build_r_package
+    run_r_cmd_check
+    upload_artifact
+
+# When asked to, please add the steps from the list above:
+# env:
+#   ENABLED_STEPS: |
+#     checkout_...
+#     setup_...
+#     setup_...
+#     get_package_...
+#     build_r_...
+#     run_r_...
+#     upload_...
 
 jobs:
   hello-world-from-r:
@@ -66,7 +70,9 @@ jobs:
         if: contains(env.ENABLED_STEPS, 'setup_r')
         uses: r-lib/actions/setup-r@v2
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - name: Setup R dependencies 🔧
+        uses: r-lib/actions/setup-r-dependencies@v2
+        if: contains(env.ENABLED_STEPS, 'setup_dependencies')
         with:
           extra-packages: any::rcmdcheck
 

From a1d982de34a6e805145af51c62a7972a4fa6051c Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 23 May 2024 11:32:59 +0200
Subject: [PATCH 37/62] Update

---
 .github/workflows/simple.yaml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 49c423e6..c6589e34 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -64,6 +64,9 @@ jobs:
         uses: actions/checkout@v4.1.1
         if: contains(env.ENABLED_STEPS, 'checkout_repository')
         with:
+          # Action inputs (arguments/parameters).
+          # In this case we clone the repository to the directory called the same
+          # as the repository name.
           path: ${{ github.event.repository.name }}
 
       - name: Setup R 🔧
@@ -75,7 +78,10 @@ jobs:
         if: contains(env.ENABLED_STEPS, 'setup_dependencies')
         with:
           extra-packages: any::rcmdcheck
+        working-directory: ${{ github.event.repository.name }}
 
+      # Get package name and version from DESCRIPTION so that we'll know
+      # what's the name of the tar.gz file with the built package.
       - name: Get package name 📦
         if: contains(env.ENABLED_STEPS, 'get_package_name')
         run: |
@@ -85,6 +91,7 @@ jobs:
         shell: bash
         working-directory: ${{ github.event.repository.name }}
 
+      # Build a package stored in a directory called ${{ github.event.repository.name }}
       - name: Build R package 🏗
         if: contains(env.ENABLED_STEPS, 'build_r_package')
         run: |
@@ -92,6 +99,7 @@ jobs:
           ls -l
         shell: bash
 
+      # Check tar.gz package built in previous step.
       - name: Run R CMD check 🏁
         if: contains(env.ENABLED_STEPS, 'run_r_cmd_check')
         run: |
@@ -101,6 +109,7 @@ jobs:
           _R_CHECK_TESTS_NLINES_: 0
           _R_CHECK_VIGNETTES_NLINES_: 0
 
+      # Upload tar.gz package as an artifact so it can be downloaded.
       - name: Upload package build ⤴
         if: contains(env.ENABLED_STEPS, 'upload_artifact')
         uses: actions/upload-artifact@v4

From 05c077b699a11b63e8910979d4f3c85a0de36cce Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 23 May 2024 11:33:37 +0200
Subject: [PATCH 38/62] Update

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

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index c6589e34..7054999f 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -78,7 +78,7 @@ jobs:
         if: contains(env.ENABLED_STEPS, 'setup_dependencies')
         with:
           extra-packages: any::rcmdcheck
-        working-directory: ${{ github.event.repository.name }}
+          working-directory: ${{ github.event.repository.name }}
 
       # Get package name and version from DESCRIPTION so that we'll know
       # what's the name of the tar.gz file with the built package.

From c80254c90d74941442eb0a967dd8e851f65ca912 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 23 May 2024 11:41:49 +0200
Subject: [PATCH 39/62] Update

---
 .github/workflows/check.yaml  | 1 +
 .github/workflows/simple.yaml | 6 ++++--
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index 0a6743f3..34df66bd 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -33,6 +33,7 @@ jobs:
   r-cmd:
     name: R CMD Check 🧬
     needs: job-setup
+    # Call a workflow from a given GitHub repository, from a given branch (or tag).
     uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
     if: >
       needs.job-setup.outputs.check_out == 'true'
diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 7054999f..fcc3574e 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -82,6 +82,8 @@ jobs:
 
       # Get package name and version from DESCRIPTION so that we'll know
       # what's the name of the tar.gz file with the built package.
+      # PKGBUILD environment variable is saved as an environment variable so this
+      # information can be accessed by subsequent steps.
       - name: Get package name 📦
         if: contains(env.ENABLED_STEPS, 'get_package_name')
         run: |
@@ -95,7 +97,7 @@ jobs:
       - name: Build R package 🏗
         if: contains(env.ENABLED_STEPS, 'build_r_package')
         run: |
-          R CMD build ${{ github.event.repository.name }}
+          R CMD build --no-manual --no-build-vignettes ${{ github.event.repository.name }}
           ls -l
         shell: bash
 
@@ -103,7 +105,7 @@ jobs:
       - name: Run R CMD check 🏁
         if: contains(env.ENABLED_STEPS, 'run_r_cmd_check')
         run: |
-          R CMD check ${{ env.PKGBUILD }}
+          R CMD check --no-manual --no-vignettes ${{ env.PKGBUILD }}
         shell: bash
         env:
           _R_CHECK_TESTS_NLINES_: 0

From b1f73cf996d68cae800136d4585dfbf5fd0c8b15 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 23 May 2024 11:47:11 +0200
Subject: [PATCH 40/62] Update

---
 tests/testthat/test-hello.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-hello.R b/tests/testthat/test-hello.R
index 0b2fa257..289310c5 100644
--- a/tests/testthat/test-hello.R
+++ b/tests/testthat/test-hello.R
@@ -7,5 +7,5 @@ test_that("hello_cli() works", {
 })
 
 test_that("fix me!!!", {
-  expect_equal(1, 2)
-})
\ No newline at end of file
+  expect_equal(1, 1)
+})

From 116e2740bbda6ef191695d5d233b655cab846750 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 23 May 2024 11:55:47 +0200
Subject: [PATCH 41/62] Update

---
 .github/workflows/check.yaml  | 22 ++++++++++++----------
 .github/workflows/simple.yaml | 26 ++++++++++++++++----------
 2 files changed, 28 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index 34df66bd..8b2c3d9a 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -2,20 +2,22 @@
 name: Check 🛠
 
 on:
-  # pull_request:
-  #   types:
-  #     - opened
-  #     - synchronize
-  #     - reopened
-  #     - ready_for_review
-  #   branches:
-  #     - main
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
+    branches:
+      - main
   push:
     branches:
       - main
-      - setup-workflows
-  workflow_dispatch:
 
+# Prerequisites to run workflows:
+# Actions -> I understand my workflows...
+# Settings -> Actions -> General -> Workflow permissions -> Read and write permissions
+# Create a PR from your own branch to main.
 
 # This reusable workflow from insightsengineering/r.pkg.template will run once a PR to main branch is created.
 jobs:
diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index fcc3574e..65394b10 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -2,23 +2,22 @@
 name: Simple workflow
 
 on:
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
+    branches:
+      - main
   push:
     branches:
       - main
-      # TODO update this
-      - setup-workflows
-  # pull_request:
-  #   types:
-  #     - opened
-  #     - synchronize
-  #     - reopened
-  #     - ready_for_review
-  #   branches:
-  #     - main
 
 # Prerequisites to run workflows:
 # Actions -> I understand my workflows...
 # Settings -> Actions -> General -> Workflow permissions -> Read and write permissions
+# Create a PR from your own branch to main.
 
 env:
   ENABLED_STEPS: |
@@ -42,6 +41,7 @@ env:
 #     upload_...
 
 jobs:
+  # First job.
   hello-world-from-r:
     name: Hello, world!
     runs-on: ubuntu-latest
@@ -55,6 +55,8 @@ jobs:
         env:
           NAME: "Your name"
 
+  # Second job - by default jobs will run in parallel, unless some dependencies
+  # are introduced between them.
   build-and-check:
     name: Build R package
     runs-on: ubuntu-latest
@@ -71,9 +73,11 @@ jobs:
 
       - name: Setup R 🔧
         if: contains(env.ENABLED_STEPS, 'setup_r')
+        # We're using a third-party GitHub Action.
         uses: r-lib/actions/setup-r@v2
 
       - name: Setup R dependencies 🔧
+        # We're using a third-party GitHub Action.
         uses: r-lib/actions/setup-r-dependencies@v2
         if: contains(env.ENABLED_STEPS, 'setup_dependencies')
         with:
@@ -94,6 +98,7 @@ jobs:
         working-directory: ${{ github.event.repository.name }}
 
       # Build a package stored in a directory called ${{ github.event.repository.name }}
+      # --no-manual --no-build-vignettes because this requires LaTeX.
       - name: Build R package 🏗
         if: contains(env.ENABLED_STEPS, 'build_r_package')
         run: |
@@ -102,6 +107,7 @@ jobs:
         shell: bash
 
       # Check tar.gz package built in previous step.
+      # --no-manual --no-vignettes because this requires LaTeX.
       - name: Run R CMD check 🏁
         if: contains(env.ENABLED_STEPS, 'run_r_cmd_check')
         run: |

From 9d59f468c5c63cdb2f23c69539a8a4a1638f33f7 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 23 May 2024 12:28:04 +0200
Subject: [PATCH 42/62] Update

---
 .github/workflows/simple.yaml | 33 ++++++++++++++++++++-------------
 1 file changed, 20 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 65394b10..465399eb 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -42,18 +42,19 @@ env:
 
 jobs:
   # First job.
-  hello-world-from-r:
-    name: Hello, world!
-    runs-on: ubuntu-latest
-    steps:
-      - name: Setup R 🔧
-        uses: r-lib/actions/setup-r@v2
+  # TODO uncomment
+  # hello-world-from-r:
+  #   name: Hello, world!
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - name: Setup R 🔧
+  #       uses: r-lib/actions/setup-r@v2
 
-      - name: Hello world! 💬
-        run: cat(paste0("Hello ", Sys.getenv("NAME"), "! 👋"))
-        shell: Rscript {0}
-        env:
-          NAME: "Your name"
+  #     - name: Hello world! 💬
+  #       run: cat(paste0("Hello ", Sys.getenv("NAME"), "! 👋"))
+  #       shell: Rscript {0}
+  #       env:
+  #         NAME: "Your name"
 
   # Second job - by default jobs will run in parallel, unless some dependencies
   # are introduced between them.
@@ -117,13 +118,19 @@ jobs:
           _R_CHECK_TESTS_NLINES_: 0
           _R_CHECK_VIGNETTES_NLINES_: 0
 
+      - name: Get tar.gz file name
+        id: tar-gz
+        uses: user-workshop-cicd/action-example@setup-action
+        with:
+          filename-beginning: ${{ github.event.repository.name }}
+
       # Upload tar.gz package as an artifact so it can be downloaded.
       - name: Upload package build ⤴
         if: contains(env.ENABLED_STEPS, 'upload_artifact')
         uses: actions/upload-artifact@v4
         with:
-          path: ${{ env.PKGBUILD }}
-          name: ${{ env.PKGBUILD }}
+          path: ${{ steps.tar-gz.outputs.full-filename }}
+          name: ${{ steps.tar-gz.outputs.full-filename }}
 
   call-reusable-workflow:
     name: Reusable workflow ♻️

From 36acdadbd0ca004f800cc4267fb094d33d8b8da0 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 23 May 2024 12:31:33 +0200
Subject: [PATCH 43/62] Update

---
 .github/workflows/simple.yaml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 465399eb..f3af4cc4 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -119,7 +119,9 @@ jobs:
           _R_CHECK_VIGNETTES_NLINES_: 0
 
       - name: Get tar.gz file name
+        if: contains(env.ENABLED_STEPS, 'upload_artifact')
         id: tar-gz
+        # Use our custom action.
         uses: user-workshop-cicd/action-example@setup-action
         with:
           filename-beginning: ${{ github.event.repository.name }}
@@ -129,6 +131,8 @@ jobs:
         if: contains(env.ENABLED_STEPS, 'upload_artifact')
         uses: actions/upload-artifact@v4
         with:
+          # Output of the custom action from the previous step
+          # are inputs of this action.
           path: ${{ steps.tar-gz.outputs.full-filename }}
           name: ${{ steps.tar-gz.outputs.full-filename }}
 

From 862e70a96e769c840b4f247fb105cf2dc818f5f9 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 23 May 2024 12:33:08 +0200
Subject: [PATCH 44/62] Update

---
 tests/testthat/test-hello.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-hello.R b/tests/testthat/test-hello.R
index 289310c5..e3cfab2a 100644
--- a/tests/testthat/test-hello.R
+++ b/tests/testthat/test-hello.R
@@ -7,5 +7,5 @@ test_that("hello_cli() works", {
 })
 
 test_that("fix me!!!", {
-  expect_equal(1, 1)
+  expect_equal(1, 2)
 })

From 1b0915fdd89b89fa8045f2324ad558352aa2d715 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Thu, 23 May 2024 12:35:58 +0200
Subject: [PATCH 45/62] Update

---
 .github/workflows/simple.yaml | 59 +++++++++++++++++------------------
 1 file changed, 29 insertions(+), 30 deletions(-)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index f3af4cc4..26e18b35 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -19,42 +19,41 @@ on:
 # Settings -> Actions -> General -> Workflow permissions -> Read and write permissions
 # Create a PR from your own branch to main.
 
-env:
-  ENABLED_STEPS: |
-    checkout_repository
-    setup_r
-    setup_dependencies
-    get_package_name
-    build_r_package
-    run_r_cmd_check
-    upload_artifact
-
-# When asked to, please add the steps from the list above:
 # env:
 #   ENABLED_STEPS: |
-#     checkout_...
-#     setup_...
-#     setup_...
-#     get_package_...
-#     build_r_...
-#     run_r_...
-#     upload_...
+#     checkout_repository
+#     setup_r
+#     setup_dependencies
+#     get_package_name
+#     build_r_package
+#     run_r_cmd_check
+#     upload_artifact
+
+# When asked to, please add the steps from the list above:
+env:
+  ENABLED_STEPS: |
+    checkout_...
+    setup_...
+    setup_...
+    get_package_...
+    build_r_...
+    run_r_...
+    upload_...
 
 jobs:
   # First job.
-  # TODO uncomment
-  # hello-world-from-r:
-  #   name: Hello, world!
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - name: Setup R 🔧
-  #       uses: r-lib/actions/setup-r@v2
+  hello-world-from-r:
+    name: Hello, world!
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup R 🔧
+        uses: r-lib/actions/setup-r@v2
 
-  #     - name: Hello world! 💬
-  #       run: cat(paste0("Hello ", Sys.getenv("NAME"), "! 👋"))
-  #       shell: Rscript {0}
-  #       env:
-  #         NAME: "Your name"
+      - name: Hello world! 💬
+        run: cat(paste0("Hello ", Sys.getenv("NAME"), "! 👋"))
+        shell: Rscript {0}
+        env:
+          NAME: "Your name"
 
   # Second job - by default jobs will run in parallel, unless some dependencies
   # are introduced between them.

From 1fe72e6612f9a4dda912916cee5f5949cfd4d3cd Mon Sep 17 00:00:00 2001
From: walkowif <walkowif@test>
Date: Fri, 24 May 2024 12:34:17 +0000
Subject: [PATCH 46/62] Empty test


From cd801db5270a5e58f663c091568bd17bc7e5f477 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Fri, 24 May 2024 14:39:20 +0200
Subject: [PATCH 47/62] Add instructions to README

---
 README.md | 49 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)

diff --git a/README.md b/README.md
index c7886d4a..d609dc14 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,52 @@
 # r.package.example
 
 An example package for the workshop.
+
+## Setting up local environment
+
+You'll need an SSH client and `git`.
+
+For example on Ubuntu, you can install them like this. If you know how to use Docker, you can run these commands in `ubuntu` image.
+```bash
+apt-get update && apt-get install -yq openssh-client git
+```
+
+Create an SSH key pair.
+```bash
+ssh-keygen -P '' -t rsa -b 4096 -C "$(whoami)@$(hostname)" -f ~/.ssh/$(whoami)-github
+eval $(ssh-agent) && ssh-add ~/.ssh/$(whoami)-github
+cat ~/.ssh/$(whoami)-github.pub
+```
+
+The result will look like this:
+```
+ssh-rsa AAAA...
+```
+
+Copy this and paste to https://github.com/settings/ssh/new.
+
+Add any title, and leave key type equal to authentication key.
+
+### Cloning the sample repository
+
+Clone the `r.package.example` repository. Replace `<url>` with an URL similar to this one: `git@github.com:user-workshop-cicd/r.package.example.git`, but `user-workshop-cicd` should be replaced with your GitHub username.
+
+```bash
+git clone <url>
+cd r.package.example
+git status
+```
+
+The output should look like:
+```
+On branch main
+Your branch is up to date with 'origin/main'.
+
+nothing to commit, working tree clean
+```
+
+Configure your name and email address - this will be required to push commits.
+```
+git config --global user.email "you@example.com"
+git config --global user.name "Your Name"
+```

From 41b2a2838eb3c5e25aa22e64335e42da27b54e9d Mon Sep 17 00:00:00 2001
From: walkowif <walkowif@example.com>
Date: Mon, 27 May 2024 10:51:00 +0200
Subject: [PATCH 48/62] Empty


From f801af41acb1eebf3813538923f43a7345fe7319 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Mon, 27 May 2024 11:13:52 +0200
Subject: [PATCH 49/62] Add git installation instructions for Windows

---
 .github/workflows/check.yaml  |  5 -----
 .github/workflows/simple.yaml |  6 +-----
 README.md                     | 27 +++++++++++++++++++++++----
 3 files changed, 24 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index 8b2c3d9a..341ec75d 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -14,11 +14,6 @@ on:
     branches:
       - main
 
-# Prerequisites to run workflows:
-# Actions -> I understand my workflows...
-# Settings -> Actions -> General -> Workflow permissions -> Read and write permissions
-# Create a PR from your own branch to main.
-
 # This reusable workflow from insightsengineering/r.pkg.template will run once a PR to main branch is created.
 jobs:
   job-setup:
diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 26e18b35..dac81c70 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -14,11 +14,7 @@ on:
     branches:
       - main
 
-# Prerequisites to run workflows:
-# Actions -> I understand my workflows...
-# Settings -> Actions -> General -> Workflow permissions -> Read and write permissions
-# Create a PR from your own branch to main.
-
+# For reference, this is how the final list of steps will look like:
 # env:
 #   ENABLED_STEPS: |
 #     checkout_repository
diff --git a/README.md b/README.md
index d609dc14..ac76c58d 100644
--- a/README.md
+++ b/README.md
@@ -2,15 +2,34 @@
 
 An example package for the workshop.
 
-## Setting up local environment
+## Install `git` and SSH client
 
-You'll need an SSH client and `git`.
+### Windows
+On Windows you can install `git` together with SSH client from https://git-scm.com/download/win.
 
-For example on Ubuntu, you can install them like this. If you know how to use Docker, you can run these commands in `ubuntu` image.
+Below you can find suggested installation customizations, but feel free to customize according to your preferences.
+
+1. Select Components → you can unselect `Windows Explorer integration` and `Scalar (Git add-on to manage large-scale repositories)`.
+1. Choosing the default editor used by Git → `Use the Nano editor by default`.
+1. Adjusting the name of the initial branch in new repositories → `Override the default branch name for new repositories` with `main`.
+1. Adjusting your PATH environment → `Use Git from Git Bash only`.
+1. Use bundled OpenSSH (default).
+1. Use the OpenSSL library (default).
+1. Configure the line ending conversions → `Checkout as-is, commit as-is`.
+1. Use MinTTY (default).
+1. Fast-forward or merge (default).
+1. Git Credential Manager (default).
+1. Enable file system caching (default).
+1. No experimental options.
+
+### Ubuntu or Docker container
+On Ubuntu, you can install them like this. If you know how to use Docker, you can run these commands in `ubuntu` image.
 ```bash
 apt-get update && apt-get install -yq openssh-client git
 ```
 
+## Setup write access to GitHub
+
 Create an SSH key pair.
 ```bash
 ssh-keygen -P '' -t rsa -b 4096 -C "$(whoami)@$(hostname)" -f ~/.ssh/$(whoami)-github
@@ -27,7 +46,7 @@ Copy this and paste to https://github.com/settings/ssh/new.
 
 Add any title, and leave key type equal to authentication key.
 
-### Cloning the sample repository
+## Cloning the sample repository
 
 Clone the `r.package.example` repository. Replace `<url>` with an URL similar to this one: `git@github.com:user-workshop-cicd/r.package.example.git`, but `user-workshop-cicd` should be replaced with your GitHub username.
 

From c59f497a281cc862fb7b9fb9359c6adbca9e5e26 Mon Sep 17 00:00:00 2001
From: walkowif <walkowif@example.com>
Date: Mon, 27 May 2024 11:27:42 +0200
Subject: [PATCH 50/62] Empty


From 4db5cf971130b3d6d8c19869d88da7460739666b Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Mon, 27 May 2024 11:29:54 +0200
Subject: [PATCH 51/62] Update readme

---
 README.md | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index ac76c58d..17eafe3e 100644
--- a/README.md
+++ b/README.md
@@ -2,9 +2,11 @@
 
 An example package for the workshop.
 
-## Install `git` and SSH client
+## Prepare your local environment for the workshop excercises
 
-### Windows
+### Install `git` and SSH client
+
+#### Windows
 On Windows you can install `git` together with SSH client from https://git-scm.com/download/win.
 
 Below you can find suggested installation customizations, but feel free to customize according to your preferences.
@@ -22,13 +24,13 @@ Below you can find suggested installation customizations, but feel free to custo
 1. Enable file system caching (default).
 1. No experimental options.
 
-### Ubuntu or Docker container
+#### Ubuntu or Docker container
 On Ubuntu, you can install them like this. If you know how to use Docker, you can run these commands in `ubuntu` image.
 ```bash
 apt-get update && apt-get install -yq openssh-client git
 ```
 
-## Setup write access to GitHub
+### Setup write access to GitHub
 
 Create an SSH key pair.
 ```bash
@@ -46,11 +48,13 @@ Copy this and paste to https://github.com/settings/ssh/new.
 
 Add any title, and leave key type equal to authentication key.
 
-## Cloning the sample repository
+### Clone the sample repository
 
 Clone the `r.package.example` repository. Replace `<url>` with an URL similar to this one: `git@github.com:user-workshop-cicd/r.package.example.git`, but `user-workshop-cicd` should be replaced with your GitHub username.
 
 ```bash
+mkdir user-workshop
+cd user-workshop
 git clone <url>
 cd r.package.example
 git status
@@ -65,6 +69,8 @@ nothing to commit, working tree clean
 ```
 
 Configure your name and email address - this will be required to push commits.
+
+You may consider using obfuscated e-mail address like `<github-username>@example.com`, and `<github-username>` as `Your Name`.
 ```
 git config --global user.email "you@example.com"
 git config --global user.name "Your Name"

From 59eb530207deb5781221dfe966e21c1a4abf2d31 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 11 Jun 2024 11:43:03 +0200
Subject: [PATCH 52/62] Remove local configuration instructions

---
 README.md | 74 -------------------------------------------------------
 1 file changed, 74 deletions(-)

diff --git a/README.md b/README.md
index 17eafe3e..c7886d4a 100644
--- a/README.md
+++ b/README.md
@@ -1,77 +1,3 @@
 # r.package.example
 
 An example package for the workshop.
-
-## Prepare your local environment for the workshop excercises
-
-### Install `git` and SSH client
-
-#### Windows
-On Windows you can install `git` together with SSH client from https://git-scm.com/download/win.
-
-Below you can find suggested installation customizations, but feel free to customize according to your preferences.
-
-1. Select Components → you can unselect `Windows Explorer integration` and `Scalar (Git add-on to manage large-scale repositories)`.
-1. Choosing the default editor used by Git → `Use the Nano editor by default`.
-1. Adjusting the name of the initial branch in new repositories → `Override the default branch name for new repositories` with `main`.
-1. Adjusting your PATH environment → `Use Git from Git Bash only`.
-1. Use bundled OpenSSH (default).
-1. Use the OpenSSL library (default).
-1. Configure the line ending conversions → `Checkout as-is, commit as-is`.
-1. Use MinTTY (default).
-1. Fast-forward or merge (default).
-1. Git Credential Manager (default).
-1. Enable file system caching (default).
-1. No experimental options.
-
-#### Ubuntu or Docker container
-On Ubuntu, you can install them like this. If you know how to use Docker, you can run these commands in `ubuntu` image.
-```bash
-apt-get update && apt-get install -yq openssh-client git
-```
-
-### Setup write access to GitHub
-
-Create an SSH key pair.
-```bash
-ssh-keygen -P '' -t rsa -b 4096 -C "$(whoami)@$(hostname)" -f ~/.ssh/$(whoami)-github
-eval $(ssh-agent) && ssh-add ~/.ssh/$(whoami)-github
-cat ~/.ssh/$(whoami)-github.pub
-```
-
-The result will look like this:
-```
-ssh-rsa AAAA...
-```
-
-Copy this and paste to https://github.com/settings/ssh/new.
-
-Add any title, and leave key type equal to authentication key.
-
-### Clone the sample repository
-
-Clone the `r.package.example` repository. Replace `<url>` with an URL similar to this one: `git@github.com:user-workshop-cicd/r.package.example.git`, but `user-workshop-cicd` should be replaced with your GitHub username.
-
-```bash
-mkdir user-workshop
-cd user-workshop
-git clone <url>
-cd r.package.example
-git status
-```
-
-The output should look like:
-```
-On branch main
-Your branch is up to date with 'origin/main'.
-
-nothing to commit, working tree clean
-```
-
-Configure your name and email address - this will be required to push commits.
-
-You may consider using obfuscated e-mail address like `<github-username>@example.com`, and `<github-username>` as `Your Name`.
-```
-git config --global user.email "you@example.com"
-git config --global user.name "Your Name"
-```

From cf99c3a2aae6e9f286d9a285c01602fe67057cdb Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 11 Jun 2024 11:43:58 +0200
Subject: [PATCH 53/62] Test step output

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

diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index 341ec75d..19a1c2c5 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -13,6 +13,7 @@ on:
   push:
     branches:
       - main
+      - setup-workflows
 
 # This reusable workflow from insightsengineering/r.pkg.template will run once a PR to main branch is created.
 jobs:
@@ -25,7 +26,7 @@ jobs:
       - name: To check or not to check?
         id: check
         run: |
-          echo "run_r_cmd_check=false" >> $GITHUB_OUTPUT
+          echo "run_r_cmd_check=true" >> $GITHUB_OUTPUT
 
   r-cmd:
     name: R CMD Check 🧬

From cf53ed2323eaa0ff80c06372c41b2dbcf5923b1c Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 11 Jun 2024 12:07:26 +0200
Subject: [PATCH 54/62] Update

---
 .github/workflows/check.yaml  |  2 +-
 .github/workflows/simple.yaml | 20 ++++++++++++--------
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index 19a1c2c5..0fb6ef7e 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -26,7 +26,7 @@ jobs:
       - name: To check or not to check?
         id: check
         run: |
-          echo "run_r_cmd_check=true" >> $GITHUB_OUTPUT
+          echo "run_r_cmd_check=false" >> $GITHUB_OUTPUT
 
   r-cmd:
     name: R CMD Check 🧬
diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index dac81c70..329b37db 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -13,6 +13,7 @@ on:
   push:
     branches:
       - main
+      - setup-workflows
 
 # For reference, this is how the final list of steps will look like:
 # env:
@@ -25,8 +26,11 @@ on:
 #     run_r_cmd_check
 #     upload_artifact
 
-# When asked to, please add the steps from the list above:
 env:
+  _R_CHECK_TESTS_NLINES_: 0
+  _R_CHECK_VIGNETTES_NLINES_: 0
+  EXTRA_CHECK_FLAGS: "--no-manual --no-vignettes"
+  # When asked to, please add the steps from the list above:
   ENABLED_STEPS: |
     checkout_...
     setup_...
@@ -82,14 +86,14 @@ jobs:
 
       # Get package name and version from DESCRIPTION so that we'll know
       # what's the name of the tar.gz file with the built package.
-      # PKGBUILD environment variable is saved as an environment variable so this
-      # information can be accessed by subsequent steps.
+      # pkgbuild is set as an output which can be accessed by subsequent steps.
       - name: Get package name 📦
         if: contains(env.ENABLED_STEPS, 'get_package_name')
+        id: package-name
         run: |
           PKGBUILD="$(Rscript -e 'cat(sprintf("%s_%s.tar.gz",(dcf <- read.dcf("DESCRIPTION"))[,"Package"], dcf[,"Version"]))')"
           echo "PKGBUILD = $PKGBUILD"
-          echo "PKGBUILD=$PKGBUILD" >> $GITHUB_ENV
+          echo "pkgbuild=$PKGBUILD" >> $GITHUB_OUTPUT
         shell: bash
         working-directory: ${{ github.event.repository.name }}
 
@@ -107,11 +111,11 @@ jobs:
       - name: Run R CMD check 🏁
         if: contains(env.ENABLED_STEPS, 'run_r_cmd_check')
         run: |
-          R CMD check --no-manual --no-vignettes ${{ env.PKGBUILD }}
+          echo "_R_CHECK_TESTS_NLINES_ = $_R_CHECK_TESTS_NLINES_"
+          echo "_R_CHECK_VIGNETTES_NLINES_ = $_R_CHECK_VIGNETTES_NLINES_"
+          echo "Let's run R CMD check..."
+          R CMD check ${EXTRA_CHECK_FLAGS} ${{ steps.package-name.outputs.pkgbuild }}
         shell: bash
-        env:
-          _R_CHECK_TESTS_NLINES_: 0
-          _R_CHECK_VIGNETTES_NLINES_: 0
 
       - name: Get tar.gz file name
         if: contains(env.ENABLED_STEPS, 'upload_artifact')

From 42dfd58f58224c76f468200b008916cc3482b55a Mon Sep 17 00:00:00 2001
From: walkowif <59475134+walkowif@users.noreply.github.com>
Date: Tue, 11 Jun 2024 12:11:04 +0200
Subject: [PATCH 55/62] Update simple.yaml

---
 .github/workflows/simple.yaml | 25 +++++++------------------
 1 file changed, 7 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 329b37db..5e9af541 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -15,30 +15,19 @@ on:
       - main
       - setup-workflows
 
-# For reference, this is how the final list of steps will look like:
-# env:
-#   ENABLED_STEPS: |
-#     checkout_repository
-#     setup_r
-#     setup_dependencies
-#     get_package_name
-#     build_r_package
-#     run_r_cmd_check
-#     upload_artifact
-
 env:
   _R_CHECK_TESTS_NLINES_: 0
   _R_CHECK_VIGNETTES_NLINES_: 0
   EXTRA_CHECK_FLAGS: "--no-manual --no-vignettes"
   # When asked to, please add the steps from the list above:
   ENABLED_STEPS: |
-    checkout_...
-    setup_...
-    setup_...
-    get_package_...
-    build_r_...
-    run_r_...
-    upload_...
+    checkout_repository
+    setup_r
+    setup_dependencies
+    get_package_name
+    build_r_package
+    run_r_cmd_check
+    upload_artifact
 
 jobs:
   # First job.

From 94032ce1a1928db864e9a4de9e5cb20eaaa260e1 Mon Sep 17 00:00:00 2001
From: walkowif <59475134+walkowif@users.noreply.github.com>
Date: Tue, 11 Jun 2024 12:14:26 +0200
Subject: [PATCH 56/62] Update .github/workflows/simple.yaml

Co-authored-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
---
 .github/workflows/simple.yaml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 5e9af541..124cd00c 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -16,9 +16,12 @@ on:
       - setup-workflows
 
 env:
+  # additional flags for `R CMD CHECK`
+  EXTRA_CHECK_FLAGS: "--no-manual --no-vignettes"
+  # additional environmental vars for `R CMD CHECK`
+  # see manual here: https://rstudio.github.io/r-manuals/r-ints/Tools.html
   _R_CHECK_TESTS_NLINES_: 0
   _R_CHECK_VIGNETTES_NLINES_: 0
-  EXTRA_CHECK_FLAGS: "--no-manual --no-vignettes"
   # When asked to, please add the steps from the list above:
   ENABLED_STEPS: |
     checkout_repository

From 6ef0ce3726fc0bdb9268f8ff62305aee605e454f Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 11 Jun 2024 12:18:41 +0200
Subject: [PATCH 57/62] Comment steps

---
 .github/workflows/simple.yaml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 124cd00c..445c9f15 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -25,12 +25,12 @@ env:
   # When asked to, please add the steps from the list above:
   ENABLED_STEPS: |
     checkout_repository
-    setup_r
-    setup_dependencies
-    get_package_name
-    build_r_package
-    run_r_cmd_check
-    upload_artifact
+#    setup_r
+#    setup_dependencies
+#    get_package_name
+#    build_r_package
+#    run_r_cmd_check
+#    upload_artifact
 
 jobs:
   # First job.

From 5518e080b9bb0c994a32d7795a0a5d277a7032f0 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 11 Jun 2024 12:43:54 +0200
Subject: [PATCH 58/62] Remove any::rcmdcheck

---
 .github/workflows/simple.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 445c9f15..71519712 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -73,7 +73,6 @@ jobs:
         uses: r-lib/actions/setup-r-dependencies@v2
         if: contains(env.ENABLED_STEPS, 'setup_dependencies')
         with:
-          extra-packages: any::rcmdcheck
           working-directory: ${{ github.event.repository.name }}
 
       # Get package name and version from DESCRIPTION so that we'll know

From 3381cc1dd86486a5c0aceb9d0393e0b392907451 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 11 Jun 2024 12:44:40 +0200
Subject: [PATCH 59/62] Uncomment steps

---
 .github/workflows/check.yaml  |  1 -
 .github/workflows/simple.yaml | 13 ++++++-------
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index 0fb6ef7e..341ec75d 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -13,7 +13,6 @@ on:
   push:
     branches:
       - main
-      - setup-workflows
 
 # This reusable workflow from insightsengineering/r.pkg.template will run once a PR to main branch is created.
 jobs:
diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 71519712..2ab27ad6 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -13,7 +13,6 @@ on:
   push:
     branches:
       - main
-      - setup-workflows
 
 env:
   # additional flags for `R CMD CHECK`
@@ -25,12 +24,12 @@ env:
   # When asked to, please add the steps from the list above:
   ENABLED_STEPS: |
     checkout_repository
-#    setup_r
-#    setup_dependencies
-#    get_package_name
-#    build_r_package
-#    run_r_cmd_check
-#    upload_artifact
+   setup_r
+   setup_dependencies
+   get_package_name
+   build_r_package
+   run_r_cmd_check
+   upload_artifact
 
 jobs:
   # First job.

From 8b71f3f3b000b8918175f561ee05f930bf68ebfb Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 11 Jun 2024 12:45:42 +0200
Subject: [PATCH 60/62] Fix yaml

---
 .github/workflows/simple.yaml | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 2ab27ad6..02ec4e41 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -21,15 +21,14 @@ env:
   # see manual here: https://rstudio.github.io/r-manuals/r-ints/Tools.html
   _R_CHECK_TESTS_NLINES_: 0
   _R_CHECK_VIGNETTES_NLINES_: 0
-  # When asked to, please add the steps from the list above:
   ENABLED_STEPS: |
     checkout_repository
-   setup_r
-   setup_dependencies
-   get_package_name
-   build_r_package
-   run_r_cmd_check
-   upload_artifact
+    setup_r
+    setup_dependencies
+    get_package_name
+    build_r_package
+    run_r_cmd_check
+    upload_artifact
 
 jobs:
   # First job.

From 6c536d158c2132f5ec9323e6d40dbb9812f6bae5 Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Tue, 11 Jun 2024 13:48:15 +0200
Subject: [PATCH 61/62] Print all R variables

---
 .github/workflows/simple.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index 02ec4e41..abc1bef2 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -100,8 +100,7 @@ jobs:
       - name: Run R CMD check 🏁
         if: contains(env.ENABLED_STEPS, 'run_r_cmd_check')
         run: |
-          echo "_R_CHECK_TESTS_NLINES_ = $_R_CHECK_TESTS_NLINES_"
-          echo "_R_CHECK_VIGNETTES_NLINES_ = $_R_CHECK_VIGNETTES_NLINES_"
+          env | grep -E '^_R'
           echo "Let's run R CMD check..."
           R CMD check ${EXTRA_CHECK_FLAGS} ${{ steps.package-name.outputs.pkgbuild }}
         shell: bash

From 0cec831bae98ef47a931c0037ee2cf80b04f7274 Mon Sep 17 00:00:00 2001
From: walkowif <59475134+walkowif@users.noreply.github.com>
Date: Tue, 11 Jun 2024 15:52:04 +0200
Subject: [PATCH 62/62] Update .github/workflows/simple.yaml

---
 .github/workflows/simple.yaml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/simple.yaml b/.github/workflows/simple.yaml
index abc1bef2..dcdd1d11 100644
--- a/.github/workflows/simple.yaml
+++ b/.github/workflows/simple.yaml
@@ -23,12 +23,12 @@ env:
   _R_CHECK_VIGNETTES_NLINES_: 0
   ENABLED_STEPS: |
     checkout_repository
-    setup_r
-    setup_dependencies
-    get_package_name
-    build_r_package
-    run_r_cmd_check
-    upload_artifact
+#    setup_r
+#    setup_dependencies
+#    get_package_name
+#    build_r_package
+#    run_r_cmd_check
+#    upload_artifact
 
 jobs:
   # First job.