From 1bf5f11ad4efe7f5c087f9bc08f6f3ca4b975326 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 24 Oct 2023 15:45:02 +0200
Subject: [PATCH 01/39] add checks for devel

---
 .github/workflows/push-docker-image.yml | 28 +++++++++++++++++++++----
 .github/workflows/r-cmd-check.yml       | 27 ++++++++++++++++--------
 2 files changed, 42 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/push-docker-image.yml b/.github/workflows/push-docker-image.yml
index d85cb83c..107ba4e6 100644
--- a/.github/workflows/push-docker-image.yml
+++ b/.github/workflows/push-docker-image.yml
@@ -47,6 +47,7 @@ jobs:
             renv_list="${{ steps.changed-files.outputs.all_changed_files }}"
           fi
           renv_list=$(echo $renv_list | sed 's/ /", "/g')
+          renv_list="$renv_list devel" # adding devel conf
           echo "renv=[\"$renv_list\"]" >> $GITHUB_OUTPUT
 
   deploy-image:
@@ -76,14 +77,20 @@ jobs:
         id: image_specs
         run: |
           package_name=$(grep "Package:" DESCRIPTION | awk '{print $NF}')
-          r_version=$(basename $(dirname ${{ matrix.value }})) # TODO: check here if legacy renv (if yes, delete _legacy suffix and add _legacy suffix to docker im?)
+          if [ "${{ matrix.value }}" == "devel" ]{
+            r_version="devel"
+          }
+          else {
+            r_version=$(basename $(dirname ${{ matrix.value }})) # TODO: check here if legacy renv (if yes, delete _legacy suffix and add _legacy suffix to docker im?)
+            renv=$(echo "${{ matrix.value }}" | tr -d '"')
+            echo "renv_lock_path=$renv" >> $GITHUB_OUTPUT
+          }
           echo "r_version=$r_version" >> $GITHUB_OUTPUT
           echo "image_name=$package_name-$r_version" >> $GITHUB_OUTPUT
-          renv=$(echo "${{ matrix.value }}" | tr -d '"')
-          echo "renv_lock_path=$renv" >> $GITHUB_OUTPUT
 
       - name: Call deploy docker image action for every renv
-        uses: insightsengineering/r-image-creator@v1
+        uses: insightsengineering/r-image-creator@create_image_from_description
+        if: ${{ matrix.value }} != 'devel'
         with:
           image-name: "${{ steps.image_specs.outputs.image_name }}"
           tag-latest: true
@@ -93,6 +100,19 @@ jobs:
           repository-owner: ${{ github.repository_owner }}
           repo-user: ${{ github.actor }}  # pharmaverse-bot
           repo-token: "${{ secrets.GITHUB_TOKEN }}" # ${{ secrets.PHARMAVERSE_BOT }}
+      
+      - name: Call deploy docker image action for every renv
+        uses: insightsengineering/r-image-creator@create_image_from_description
+        if: ${{ matrix.value }} == 'devel'
+        with:
+          image-name: "${{ steps.image_specs.outputs.image_name }}"
+          tag-latest: true
+          base-image: "rocker/rstudio:${{ steps.image_specs.outputs.r_version }}"
+          sysdeps: qpdf,libxt-dev,curl,npm,libicu-dev,libcurl4-openssl-dev,libssl-dev,make,zlib1g-dev,libfontconfig1-dev,libfreetype6-dev,libfribidi-dev,libharfbuzz-dev,libjpeg-dev,libpng-dev,libtiff-dev,pandoc,libxml2-dev,libgit2-dev,libgit2-dev,jq
+          description-file: "./DESCRIPTION"
+          repository-owner: ${{ github.repository_owner }}
+          repo-user: ${{ github.actor }}  # pharmaverse-bot
+          repo-token: "${{ secrets.GITHUB_TOKEN }}" # ${{ secrets.PHARMAVERSE_BOT }}
 
 # note: in case of 403 error when pushing to ghcr : link current repo to the given package registry - https://github.com/docker/build-push-action/issues/687
 # (got to https://github.com/<user name>?tab=packages to go to packages settings) and there https://github.com/users/<user name>/packages/container/admiralci-4.0/settings
\ No newline at end of file
diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
index 93f487ba..55cb54b8 100644
--- a/.github/workflows/r-cmd-check.yml
+++ b/.github/workflows/r-cmd-check.yml
@@ -37,6 +37,7 @@ jobs:
           - {r: '4.1', repos: 'https://packagemanager.posit.co/cran/2021-05-03/'}
           - {r: '4.2', repos: 'https://packagemanager.posit.co/cran/2022-01-03/'}
           - {r: '4.3', repos: 'https://packagemanager.posit.co/cran/__linux__/focal/latest'}
+          - {r: 'devel', repos: 'https://packagemanager.posit.co/cran/__linux__/focal/latest'} # not needed for devel ?
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -86,22 +87,30 @@ jobs:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
           _R_CHECK_FORCE_SUGGESTS_: false
         run: |
-          if (!requireNamespace("rcmdcheck", quietly = TRUE)) install.packages("rcmdcheck")
+          script=$(cat <<EOF
           options(crayon.enabled = TRUE)
-          check_error_on <- "${{ inputs.error-on }}"
-          if (check_error_on == "") {
-            check_error_on <- "note"
+          check_error_on <- '${{ inputs.error-on }}'
+          if (check_error_on == '') {
+            check_error_on <- 'note'
           }
           rcmdcheck::rcmdcheck(
-            args = c("--no-manual", "--as-cran"),
+            args = c('--no-manual', '--as-cran'),
             error_on = check_error_on,
-            check_dir = "check"
+            check_dir = 'check'
           )
-        shell: Rscript {0}
+          EOF
+          )
+
+          if [ ${{ matrix.config.r }} == "devel" ]; then
+            Rscript --vanilla --no-renv -e $script
+          else
+            Rscript {0} -e $script
+          fi
+        shell: bash
 
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@main
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          name: r${{ matrix.config.r }}-results
+          path: check
\ No newline at end of file

From 6097514a988c39d6738f60da96f26ffd0fda825a Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 24 Oct 2023 15:58:12 +0200
Subject: [PATCH 02/39] fix branch name

---
 .github/workflows/push-docker-image.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/push-docker-image.yml b/.github/workflows/push-docker-image.yml
index 107ba4e6..d957dd05 100644
--- a/.github/workflows/push-docker-image.yml
+++ b/.github/workflows/push-docker-image.yml
@@ -89,7 +89,7 @@ jobs:
           echo "image_name=$package_name-$r_version" >> $GITHUB_OUTPUT
 
       - name: Call deploy docker image action for every renv
-        uses: insightsengineering/r-image-creator@create_image_from_description
+        uses: insightsengineering/r-image-creator@feature/create_image_from_description
         if: ${{ matrix.value }} != 'devel'
         with:
           image-name: "${{ steps.image_specs.outputs.image_name }}"
@@ -102,7 +102,7 @@ jobs:
           repo-token: "${{ secrets.GITHUB_TOKEN }}" # ${{ secrets.PHARMAVERSE_BOT }}
       
       - name: Call deploy docker image action for every renv
-        uses: insightsengineering/r-image-creator@create_image_from_description
+        uses: insightsengineering/r-image-creator@feature/create_image_from_description
         if: ${{ matrix.value }} == 'devel'
         with:
           image-name: "${{ steps.image_specs.outputs.image_name }}"

From 1236e00dc3c87c3583bcfca3f281561636fa1c62 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 24 Oct 2023 17:55:20 +0200
Subject: [PATCH 03/39] update push job

---
 .github/workflows/push-docker-image.yml | 44 +++++++++++++++++--------
 1 file changed, 30 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/push-docker-image.yml b/.github/workflows/push-docker-image.yml
index d957dd05..75c89519 100644
--- a/.github/workflows/push-docker-image.yml
+++ b/.github/workflows/push-docker-image.yml
@@ -47,7 +47,6 @@ jobs:
             renv_list="${{ steps.changed-files.outputs.all_changed_files }}"
           fi
           renv_list=$(echo $renv_list | sed 's/ /", "/g')
-          renv_list="$renv_list devel" # adding devel conf
           echo "renv=[\"$renv_list\"]" >> $GITHUB_OUTPUT
 
   deploy-image:
@@ -77,20 +76,14 @@ jobs:
         id: image_specs
         run: |
           package_name=$(grep "Package:" DESCRIPTION | awk '{print $NF}')
-          if [ "${{ matrix.value }}" == "devel" ]{
-            r_version="devel"
-          }
-          else {
-            r_version=$(basename $(dirname ${{ matrix.value }})) # TODO: check here if legacy renv (if yes, delete _legacy suffix and add _legacy suffix to docker im?)
-            renv=$(echo "${{ matrix.value }}" | tr -d '"')
-            echo "renv_lock_path=$renv" >> $GITHUB_OUTPUT
-          }
+          r_version=$(basename $(dirname ${{ matrix.value }})) # TODO: check here if legacy renv (if yes, delete _legacy suffix and add _legacy suffix to docker im?)
+          renv=$(echo "${{ matrix.value }}" | tr -d '"')
+          echo "renv_lock_path=$renv" >> $GITHUB_OUTPUT
           echo "r_version=$r_version" >> $GITHUB_OUTPUT
           echo "image_name=$package_name-$r_version" >> $GITHUB_OUTPUT
 
       - name: Call deploy docker image action for every renv
         uses: insightsengineering/r-image-creator@feature/create_image_from_description
-        if: ${{ matrix.value }} != 'devel'
         with:
           image-name: "${{ steps.image_specs.outputs.image_name }}"
           tag-latest: true
@@ -100,19 +93,42 @@ jobs:
           repository-owner: ${{ github.repository_owner }}
           repo-user: ${{ github.actor }}  # pharmaverse-bot
           repo-token: "${{ secrets.GITHUB_TOKEN }}" # ${{ secrets.PHARMAVERSE_BOT }}
-      
-      - name: Call deploy docker image action for every renv
+
+  deploy-image-devel:
+    runs-on: ubuntu-latest
+
+    # Token permissions
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set image specs
+        id: image_specs
+        run: |
+          package_name=$(grep "Package:" DESCRIPTION | awk '{print $NF}')
+          echo "image_name=$package_name-devel" >> $GITHUB_OUTPUT
+    
+      - name: Call deploy docker image action devel
         uses: insightsengineering/r-image-creator@feature/create_image_from_description
-        if: ${{ matrix.value }} == 'devel'
         with:
           image-name: "${{ steps.image_specs.outputs.image_name }}"
           tag-latest: true
-          base-image: "rocker/rstudio:${{ steps.image_specs.outputs.r_version }}"
+          base-image: "rocker/rstudio:devel"
           sysdeps: qpdf,libxt-dev,curl,npm,libicu-dev,libcurl4-openssl-dev,libssl-dev,make,zlib1g-dev,libfontconfig1-dev,libfreetype6-dev,libfribidi-dev,libharfbuzz-dev,libjpeg-dev,libpng-dev,libtiff-dev,pandoc,libxml2-dev,libgit2-dev,libgit2-dev,jq
           description-file: "./DESCRIPTION"
           repository-owner: ${{ github.repository_owner }}
           repo-user: ${{ github.actor }}  # pharmaverse-bot
           repo-token: "${{ secrets.GITHUB_TOKEN }}" # ${{ secrets.PHARMAVERSE_BOT }}
 
+
+# refacto todo: image-name, sysdeps on get-renv-list job
+
+
 # note: in case of 403 error when pushing to ghcr : link current repo to the given package registry - https://github.com/docker/build-push-action/issues/687
 # (got to https://github.com/<user name>?tab=packages to go to packages settings) and there https://github.com/users/<user name>/packages/container/admiralci-4.0/settings
\ No newline at end of file

From 80516dac35b2b4016aa36b52dceb84267450aa2d Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 24 Oct 2023 17:57:28 +0200
Subject: [PATCH 04/39] re-test

---
 .github/workflows/push-docker-image.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/push-docker-image.yml b/.github/workflows/push-docker-image.yml
index 75c89519..d8977196 100644
--- a/.github/workflows/push-docker-image.yml
+++ b/.github/workflows/push-docker-image.yml
@@ -71,6 +71,7 @@ jobs:
       - name: Print message
         run: |
           echo "updating docker image for renv ${{ matrix.value }}"
+          exit 1 # TODO: del (for testing)
 
       - name: Set image specs
         id: image_specs

From e79372ccc4dfb84144d2d94861c190c7fe071e6d Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Wed, 25 Oct 2023 10:14:16 +0200
Subject: [PATCH 05/39] fix checks

---
 .github/workflows/r-cmd-check.yml | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
index 55cb54b8..d03b30a1 100644
--- a/.github/workflows/r-cmd-check.yml
+++ b/.github/workflows/r-cmd-check.yml
@@ -102,9 +102,15 @@ jobs:
           )
 
           if [ ${{ matrix.config.r }} == "devel" ]; then
-            Rscript --vanilla --no-renv -e $script
+            # deactivate renv for devel checks
+            script=$(cat <<EOF
+            renv::deactivate()
+            $script
+            EOF
+            )
+            Rscript --vanilla -e $script
           else
-            Rscript {0} -e $script
+            Rscript --vanilla -e $script
           fi
         shell: bash
 

From eef1305b380fcfc5de4cf1d37a082a3725ea4304 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Wed, 25 Oct 2023 10:55:22 +0200
Subject: [PATCH 06/39] fix typo

---
 .github/workflows/r-cmd-check.yml | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
index d03b30a1..352d41ce 100644
--- a/.github/workflows/r-cmd-check.yml
+++ b/.github/workflows/r-cmd-check.yml
@@ -87,7 +87,7 @@ jobs:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
           _R_CHECK_FORCE_SUGGESTS_: false
         run: |
-          script=$(cat <<EOF
+          script="
           options(crayon.enabled = TRUE)
           check_error_on <- '${{ inputs.error-on }}'
           if (check_error_on == '') {
@@ -97,17 +97,12 @@ jobs:
             args = c('--no-manual', '--as-cran'),
             error_on = check_error_on,
             check_dir = 'check'
-          )
-          EOF
-          )
+          )"
 
           if [ ${{ matrix.config.r }} == "devel" ]; then
             # deactivate renv for devel checks
-            script=$(cat <<EOF
-            renv::deactivate()
-            $script
-            EOF
-            )
+            script="renv::deactivate()
+            $script"
             Rscript --vanilla -e $script
           else
             Rscript --vanilla -e $script

From 506ff15c98a47eca7a33abb3d6ec5bd9542c6572 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Wed, 25 Oct 2023 11:30:27 +0200
Subject: [PATCH 07/39] fix

---
 .github/workflows/r-cmd-check.yml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
index 352d41ce..c9c6e96e 100644
--- a/.github/workflows/r-cmd-check.yml
+++ b/.github/workflows/r-cmd-check.yml
@@ -101,12 +101,13 @@ jobs:
 
           if [ ${{ matrix.config.r }} == "devel" ]; then
             # deactivate renv for devel checks
-            script="renv::deactivate()
+            script="
+            renv::deactivate()
             $script"
-            Rscript --vanilla -e $script
-          else
-            Rscript --vanilla -e $script
+            echo "$script" > checks.R
           fi
+
+          Rscript --vanilla checks.R
         shell: bash
 
       - name: Upload check results

From 2ce17dbeaae10180834d907673e4d470e2a6962b Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Wed, 25 Oct 2023 11:36:47 +0200
Subject: [PATCH 08/39] fix

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

diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
index c9c6e96e..56e062c9 100644
--- a/.github/workflows/r-cmd-check.yml
+++ b/.github/workflows/r-cmd-check.yml
@@ -104,9 +104,10 @@ jobs:
             script="
             renv::deactivate()
             $script"
-            echo "$script" > checks.R
           fi
 
+          echo "$script" > checks.R
+
           Rscript --vanilla checks.R
         shell: bash
 

From a5b603639fd11aeca63d6a4696394d21dca99474 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Wed, 25 Oct 2023 11:38:17 +0200
Subject: [PATCH 09/39] fix

---
 .github/workflows/r-cmd-check.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
index 56e062c9..3431667b 100644
--- a/.github/workflows/r-cmd-check.yml
+++ b/.github/workflows/r-cmd-check.yml
@@ -99,12 +99,12 @@ jobs:
             check_dir = 'check'
           )"
 
-          if [ ${{ matrix.config.r }} == "devel" ]; then
-            # deactivate renv for devel checks
-            script="
-            renv::deactivate()
-            $script"
-          fi
+          # if [ ${{ matrix.config.r }} == "devel" ]; then
+          #   # deactivate renv for devel checks
+          #   script="
+          #   renv::deactivate()
+          #   $script"
+          # fi
 
           echo "$script" > checks.R
 

From 40a30b0208330362a1ba4034fe2bd5aca68c9864 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Wed, 25 Oct 2023 11:54:22 +0200
Subject: [PATCH 10/39] install rcmdcheck for devel im

---
 .github/workflows/r-cmd-check.yml | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
index 3431667b..5efa7fc2 100644
--- a/.github/workflows/r-cmd-check.yml
+++ b/.github/workflows/r-cmd-check.yml
@@ -99,16 +99,13 @@ jobs:
             check_dir = 'check'
           )"
 
-          # if [ ${{ matrix.config.r }} == "devel" ]; then
-          #   # deactivate renv for devel checks
-          #   script="
-          #   renv::deactivate()
-          #   $script"
-          # fi
+          if [ ${{ matrix.config.r }} == "devel" ]; then
+            R -e "install.packages('rcmdcheck')"
+          fi
 
           echo "$script" > checks.R
 
-          Rscript --vanilla checks.R
+          Rscript checks.R
         shell: bash
 
       - name: Upload check results

From 1dc13897d1d5f0fc22def44c01a2b20a9e021ea2 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Fri, 27 Oct 2023 10:13:25 +0200
Subject: [PATCH 11/39] templates: retrieve temp folder

---
 .github/workflows/check-templates.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/check-templates.yml b/.github/workflows/check-templates.yml
index d373e019..c59dc9e2 100644
--- a/.github/workflows/check-templates.yml
+++ b/.github/workflows/check-templates.yml
@@ -198,6 +198,13 @@ jobs:
           }
         shell: Rscript {0}
 
+      - name: Get temp dir
+        run: |
+          folder_id=$(dirname $(find /tmp/ 2>/dev/null | grep .rda | head -n 1))
+          echo "folder id: $folder_id"
+          # copy data from tmp folder
+          cp -r "/tmp/${folder_id}/." "$GITHUB_WORKSPACE/tmp/"
+
       - name: Add other data formats and suffixes, exclude data
         if: inputs.push-templates-data
         run: |

From aad06e3014185923e456f0f59ba54eeeeeeffe70 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Fri, 27 Oct 2023 10:38:34 +0200
Subject: [PATCH 12/39] add checks on existing branches - templates

---
 .github/workflows/check-templates.yml | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/check-templates.yml b/.github/workflows/check-templates.yml
index c59dc9e2..a0125ab6 100644
--- a/.github/workflows/check-templates.yml
+++ b/.github/workflows/check-templates.yml
@@ -384,13 +384,18 @@ jobs:
         id: branch
         run: |
           repo_name=$(basename "${{ github.repository }}")
-          echo "source-branch=${{ env.source-branch }}_${repo_name}@devel" >> $GITHUB_OUTPUT
+          source_br="${{ env.source-branch }}_${repo_name}@devel"
+          source_grep=$(git branch -a | grep $source_br)
+          if [ -z $source_grep ]; then branch_exists=false; else branch_exists=true; fi
+          echo "source-branch=$source_br" >> $GITHUB_OUTPUT
+          echo "branch-exists=$branch_exists" >> $GITHUB_OUTPUT
+          warn_msg="WARNING:: the branch $source_br already exists in pharmaverseadam, please merge it and delete it, and re-execute this job"
+          if [ ${{ steps.changes.outputs.diff }} == 'true' ] && [ "$branch_exists" == 'true' ]; then echo "$warn_msg"; fi
         shell: bash {0}
 
-
       # if diff detected, push changes
       - name: Commit and push changes in {{ env.repo }}
-        if: ${{ inputs.push-templates-data && steps.changes.outputs.diff == 'true' }}
+        if: ${{ inputs.push-templates-data && steps.changes.outputs.diff == 'true' && steps.branch.outputs.branch-exists == 'false' }}
         uses: stefanzweifel/git-auto-commit-action@v4
         with:
           commit_message: templates data updates from ${{ github.repository }}
@@ -401,7 +406,7 @@ jobs:
           create_branch: true
 
       - name: Create Pull Request
-        if: ${{ inputs.push-templates-data && steps.changes.outputs.diff == 'true' }}
+        if: ${{ inputs.push-templates-data && steps.changes.outputs.diff == 'true' && steps.branch.outputs.branch-exists == 'false' }}
         uses: actions/github-script@v6
         with:
           github-token: ${{ secrets.PHARMAVERSE_BOT }}

From 06ce9fc033dcc8601a241f46661edac9c7c08802 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Fri, 27 Oct 2023 11:04:46 +0200
Subject: [PATCH 13/39] debug traces

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

diff --git a/.github/workflows/check-templates.yml b/.github/workflows/check-templates.yml
index a0125ab6..eb269ab1 100644
--- a/.github/workflows/check-templates.yml
+++ b/.github/workflows/check-templates.yml
@@ -200,7 +200,9 @@ jobs:
 
       - name: Get temp dir
         run: |
-          folder_id=$(dirname $(find /tmp/ 2>/dev/null | grep .rda | head -n 1))
+          find /tmp/ 2>/dev/null | grep .rda
+          rda_files=$(find /tmp/ 2>/dev/null | grep .rda | head -n 1)
+          folder_id=$(dirname $rda_files)
           echo "folder id: $folder_id"
           # copy data from tmp folder
           cp -r "/tmp/${folder_id}/." "$GITHUB_WORKSPACE/tmp/"

From 466e5fa441d620b311f0f43e6fb334541f4e7113 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Fri, 27 Oct 2023 11:16:49 +0200
Subject: [PATCH 14/39] fix cp cmd

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

diff --git a/.github/workflows/check-templates.yml b/.github/workflows/check-templates.yml
index eb269ab1..57449a16 100644
--- a/.github/workflows/check-templates.yml
+++ b/.github/workflows/check-templates.yml
@@ -205,7 +205,8 @@ jobs:
           folder_id=$(dirname $rda_files)
           echo "folder id: $folder_id"
           # copy data from tmp folder
-          cp -r "/tmp/${folder_id}/." "$GITHUB_WORKSPACE/tmp/"
+          mkdir -p "$GITHUB_WORKSPACE/tmp/"
+          cp -r "${folder_id}/." "$GITHUB_WORKSPACE/tmp/"
 
       - name: Add other data formats and suffixes, exclude data
         if: inputs.push-templates-data

From 91acb1d70c1c16b3aa4ca1c08c808c293c8eb7f9 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Fri, 27 Oct 2023 11:24:50 +0200
Subject: [PATCH 15/39] fix

---
 .github/workflows/check-templates.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/check-templates.yml b/.github/workflows/check-templates.yml
index 57449a16..ad4b2c24 100644
--- a/.github/workflows/check-templates.yml
+++ b/.github/workflows/check-templates.yml
@@ -207,6 +207,7 @@ jobs:
           # copy data from tmp folder
           mkdir -p "$GITHUB_WORKSPACE/tmp/"
           cp -r "${folder_id}/." "$GITHUB_WORKSPACE/tmp/"
+        shell: bash
 
       - name: Add other data formats and suffixes, exclude data
         if: inputs.push-templates-data

From d0e2ad902cf80e66448181edb41966fe2575e29d Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Fri, 27 Oct 2023 11:39:05 +0200
Subject: [PATCH 16/39] debug traces

---
 .github/workflows/check-templates.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/check-templates.yml b/.github/workflows/check-templates.yml
index ad4b2c24..fe30b12e 100644
--- a/.github/workflows/check-templates.yml
+++ b/.github/workflows/check-templates.yml
@@ -200,8 +200,12 @@ jobs:
 
       - name: Get temp dir
         run: |
+          find /tmp/ 2>/dev/null
+          echo "debug1"
           find /tmp/ 2>/dev/null | grep .rda
+          echo "debug2"
           rda_files=$(find /tmp/ 2>/dev/null | grep .rda | head -n 1)
+          echo "debug3"
           folder_id=$(dirname $rda_files)
           echo "folder id: $folder_id"
           # copy data from tmp folder

From 1f82e55b90952dd69a25a27e3ad3110a5a39511c Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Fri, 27 Oct 2023 15:24:18 +0200
Subject: [PATCH 17/39] add other debug traces

---
 .github/workflows/check-templates.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/check-templates.yml b/.github/workflows/check-templates.yml
index fe30b12e..0cda3db9 100644
--- a/.github/workflows/check-templates.yml
+++ b/.github/workflows/check-templates.yml
@@ -201,6 +201,7 @@ jobs:
       - name: Get temp dir
         run: |
           find /tmp/ 2>/dev/null
+          ls -al /tmp
           echo "debug1"
           find /tmp/ 2>/dev/null | grep .rda
           echo "debug2"

From 9b0a4b62b585a2a2e62e0ed7c21183989e4dff22 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Fri, 27 Oct 2023 15:48:21 +0200
Subject: [PATCH 18/39] update

---
 .github/workflows/check-templates.yml | 24 ++++++++----------------
 1 file changed, 8 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/check-templates.yml b/.github/workflows/check-templates.yml
index 0cda3db9..9c7b6c40 100644
--- a/.github/workflows/check-templates.yml
+++ b/.github/workflows/check-templates.yml
@@ -186,6 +186,14 @@ jobs:
             exit_codes <- purrr::map_chr(templates, function(file) {
               cmd <- sprintf("Rscript --vanilla %s", file)
               system(cmd)
+              # move produced rda file to another location
+              subdirectories <- list.dirs("/tmp", full.names = TRUE)
+              rda_files <- list.files(subdirectories, pattern = "\\.rda$", recursive = TRUE, full.names = TRUE)
+              if (length(rda_files) > 0) {
+                current_rda_file <- rda_files[1]
+                file.copy(current_rda_file, file.path(file.path(Sys.getenv("GITHUB_WORKSPACE"), "tmp"), basename(current_rda_file)))
+                file.remove(current_rda_file)
+              }
             })
             if (any(exit_codes == 1L)) {
               failed_scripts <- basename(templates)[which(exit_codes == 1L)]
@@ -198,22 +206,6 @@ jobs:
           }
         shell: Rscript {0}
 
-      - name: Get temp dir
-        run: |
-          find /tmp/ 2>/dev/null
-          ls -al /tmp
-          echo "debug1"
-          find /tmp/ 2>/dev/null | grep .rda
-          echo "debug2"
-          rda_files=$(find /tmp/ 2>/dev/null | grep .rda | head -n 1)
-          echo "debug3"
-          folder_id=$(dirname $rda_files)
-          echo "folder id: $folder_id"
-          # copy data from tmp folder
-          mkdir -p "$GITHUB_WORKSPACE/tmp/"
-          cp -r "${folder_id}/." "$GITHUB_WORKSPACE/tmp/"
-        shell: bash
-
       - name: Add other data formats and suffixes, exclude data
         if: inputs.push-templates-data
         run: |

From d3011fe96465f0b0e00cf720227fdbd8a724ed74 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Fri, 27 Oct 2023 17:17:55 +0200
Subject: [PATCH 19/39] add other debug traces

---
 .github/workflows/check-templates.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/check-templates.yml b/.github/workflows/check-templates.yml
index 9c7b6c40..7c03f782 100644
--- a/.github/workflows/check-templates.yml
+++ b/.github/workflows/check-templates.yml
@@ -188,9 +188,16 @@ jobs:
               system(cmd)
               # move produced rda file to another location
               subdirectories <- list.dirs("/tmp", full.names = TRUE)
+              print("subdirectories")
+              print(subdirectories)
               rda_files <- list.files(subdirectories, pattern = "\\.rda$", recursive = TRUE, full.names = TRUE)
+              print("rda_files")
+              print(rda_files)
               if (length(rda_files) > 0) {
                 current_rda_file <- rda_files[1]
+                print("other traces")
+                print(current_rda_file)
+                print(file.path(file.path(Sys.getenv("GITHUB_WORKSPACE"), "tmp"), basename(current_rda_file)))
                 file.copy(current_rda_file, file.path(file.path(Sys.getenv("GITHUB_WORKSPACE"), "tmp"), basename(current_rda_file)))
                 file.remove(current_rda_file)
               }

From 64455140f0d6ac36dbdeb93c09666cd5d9cc1895 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Fri, 27 Oct 2023 17:56:14 +0200
Subject: [PATCH 20/39] test other folder

---
 .github/workflows/check-templates.yml | 37 ++++++++++++++++-----------
 1 file changed, 22 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/check-templates.yml b/.github/workflows/check-templates.yml
index 7c03f782..ce05d01c 100644
--- a/.github/workflows/check-templates.yml
+++ b/.github/workflows/check-templates.yml
@@ -186,21 +186,21 @@ jobs:
             exit_codes <- purrr::map_chr(templates, function(file) {
               cmd <- sprintf("Rscript --vanilla %s", file)
               system(cmd)
-              # move produced rda file to another location
-              subdirectories <- list.dirs("/tmp", full.names = TRUE)
-              print("subdirectories")
-              print(subdirectories)
-              rda_files <- list.files(subdirectories, pattern = "\\.rda$", recursive = TRUE, full.names = TRUE)
-              print("rda_files")
-              print(rda_files)
-              if (length(rda_files) > 0) {
-                current_rda_file <- rda_files[1]
-                print("other traces")
-                print(current_rda_file)
-                print(file.path(file.path(Sys.getenv("GITHUB_WORKSPACE"), "tmp"), basename(current_rda_file)))
-                file.copy(current_rda_file, file.path(file.path(Sys.getenv("GITHUB_WORKSPACE"), "tmp"), basename(current_rda_file)))
-                file.remove(current_rda_file)
-              }
+              # # move produced rda file to another location
+              # subdirectories <- list.dirs("/tmp", full.names = TRUE)
+              # print("subdirectories")
+              # print(subdirectories)
+              # rda_files <- list.files(subdirectories, pattern = "\\.rda$", recursive = TRUE, full.names = TRUE)
+              # print("rda_files")
+              # print(rda_files)
+              # if (length(rda_files) > 0) {
+              #   current_rda_file <- rda_files[1]
+              #   print("other traces")
+              #   print(current_rda_file)
+              #   print(file.path(file.path(Sys.getenv("GITHUB_WORKSPACE"), "tmp"), basename(current_rda_file)))
+              #   file.copy(current_rda_file, file.path(file.path(Sys.getenv("GITHUB_WORKSPACE"), "tmp"), basename(current_rda_file)))
+              #   file.remove(current_rda_file)
+              # }
             })
             if (any(exit_codes == 1L)) {
               failed_scripts <- basename(templates)[which(exit_codes == 1L)]
@@ -212,6 +212,13 @@ jobs:
             }
           }
         shell: Rscript {0}
+      
+      - name: Test tmp folder
+        run: |
+          ls /tmp/
+          find /tmp/
+          ls /tmp/templates_data
+          cp -r /tmp/templates_data/. "$GITHUB_WORKSPACE/tmp"
 
       - name: Add other data formats and suffixes, exclude data
         if: inputs.push-templates-data

From b2c7ab6a4d40d9aa76831d147960f5f89e87531c Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Fri, 27 Oct 2023 18:07:48 +0200
Subject: [PATCH 21/39] fix condition branch

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

diff --git a/.github/workflows/check-templates.yml b/.github/workflows/check-templates.yml
index ce05d01c..5e155526 100644
--- a/.github/workflows/check-templates.yml
+++ b/.github/workflows/check-templates.yml
@@ -405,7 +405,7 @@ jobs:
           echo "source-branch=$source_br" >> $GITHUB_OUTPUT
           echo "branch-exists=$branch_exists" >> $GITHUB_OUTPUT
           warn_msg="WARNING:: the branch $source_br already exists in pharmaverseadam, please merge it and delete it, and re-execute this job"
-          if [ ${{ steps.changes.outputs.diff }} == 'true' ] && [ "$branch_exists" == 'true' ]; then echo "$warn_msg"; fi
+          if [ '${{ steps.changes.outputs.diff }}' == 'true' ] && [ '$branch_exists' == 'true' ]; then echo "$warn_msg"; fi
         shell: bash {0}
 
       # if diff detected, push changes

From d34d1ea1e958dbf8ba5d0051bae0e89702671ee3 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 7 Nov 2023 10:44:51 +0100
Subject: [PATCH 22/39] fix checks

---
 .github/workflows/push-docker-image.yml | 1 -
 .github/workflows/r-cmd-check.yml       | 2 ++
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/push-docker-image.yml b/.github/workflows/push-docker-image.yml
index d8977196..75c89519 100644
--- a/.github/workflows/push-docker-image.yml
+++ b/.github/workflows/push-docker-image.yml
@@ -71,7 +71,6 @@ jobs:
       - name: Print message
         run: |
           echo "updating docker image for renv ${{ matrix.value }}"
-          exit 1 # TODO: del (for testing)
 
       - name: Set image specs
         id: image_specs
diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
index 5efa7fc2..d0cdce37 100644
--- a/.github/workflows/r-cmd-check.yml
+++ b/.github/workflows/r-cmd-check.yml
@@ -106,6 +106,8 @@ jobs:
           echo "$script" > checks.R
 
           Rscript checks.R
+
+          rm -f checks.R
         shell: bash
 
       - name: Upload check results

From 40aa7d3edf9389c84a2ad29ab4d79fe5ee956c64 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 7 Nov 2023 11:15:33 +0100
Subject: [PATCH 23/39] test checks on maintenance versions

---
 .github/workflows/r-cmd-check.yml | 48 ++++++++++++++++++++-----------
 DESCRIPTION                       |  2 +-
 2 files changed, 32 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
index d0cdce37..46c4e2e0 100644
--- a/.github/workflows/r-cmd-check.yml
+++ b/.github/workflows/r-cmd-check.yml
@@ -87,28 +87,42 @@ jobs:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
           _R_CHECK_FORCE_SUGGESTS_: false
         run: |
-          script="
+          description_old <- readLines("DESCRIPTION")
+          description_dat <- description_old
+          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 yes, temp update the DESCRIPTION for rcmdchecks
+              if (length(version_parts) == 4) {
+                print("Maintenance version detected (format X.Y.Z.M with M >= 9000)")
+                version_parts <- version_parts[1:3]
+              }
+              
+              new_version <- paste(version_parts, collapse = ".")
+              description_dat[i] <- paste("Version: ", new_version)
+            }
+          }
+          
+          # Write the updated DESCRIPTION file back
+          writeLines(description_dat, con = description_file_path)
+        
+          if (!requireNamespace("rcmdcheck", quietly = TRUE)) install.packages("rcmdcheck")
           options(crayon.enabled = TRUE)
-          check_error_on <- '${{ inputs.error-on }}'
-          if (check_error_on == '') {
-            check_error_on <- 'note'
+          check_error_on <- "${{ inputs.error-on }}"
+          if (check_error_on == "") {
+            check_error_on <- "note"
           }
           rcmdcheck::rcmdcheck(
-            args = c('--no-manual', '--as-cran'),
+            args = c("--no-manual", "--as-cran"),
             error_on = check_error_on,
-            check_dir = 'check'
-          )"
-
-          if [ ${{ matrix.config.r }} == "devel" ]; then
-            R -e "install.packages('rcmdcheck')"
-          fi
-
-          echo "$script" > checks.R
-
-          Rscript checks.R
+            check_dir = "check"
+          )
 
-          rm -f checks.R
-        shell: bash
+          # Write back initial description file
+          writeLines(description_dat, con = description_file_path)
+        shell: Rscript {0}
 
       - name: Upload check results
         if: failure()
diff --git a/DESCRIPTION b/DESCRIPTION
index 3fb8017e..c89d1fcf 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: admiralci
 Type: Package
 Title: ADaM in R Asset Library - CI/CD Workflows
-Version: 0.0.1
+Version: 0.0.1.9001
 Authors@R: c(
     person("Open", "Source", email = "admiralci@pharmaverse.com", role = c("aut", "cre")))
 Description: A set of common CI/CD workflows originally designed and developed for

From 31f569e9765b3ea298f518d6474097e11fc05084 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 7 Nov 2023 11:17:22 +0100
Subject: [PATCH 24/39] fix

---
 .github/workflows/r-cmd-check.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
index 46c4e2e0..8d74f133 100644
--- a/.github/workflows/r-cmd-check.yml
+++ b/.github/workflows/r-cmd-check.yml
@@ -106,7 +106,7 @@ jobs:
           }
           
           # Write the updated DESCRIPTION file back
-          writeLines(description_dat, con = description_file_path)
+          writeLines(description_dat, con = "DESCRIPTION")
         
           if (!requireNamespace("rcmdcheck", quietly = TRUE)) install.packages("rcmdcheck")
           options(crayon.enabled = TRUE)
@@ -121,7 +121,7 @@ jobs:
           )
 
           # Write back initial description file
-          writeLines(description_dat, con = description_file_path)
+          writeLines(description_dat, con = "DESCRIPTION")
         shell: Rscript {0}
 
       - name: Upload check results

From c43f3f45ed325d9c12cf39e6bee245cf1cb032ca Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 7 Nov 2023 11:24:56 +0100
Subject: [PATCH 25/39] trigger checks

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

diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
index 8d74f133..b9725ff2 100644
--- a/.github/workflows/r-cmd-check.yml
+++ b/.github/workflows/r-cmd-check.yml
@@ -106,7 +106,7 @@ jobs:
           }
           
           # Write the updated DESCRIPTION file back
-          writeLines(description_dat, con = "DESCRIPTION")
+          #writeLines(description_dat, con = "DESCRIPTION")
         
           if (!requireNamespace("rcmdcheck", quietly = TRUE)) install.packages("rcmdcheck")
           options(crayon.enabled = TRUE)

From 9f978eb5fd8a7832e7979e5efd9b736684585ecd Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 7 Nov 2023 11:28:37 +0100
Subject: [PATCH 26/39] try ignore note

---
 .Rbuildignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.Rbuildignore b/.Rbuildignore
index 97cadc2e..a19b2a9d 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -28,3 +28,4 @@
 ^staged_dependencies.yaml$
 ^README.Rmd$
 ^.devcontainer
+^Version contains large components|^*NOTE*:
\ No newline at end of file

From f93f2b1e61f2eee65454ba6892ec5cd7d065daeb Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 7 Nov 2023 11:30:56 +0100
Subject: [PATCH 27/39] retry

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

diff --git a/.Rbuildignore b/.Rbuildignore
index a19b2a9d..11b81b8f 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -28,4 +28,4 @@
 ^staged_dependencies.yaml$
 ^README.Rmd$
 ^.devcontainer
-^Version contains large components|^*NOTE*:
\ No newline at end of file
+^Version contains large components|^\*NOTE\*:
\ No newline at end of file

From 5148dad7d6ed02eac92fdf8102d67242b4ea3d1b Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 7 Nov 2023 11:33:58 +0100
Subject: [PATCH 28/39] try another regexp

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

diff --git a/.Rbuildignore b/.Rbuildignore
index 11b81b8f..5a720691 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -28,4 +28,4 @@
 ^staged_dependencies.yaml$
 ^README.Rmd$
 ^.devcontainer
-^Version contains large components|^\*NOTE\*:
\ No newline at end of file
+^Version contains large components \(\d+\.\d+\.\d+\.\d+\)|^\*NOTE\*:
\ No newline at end of file

From a12985d4704c791820c587217265bdab69ea485b Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 7 Nov 2023 11:37:21 +0100
Subject: [PATCH 29/39] retry

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

diff --git a/.Rbuildignore b/.Rbuildignore
index 5a720691..5f1ca6ae 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -28,4 +28,4 @@
 ^staged_dependencies.yaml$
 ^README.Rmd$
 ^.devcontainer
-^Version contains large components \(\d+\.\d+\.\d+\.\d+\)|^\*NOTE\*:
\ No newline at end of file
+^Version contains large components.*|^\*NOTE\*:
\ No newline at end of file

From 82e47cdc887abaea0389b66c46705c7608777ffb Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 7 Nov 2023 13:49:28 +0100
Subject: [PATCH 30/39] rework rcmdcheck

---
 .github/workflows/propagate.yml   |  1 +
 .github/workflows/r-cmd-check.yml | 32 ++++++++++++++-----------------
 2 files changed, 15 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/propagate.yml b/.github/workflows/propagate.yml
index 3160f9db..ef04b288 100644
--- a/.github/workflows/propagate.yml
+++ b/.github/workflows/propagate.yml
@@ -13,6 +13,7 @@ on:
       - renv/**
       - .Rprofile
       - .devcontainer/*
+  workflow_dispatch: # give possibility to run it manually
 
 jobs:
   integrity:
diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
index b9725ff2..4ba4cdf1 100644
--- a/.github/workflows/r-cmd-check.yml
+++ b/.github/workflows/r-cmd-check.yml
@@ -82,32 +82,31 @@ jobs:
           GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       #####################c#####################
 
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-          _R_CHECK_FORCE_SUGGESTS_: false
+      - name: Check Version
+        id: check_version
         run: |
-          description_old <- readLines("DESCRIPTION")
-          description_dat <- description_old
+          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 yes, temp update the DESCRIPTION for rcmdchecks
               if (length(version_parts) == 4) {
                 print("Maintenance version detected (format X.Y.Z.M with M >= 9000)")
-                version_parts <- version_parts[1:3]
+                maintenance_version="T"
               }
-              
-              new_version <- paste(version_parts, collapse = ".")
-              description_dat[i] <- paste("Version: ", new_version)
             }
           }
-          
-          # Write the updated DESCRIPTION file back
-          #writeLines(description_dat, con = "DESCRIPTION")
-        
+          cat(paste("maintenance_version=", maintenance_version), file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
+
+      - name: Check
+        env:
+          _R_CHECK_FORCE_SUGGESTS_: false
+        run: |
+          if ( "${{ steps.check_version.outputs.maintenance_version }}" == "T" ){
+            Sys.setenv(_R_CHECK_CRAN_INCOMING_REMOTE_ = TRUE) # we do not check if package is suitable for publication on CRAN in case of maintenance version
+          }
           if (!requireNamespace("rcmdcheck", quietly = TRUE)) install.packages("rcmdcheck")
           options(crayon.enabled = TRUE)
           check_error_on <- "${{ inputs.error-on }}"
@@ -119,9 +118,6 @@ jobs:
             error_on = check_error_on,
             check_dir = "check"
           )
-
-          # Write back initial description file
-          writeLines(description_dat, con = "DESCRIPTION")
         shell: Rscript {0}
 
       - name: Upload check results

From 8e817e12c271fee4e9d68d6c74cfb964e4a8d058 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 7 Nov 2023 13:52:55 +0100
Subject: [PATCH 31/39] fix

---
 .github/workflows/r-cmd-check.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
index 4ba4cdf1..b3db1942 100644
--- a/.github/workflows/r-cmd-check.yml
+++ b/.github/workflows/r-cmd-check.yml
@@ -99,6 +99,7 @@ jobs:
             }
           }
           cat(paste("maintenance_version=", maintenance_version), file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
+        shell: Rscript {0}
 
       - name: Check
         env:

From 381d596f199e3abc2963cc1bbcf18a3459d323a1 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 7 Nov 2023 13:56:09 +0100
Subject: [PATCH 32/39] fix

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

diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
index b3db1942..5cc9d1e7 100644
--- a/.github/workflows/r-cmd-check.yml
+++ b/.github/workflows/r-cmd-check.yml
@@ -105,7 +105,7 @@ jobs:
         env:
           _R_CHECK_FORCE_SUGGESTS_: false
         run: |
-          if ( "${{ steps.check_version.outputs.maintenance_version }}" == "T" ){
+          if ("${{steps.check_version.outputs.maintenance_version}}" == "T"){
             Sys.setenv(_R_CHECK_CRAN_INCOMING_REMOTE_ = TRUE) # we do not check if package is suitable for publication on CRAN in case of maintenance version
           }
           if (!requireNamespace("rcmdcheck", quietly = TRUE)) install.packages("rcmdcheck")

From 19cfc995355ebc0955e23d2a443ce86c104767d4 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 7 Nov 2023 14:00:06 +0100
Subject: [PATCH 33/39] fix

---
 .github/workflows/r-cmd-check.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
index 5cc9d1e7..697c53df 100644
--- a/.github/workflows/r-cmd-check.yml
+++ b/.github/workflows/r-cmd-check.yml
@@ -98,7 +98,7 @@ jobs:
               }
             }
           }
-          cat(paste("maintenance_version=", maintenance_version), file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
+          cat(sprintf("maintenance_version=%s", maintenance_version), file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
         shell: Rscript {0}
 
       - name: Check
@@ -106,7 +106,7 @@ jobs:
           _R_CHECK_FORCE_SUGGESTS_: false
         run: |
           if ("${{steps.check_version.outputs.maintenance_version}}" == "T"){
-            Sys.setenv(_R_CHECK_CRAN_INCOMING_REMOTE_ = TRUE) # we do not check if package is suitable for publication on CRAN in case of maintenance version
+            Sys.setenv("_R_CHECK_CRAN_INCOMING_REMOTE_" = TRUE)
           }
           if (!requireNamespace("rcmdcheck", quietly = TRUE)) install.packages("rcmdcheck")
           options(crayon.enabled = TRUE)

From b272317df2573f57a198a58d9d3a49018892e94d Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 7 Nov 2023 14:10:13 +0100
Subject: [PATCH 34/39] fix

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

diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
index 697c53df..9167ba10 100644
--- a/.github/workflows/r-cmd-check.yml
+++ b/.github/workflows/r-cmd-check.yml
@@ -103,10 +103,11 @@ jobs:
 
       - name: Check
         env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
           _R_CHECK_FORCE_SUGGESTS_: false
         run: |
           if ("${{steps.check_version.outputs.maintenance_version}}" == "T"){
-            Sys.setenv("_R_CHECK_CRAN_INCOMING_REMOTE_" = TRUE)
+            Sys.setenv("_R_CHECK_CRAN_INCOMING_" = TRUE)
           }
           if (!requireNamespace("rcmdcheck", quietly = TRUE)) install.packages("rcmdcheck")
           options(crayon.enabled = TRUE)

From b6a0f89ba9f7ca577c68859e380d50a967a9f665 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 7 Nov 2023 14:16:43 +0100
Subject: [PATCH 35/39] fix

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

diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
index 9167ba10..8af921dd 100644
--- a/.github/workflows/r-cmd-check.yml
+++ b/.github/workflows/r-cmd-check.yml
@@ -107,7 +107,7 @@ jobs:
           _R_CHECK_FORCE_SUGGESTS_: false
         run: |
           if ("${{steps.check_version.outputs.maintenance_version}}" == "T"){
-            Sys.setenv("_R_CHECK_CRAN_INCOMING_" = TRUE)
+            Sys.setenv("_R_CHECK_CRAN_INCOMING_SKIP_LARGE_VERSION_" = TRUE)
           }
           if (!requireNamespace("rcmdcheck", quietly = TRUE)) install.packages("rcmdcheck")
           options(crayon.enabled = TRUE)

From 889d1f98fa04d7e399ecc0ea3a66478fbeb5426e Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 7 Nov 2023 14:50:08 +0100
Subject: [PATCH 36/39] cleanup

---
 .Rbuildignore                         |  3 +--
 .github/workflows/check-templates.yml | 22 ----------------------
 DESCRIPTION                           |  2 +-
 3 files changed, 2 insertions(+), 25 deletions(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index 5f1ca6ae..531fcbbf 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -27,5 +27,4 @@
 ^admiralci.*\.tgz$
 ^staged_dependencies.yaml$
 ^README.Rmd$
-^.devcontainer
-^Version contains large components.*|^\*NOTE\*:
\ No newline at end of file
+^.devcontainer
\ No newline at end of file
diff --git a/.github/workflows/check-templates.yml b/.github/workflows/check-templates.yml
index 76ad589a..37b9214d 100644
--- a/.github/workflows/check-templates.yml
+++ b/.github/workflows/check-templates.yml
@@ -174,21 +174,6 @@ jobs:
             exit_codes <- purrr::map_chr(templates, function(file) {
               cmd <- sprintf("Rscript --vanilla %s", file)
               system(cmd)
-              # # move produced rda file to another location
-              # subdirectories <- list.dirs("/tmp", full.names = TRUE)
-              # print("subdirectories")
-              # print(subdirectories)
-              # rda_files <- list.files(subdirectories, pattern = "\\.rda$", recursive = TRUE, full.names = TRUE)
-              # print("rda_files")
-              # print(rda_files)
-              # if (length(rda_files) > 0) {
-              #   current_rda_file <- rda_files[1]
-              #   print("other traces")
-              #   print(current_rda_file)
-              #   print(file.path(file.path(Sys.getenv("GITHUB_WORKSPACE"), "tmp"), basename(current_rda_file)))
-              #   file.copy(current_rda_file, file.path(file.path(Sys.getenv("GITHUB_WORKSPACE"), "tmp"), basename(current_rda_file)))
-              #   file.remove(current_rda_file)
-              # }
             })
             if (any(exit_codes == 1L)) {
               failed_scripts <- basename(templates)[which(exit_codes == 1L)]
@@ -200,13 +185,6 @@ jobs:
             }
           }
         shell: Rscript {0}
-      
-      - name: Test tmp folder
-        run: |
-          ls /tmp/
-          find /tmp/
-          ls /tmp/templates_data
-          cp -r /tmp/templates_data/. "$GITHUB_WORKSPACE/tmp"
 
       - name: Add other data formats and suffixes, exclude data
         if: inputs.push-templates-data
diff --git a/DESCRIPTION b/DESCRIPTION
index c89d1fcf..3fb8017e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: admiralci
 Type: Package
 Title: ADaM in R Asset Library - CI/CD Workflows
-Version: 0.0.1.9001
+Version: 0.0.1
 Authors@R: c(
     person("Open", "Source", email = "admiralci@pharmaverse.com", role = c("aut", "cre")))
 Description: A set of common CI/CD workflows originally designed and developed for

From c021700d1faeb6ccdb5758498143d6aa33ec6419 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Tue, 7 Nov 2023 15:11:34 +0100
Subject: [PATCH 37/39] change r-im-creator tag

---
 .github/workflows/push-docker-image.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/push-docker-image.yml b/.github/workflows/push-docker-image.yml
index 75c89519..3ae3c77b 100644
--- a/.github/workflows/push-docker-image.yml
+++ b/.github/workflows/push-docker-image.yml
@@ -83,7 +83,7 @@ jobs:
           echo "image_name=$package_name-$r_version" >> $GITHUB_OUTPUT
 
       - name: Call deploy docker image action for every renv
-        uses: insightsengineering/r-image-creator@feature/create_image_from_description
+        uses: insightsengineering/r-image-creator@v1
         with:
           image-name: "${{ steps.image_specs.outputs.image_name }}"
           tag-latest: true
@@ -115,7 +115,7 @@ jobs:
           echo "image_name=$package_name-devel" >> $GITHUB_OUTPUT
     
       - name: Call deploy docker image action devel
-        uses: insightsengineering/r-image-creator@feature/create_image_from_description
+        uses: insightsengineering/r-image-creator@v1
         with:
           image-name: "${{ steps.image_specs.outputs.image_name }}"
           tag-latest: true

From e7c2913b334b8b8678b82cd99c8645858c6be2fc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Daphn=C3=A9=20Grasselly?=
 <56442075+dgrassellyb@users.noreply.github.com>
Date: Wed, 8 Nov 2023 16:09:32 +0100
Subject: [PATCH 38/39] Update check-templates.yml

remove @devel
---
 .github/workflows/check-templates.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/check-templates.yml b/.github/workflows/check-templates.yml
index 37b9214d..059c44ae 100644
--- a/.github/workflows/check-templates.yml
+++ b/.github/workflows/check-templates.yml
@@ -365,7 +365,7 @@ jobs:
         id: branch
         run: |
           repo_name=$(basename "${{ github.repository }}")
-          source_br="${{ env.source-branch }}_${repo_name}@devel"
+          source_br="${{ env.source-branch }}_${repo_name}"
           source_grep=$(git branch -a | grep $source_br)
           if [ -z $source_grep ]; then branch_exists=false; else branch_exists=true; fi
           echo "source-branch=$source_br" >> $GITHUB_OUTPUT

From ea523c719db282c5d2e80b7460a02c5722ee7d84 Mon Sep 17 00:00:00 2001
From: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com>
Date: Wed, 8 Nov 2023 16:49:56 +0100
Subject: [PATCH 39/39] add cron job

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

diff --git a/.github/workflows/push-docker-image.yml b/.github/workflows/push-docker-image.yml
index 3ae3c77b..5d2677ec 100644
--- a/.github/workflows/push-docker-image.yml
+++ b/.github/workflows/push-docker-image.yml
@@ -8,6 +8,8 @@ on:
     paths:
       - 'renv/profiles/**/renv.lock'
   workflow_dispatch: # give possibility to run it manually
+  schedule:
+    - cron: '0 0 * * *' # Run every day at midnight UTC
 
 permissions: write-all
 env:
@@ -50,6 +52,7 @@ jobs:
           echo "renv=[\"$renv_list\"]" >> $GITHUB_OUTPUT
 
   deploy-image:
+    if: github.event_name != 'schedule'
     needs: [ get_renv_list ]
     runs-on: ubuntu-latest
     strategy:
@@ -96,7 +99,6 @@ jobs:
 
   deploy-image-devel:
     runs-on: ubuntu-latest
-
     # Token permissions
     permissions:
       contents: read