From 108151a49ff6264e3f49b38d2f6383cbb09a129e Mon Sep 17 00:00:00 2001
From: Patrice Lecharpentier <patrice.lecharpentier@inrae.fr>
Date: Fri, 9 Jan 2026 14:12:58 +0100
Subject: [PATCH 1/4] Update GitHub Actions workflow for branch handling

---
 .github/workflows/R-CMD-check.yaml | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 87e20eb..2412fb2 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -42,8 +42,25 @@ jobs:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      # set environment variables from the client payload for convenience
+      SOURCE_REPO: ${{ github.event.client_payload.repo }}
+      SOURCE_REF: ${{ github.event.client_payload.ref }}
+      SOURCE_SHA: ${{ github.event.client_payload.sha }}
+      # get trigerring info
+      STICSRPACKS_BRANCH: main
+      CROPLOTR_BRANCH: main
+      CROPTIMIZR_BRANCH: main
+      STICSONR_BRANCH: main
+      STICSRFILES_BRANCH: main
+      
 
     steps:
+      - name: fix branches names
+        if: ${{ env.SOURCE_REPO == 'SticsRPacks' }}
+        run: echo "Triggering repository $SOURCE_REPOS"
+        env:
+          ${{ env.STICSRPACKS_BRANCH }}: ${{ SOURCE_REF }}
+          
       - name: install libxslt
         if: runner.os  != 'Windows'
         run: |
@@ -99,7 +116,7 @@ jobs:
           # Instal dependencies without upgrade
           remotes::install_deps(dependencies = TRUE, upgrade = "never")
           remotes::install_cran("rcmdcheck", upgrade = "never")
-          remotes::install_github("SticsRPacks/SticsRPacks@main", dependencies = FALSE, upgrade = "never")
+          remotes::install_github("SticsRPacks/SticsRPacks", ref = "$STICSRPACKS_BRANCH", dependencies = FALSE, upgrade = "never")
           remotes::install_github("SticsRPacks/CroPlotR@main", dependencies = FALSE, upgrade = "never")
           remotes::install_github("SticsRPacks/CroptimizR@main", dependencies = FALSE, upgrade = "never")
           remotes::install_github("SticsRPacks/SticsOnR@main", dependencies = FALSE, upgrade = "never")

From 9ab46031624e480f0a766adc6d19c75e214e7490 Mon Sep 17 00:00:00 2001
From: Patrice Lecharpentier <patrice.lecharpentier@inrae.fr>
Date: Fri, 9 Jan 2026 14:17:19 +0100
Subject: [PATCH 2/4] Fix environment variable reference in workflow

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

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 2412fb2..0e84152 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -59,7 +59,7 @@ jobs:
         if: ${{ env.SOURCE_REPO == 'SticsRPacks' }}
         run: echo "Triggering repository $SOURCE_REPOS"
         env:
-          ${{ env.STICSRPACKS_BRANCH }}: ${{ SOURCE_REF }}
+          ${{ env.STICSRPACKS_BRANCH }}: ${{ env.SOURCE_REF }}
           
       - name: install libxslt
         if: runner.os  != 'Windows'

From eee1e74032ae9ed43983325c2b6344d139fc1cc8 Mon Sep 17 00:00:00 2001
From: Patrice Lecharpentier <patrice.lecharpentier@inrae.fr>
Date: Fri, 9 Jan 2026 14:38:25 +0100
Subject: [PATCH 3/4] Fix environment variable usage in R-CMD-check.yaml

---
 .github/workflows/R-CMD-check.yaml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 0e84152..9a394f4 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -57,9 +57,11 @@ jobs:
     steps:
       - name: fix branches names
         if: ${{ env.SOURCE_REPO == 'SticsRPacks' }}
-        run: echo "Triggering repository $SOURCE_REPOS"
+        run: |
+          echo "Triggering repository $SOURCE_REPOS"
+          echo "Branch ref $SOURCE_REF"
         env:
-          ${{ env.STICSRPACKS_BRANCH }}: ${{ env.SOURCE_REF }}
+          ${{ STICSRPACKS_BRANCH }}: ${{ SOURCE_REF }}
           
       - name: install libxslt
         if: runner.os  != 'Windows'
@@ -116,7 +118,7 @@ jobs:
           # Instal dependencies without upgrade
           remotes::install_deps(dependencies = TRUE, upgrade = "never")
           remotes::install_cran("rcmdcheck", upgrade = "never")
-          remotes::install_github("SticsRPacks/SticsRPacks", ref = "$STICSRPACKS_BRANCH", dependencies = FALSE, upgrade = "never")
+          remotes::install_github("SticsRPacks/SticsRPacks", ref = "$env.STICSRPACKS_BRANCH", dependencies = FALSE, upgrade = "never")
           remotes::install_github("SticsRPacks/CroPlotR@main", dependencies = FALSE, upgrade = "never")
           remotes::install_github("SticsRPacks/CroptimizR@main", dependencies = FALSE, upgrade = "never")
           remotes::install_github("SticsRPacks/SticsOnR@main", dependencies = FALSE, upgrade = "never")

From 1a1d01e96c5cd9c5a37acaeefae7cdf80c18e7cf Mon Sep 17 00:00:00 2001
From: Patrice Lecharpentier <patrice.lecharpentier@inrae.fr>
Date: Fri, 9 Jan 2026 14:40:01 +0100
Subject: [PATCH 4/4] Fix environment variable reference in workflow

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

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 9a394f4..6a75b32 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -61,7 +61,7 @@ jobs:
           echo "Triggering repository $SOURCE_REPOS"
           echo "Branch ref $SOURCE_REF"
         env:
-          ${{ STICSRPACKS_BRANCH }}: ${{ SOURCE_REF }}
+          ${{ env.STICSRPACKS_BRANCH }}: ${{ env.SOURCE_REF }}
           
       - name: install libxslt
         if: runner.os  != 'Windows'