From 5575c50da03b9346e9500659b35a1630dbd63a76 Mon Sep 17 00:00:00 2001
From: akselthomsen <thomsenaksel@gmail.com>
Date: Mon, 9 Dec 2024 18:47:31 +0100
Subject: [PATCH] ci: debug

---
 .github/workflows/check_and_co.yaml | 72 +++++++++++++--------------
 .github/workflows/debug.yaml        | 76 +++++++++++++++++++++++++++++
 2 files changed, 112 insertions(+), 36 deletions(-)
 create mode 100644 .github/workflows/debug.yaml

diff --git a/.github/workflows/check_and_co.yaml b/.github/workflows/check_and_co.yaml
index 1fbdfdf..e37ac54 100644
--- a/.github/workflows/check_and_co.yaml
+++ b/.github/workflows/check_and_co.yaml
@@ -1,36 +1,36 @@
-on:
-  push:
-    branches:
-      - main
-      - master
-  pull_request:
-    branches:
-      - main
-      - master
-name: All actions
-jobs:
-  check-current-version:
-    name: Check current version
-    uses: >-
-      NovoNordisk-OpenSource/r.workflows/.github/workflows/check_current_version.yaml@main
-    with:
-      use_local_setup_action: true
-  check-nn-version:
-    name: Check NN version
-    uses: >-
-      NovoNordisk-OpenSource/r.workflows/.github/workflows/check_nn_versions.yaml@main
-    with:
-      use_local_setup_action: true
-  pkgdown:
-    name: Pkgdown site
-    uses: NovoNordisk-OpenSource/r.workflows/.github/workflows/pkgdown.yaml@main
-    with:
-      use_local_setup_action: true
-  coverage:
-    name: Coverage report
-    uses: NovoNordisk-OpenSource/r.workflows/.github/workflows/coverage.yaml@main
-    with:
-      use_local_setup_action: true
-  megalinter:
-    name: Megalinter
-    uses: NovoNordisk-OpenSource/r.workflows/.github/workflows/megalinter.yaml@main
+# on:
+#   push:
+#     branches:
+#       - main
+#       - master
+#   pull_request:
+#     branches:
+#       - main
+#       - master
+# name: All actions
+# jobs:
+#   check-current-version:
+#     name: Check current version
+#     uses: >-
+#       NovoNordisk-OpenSource/r.workflows/.github/workflows/check_current_version.yaml@main
+#     with:
+#       use_local_setup_action: true
+#   check-nn-version:
+#     name: Check NN version
+#     uses: >-
+#       NovoNordisk-OpenSource/r.workflows/.github/workflows/check_nn_versions.yaml@main
+#     with:
+#       use_local_setup_action: true
+#   pkgdown:
+#     name: Pkgdown site
+#     uses: NovoNordisk-OpenSource/r.workflows/.github/workflows/pkgdown.yaml@main
+#     with:
+#       use_local_setup_action: true
+#   coverage:
+#     name: Coverage report
+#     uses: NovoNordisk-OpenSource/r.workflows/.github/workflows/coverage.yaml@main
+#     with:
+#       use_local_setup_action: true
+#   megalinter:
+#     name: Megalinter
+#     uses: NovoNordisk-OpenSource/r.workflows/.github/workflows/megalinter.yaml@main
diff --git a/.github/workflows/debug.yaml b/.github/workflows/debug.yaml
new file mode 100644
index 0000000..02b960b
--- /dev/null
+++ b/.github/workflows/debug.yaml
@@ -0,0 +1,76 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: debug R-CMD-check standard
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  R-CMD-check:
+    runs-on: '${{ matrix.config.os }}'
+    name: '${{ matrix.config.os }} (${{ matrix.config.r }})'
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - os: ubuntu-latest
+            r: release
+    env:
+      R_KEEP_PKG_SOURCE: true
+    steps:
+      - uses: actions/checkout@v4
+      - name: Allow strace to attach to a process
+        if: runner.os == 'Linux'
+        shell: bash
+        run: |
+          echo 0 | sudo tee /proc/sys/kernel/yama/ptrace_scope
+
+      - name: Install Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: (Linux) Install jupyter
+        if: runner.os == 'Linux'
+        shell: bash
+        run: python3 -m pip install jupyter
+
+      - name: (macOS) Install jupyter
+        if: runner.os == 'macOS'
+        shell: bash
+        run: python3 -m pip install --break-system-packages jupyter
+
+      - name: (Windows) Install jupyter
+        if: runner.os == 'Windows'
+        shell: bash
+        run: py -m pip install jupyter
+
+      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: '${{matrix.config.r}}'
+          http-user-agent: '${{matrix.config.http-user-agent}}'
+          use-public-rspm: true
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: 'any::rcmdcheck'
+          needs: check
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true