From 7b072877d5947320301d2e603d8e3c8b68457958 Mon Sep 17 00:00:00 2001
From: Ian D Buller <ian.d.buller@gmail.com>
Date: Tue, 9 Jul 2024 16:30:17 -0400
Subject: [PATCH] :stethoscope: Update R CMD check in GitHub Actions

* test solution for #8 (attempt 2)
* suspect #8 is lack of 'sf' dependencies in earlier Ubuntu releases (i.e., GDAL)
* now install 'sf' dependencies based on R CMD check in GitHub Actions of pfizer-opensource/deprivateR
---
 .github/workflows/R-CMD-check.yaml | 94 +++++++++++++++++++++++++-----
 1 file changed, 78 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index a3ac618..8a12fe0 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -1,10 +1,10 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
-# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: 
+    - main
   pull_request:
-    branches: [main, master]
+    branches: 
+    - main
 
 name: R-CMD-check
 
@@ -18,32 +18,94 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'devel'}
           - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
-
+          - {os: windows-latest, r: '3.6'} # Use 3.6 to trigger usage of RTools35
+          - {os: windows-latest, r: '4.1'} # use 4.1 to check with rtools40's older compiler
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'oldrel-2'}
+          - {os: ubuntu-latest,  r: 'oldrel-3'}
+          - {os: ubuntu-latest,  r: 'oldrel-4'}
+          - {os: ubuntu-latest,  r: 'oldrel-5'}
+          
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
 
     steps:
-      - uses: actions/checkout@v3
-
-      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r@v2.9.0
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
+          
+      - uses: r-lib/actions/setup-pandoc@v2
+      
+      # For file snapshot that uses png
+      - name: Install xquartz
+        if: runner.os == 'macOS'
+        run: brew install --cask xquartz
+
+      # - uses: r-lib/actions/setup-r-dependencies@v2.9.0
+      #   with:
+      #     extra-packages: any::rcmdcheck
+      #     needs: check
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
         with:
-          extra-packages: any::rcmdcheck
-          needs: check
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-r-${{ matrix.config.r }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-1-
+
+      - name: Install macOS specific dependencies for sf
+        if: runner.os == 'macOS'
+        run: brew install udunits gdal proj
+
+      - name: Install Linux specific dependencies for sf
+        if: runner.os == 'Linux'
+        run: sudo apt-get install libgdal-dev libproj-dev libgeos-dev libudunits2-dev
 
-      - uses: r-lib/actions/check-r-package@v2
+      - name: Install language dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE, build = FALSE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+      
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, 'Package']
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+        
+      - uses: r-lib/actions/check-r-package@v2.9.0
         with:
           upload-snapshots: true
+        
+     - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check