Adding new workflow and working on R CMD check

Author: gvegayon

.devcontainer/devcontainer.json

@@ -1,7 +1,7 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the
 // README at: https://github.com/devcontainers/templates/tree/main/src/cpp
 {
-	"name": "epiworldR",
+	"name": "netdiffuseR",
 	"build": {
 		"dockerfile": "Dockerfile"
 	},
@@ -11,7 +11,8 @@
 				"reditorsupport.r",
 				"rdebugger.r-debugger",
 				"quarto.quarto",
-				"tianyishi.rmarkdown"
+				"tianyishi.rmarkdown",
+				"github.vscode-github-actions"
 			]
 		}
 	},

.github/workflows/build-targz.yml

@@ -0,0 +1,38 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+  workflow_dispatch:
+
+name: Build and upload the tar.gz
+
+jobs:
+  R-build:
+    runs-on: ubuntu-latest
+    name: Build the package
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+      
+      - name: Build the package
+        run: R CMD build .
+
+      - name: Upload the artifact
+        uses: actions/upload-artifact@v5
+        with:
+          name: package
+          path: "*.tar.gz"

.github/workflows/pkgdown.yml

@@ -44,7 +44,7 @@ jobs:
           shell: Rscript {0}
 
         - name: Upload artifact for GH pages deployment
-          uses: actions/upload-pages-artifact@v3
+          uses: actions/upload-pages-artifact@v5
           with:
             path: "docs/"
 

.github/workflows/r.yml

@@ -22,11 +22,12 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-latest, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-latest, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-latest, r: 'devel', valgrind: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: windows-latest, r: 'release', valgrind: false}
+          - {os: macOS-latest, r: 'release', valgrind: false}
+          - {os: ubuntu-latest, r: 'release', valgrind: false}
+          - {os: ubuntu-latest, r: 'devel', valgrind: false}
+          - {os: ubuntu-latest, r: 'devel', valgrind: true}
+          - {os: macos-26, r: 'release', valgrind: false}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -42,73 +43,23 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Restore R package cache
-        if: runner.os != 'Windows'
-        uses: actions/cache@v4
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        if: ${{ matrix.config.valgrind != true }}
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
 
-      - name: Setup valgrind
-        if: ${{ matrix.config.valgrind == true }}
+      - name: Install valgrind
+        if: ${{ matrix.config.valgrind }}
         run: |
           sudo apt-get update
-          sudo apt-get install -y valgrind --no-install-recommends
-        shell: bash
+          sudo apt-get install -y --no-install-recommends valgrind
 
-      - name: Check with Valgrind
-        if: ${{ matrix.config.valgrind == true }}
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--use-valgrind"), error_on = "error", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
+        if: ${{ matrix.config.valgrind }}
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          args: 'c("--as-cran", "--use-valgrind")'
+
+      - uses: r-lib/actions/check-r-package@v2
+        if: ${{ !matrix.config.valgrind }}
+
+
+      
 
-      - name: Build the package
-        if: ${{ matrix.config.os == 'ubuntu-latest' && (matrix.config.r == 'release' || matrix.config.r == 'devel') && (matrix.config.valgrind != true) }}
-        run: R CMD build .
 
-      - uses: actions/upload-artifact@v4
-        if: ${{ matrix.config.os == 'ubuntu-latest' && (matrix.config.r == 'release' || matrix.config.r == 'devel') && (matrix.config.valgrind != true) }}
-        with:
-          name: netdiffuseR-built-package-${{ matrix.config.os }}-${{ matrix.config.r }}
-          path: netdiffuseR_*.tar.gz
-          retention-days: 7