fixing the GHA for deployment

Author: federicomarini

.github/workflows/basic_checks.yaml

@@ -3,17 +3,21 @@ name: Check, build, and push image
 on: [push, pull_request]
 
 env:
-  cache-version: v4
+  cache-version: v1
 
 jobs:
   r-build-and-check:
     runs-on: ubuntu-latest
     container: bioconductor/bioconductor_docker:devel
+
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: TRUE
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest
+
     steps:
-      - uses: actions/checkout@v2
+      - name: Checkout Repository
+        uses: actions/checkout@v4
 
       - name: Query dependencies and update old packages
         run: |
@@ -29,16 +33,6 @@ jobs:
           key: ${{ env.cache-version }}-${{ runner.os }}-r-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ env.cache-version }}-${{ runner.os }}-r-
 
-      # This lets us augment with additional dependencies
-      - name: Install system dependencies (Linux)
-        if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-        uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::rcmdcheck
-          pak-version: devel
-
       - name: Install dependencies
         run: |
           BiocManager::repositories()
@@ -49,10 +43,9 @@ jobs:
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check")
+        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
-
       - name: Build pkgdown
         run: |
            PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site(".")'
@@ -64,11 +57,12 @@ jobs:
           apt-get -y install rsync
 
       - name: Deploy 🚀
-        uses: JamesIves/github-pages-deploy-action@releases/v4
+        uses: JamesIves/github-pages-deploy-action@v4
         with:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          TOKEN: ${{ secrets.GITHUB_TOKEN }}
           BRANCH: gh-pages # The branch the action should deploy to.
           FOLDER: docs # The folder the action should deploy.
+
   docker-build-and-push:
     #needs: r-build-and-check
     runs-on: ubuntu-latest
@@ -80,8 +74,8 @@ jobs:
       id-token: write
 
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v2
+      - name: Checkout Repository
+        uses: actions/checkout@v4
 
       - name: Set Environment Variables
         run: |
@@ -96,25 +90,20 @@ jobs:
         run: |
           env
 
-
       # Install the cosign tool except on PR
       # https://github.com/sigstore/cosign-installer
       - name: Install cosign
         if: github.event_name != 'pull_request'
-        uses: sigstore/cosign-installer@1e95c1de343b5b0c23352d6417ee3e48d5bcd422
-        with:
-          cosign-release: 'v1.4.0'
+        uses: sigstore/cosign-installer@v3
 
-
-      # Workaround: https://github.com/docker/build-push-action/issues/461
       - name: Setup Docker buildx
-        uses: docker/setup-buildx-action@79abd3f86f79a9d68a23c75a09a9a85889262adf
+        uses: docker/setup-buildx-action@v3
 
       # Login against a Docker registry except on PR
       # https://github.com/docker/login-action
       - name: Log into registry ${{ env.REGISTRY }}
         if: github.event_name != 'pull_request'
-        uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+        uses: docker/login-action@v3
         with:
           registry: ${{ env.REGISTRY }}
           username: ${{ github.actor }}
@@ -124,19 +113,18 @@ jobs:
       # https://github.com/docker/metadata-action
       - name: Extract Docker metadata
         id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        uses: docker/metadata-action@v5
         with:
           images: ${{ env.IMAGE }}
 
       # Build and push Docker image with Buildx (don't push on PR)
       # https://github.com/docker/build-push-action
       - name: Build and push Docker image
         id: build-and-push
-        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        uses: docker/build-push-action@v5
         with:
           context: .
           push: ${{ github.event_name != 'pull_request' }}
           tags: |
             ${{ env.IMAGE }}:latest
             ${{ env.IMAGE }}:${{ env.GIT_SHA }}
-