From 6bcad526f56ad0b150fe5399b7ecbdbb2b50840a Mon Sep 17 00:00:00 2001
From: cicdguy <26552821+cicdguy@users.noreply.github.com>
Date: Tue, 7 Nov 2023 08:06:46 -0600
Subject: [PATCH] New R and BioC versions (#87)

Upgrade to R 4.3.2 and BioC 3.18
---
 .github/workflows/deploy.yaml        |  8 +++++---
 .github/workflows/linter.yaml        |  4 ++--
 .github/workflows/scheduled.yaml     | 18 +++++++++---------
 .github/workflows/security-scan.yaml |  8 ++++----
 Dockerfile                           |  4 ++--
 5 files changed, 22 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
index 33a8aff..9dc7471 100755
--- a/.github/workflows/deploy.yaml
+++ b/.github/workflows/deploy.yaml
@@ -46,29 +46,31 @@ on:
           - "4.2.2"
           - "4.3.0"
           - "4.3.1"
+          - "4.3.2"
           - "latest"
       latest_r_version:
         description: R Version to be used as latest
         required: false
         type: string
-        default: "4.3.1"
+        default: "4.3.2"
       bioc_version:
         description: BioConductor Release
         required: true
         type: choice
-        default: "3.17"
+        default: "3.18"
         options:
           - "3.13"
           - "3.14"
           - "3.15"
           - "3.16"
           - "3.17"
+          - "3.18"
           - "devel"
       latest_bioc_version:
         description: BioC version to be used as latest
         required: false
         type: string
-        default: "3.17"
+        default: "3.18"
       tag:
         description: |
           Custom Image Tag/Version. Defaults to current date in the `YYYY.MM.DD` format if unspecified.
diff --git a/.github/workflows/linter.yaml b/.github/workflows/linter.yaml
index 7f94c68..4849d89 100755
--- a/.github/workflows/linter.yaml
+++ b/.github/workflows/linter.yaml
@@ -12,12 +12,12 @@ jobs:
 
     steps:
       - name: Checkout repo 🛎
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Lint Code Base 🧶
-        uses: github/super-linter/slim@v4
+        uses: github/super-linter/slim@v5
         env:
           VALIDATE_ALL_CODEBASE: false
           DEFAULT_BRANCH: main
diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml
index d290f65..7d5bf7c 100644
--- a/.github/workflows/scheduled.yaml
+++ b/.github/workflows/scheduled.yaml
@@ -36,12 +36,12 @@ jobs:
     strategy:
       matrix:
         image:
-          - distro_tag: '4.3.1'
-            bioc: '3.17'
+          - distro_tag: '4.3.2'
+            bioc: '3.18'
             distro: rstudio-local
             origin: rocker
-          - distro_tag: '4.3.1'
-            bioc: '3.17'
+          - distro_tag: '4.3.2'
+            bioc: '3.18'
             distro: rstudio
             origin: rocker
           - distro_tag: 'latest'
@@ -61,18 +61,18 @@ jobs:
             distro: fedora-gcc-devel
             origin: rhub
           - distro_tag: 'latest'
-            bioc: '3.17'
+            bioc: '3.18'
             distro: debian-gcc-patched
             origin: rhub
           - distro_tag: 'latest'
-            bioc: '3.17'
+            bioc: '3.18'
             distro: debian-gcc-release
             origin: rhub
 
     # Trigger steps
     steps:
       - name: Checkout repository 💳
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: main
 
@@ -87,8 +87,8 @@ jobs:
               "distribution": "${{ matrix.image.distro }}",
               "r_version": "${{ matrix.image.distro_tag }}",
               "bioc_version": "${{ matrix.image.bioc }}",
-              "latest_r_version": "4.3.1",
-              "latest_bioc_version": "3.17",
+              "latest_r_version": "4.3.2",
+              "latest_bioc_version": "3.18",
               "tag": "",
               "tag_latest": "true",
               "release_tag": "${{ needs.create-release.outputs.release_tag }}"
diff --git a/.github/workflows/security-scan.yaml b/.github/workflows/security-scan.yaml
index 311ae2c..a965abe 100644
--- a/.github/workflows/security-scan.yaml
+++ b/.github/workflows/security-scan.yaml
@@ -15,19 +15,19 @@ jobs:
     strategy:
       matrix:
         image:
-          - r: '4.3.1'
-            bioc: '3.17'
+          - r: '4.3.2'
+            bioc: '3.18'
             distro: rstudio-local
     steps:
       - name: Log in to the Container registry 🗝
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ${{ env.REGISTRY }}
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Run Trivy vulnerability scanner 🚓
-        uses: aquasecurity/trivy-action@0.11.2
+        uses: aquasecurity/trivy-action@0.14.0
         with:
           scan-type: image
           image-ref: ${{ env.REGISTRY }}/${{ github.repository_owner }}/${{ matrix.image.distro }}_${{ matrix.image.r }}_bioc_${{ matrix.image.bioc }}:latest
diff --git a/Dockerfile b/Dockerfile
index 6fd6f9e..f85a14b 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,14 +1,14 @@
 # Build arguments
 ARG ORIGIN=rocker
 ARG ORIGIN_DISTRIBUTION=rstudio
-ARG R_VERSION=4.3.1
+ARG R_VERSION=4.3.2
 
 # Fetch base image
 FROM ${ORIGIN}/${ORIGIN_DISTRIBUTION}:${R_VERSION}
 
 # Reset args in build context
 ARG DISTRIBUTION=rstudio-local
-ARG BIOC_VERSION=3.17
+ARG BIOC_VERSION=3.18
 
 # Set image metadata
 LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \