From 23e02121ef778c8be3bc39a6ca7ca5f9ab40d54d Mon Sep 17 00:00:00 2001
From: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: Mon, 28 Oct 2024 10:54:54 +0800
Subject: [PATCH] update actions versions

---
 .github/workflows/check-bioc.yml     | 18 +++++++++---------
 .github/workflows/lint.yaml          |  2 +-
 .github/workflows/pr-commands.yaml   |  4 ++--
 .github/workflows/test-coverage.yaml |  2 +-
 4 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
index 5927ff7e..6263b116 100644
--- a/.github/workflows/check-bioc.yml
+++ b/.github/workflows/check-bioc.yml
@@ -40,7 +40,7 @@ env:
   run_covr: 'false'
   run_pkgdown: 'false'
   has_RUnit: 'false'
-  cache-version: 'cache-v3'
+  cache-version: 'cache-v4'
   run_docker: 'false'
 
 jobs:
@@ -54,9 +54,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.3', bioc: '3.18'}
-            ##- { os: windows-latest, r: '4.3', bioc: '3.18'}
+          - { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: '4.4', bioc: '3.19'}
+          - { os: windows-latest, r: '4.4', bioc: '3.19'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -81,7 +81,7 @@ jobs:
       ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
       ## If they update their steps, we will also need to update ours.
       - name: Checkout Repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
@@ -104,7 +104,7 @@ jobs:
 
       - name: Restore R package cache
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE-r-4.3-${{ hashFiles('.github/depends.Rds') }}
@@ -112,7 +112,7 @@ jobs:
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: /home/runner/work/_temp/Library
           key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.3-${{ hashFiles('.github/depends.Rds') }}
@@ -337,9 +337,9 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE-r-4.3-results
+          name: ${{ runner.os }}-biocversion-RELEASE-r-4.4-results
           path: check
 
       - uses: docker/build-push-action@v1
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
index 9daaa663..aa29e0f1 100644
--- a/.github/workflows/lint.yaml
+++ b/.github/workflows/lint.yaml
@@ -15,7 +15,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
index 98ca228b..35d14666 100644
--- a/.github/workflows/pr-commands.yaml
+++ b/.github/workflows/pr-commands.yaml
@@ -14,7 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -49,7 +49,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index a1b6e36e..58383454 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -16,7 +16,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with: