From 2c9db6ac51cb5fb976c369e3dace21dbcf666737 Mon Sep 17 00:00:00 2001
From: Stefano Mangiola <mangiolastefano@gmail.com>
Date: Tue, 15 Nov 2022 08:47:58 +1100
Subject: [PATCH] Fix actions

---
 .github/workflows/check-bioc.yml | 31 ++++++++++++++++---------------
 1 file changed, 16 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
index ed9c4e1..7c7151e 100755
--- a/.github/workflows/check-bioc.yml
+++ b/.github/workflows/check-bioc.yml
@@ -51,9 +51,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.2', bioc: '3.15', cont: "bioconductor/bioconductor_docker:RELEASE_3_15", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.2', bioc: '3.15'}
-          - { os: windows-latest, r: '4.2', bioc: '3.15'}
+          - { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: '4.2', bioc: '3.16'}
+          - { os: windows-latest, r: '4.2', bioc: '3.16'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -81,14 +81,14 @@ jobs:
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-r@master
+        uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
       ## pandoc is already included in the Bioconductor docker images
       - name: Setup pandoc from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-pandoc@master
+        uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -98,19 +98,19 @@ jobs:
 
       - name: Cache R packages
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
 
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
@@ -239,7 +239,9 @@ jobs:
               dir('check', 'tar.gz$', full.names = TRUE),
               `quit-with-status` = TRUE,
               `no-check-R-ver` = TRUE,
-              `no-check-bioc-help` = TRUE
+              `no-check-bioc-help` = TRUE,
+              `no-check-library-calls` = TRUE,
+              `no-check-coding-practices` = TRUE
           )
         shell: Rscript {0}
 
@@ -270,8 +272,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@master
+        uses: actions/upload-artifact@v3
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-results
+          name: ${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-results
           path: check
-