From 10881f32ddb6aab1d90826e37e57b581bde6aa66 Mon Sep 17 00:00:00 2001
From: Zewen Kelvin Tuong <z.tuong@uq.edu.au>
Date: Tue, 30 Apr 2024 09:29:23 +1000
Subject: [PATCH] fix R

---
 .github/workflows/tests.yml        | 18 +++++++-----------
 .github/workflows/tests_weekly.yml | 18 +++++++-----------
 2 files changed, 14 insertions(+), 22 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index c709d4952..9c4c39709 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -81,6 +81,9 @@ jobs:
         run: |
           brew install cairo pkg-config autoconf automake libtool
 
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+
       - name: Cache conda
         uses: actions/cache@v3
         env:
@@ -126,33 +129,26 @@ jobs:
       - id: R
         name: Check R version
         run: |
-          R --version > VERSION
-          echo "version=$(head -1 VERSION | awk '{print $3}')" >> $GITHUB_OUTPUT
           echo "mainbiocversion=$(Rscript -e 'cat(unlist(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $1}')" >> $GITHUB_OUTPUT
           echo "subbiocversion=$(Rscript -e 'cat(unlist(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $2}')" >> $GITHUB_OUTPUT
           echo "biocversion=$(Rscript -e 'cat(as.character(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $1}')" >> $GITHUB_OUTPUT
         shell: bash -l {0}
 
-      - name: Set up R
-        uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: ${{ steps.R.outputs.version}}
-
       - name: Cache ubuntu R packages
         if: "!contains(github.event.head_commit.message, '/nocache') && matrix.config.os == 'ubuntu-latest'"
         uses: actions/cache@v3
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-r-${{ steps.R.outputs.version}}-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-r-${{ steps.R.outputs.version}}-
+          key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-
 
       - name: Cache macOS R packages
         if: "!contains(github.event.head_commit.message, '/nocache') && matrix.config.os != 'ubuntu-latest'"
         uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-r-${{ steps.R.outputs.version}}-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-r-${{ steps.R.outputs.version}}-
+          key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-
 
       - name: Setup r-lib/remotes
         run: |
diff --git a/.github/workflows/tests_weekly.yml b/.github/workflows/tests_weekly.yml
index 3e69a0413..e543d72be 100644
--- a/.github/workflows/tests_weekly.yml
+++ b/.github/workflows/tests_weekly.yml
@@ -57,6 +57,9 @@ jobs:
         run: |
           brew install cairo pkg-config autoconf automake libtool
 
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+
       - name: Cache conda
         uses: actions/cache@v3
         env:
@@ -102,33 +105,26 @@ jobs:
       - id: R
         name: Check R version
         run: |
-          R --version > VERSION
-          echo "version=$(head -1 VERSION | awk '{print $3}')" >> $GITHUB_OUTPUT
           echo "mainbiocversion=$(Rscript -e 'cat(unlist(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $1}')" >> $GITHUB_OUTPUT
           echo "subbiocversion=$(Rscript -e 'cat(unlist(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $2}')" >> $GITHUB_OUTPUT
           echo "biocversion=$(Rscript -e 'cat(as.character(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $1}')" >> $GITHUB_OUTPUT
         shell: bash -l {0}
 
-      - name: Set up R
-        uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: ${{ steps.R.outputs.version}}
-
       - name: Cache ubuntu R packages
         if: "!contains(github.event.head_commit.message, '/nocache') && matrix.config.os == 'ubuntu-latest'"
         uses: actions/cache@v3
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-r-${{ steps.R.outputs.version}}-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-r-${{ steps.R.outputs.version}}-
+          key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-
 
       - name: Cache macOS R packages
         if: "!contains(github.event.head_commit.message, '/nocache') && matrix.config.os != 'ubuntu-latest'"
         uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-r-${{ steps.R.outputs.version}}-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-r-${{ steps.R.outputs.version}}-
+          key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.R.outputs.mainbiocversion}}_${{ steps.R.outputs.subbiocversion}}-
 
       - name: Setup r-lib/remotes
         run: |