Merge pull request #1 from danro9685/development

Development
danro9685 · Oct 26, 2022 · 8c4f643 · 8c4f643
2 parents f16ec16 + f736456
commit 8c4f643
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diff --git a/.github/workflows/check-development.yml b/.github/workflows/check-development.yml
@@ -128,7 +128,7 @@ jobs:
       ## Most of these steps are the same as the ones in
       ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
       ## If they update their steps, we will also need to update ours.
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Install dependencies
         run: |
@@ -137,11 +137,11 @@ jobs:
           sudo apt-get install libharfbuzz-dev
           sudo apt-get install libfribidi-dev
           sudo apt-get install texlive-fonts-extra
-      - uses: r-lib/actions/setup-tinytex@master
+      - uses: r-lib/actions/setup-tinytex@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Install latex packages
         run: |
@@ -347,8 +347,8 @@ jobs:
       matrix:
         config:
           ## Comment/Un-comment in case you also want to run other versions
-          - {os: windows-latest}
-          - {os: macOS-latest}
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
           # - {os: ubuntu-16.04, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
 
     env:
@@ -358,18 +358,19 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Setup R from r-lib
-        uses: r-lib/actions/setup-r@master
+        uses: r-lib/actions/setup-r@v2
         with:
-          r-version: ${{ needs.R-CMD-check-bioc.outputs.rversion }}
+          r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
 
       - name: Setup pandoc from r-lib
-        uses: r-lib/actions/setup-pandoc@master
+        uses: r-lib/actions/setup-pandoc@v2
 
       - name: Setup tinytex from r-lib
-        uses: r-lib/actions/setup-tinytex@master
+        uses: r-lib/actions/setup-tinytex@v2
 
       - name: Install latex packages
         run: |

diff --git a/.github/workflows/check-master.yml b/.github/workflows/check-master.yml
@@ -29,11 +29,9 @@
 ## http://bioconductor.org/developers/how-to/git/
 on:
   push:
-    branches:
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - master
+    branches: [main, master]
 
 name: check-master
 
@@ -131,7 +129,7 @@ jobs:
       ## Most of these steps are the same as the ones in
       ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
       ## If they update their steps, we will also need to update ours.
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Install dependencies
         run: |
@@ -140,11 +138,11 @@ jobs:
           sudo apt-get install libharfbuzz-dev
           sudo apt-get install libfribidi-dev
           sudo apt-get install texlive-fonts-extra
-      - uses: r-lib/actions/setup-tinytex@master
+      - uses: r-lib/actions/setup-tinytex@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Install latex packages
         run: |
@@ -350,8 +348,8 @@ jobs:
       matrix:
         config:
           ## Comment/Un-comment in case you also want to run other versions
-          - {os: windows-latest}
-          - {os: macOS-latest}
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
           # - {os: ubuntu-16.04, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
 
     env:
@@ -361,18 +359,19 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Setup R from r-lib
-        uses: r-lib/actions/setup-r@master
+        uses: r-lib/actions/setup-r@v2
         with:
-          r-version: ${{ needs.R-CMD-check-bioc.outputs.rversion }}
+          r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
 
       - name: Setup pandoc from r-lib
-        uses: r-lib/actions/setup-pandoc@master
+        uses: r-lib/actions/setup-pandoc@v2
 
       - name: Setup tinytex from r-lib
-        uses: r-lib/actions/setup-tinytex@master
+        uses: r-lib/actions/setup-tinytex@v2
 
       - name: Install latex packages
         run: |