master to main

.github/workflows/check-bioc.yml

@@ -48,7 +48,7 @@ jobs:
     ## Environment variables unique to this job.
 
     strategy:
-      fail-fast: false 
+      fail-fast: false
       matrix:
         config:
           - { os: ubuntu-latest, r: '4.1.3', bioc: '3.14', cont: "bioconductor/bioconductor_docker:RELEASE_3_14", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
@@ -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@main
         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@main
 
       - name: Query dependencies
         run: |
@@ -120,7 +120,7 @@ jobs:
           sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y libicu-dev pandoc libpq-dev" )')
           echo $sysreqs
           sudo -s eval "$sysreqs"
-          
+
 
       - name: Install macOS system dependencies
         if: matrix.config.os == 'macOS-latest'
@@ -169,7 +169,7 @@ jobs:
           remotes::install_github("ropensci/bibtex")
           remotes::install_github("ropensci/RefManageR")
           remotes::install_github("cboettig/knitcitations")
-          
+
 
           ## Pass #1 at installing dependencies
           message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
@@ -193,13 +193,13 @@ jobs:
         shell: Rscript {0}
 
       - name: Install covr
-        if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux'
         run: |
           remotes::install_cran("covr")
         shell: Rscript {0}
 
       - name: Install pkgdown
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/mastr' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
           remotes::install_cran("pkgdown")
         shell: Rscript {0}
@@ -246,22 +246,22 @@ jobs:
               `no-check-R-ver` = TRUE,
               `no-check-bioc-help` = TRUE,
               `no-check-dependencies` = TRUE
-              
+
           )
         shell: Rscript {0}
 
       - name: Test coverage
-        if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux'
         run: |
           covr::codecov()
         shell: Rscript {0}
 
       - name: Install package
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: R CMD INSTALL .
 
       - name: Deploy package
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
           git config --local user.email "[email protected]"
           git config --local user.name "GitHub Actions"
@@ -274,7 +274,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@master
+        uses: actions/upload-artifact@main
         with:
           name: ${{ runner.os }}-biocversion-r-4.1.3-results
           path: check