Updated GHA workflow

.github/workflows/check-bioc.yml

@@ -38,7 +38,7 @@ env:
   run_covr: 'true'
   run_pkgdown: 'true'
   has_RUnit: 'false'
-  cache-version: 'cache-v4'
+  cache-version: 'cache-v3'
   run_docker: 'false'
 
 jobs:
@@ -52,8 +52,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.3', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-
+          - { 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" }
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -71,9 +70,10 @@ jobs:
         run: |
           mkdir /__w/_temp/Library
           echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile
-          
+
           git config --global --add safe.directory /__w/doubletrouble/doubletrouble
 
+
       - name: Checkout Repository
         uses: actions/checkout@v2
 
@@ -83,7 +83,6 @@ jobs:
         uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
 
       ## pandoc is already included in the Bioconductor docker images
       - name: Setup pandoc from r-lib
@@ -96,7 +95,7 @@ jobs:
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
         shell: Rscript {0}
 
-      - name: Restore R package cache
+      - name: Cache R packages
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
         uses: actions/cache@v2
         with:
@@ -136,14 +135,15 @@ jobs:
           ## For installing usethis's dependency gert
           brew install libgit2
 
-          ## Required for tcltk
-          brew install xquartz --cask
-
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'
         run: |
           ## Edit below if you have any Windows system dependencies
-        shell: Rscript {0}
+          ## Add code here to install dependencies
+          # yes | pacman -Sy mingw-w64-x86_64-glpk
+          # yes | pacman -Sy mingw-w64-x86_64-libxml2
+
+        shell: bash
 
       - name: Install BiocManager
         run: |
@@ -165,37 +165,22 @@ jobs:
           ## https://github.com/r-lib/remotes/issues/296
           ## Ideally, all dependencies should get installed in the first pass.
 
-          ## Set the repos source depending on the OS
-          ## Alternatively use https://storage.googleapis.com/bioconductor_docker/packages/
-          ## though based on https://bit.ly/bioc2021-package-binaries
-          ## the Azure link will be the main one going forward.
-          gha_repos <- if(
-              .Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin"
-          ) c(
-              "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.15/bioc",
-              BiocManager::repositories()
-              ) else BiocManager::repositories()
-
-          ## For running the checks
-          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
-          install.packages(c("rcmdcheck", "BiocCheck"), repos = gha_repos)
-
           ## Pass #1 at installing dependencies
-          ## This pass uses AnVIL-powered fast binaries
-          ## details at https://github.com/nturaga/bioc2021-bioconductor-binaries
-          ## The speed gains only apply to the docker builds.
           message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
-          remotes::install_local(dependencies = TRUE, repos = gha_repos, build_vignettes = FALSE, upgrade = TRUE)
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
         continue-on-error: true
         shell: Rscript {0}
 
       - name: Install dependencies pass 2
         run: |
           ## Pass #2 at installing dependencies
-          ## This pass does not use AnVIL and will thus update any packages
-          ## that have seen been updated in Bioconductor
           message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
           remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
+
+          ## For running the checks
+          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
+          remotes::install_cran("rcmdcheck")
+          BiocManager::install("BiocCheck")
         shell: Rscript {0}
 
       - name: Install BiocGenerics
@@ -227,12 +212,10 @@ jobs:
       - name: Run CMD check
         env:
           _R_CHECK_CRAN_INCOMING_: false
-          DISPLAY: 99.0
         run: |
-          options(crayon.enabled = TRUE)
           rcmdcheck::rcmdcheck(
-              args = c("--no-manual", "--no-vignettes", "--timings"),
-              build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
+              args = c("--no-build-vignettes", "--no-manual", "--timings"),
+              build_args = c("--no-manual", "--no-resave-data"),
               error_on = "warning",
               check_dir = "check"
           )
@@ -248,23 +231,14 @@ jobs:
         run: |
           BiocGenerics:::testPackage()
         shell: Rscript {0}
-
-      - name: (Temporarily) Install correct version of BiocCheck
-        run: |
-          remotes::install_github("Bioconductor/BiocCheck@0a217b4")
-        shell: Rscript {0}
-
+
       - name: Run BiocCheck
-        env:
-          DISPLAY: 99.0
         run: |
           BiocCheck::BiocCheck(
-              package = ".",
+              dir('check', 'tar.gz$', full.names = TRUE),
               `quit-with-status` = TRUE,
               `no-check-R-ver` = TRUE,
-              `no-check-bioc-help` = TRUE,
-              `no-check-coding-practices` = TRUE,
-              `no-check-version-num` = TRUE
+              `no-check-bioc-help` = TRUE
           )
         shell: Rscript {0}
 
@@ -278,11 +252,11 @@ jobs:
         if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: R CMD INSTALL .
 
-      - name: Build and deploy pkgdown site
+      - name: Deploy package
         if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected]"
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Actions"
           Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
         shell: bash {0}
         ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
@@ -297,12 +271,6 @@ jobs:
           name: ${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-results
           path: check
 
-        ## Note that DOCKER_PASSWORD is really a token for your dockerhub
-        ## account, not your actual dockerhub account password.
-        ## This comes from
-        ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html#6-add-secrets-to-github-repo
-        ## Check https://github.com/docker/build-push-action/tree/releases/v1
-        ## for more details.
       - uses: docker/build-push-action@v1
         if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' "
         with: