@@ -38,7 +38,8 @@ env:

   run_covr: 'true'

   run_pkgdown: 'true'

   has_RUnit: 'false'

-  cache-version: 'cache-v2'

+  cache-version: 'cache-v1'

+  run_docker: 'false'

 jobs:

   build-check:

@@ -51,9 +52,11 @@ jobs:

       fail-fast: false

       matrix:

         config:

-          - { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }

+          - { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }

           - { os: macOS-latest, r: '4.2', bioc: '3.16'}

           - { os: windows-latest, r: '4.2', bioc: '3.16'}

+          ## Check https://github.com/r-lib/actions/tree/master/examples

+          ## for examples using the http-user-agent

     env:

       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

       RSPM: ${{ matrix.config.rspm }}

@@ -76,19 +79,20 @@ jobs:

       ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml

       ## If they update their steps, we will also need to update ours.

       - name: Checkout Repository

-        uses: actions/checkout@v2

+        uses: actions/checkout@v3

       ## 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 }}

+          http-user-agent: ${{ matrix.config.http-user-agent }}

       ## 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: |

@@ -96,9 +100,9 @@ jobs:

           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)

         shell: Rscript {0}

-      - name: Cache R packages

+      - name: Restore R package cache

         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-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}

@@ -106,7 +110,7 @@ jobs:

       - 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-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}

@@ -136,6 +140,9 @@ 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: |

@@ -150,7 +157,7 @@ jobs:

       - name: Set BiocVersion

         run: |

-          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)

+          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)

         shell: Rscript {0}

       - name: Install dependencies pass 1

@@ -162,22 +169,37 @@ 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/3.17/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 = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)

+          remotes::install_local(dependencies = TRUE, repos = gha_repos, build_vignettes = FALSE, upgrade = 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)

-

-          ## For running the checks

-          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))

-          remotes::install_cran("rcmdcheck")

-          BiocManager::install("BiocCheck")

+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)

         shell: Rscript {0}

       - name: Install BiocGenerics

@@ -196,7 +218,7 @@ jobs:

       - name: Install pkgdown

         if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'

         run: |

-          remotes::install_cran("pkgdown")

+          remotes::install_github("r-lib/pkgdown")

         shell: Rscript {0}

       - name: Session info

@@ -209,10 +231,12 @@ jobs:

       - name: Run CMD check

         env:

           _R_CHECK_CRAN_INCOMING_: false

+          DISPLAY: 99.0

         run: |

+          options(crayon.enabled = TRUE)

           rcmdcheck::rcmdcheck(

-              args = c("--no-build-vignettes", "--no-manual", "--timings"),

-              build_args = c("--no-manual", "--no-resave-data"),

+              args = c("--no-manual", "--no-vignettes", "--timings"),

+              build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),

               error_on = "warning",

               check_dir = "check"

           )

@@ -230,13 +254,15 @@ jobs:

         shell: Rscript {0}

       - name: Run BiocCheck

+        env:

+          DISPLAY: 99.0

         run: |

           BiocCheck::BiocCheck(

               dir('check', 'tar.gz$', full.names = TRUE),

               `quit-with-status` = TRUE,

               `no-check-R-ver` = TRUE,

-              `no-check-pkg-size` = TRUE,

-              `no-check-bioc-help` = TRUE

+              `no-check-bioc-help` = TRUE,

+              `no-check-pkg-size` = TRUE

           )

         shell: Rscript {0}

@@ -250,24 +276,80 @@ jobs:

         if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'

         run: R CMD INSTALL .

-      - name: work around permission issue (since Apr 2022)

-        run: git config --global --add safe.directory /__w/Gviz/Gviz

-

-      - name: Deploy package

+      - name: Build pkgdown site

         if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'

-        run: |

-          git config --local user.email "actions@github.com"

-          git config --local user.name "GitHub Actions"

-          Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"

-        shell: bash {0}

+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)

+        shell: Rscript {0}

         ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)

         ## at least one locally before this will work. This creates the gh-pages

         ## branch (erasing anything you haven't version controlled!) and

         ## makes the git history recognizable by pkgdown.

+      - name: Install deploy dependencies

+        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'

+        run: |

+          apt-get update && apt-get -y install rsync

+

+      - name: Deploy pkgdown site to GitHub pages 🚀

+        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'

+        uses: JamesIves/github-pages-deploy-action@releases/v4

+        with:

+          clean: false

+          branch: gh-pages

+          folder: docs

+

       - name: Upload check results

         if: failure()

         uses: actions/upload-artifact@master

         with:

           name: ${{ runner.os }}-biocversion-devel-r-devel-results

           path: check

+

+

+  ## Code adapted from

+  ## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92

+  docker-build-and-push:

+    runs-on: ubuntu-latest

+    needs: build-check

+    steps:

+      - name: Checkout Repository

+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/master' "

+        uses: actions/checkout@v3

+

+      - name: Register repo name

+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/master' "

+        id: reg_repo_name

+        run: |

+          echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV

+

+      - name: Set up QEMU

+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/master' "

+        uses: docker/setup-qemu-action@v2

+

+      - name: Set up Docker Buildx

+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/master' "

+        uses: docker/setup-buildx-action@v2

+

+      - name: Login to Docker Hub

+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/master' "

+        uses: docker/login-action@v2

+        with:

+          username: ${{ secrets.DOCKERHUB_USERNAME }}

+          password: ${{ secrets.DOCKERHUB_TOKEN }}

+      ## Note that DOCKERHUB_TOKEN is really a token for your dockerhub

+      ## account, not your actual dockerhub account password. You can get it

+      ## from https://hub.docker.com/settings/security.

+      ## Check https://github.com/docker/build-push-action/tree/v4.0.0

+      ## for more details.

+      ## Alternatively, try checking

+      ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html.

+

+      - name: Build and Push Docker

+        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/master' && success()"

+        uses: docker/build-push-action@v4

+        with:

+          context: .

+          push: true

+          tags: >

+            ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest,

+            ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel