@@ -34,8 +34,8 @@ name: R-CMD-check-bioc

 ## Note that you can always run a GHA test without the cache by using the word

 ## "/nocache" in the commit message.

 env:

-  has_testthat: 'true'

-  run_covr: 'true'

+  has_testthat: 'false'

+  run_covr: 'false'

   run_pkgdown: 'false'

   has_RUnit: 'false'

   cache-version: 'cache-v1'

@@ -52,7 +52,7 @@ jobs:

       fail-fast: false

       matrix:

         config:

-          - { os: ubuntu-latest, r: '4.3', bioc: '3.17', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }

+          - { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }

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

           ## for examples using the http-user-agent

     env:

@@ -103,16 +103,16 @@ jobs:

         uses: actions/cache@v3

         with:

           path: ${{ env.R_LIBS_USER }}

-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}

-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-

+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-${{ hashFiles('.github/depends.Rds') }}

+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-

       - name: Cache R packages on Linux

         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "

         uses: actions/cache@v3

         with:

           path: /home/runner/work/_temp/Library

-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}

-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-

+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-${{ hashFiles('.github/depends.Rds') }}

+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-

       - name: Install Linux system dependencies

         if: runner.os == 'Linux'

@@ -124,11 +124,11 @@ jobs:

       - name: Install GATK4

         if: runner.os == 'Linux'

         run: |

-           wget --no-verbose https://github.com/broadinstitute/gatk/releases/download/4.4.0.0/gatk-4.4.0.0.zip

+           wget --no-verbose https://github.com/broadinstitute/gatk/releases/download/4.6.1.0/gatk-4.6.1.0.zip

            mkdir $HOME/tools

-           unzip gatk-4.4.0.0.zip -d $HOME/tools

-           sudo -s ln -s "$HOME/tools/gatk-4.4.0.0/gatk" /usr/local/bin/gatk

-           rm gatk-4.4.0.0.zip

+           unzip gatk-4.6.1.0.zip -d $HOME/tools

+           sudo -s ln -s "$HOME/tools/gatk-4.6.1.0/gatk" /usr/local/bin/gatk

+           rm gatk-4.6.1.0.zip

       - name: Show GATK4 version

         if: runner.os == 'Linux'

@@ -136,32 +136,6 @@ jobs:

            echo "$PATH"

            gatk --version

-      - name: Install macOS system dependencies

-        if: matrix.config.os == 'macOS-latest'

-        run: |

-          ## Enable installing XML from source if needed

-          brew install libxml2

-          echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV

-

-          ## Required to install magick as noted at

-          ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2

-          brew install imagemagick@6

-

-          ## For textshaping, required by ragg, and required by pkgdown

-          brew install harfbuzz fribidi

-

-          ## 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}

-

       - name: Install BiocManager

         run: |

           message(paste('****', Sys.time(), 'installing BiocManager ****'))

@@ -182,35 +156,19 @@ 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)

+          install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories())

           ## 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 = 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, force = TRUE)

         shell: Rscript {0}

@@ -274,7 +232,6 @@ jobs:

               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

           )

         shell: Rscript {0}

@@ -282,7 +239,7 @@ jobs:

       - name: Test coverage

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

         run: |

-          covr::codecov()

+          covr::codecov(coverage = covr::package_coverage(type = "all"))

         shell: Rscript {0}

       - name: Install package

@@ -315,6 +272,54 @@ jobs:

         if: failure()

         uses: actions/upload-artifact@master

         with:

-          name: ${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-results

+          name: ${{ runner.os }}-biocversion-RELEASE_3_19-r-4.4-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/devel'"

+        uses: actions/checkout@v3

+

+      - name: Register repo name

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

+        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/devel'"

+        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/devel'"

+        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/devel'"

+        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/devel' && 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