diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index 5616f0a..630464d 100644 --- a/.github/workflows/check-bioc.yml +++ b/.github/workflows/check-bioc.yml @@ -52,9 +52,9 @@ jobs: fail-fast: false matrix: config: - - { 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'} + - { 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: macOS-latest, r: '4.3', bioc: '3.17'} + - { os: windows-latest, r: '4.3', bioc: '3.17'} ## Check https://github.com/r-lib/actions/tree/master/examples ## for examples using the http-user-agent env: @@ -105,16 +105,16 @@ jobs: uses: actions/cache@v3 with: path: ${{ env.R_LIBS_USER }} - key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2- + 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- - 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_16-r-4.2-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2- + 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- - name: Install Linux system dependencies if: runner.os == 'Linux' @@ -169,35 +169,19 @@ 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/3.16/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} @@ -305,7 +289,7 @@ jobs: if: failure() uses: actions/upload-artifact@master with: - name: ${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-results + name: ${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-results path: check @@ -316,25 +300,25 @@ jobs: needs: build-check steps: - name: Checkout Repository - if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' " + if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" uses: actions/checkout@v3 - name: Register repo name - if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' " + if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" id: reg_repo_name run: | echo CONT_IMG_NAME=$(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' " + 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' " + 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' " + 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 }}