diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index 0738b9a..65a51f9 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: '3.15', cont: "bioconductor/bioconductor_docker:RELEASE_3_15", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } - - { os: macOS-latest, r: '4.2', bioc: '3.15'} - - { os: windows-latest, r: '4.2', bioc: '3.15'} + - { os: ubuntu-latest, r: 'devel', bioc: '3.20', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" } + - { os: macOS-latest, r: 'devel', bioc: '3.20'} + - { os: windows-latest, r: 'devel', bioc: '3.20'} ## Check https://github.com/r-lib/actions/tree/master/examples ## for examples using the http-user-agent env: @@ -79,12 +79,12 @@ 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 }} @@ -92,7 +92,7 @@ jobs: ## 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: | @@ -102,19 +102,19 @@ jobs: - 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-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2- + key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel- - 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-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2- + key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel- - name: Install Linux system dependencies if: runner.os == 'Linux' @@ -128,7 +128,7 @@ jobs: run: | ## Enable installing XML from source if needed brew install libxml2 - echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV + echo "XML_CONFIG=/opt/homebrew/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV ## Required to install magick as noted at ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 @@ -143,6 +143,21 @@ jobs: ## Required for tcltk brew install xquartz --cask + ## Required for terra + brew install gdal + + ## Temporary fix for freetype (https://github.com/r-lib/ragg/issues/170; Sep 2024) + #brew install --cask https://raw.githubusercontent.com/Homebrew/homebrew-core/d28afc3bfdb5d24eab02157bfffcc9e17ed6666c/Formula/f/freetype.rb + brew unlink freetype + curl -L https://raw.githubusercontent.com/Homebrew/homebrew-core/3db6dc6c4baf5a75e345f380cc4e8224c1ae5ae0/Formula/f/freetype.rb > freetype.rb && brew install freetype.rb + + - name: Install binary units for macOS + if: matrix.config.os == 'macOS-latest' + run: | + ## temporary fix due to issue in udunits (Sep 2024) + install.packages('https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/units_0.8-5.tgz') + shell: Rscript {0} + - name: Install Windows system dependencies if: runner.os == 'Windows' run: | @@ -176,7 +191,7 @@ jobs: gha_repos <- if( .Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin" ) c( - "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.15/bioc", + "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.20/bioc", BiocManager::repositories() ) else BiocManager::repositories() @@ -210,13 +225,13 @@ jobs: shell: Rscript {0} - name: Install covr - if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux' + if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' run: | remotes::install_cran("covr") shell: Rscript {0} - name: Install pkgdown - if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux' + if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' run: | remotes::install_cran("pkgdown") shell: Rscript {0} @@ -237,7 +252,7 @@ jobs: rcmdcheck::rcmdcheck( args = c("--no-manual", "--no-vignettes", "--timings"), build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"), - error_on = "error", + error_on = "warning", check_dir = "check" ) shell: Rscript {0} @@ -259,28 +274,28 @@ jobs: run: | BiocCheck::BiocCheck( dir('check', 'tar.gz$', full.names = TRUE), - `quit-with-status` = TRUE, + `quit-with-status` = FALSE, `no-check-R-ver` = TRUE, `no-check-bioc-help` = TRUE ) shell: Rscript {0} - name: Test coverage - if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux' + if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' run: | covr::codecov() shell: Rscript {0} - name: Install package - if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux' + if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' run: R CMD INSTALL . - name: Build and deploy pkgdown site - if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux' + if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' run: | git config --global user.name "$GITHUB_ACTOR" git config --global user.email "$GITHUB_ACTOR@users.noreply.github.com" - git config --global --add safe.directory /__w/iSEEhex/iSEEhex + git config --global --add safe.directory /__w/iSEE/iSEEhex 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) @@ -292,7 +307,7 @@ jobs: if: failure() uses: actions/upload-artifact@master with: - name: ${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-results + name: ${{ runner.os }}-biocversion-devel-r-devel-results path: check - uses: docker/build-push-action@v1 @@ -300,7 +315,7 @@ jobs: with: username: ${{ secrets.DOCKER_USERNAME }} password: ${{ secrets.DOCKER_PASSWORD }} - repository: iseedevelopers/iseehex + repository: isee/iseehex tag_with_ref: true tag_with_sha: true tags: latest