Update jsonlite to v1.8.8 for compatibility with R 4.4.0 #106
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| name: CI | |
| on: | |
| push: | |
| # The docker branch tracks master, so it doesn't need testing separately | |
| branches-ignore: | |
| docker | |
| pull_request: | |
| defaults: | |
| run: | |
| shell: bash | |
| jobs: | |
| # Main TractoR tests, on Linux only | |
| integration-check: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| R: [ '3.5.0', '4.0.0', 'release' ] | |
| steps: | |
| - name: Check out code | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: true | |
| - name: Install and set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.R }} | |
| # igraph depends on glpk in the 2.0.x series, so this is required for deep testing | |
| - name: Install upstream system dependencies | |
| run: sudo apt-get install -y libglpk-dev | |
| - name: Cache dependencies | |
| id: cache-deps | |
| uses: actions/cache@v4 | |
| with: | |
| path: lib/R | |
| key: ${{ runner.os }}-deps-${{ matrix.R }}-${{ hashFiles('lib/*/DESCRIPTION') }} | |
| - name: Install dependencies | |
| if: ${{ steps.cache-deps.outputs.cache-hit != 'true' }} | |
| run: make install-libs | |
| - name: Install main packages | |
| run: make install-main | |
| - name: Run tests | |
| run: make deeptest | |
| # Standard R CMD check on tractor.base package (Linux and Windows) | |
| base-check: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-latest, windows-latest ] | |
| R: [ release, devel ] | |
| runs-on: ${{ matrix.os }} | |
| # No submodules needed in this case, as we'll install dependencies from CRAN | |
| steps: | |
| - name: Check out code | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: false | |
| - name: Install and set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.R }} | |
| - name: Parse and install dependencies | |
| run: | | |
| deps <- read.dcf(file.path("tractor.base","DESCRIPTION"), c("Depends","Imports","LinkingTo","Suggests","Enhances")) | |
| deps <- na.omit(unlist(strsplit(deps, "\\s*,\\s*", perl=TRUE))) | |
| deps <- setdiff(unique(sub("\\s*\\([^\\)]+\\)\\s*$", "", deps, perl=TRUE)), c("R", rownames(installed.packages()))) | |
| install.packages(deps) | |
| shell: Rscript {0} | |
| - name: Build package | |
| run: R CMD build tractor.base | |
| - name: Check package | |
| run: R CMD check --no-manual tractor.base*tar.gz | |
| # Upload the check directory as an artefact on failure | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ matrix.os }}-R${{ matrix.R }}-check | |
| path: tractor.base.Rcheck |