fix notes/warnings in data.land package #4796
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - develop | |
| tags: | |
| - '*' | |
| pull_request: | |
| merge_group: | |
| issue_comment: | |
| types: | |
| - created | |
| env: | |
| R_LIBS_USER: /usr/local/lib/R/site-library | |
| LC_ALL: en_US.UTF-8 | |
| NCPUS: 2 | |
| PGHOST: postgres | |
| CI: true | |
| jobs: | |
| # ---------------------------------------------------------------------- | |
| # R TEST | |
| # ---------------------------------------------------------------------- | |
| test: | |
| if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build') | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| R: | |
| - "4.0" | |
| - "4.1" | |
| services: | |
| postgres: | |
| image: mdillon/postgis:9.5 | |
| options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5 | |
| container: | |
| image: pecan/depends:R${{ matrix.R }} | |
| steps: | |
| # checkout source code | |
| - name: work around https://github.com/actions/checkout/issues/766 | |
| run: git config --global --add safe.directory "$GITHUB_WORKSPACE" | |
| - uses: actions/checkout@v3 | |
| with: | |
| set-safe-directory: false | |
| # install additional tools needed | |
| - name: install utils | |
| run: apt-get update && apt-get install -y postgresql-client qpdf | |
| - name: update dependency lists | |
| run: Rscript scripts/generate_dependencies.R | |
| - name: check for out-of-date dependencies files | |
| uses: infotroph/tree-is-clean@v1 | |
| - name: install newly-added dependencies | |
| run: Rscript docker/depends/pecan.depends.R | |
| # initialize database | |
| - name: db setup | |
| uses: docker://pecan/db:ci | |
| - name: add models to db | |
| run: ./scripts/add.models.sh | |
| # run PEcAn tests | |
| - name: test | |
| run: make -j1 test | |
| - name: check for out-of-date files | |
| uses: infotroph/tree-is-clean@v1 | |
| # ---------------------------------------------------------------------- | |
| # R CHECK | |
| # ---------------------------------------------------------------------- | |
| check_base: | |
| if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build') | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| R: | |
| - "4.0" | |
| - "4.1" | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| _R_CHECK_LENGTH_1_CONDITION_: true | |
| _R_CHECK_LENGTH_1_LOGIC2_: true | |
| # Avoid compilation check warnings that come from the system Makevars | |
| # See https://stat.ethz.ch/pipermail/r-package-devel/2019q2/003898.html | |
| _R_CHECK_COMPILATION_FLAGS_KNOWN_: -Wformat -Werror=format-security -Wdate-time | |
| # Keep R checks from trying to consult the very flaky worldclockapi.com | |
| _R_CHECK_SYSTEM_CLOCK_: 0 | |
| container: | |
| image: pecan/depends:R${{ matrix.R }} | |
| steps: | |
| # checkout source code | |
| - name: work around https://github.com/actions/checkout/issues/766 | |
| run: git config --global --add safe.directory "$GITHUB_WORKSPACE" | |
| - uses: actions/checkout@v3 | |
| with: | |
| set-safe-directory: false | |
| # Forbid spaces in names. Yes, *we* know it's not 1980 anymore, but Make doesn't. | |
| - name: check for filenames that would confuse Make | |
| run: | | |
| SPACENAMES=`find . -name '* *'` | |
| if [ -n "$SPACENAMES" ]; then | |
| echo "::error file=${SPACENAMES}::Spaces in filename(s): ${SPACENAMES}. Please rename these files by converting spaces to underscores." | |
| exit 1 | |
| fi | |
| # install additional tools needed | |
| - name: install utils | |
| run: apt-get update && apt-get install -y postgresql-client qpdf | |
| - name: install new dependencies | |
| run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R | |
| # run PEcAn checks | |
| - name: check | |
| run: make -j1 check_base | |
| env: | |
| REBUILD_DOCS: "FALSE" | |
| RUN_TESTS: "FALSE" | |
| - name: check for out-of-date files | |
| uses: infotroph/tree-is-clean@v1 | |
| check_modules: | |
| if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build') | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| R: | |
| - "4.0" | |
| - "4.1" | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| _R_CHECK_LENGTH_1_CONDITION_: true | |
| _R_CHECK_LENGTH_1_LOGIC2_: true | |
| # Avoid compilation check warnings that come from the system Makevars | |
| # See https://stat.ethz.ch/pipermail/r-package-devel/2019q2/003898.html | |
| _R_CHECK_COMPILATION_FLAGS_KNOWN_: -Wformat -Werror=format-security -Wdate-time | |
| # Keep R checks from trying to consult the very flaky worldclockapi.com | |
| _R_CHECK_SYSTEM_CLOCK_: 0 | |
| container: | |
| image: pecan/depends:R${{ matrix.R }} | |
| steps: | |
| # checkout source code | |
| - name: work around https://github.com/actions/checkout/issues/766 | |
| run: git config --global --add safe.directory "$GITHUB_WORKSPACE" | |
| - uses: actions/checkout@v3 | |
| with: | |
| set-safe-directory: false | |
| # Forbid spaces in names. Yes, *we* know it's not 1980 anymore, but Make doesn't. | |
| - name: check for filenames that would confuse Make | |
| run: | | |
| SPACENAMES=`find . -name '* *'` | |
| if [ -n "$SPACENAMES" ]; then | |
| echo "::error file=${SPACENAMES}::Spaces in filename(s): ${SPACENAMES}. Please rename these files by converting spaces to underscores." | |
| exit 1 | |
| fi | |
| # install additional tools needed | |
| - name: install utils | |
| run: apt-get update && apt-get install -y postgresql-client qpdf | |
| - name: install new dependencies | |
| run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R | |
| # run PEcAn checks | |
| - name: check | |
| run: make -j1 check_modules | |
| env: | |
| REBUILD_DOCS: "FALSE" | |
| RUN_TESTS: "FALSE" | |
| - name: check for out-of-date files | |
| uses: infotroph/tree-is-clean@v1 | |
| check_models: | |
| if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build') | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| R: | |
| - "4.0" | |
| - "4.1" | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| _R_CHECK_LENGTH_1_CONDITION_: true | |
| _R_CHECK_LENGTH_1_LOGIC2_: true | |
| # Avoid compilation check warnings that come from the system Makevars | |
| # See https://stat.ethz.ch/pipermail/r-package-devel/2019q2/003898.html | |
| _R_CHECK_COMPILATION_FLAGS_KNOWN_: -Wformat -Werror=format-security -Wdate-time | |
| # Keep R checks from trying to consult the very flaky worldclockapi.com | |
| _R_CHECK_SYSTEM_CLOCK_: 0 | |
| container: | |
| image: pecan/depends:R${{ matrix.R }} | |
| steps: | |
| # checkout source code | |
| - name: work around https://github.com/actions/checkout/issues/766 | |
| run: git config --global --add safe.directory "$GITHUB_WORKSPACE" | |
| - uses: actions/checkout@v3 | |
| with: | |
| set-safe-directory: false | |
| # Forbid spaces in names. Yes, *we* know it's not 1980 anymore, but Make doesn't. | |
| - name: check for filenames that would confuse Make | |
| run: | | |
| SPACENAMES=`find . -name '* *'` | |
| if [ -n "$SPACENAMES" ]; then | |
| echo "::error file=${SPACENAMES}::Spaces in filename(s): ${SPACENAMES}. Please rename these files by converting spaces to underscores." | |
| exit 1 | |
| fi | |
| # install additional tools needed | |
| - name: install utils | |
| run: apt-get update && apt-get install -y postgresql-client qpdf | |
| - name: install new dependencies | |
| run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R | |
| # run PEcAn checks | |
| - name: check | |
| run: make -j1 check_models | |
| env: | |
| REBUILD_DOCS: "FALSE" | |
| RUN_TESTS: "FALSE" | |
| - name: check for out-of-date files | |
| uses: infotroph/tree-is-clean@v1 | |
| # ---------------------------------------------------------------------- | |
| # SIPNET TESTS | |
| # ---------------------------------------------------------------------- | |
| sipnet: | |
| if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build') | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| R: | |
| - "4.0" | |
| - "4.1" | |
| services: | |
| postgres: | |
| image: mdillon/postgis:9.5 | |
| options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5 | |
| container: | |
| image: pecan/depends:R${{ matrix.R }} | |
| steps: | |
| # checkout source code | |
| - name: work around https://github.com/actions/checkout/issues/766 | |
| run: git config --global --add safe.directory "$GITHUB_WORKSPACE" | |
| - uses: actions/checkout@v3 | |
| with: | |
| set-safe-directory: false | |
| # install additional tools needed | |
| - name: install utils | |
| run: apt-get update && apt-get install -y postgresql-client qpdf | |
| - name: install new dependencies | |
| run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R | |
| # initialize database | |
| - name: db setup | |
| uses: docker://pecan/db:ci | |
| - name: add models to db | |
| run: ./scripts/add.models.sh | |
| # install sipnet | |
| - name: Check out SIPNET | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: PecanProject/sipnet | |
| path: sipnet | |
| set-safe-directory: false | |
| - name: install sipnet | |
| run: | | |
| cd ${GITHUB_WORKSPACE}/sipnet | |
| make | |
| # compile PEcAn code | |
| - name: build | |
| run: make -j1 | |
| # run SIPNET test | |
| - name: integration test | |
| run: ./tests/integration.sh ghaction |