test: Enable remaining Arrow tests #1396
Workflow file for this run
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| # Adapted from backends.yaml, with contents from odbc/db.yaml | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - master | |
| pull_request: | |
| branches: | |
| - main | |
| - master | |
| schedule: | |
| - cron: '0 8 * * *' | |
| name: backends odbc | |
| jobs: | |
| matrix: | |
| runs-on: ubuntu-20.04 | |
| outputs: | |
| matrix: ${{ steps.set-matrix.outputs.matrix }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| # https://github.blog/changelog/2020-04-15-github-actions-new-workflow-features/ | |
| - id: set-matrix | |
| run: | | |
| matrix=$(( | |
| echo '{ "include" : [' | |
| sed -n "/^REVDEP *:= */ { s///; p }" revdep-dev/Makefile | sed 's/ /,\n/g' | grep odbc | sed -r 's/^odbc-([^,]*)(,?)$/{ "database": "\1", "package": "odbc" }\2/' | |
| echo " ]}" | |
| ) | jq -c .) | |
| echo $matrix | |
| echo $matrix | jq . | |
| echo "matrix=$matrix" >> $GITHUB_OUTPUT | |
| check-matrix: | |
| runs-on: ubuntu-latest | |
| needs: matrix | |
| steps: | |
| - name: Install json2yaml | |
| run: | | |
| sudo npm install -g json2yaml | |
| - name: Check matrix definition | |
| run: | | |
| matrix='${{ needs.matrix.outputs.matrix }}' | |
| echo $matrix | |
| echo $matrix | jq . | |
| echo $matrix | json2yaml | |
| backend: | |
| needs: matrix | |
| # Need Ubuntu 20.04 for remotes::system_requirements() | |
| runs-on: ubuntu-20.04 | |
| services: | |
| postgres: | |
| image: postgres | |
| ports: | |
| - 5432:5432 | |
| env: | |
| POSTGRES_USER: postgres | |
| POSTGRES_PASSWORD: password | |
| POSTGRES_DB: test | |
| options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5 | |
| sqlserver: | |
| image: mcr.microsoft.com/mssql/server:2017-latest-ubuntu | |
| ports: | |
| - 1433:1433 | |
| env: | |
| ACCEPT_EULA: Y | |
| SA_PASSWORD: Password12 | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{fromJson(needs.matrix.outputs.matrix)}} | |
| name: ${{ matrix.database }} | |
| env: | |
| RSPM: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" | |
| ODBCSYSINI: ${{ github.workspace }}/.github/odbc | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Check rate limits | |
| run: | | |
| curl -s --header "authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" https://api.github.com/rate_limit | |
| shell: bash | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-r@v2 | |
| - name: Install remotes | |
| run: | | |
| if (!requireNamespace("curl", quietly = TRUE)) install.packages("curl") | |
| if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes") | |
| shell: Rscript {0} | |
| - name: Clone backend | |
| run: | | |
| make -C revdep-dev ${{ matrix.package }} | |
| - name: Prepare cache keys | |
| if: runner.os != 'Windows' | |
| run: | | |
| saveRDS(remotes::dev_package_deps("revdep-dev/${{ matrix.package }}", dependencies = TRUE, type = .Platform$pkgType), ".github/depends.Rds", version = 2) | |
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: backends-${{ hashFiles('.github/R-version') }}-2-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: backends-${{ hashFiles('.github/R-version') }}-2- | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| # "22.04" fails here | |
| run: | | |
| while read -r cmd | |
| do | |
| eval sudo $cmd | |
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04", path = "revdep-dev/${{ matrix.package }}"))') | |
| - name: Install package and dependencies | |
| run: | | |
| remotes::install_local("revdep-dev/${{ matrix.package }}", dependencies = TRUE, type = .Platform$pkgType) | |
| remotes::install_local(".", type = .Platform$pkgType, force = TRUE) | |
| remotes::install_cran("pkgbuild") | |
| shell: Rscript {0} | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| if (!requireNamespace("sessioninfo", quietly = TRUE)) install.packages("sessioninfo") | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| # Begin custom: after install | |
| - name: Setup MySQL | |
| if: matrix.database == 'mysql' | |
| run: | | |
| sudo systemctl start mysql.service | |
| mysql -uroot -h127.0.0.1 -proot -e 'CREATE DATABASE `test`;' | |
| .github/odbc/install-mariadb-driver.sh | |
| - name: Install SQLite Driver | |
| if: matrix.database == 'sqlite' | |
| run: | | |
| sudo apt-get install -y libsqliteodbc | |
| - name: Install PostgreSQL Driver | |
| if: matrix.database == 'postgres' | |
| run: | | |
| sudo apt-get install -y unixodbc-dev odbc-postgresql devscripts | |
| - name: Install SQL Server Driver | |
| if: matrix.database == 'sql-server' | |
| run: | | |
| curl https://packages.microsoft.com/keys/microsoft.asc | apt-key add - | |
| curl https://packages.microsoft.com/config/ubuntu/20.04/prod.list > /etc/apt/sources.list.d/mssql-release.list | |
| apt-get update | |
| ACCEPT_EULA=Y apt-get install -y msodbcsql17 | |
| ln -s /opt/microsoft/msodbcsql17/lib64/libmsodbcsql-17.*.so.* /opt/microsoft/msodbcsql17/lib64/libmsodbcsql-17.so | |
| shell: sudo bash {0} | |
| - name: Install locally to avoid error with test_local() | |
| run: | | |
| R CMD INSTALL revdep-dev/${{ matrix.package }} | |
| env: | |
| LIB_DIR: /usr/lib/x86_64-linux-gnu/ | |
| INCLUDE_DIR: /usr/include | |
| # End custom: after install | |
| - name: Test backend | |
| run: | | |
| make -C revdep-dev test-${{ matrix.package }}-${{ matrix.database }} | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| path: revdep-dev/${{ matrix.package }} | |
| - name: Check rate limits | |
| if: always() | |
| run: | | |
| curl -s --header "authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" https://api.github.com/rate_limit | |
| shell: bash |