removing symbolic links in duckdb repo because R package build falls … #5
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| name: R | |
| on: | |
| workflow_dispatch: | |
| repository_dispatch: | |
| push: | |
| pull_request: | |
| env: | |
| GH_TOKEN: ${{ secrets.GH_TOKEN }} | |
| jobs: | |
| rstats-linux: | |
| name: R Package Linux | |
| runs-on: ubuntu-20.04 | |
| env: | |
| LIBARROW_BINARY: 'false' | |
| ARROW_USER_SIMD_LEVEL: 'AVX2' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| submodules: 'true' | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.7' | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'devel' | |
| - name: Install | |
| env: | |
| GITHUB_PAT: ${{ github.token }} | |
| shell: bash | |
| run: | | |
| sudo apt-get update -y -qq && sudo apt-get install -y -qq ninja-build texlive-latex-base texlive-fonts-extra libcurl4-openssl-dev valgrind pandoc tidy | |
| mkdir -p $HOME/.R | |
| R -f dependencies.R | |
| - name: Prepare | |
| shell: bash | |
| run: | | |
| rm -rf duckdb/test/sql/copy/csv/data/glob/crawl/.symbolic_link | |
| mkdir -p /tmp/duckdb_extensions | |
| ./configure | |
| R CMD build . | |
| - name: Tests | |
| shell: bash | |
| run: | | |
| ls /tmp/duckdb_extensions | |
| R CMD INSTALL -d duckdb_*.tar.gz | |
| (cd tests && R -f testthat.R) | |
| - name: R CMD check | |
| shell: bash | |
| run: | | |
| _R_CHECK_CRAN_INCOMING_=FALSE _R_CHECK_PKG_SIZES_=FALSE R CMD check --as-cran -o /tmp duckdb_*.tar.gz | |
| if egrep 'NOTE|WARNING|ERROR' /tmp/duckdb.Rcheck/00check.log ; then exit 1; fi | |
| - name: Print R log (1) | |
| # Print logs now only if success, for the case of failure there's another identical step below. | |
| if: ${{ success() }} | |
| shell: bash | |
| run: | | |
| cat /tmp/duckdb.Rcheck/00check.log | |
| find /tmp/duckdb.Rcheck/ -type f -name "*.Rout*" -print0 | tee /dev/stderr | xargs -0 cat | |
| - name: Valgrind | |
| shell: bash | |
| run: | | |
| export NOT_CRAN='false' | |
| _R_CHECK_CRAN_INCOMING_=FALSE _R_CHECK_PKG_SIZES_=FALSE R CMD check --use-valgrind -o /tmp duckdb_*.tar.gz | |
| - name: Print check directory tree | |
| if: ${{ always() }} | |
| shell: bash | |
| run: | | |
| ls -R /tmp/duckdb.Rcheck | |
| - name: Print R log (2) | |
| if: ${{ always() }} | |
| shell: bash | |
| run: | | |
| cat /tmp/duckdb.Rcheck/00check.log | |
| find /tmp/duckdb.Rcheck/ -type f -name "*.Rout*" -print0 | tee /dev/stderr | xargs -0 cat | |
| - name: Coverage | |
| env: | |
| DUCKDB_R_DEBUG: 1 | |
| shell: Rscript {0} | |
| run: | | |
| pkgload::load_all(".") | |
| cov <- covr::codecov(".", relative_path = ".") | |
| - name: Deploy | |
| shell: bash | |
| run: python duckdb/scripts/asset-upload-gha.py duckdb_*.tar.gz | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: r-package-source | |
| path: | | |
| duckdb_*.tar.gz | |
| rstats-linux-debug: | |
| name: R Package Linux debug mode | |
| runs-on: ubuntu-20.04 | |
| needs: rstats-linux | |
| env: | |
| LIBARROW_BINARY: 'false' | |
| ARROW_USER_SIMD_LEVEL: 'AVX2' | |
| DUCKDB_R_DEBUG: 1 | |
| DUCKDB_DEBUG_MOVE: 1 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| submodules: 'true' | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.7' | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'devel' | |
| - name: Install | |
| env: | |
| GITHUB_PAT: ${{ github.token }} | |
| shell: bash | |
| run: | | |
| sudo apt-get update -y -qq && sudo apt-get install -y -qq ninja-build libcurl4-openssl-dev | |
| mkdir -p $HOME/.R | |
| R -f dependencies.R | |
| - name: Setup Ccache | |
| uses: hendrikmuhs/ccache-action@main | |
| with: | |
| key: ${{ github.job }} | |
| save: ${{ github.ref == 'refs/heads/main' || github.repository != 'duckdb/duckdb' }} | |
| - name: Build | |
| shell: bash | |
| run: | | |
| rm -rf duckdb/test/sql/copy/csv/data/glob/crawl/.symbolic_link | |
| ./configure | |
| R CMD INSTALL . | |
| rstats-windows: | |
| # Builds binaries for windows_amd64_rtools | |
| name: R Package Windows | |
| needs: rstats-linux | |
| runs-on: windows-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| submodules: 'true' | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.7' | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'devel' | |
| update-rtools: true | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Setup Ccache | |
| uses: hendrikmuhs/ccache-action@main | |
| with: | |
| key: ${{ github.job }} | |
| save: ${{ github.ref == 'refs/heads/main' || github.repository != 'duckdb/duckdb' }} | |
| - name: Install | |
| shell: bash | |
| run: | | |
| R -f dependencies.R | |
| - name: Build | |
| shell: bash | |
| run: | | |
| rm -rf duckdb/test/sql/copy/csv/data/glob/crawl/.symbolic_link | |
| ./configure | |
| R CMD build . | |
| R CMD INSTALL duckdb_*.tar.gz | |
| (cd tests && R -f testthat.R) | |
| _R_CHECK_CRAN_INCOMING_=FALSE _R_CHECK_PKG_SIZES_=FALSE R CMD check --as-cran --no-manual -o /tmp duckdb_*.tar.gz | |
| if egrep 'NOTE|WARNING|ERROR' /tmp/duckdb.Rcheck/00check.log ; then exit 1; fi | |
| rstats-windows-extensions: | |
| # Builds extensions for windows_amd64_rtools | |
| name: R Package Windows (Extensions) | |
| if: startsWith(github.ref, 'refs/tags/v') || github.ref == 'refs/heads/main' | |
| needs: rstats-linux | |
| runs-on: windows-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| submodules: 'true' | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.7' | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'devel' | |
| update-rtools: true | |
| rtools-version: '42' # linker bug in 43 ^^ | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Setup Ccache | |
| uses: hendrikmuhs/ccache-action@main | |
| with: | |
| key: ${{ github.job }} | |
| save: ${{ github.ref == 'refs/heads/main' || github.repository != 'duckdb/duckdb' }} | |
| - uses: ./.github/actions/build_extensions | |
| with: | |
| deploy_as: windows_amd64_rtools | |
| treat_warn_as_error: 0 | |
| s3_id: ${{ secrets.S3_ID }} | |
| s3_key: ${{ secrets.S3_KEY }} | |
| signing_pk: ${{ secrets.DUCKDB_EXTENSION_SIGNING_PK }} | |
| override_cc: gcc | |
| override_cxx: g++ | |
| openssl_path: C:/rtools43/x86_64-w64-mingw32.static.posix # not sure if this is required, there seems to be an openssl there | |
| run_tests: 0 | |
| build_out_of_tree_extensions: 0 | |
| vcpkg_build: 0 | |
| no_static_linking: 1 | |
| - name: Install R package | |
| shell: bash | |
| run: | | |
| rm -rf duckdb/test/sql/copy/csv/data/glob/crawl/.symbolic_link | |
| R -e 'install.packages("DBI", repos = "https://cloud.r-project.org")' | |
| ./configure | |
| R CMD build . | |
| R CMD INSTALL duckdb_*.tar.gz | |
| - name: Test Load | |
| shell: bash | |
| run: | | |
| R -e 'con <- DBI::dbConnect(duckdb::duckdb(config = list("allow_unsigned_extensions" = "true")), debug=TRUE); lapply(Sys.glob("build/release/extension/*/*.duckdb_extension"), function(x) DBI::dbExecute(con, sprintf("LOAD \"%s\"", x))); DBI::dbDisconnect(con, shutdown=TRUE);' |