Update stan submodule #612
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| # Github Actions workflow to check and build StanHeaders and RStan | |
| # yamllint disable rule:line-length | |
| name: R-CMD-check | |
| 'on': | |
| push: | |
| branches: | |
| - develop | |
| - experimental | |
| - StanHeaders_* | |
| pull_request: | |
| branches: | |
| - develop | |
| - experimental | |
| - StanHeaders_* | |
| jobs: | |
| R-CMD-check: | |
| if: "! contains(github.event.head_commit.message, '[ci skip]')" | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| config: | |
| - {os: macOS-latest, r: 'release'} | |
| - {os: macOS-latest, r: 'oldrel'} | |
| - {os: windows-latest, r: 'release'} | |
| - {os: windows-latest, r: 'oldrel'} | |
| - {os: ubuntu-20.04, r: 'devel'} | |
| - {os: ubuntu-20.04, r: 'release'} | |
| - {os: ubuntu-20.04, r: 'oldrel'} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Query dependencies | |
| run: | | |
| options(install.packages.check.source = "no") | |
| options(pkgType = ifelse(grepl("linux", R.version$os), "source", "binary")) | |
| install.packages('remotes') | |
| install.packages('V8') | |
| saveRDS(remotes::dev_package_deps(pkg = "./rstan/rstan", dependencies = TRUE), ".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@v2 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| env: | |
| RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | |
| run: | | |
| Rscript -e "remotes::install_github('r-hub/sysreqs')" | |
| sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('./rstan/rstan/DESCRIPTION'))") | |
| sudo -s eval "$sysreqs" | |
| shell: bash | |
| - name: Install dependencies | |
| run: | | |
| remotes::install_deps(pkg = "./rstan/rstan", dependencies = TRUE) | |
| remotes::install_cran("rcmdcheck") | |
| remotes::install_cran("rstantools", type = "source") | |
| remotes::install_cran("sessioninfo") | |
| if (utils::packageVersion("sessioninfo") >= "1.2.1") { | |
| sessioninfo::session_info(pkgs = "installed", include_base = TRUE) | |
| } else { | |
| options(width = 200) | |
| sessioninfo::session_info(rownames(installed.packages()), include_base = TRUE) | |
| } | |
| shell: Rscript {0} | |
| - name: Install StanHeaders | |
| run: | | |
| try(system("sh sh_b.sh --no-build-vignettes --no-manual")) | |
| shell: Rscript {0} | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| - name: Verify Math Version | |
| run: | | |
| readLines(system.file("include","stan","math","version.hpp", package="StanHeaders")) | |
| shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: false | |
| run: | | |
| if (R.version$major < 4 && isTRUE(.Platform$OS.type == "windows")) { | |
| dotR <- file.path(Sys.getenv("HOME"), ".R") | |
| if (!file.exists(dotR)) dir.create(dotR) | |
| path_makevars <- ifelse(.Platform$OS.type == "windows", "Makevars.win", "Makevars") | |
| M <- file.path(dotR, path_makevars) | |
| if (!file.exists(M)) file.create(M) | |
| cat("\nCXX14FLAGS=-O3", | |
| "CXX14 = $(BINPREF)g++ -m$(WIN) -std=c++1y", | |
| "CXX11FLAGS=-O3", | |
| file = M, sep = "\n", append = TRUE) | |
| } | |
| rcmdcheck::rcmdcheck(path = "./rstan/rstan", args = c("--no-manual", "--as-cran", "--ignore-vignettes"), build_args = c("--no-build-vignettes"), error_on = "warning", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Show testthat output | |
| if: always() | |
| run: | | |
| rm -rf check/rstan.Rcheck/rstan check/rstan.Rcheck/*pkg_src | |
| find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| path: check | |
| - name: Extract version and check StanHeaders source package | |
| run: | | |
| set -x | |
| echo "STANHEADERS_VERSION=$(grep '^Version' StanHeaders/DESCRIPTION | sed 's/.*: *//')" >> $GITHUB_ENV | |
| echo "RSTAN_VERSION=$(grep '^Version' rstan/rstan/DESCRIPTION | sed 's/.*: *//')" >> $GITHUB_ENV | |
| if [[ ! -f StanHeaders_*.tar.gz ]]; then | |
| sh sh_b.sh --no-build-vignettes --no-manual || true | |
| fi | |
| mkdir -p build || true | |
| cp -v StanHeaders_*.tar.gz build/ || true | |
| ls -R build/ | |
| shell: bash | |
| - name: Build RStan source package | |
| if: matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'devel' | |
| run: | | |
| src_rstan <- pkgbuild::build("./rstan/rstan", dest_path = tempdir(), vignettes = FALSE, manual = FALSE) | |
| file.copy(src_rstan, "build") | |
| shell: Rscript {0} | |
| - name: Build binary packages | |
| run: | | |
| bin1 <- pkgbuild::build("./build/StanHeaders_${{ env.STANHEADERS_VERSION }}.tar.gz", dest_path = tempdir(), vignettes = FALSE, manual = FALSE, binary = TRUE) | |
| bin2 <- pkgbuild::build("./rstan/rstan", dest_path = tempdir(), vignettes = FALSE, manual = FALSE, binary = TRUE) | |
| dir.create("build_bin") | |
| file.copy(c(bin1, bin2), "build_bin") | |
| shell: Rscript {0} | |
| - name: Upload StanHeaders source package | |
| if: matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'devel' | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: StanHeaders_${{ env.STANHEADERS_VERSION }}.tar.gz | |
| path: build/StanHeaders_${{ env.STANHEADERS_VERSION }}.tar.gz | |
| - name: Upload RStan source package | |
| if: matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'devel' | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: rstan_${{ env.RSTAN_VERSION }}.tar.gz | |
| path: build/rstan_${{ env.RSTAN_VERSION }}.tar.gz | |
| - name: Upload binary packages | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: R-${{ matrix.config.r }}_${{ matrix.config.os }} | |
| path: build_bin |