Update stan submodule #675
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| --- | |
| # 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 |