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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| # Some of this workflow was borrowed from https://github.com/stan-dev/cmdstanr/blob/master/.github/workflows | ||
| # This workflow file is from https://github.com/stan-dev/cmdstanr/blob/master/.github/workflows | ||
| # under the BSD 3-Clause License: https://github.com/stan-dev/cmdstanr/blob/master/LICENSE.md. | ||
| # | ||
| # BSD 3-Clause License | ||
|
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@@ -37,6 +37,7 @@ name: check | |
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| jobs: | ||
| check: | ||
| if: "! contains(github.event.head_commit.message, '[ci skip]')" | ||
| runs-on: ${{ matrix.config.os }} | ||
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| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | ||
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@@ -45,109 +46,95 @@ jobs: | |
| fail-fast: false | ||
| matrix: | ||
| config: | ||
| - {os: macOS-latest, r: 'release'} | ||
| - {os: macOS-latest, r: 'devel', rtools: ''} | ||
| - {os: macOS-latest, r: 'release', rtools: ''} | ||
| - {os: windows-latest, r: 'devel', rtools: '42'} | ||
| - {os: windows-latest, r: 'release', rtools: '42'} | ||
| - {os: ubuntu-20.04, r: 'devel', http-user-agent: 'release'} | ||
| - {os: ubuntu-20.04, r: 'release'} | ||
| - {os: ubuntu-20.04, r: 'oldrel-1'} | ||
| - {os: ubuntu-20.04, r: 'oldrel-2'} | ||
| - {os: ubuntu-20.04, r: 'oldrel-3'} | ||
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| - {os: windows-latest, r: 'oldrel', rtools: '40'} | ||
| - {os: ubuntu-20.04, r: 'devel', rtools: ''} | ||
| - {os: ubuntu-20.04, r: 'release', rtools: ''} | ||
| - {os: ubuntu-20.04, r: 'oldrel', rtools: ''} | ||
| env: | ||
| RSPM: ${{ matrix.config.rspm }} | ||
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: false | ||
| NOT_CRAN: true | ||
| CMDSTAN_VERSION: 2.30.1 | ||
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||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: cmdstan env vars | ||
| run: | | ||
| echo "CMDSTAN_PATH=${HOME}/.cmdstan" >> $GITHUB_ENV | ||
| shell: bash | ||
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||
| - uses: n1hility/cancel-previous-runs@v2 | ||
| with: | ||
| token: ${{ secrets.GITHUB_TOKEN }} | ||
| if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master'" | ||
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| - uses: actions/checkout@v3 | ||
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| - name: Install system dependencies | ||
| if: runner.os == 'Linux' | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install -y libcurl4-openssl-dev || true | ||
| sudo apt-get install -y openmpi-bin openmpi-common libopenmpi-dev || true | ||
| - uses: r-lib/actions/[email protected] | ||
| with: | ||
| r-version: ${{ matrix.config.r }} | ||
| rtools-version: ${{ matrix.config.rtools }} | ||
| - uses: r-lib/actions/setup-pandoc@v1 | ||
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| - name: Platform-independent cmdstan path | ||
| run: | | ||
| path <- normalizePath(file.path("~", ".cmdstanr"), mustWork = FALSE) | ||
| print(path) | ||
| writeLines(path, ".github/cmdstan_path") | ||
| shell: Rscript {0} | ||
|
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| - name: cmdstan env vars | ||
| run: echo "CMDSTAN_PATH=$(cat .github/cmdstan_path)" >> $GITHUB_ENV | ||
| shell: bash | ||
|
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| - uses: r-lib/actions/setup-pandoc@master | ||
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| - name: Query dependencies | ||
| run: | | ||
| install.packages('remotes') | ||
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | ||
| shell: Rscript {0} | ||
|
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| - name: Cache R packages | ||
| uses: actions/cache@v2 | ||
| if: runner.os != 'Windows' | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: ${{ env.R_LIBS_USER }} | ||
| key: ${{ runner.os }}-r-${{ matrix.config.r }}-1-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-1- | ||
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| - name: Install Linux system dependencies | ||
| if: runner.os == 'Linux' | ||
| env: | ||
| RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install -y libglpk-dev libcurl4-openssl-dev texlive-latex-base | ||
| sudo apt-get install -y openmpi-bin openmpi-common libopenmpi-dev || true | ||
| Rscript -e "remotes::install_github('r-hub/sysreqs')" | ||
| sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") | ||
| sudo -s eval "$sysreqs" | ||
| key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- | ||
|
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||
| - name: Install dependencies | ||
| run: | | ||
| remotes::install_cran("knitr") | ||
| suppressWarnings(remotes::install_deps(dependencies = TRUE)) | ||
| remotes::install_deps(dependencies = TRUE) | ||
| remotes::install_cran("rcmdcheck") | ||
| remotes::install_local(path = ".") | ||
| install.packages("curl") | ||
| shell: Rscript {0} | ||
|
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| - name: Cache cmdstan | ||
| uses: actions/cache@v2 | ||
| with: | ||
| path: ${{ env.CMDSTAN_PATH }} | ||
| key: ${{ runner.os }}-cmdstan-2-${{ env.CMDSTAN_VERSION }} | ||
|
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| - name: Install cmdstan | ||
| run: | | ||
| version <- Sys.getenv("CMDSTAN_VERSION") | ||
| url <- sprintf("https://github.com/stan-dev/cmdstan/releases/download/v%s/cmdstan-%s.tar.gz", version, version) | ||
| cmdstanr::check_cmdstan_toolchain(fix = TRUE) | ||
| cmdstanr::install_cmdstan(cores = 2, release_url = url) | ||
| cmdstanr::install_cmdstan(cores = 2) | ||
| shell: Rscript {0} | ||
|
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| - name: Test cmdstan | ||
| - name: Session info | ||
| run: | | ||
| cmdstanr::check_cmdstan_toolchain() | ||
| print(cmdstanr::cmdstan_path()) | ||
| file <- file.path(cmdstanr::cmdstan_path(), "examples", "bernoulli", "bernoulli.stan") | ||
| temp <- tempfile(fileext = ".stan") | ||
| file.copy(file, temp) | ||
| model <- cmdstanr::cmdstan_model(temp) | ||
| print(model) | ||
| options(width = 100) | ||
| pkgs <- installed.packages()[, "Package"] | ||
| sessioninfo::session_info(pkgs, include_base = TRUE) | ||
| shell: Rscript {0} | ||
|
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| - name: Check | ||
| env: | ||
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | ||
| _R_CHECK_FORCE_SUGGESTS_: false | ||
| run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check") | ||
| _R_CHECK_CRAN_INCOMING_: false | ||
| run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") | ||
| shell: Rscript {0} | ||
|
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| - name: Show testthat output | ||
| if: always() | ||
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | ||
| shell: bash | ||
|
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| - name: Upload check results | ||
| if: failure() | ||
| uses: actions/upload-artifact@master | ||
| uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | ||
| path: check | ||
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