diff --git a/.github/workflows/R-CMD-as-cran-check.yaml b/.github/workflows/R-CMD-as-cran-check.yaml index 16104203f..a3881bc64 100644 --- a/.github/workflows/R-CMD-as-cran-check.yaml +++ b/.github/workflows/R-CMD-as-cran-check.yaml @@ -36,9 +36,17 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::rcmdcheck - needs: check + dependencies: NA + extra-packages: | + stan-dev/cmdstanr + testthat + + - name: Install cmdstan + run: | + cmdstanr::check_cmdstan_toolchain(fix = TRUE) + cmdstanr::install_cmdstan(cores = 2, quiet = TRUE) + shell: Rscript {0} - uses: r-lib/actions/check-r-package@v2 with: - upload-snapshots: true \ No newline at end of file + upload-snapshots: true diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index bf666a780..d2e42d93f 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -47,13 +47,6 @@ jobs: steps: - uses: actions/checkout@v4 - - name: Install cmdstan Linux 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 - sudo apt-get install -y libpng-dev || true - uses: r-lib/actions/setup-pandoc@v2 - uses: r-lib/actions/setup-r@v2 @@ -65,8 +58,16 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::rcmdcheck - needs: check + dependencies: NA + extra-packages: | + stan-dev/cmdstanr + testthat + + - name: Install cmdstan + run: | + cmdstanr::check_cmdstan_toolchain(fix = TRUE) + cmdstanr::install_cmdstan(cores = 2, quiet = TRUE) + shell: Rscript {0} - uses: r-lib/actions/check-r-package@v2 with: diff --git a/.github/workflows/lint-only-changed-files.yaml b/.github/workflows/lint-only-changed-files.yaml index bdceceaeb..9d16256bf 100644 --- a/.github/workflows/lint-only-changed-files.yaml +++ b/.github/workflows/lint-only-changed-files.yaml @@ -21,6 +21,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: + dependencies: NA extra-packages: | any::gh any::lintr @@ -44,4 +45,4 @@ jobs: lintr::lint_package(exclusions = exclusions_list) shell: Rscript {0} env: - LINTR_ERROR_ON_LINT: true \ No newline at end of file + LINTR_ERROR_ON_LINT: true diff --git a/.github/workflows/synthetic-validation.yaml b/.github/workflows/synthetic-validation.yaml index 30671cfc4..0362bfee6 100644 --- a/.github/workflows/synthetic-validation.yaml +++ b/.github/workflows/synthetic-validation.yaml @@ -24,6 +24,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: + dependencies: NA extra-packages: | dplyr tidyr @@ -48,4 +49,4 @@ jobs: with: name: fits retention-days: 5 - path: synthetic.rds \ No newline at end of file + path: synthetic.rds diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 664af0f84..f352c2870 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -26,9 +26,18 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::covr - needs: coverage + dependencies: NA + extra-packages: | + covr + stan-dev/cmdstanr + testthat + + - name: Install cmdstan + run: | + cmdstanr::check_cmdstan_toolchain(fix = TRUE) + cmdstanr::install_cmdstan(cores = 2, quiet = TRUE) + shell: Rscript {0} - name: Test coverage run: covr::codecov(quiet = FALSE) - shell: Rscript {0} \ No newline at end of file + shell: Rscript {0}