diff --git a/.github/environment/pixi.toml b/.github/environment/pixi.toml index aa9a5b89..eed0e558 100644 --- a/.github/environment/pixi.toml +++ b/.github/environment/pixi.toml @@ -30,6 +30,7 @@ r44 = {features = ["r44"]} [dependencies] "gsl" = "*" "bioconductor-bioccheck" = "*" +"r-rcpparmadillo" = ">=15" "r-devtools" = "*" "r-rcmdcheck" = "*" "r-covr" = "*" diff --git a/.github/recipe/recipe.yaml b/.github/recipe/recipe.yaml index d04856cf..dc9245b3 100644 --- a/.github/recipe/recipe.yaml +++ b/.github/recipe/recipe.yaml @@ -20,8 +20,8 @@ build: requirements: build: - ${{ compiler('c') }} + - ${{ stdlib('c') }} - ${{ compiler('cxx') }} - - ${{ compiler('fortran') }} host: - bioconductor-iranges - bioconductor-qvalue diff --git a/.github/recipe/variant_r43.yaml b/.github/recipe/variant_r43.yaml index 21bfbbff..3973de52 100644 --- a/.github/recipe/variant_r43.yaml +++ b/.github/recipe/variant_r43.yaml @@ -1,2 +1,14 @@ +MACOSX_DEPLOYMENT_TARGET: + - '11.0' +c_stdlib_version: + - if: linux + then: 2.17 + - if: osx + then: 11.0 +c_stdlib: + - if: linux + then: sysroot + - if: osx + then: macosx_deployment_target r_base: - 4.3 diff --git a/.github/recipe/variant_r44.yaml b/.github/recipe/variant_r44.yaml index b69c4278..ccd3b536 100644 --- a/.github/recipe/variant_r44.yaml +++ b/.github/recipe/variant_r44.yaml @@ -1,2 +1,14 @@ +MACOSX_DEPLOYMENT_TARGET: + - '11.0' +c_stdlib_version: + - if: linux + then: 2.17 + - if: osx + then: 11.0 +c_stdlib: + - if: linux + then: sysroot + - if: osx + then: macosx_deployment_target r_base: - 4.4 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 549e6bd5..f70081a9 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -44,39 +44,7 @@ jobs: #- name: Run BiocCheck #run: pixi run bioccheck - - ci_osx-64: - name: osx-64 CI - runs-on: macos-13 - strategy: - fail-fast: false - matrix: - environment: ["r43", "r44"] - - steps: - - name: Checkout pull request branch - uses: actions/checkout@v4 - with: - fetch-depth: 0 - - name: Create TOML from recipe - run: .github/workflows/create_toml_from_yaml.sh ${GITHUB_WORKSPACE} - - - name: Setup pixi - uses: prefix-dev/setup-pixi@v0.9.2 - - - name: Run unit tests - run: pixi run --environment ${{ matrix.environment }} devtools_test - - #- name: Run R CMD CHECK - #run: pixi run rcmdcheck - - #- name: Run BiocCheckGitClone - #run: pixi run bioccheck_git_clone - - #- name: Run BiocCheck - #run: pixi run bioccheck - ci_osx-arm64: name: osx-arm64 CI runs-on: macos-14 @@ -84,7 +52,7 @@ jobs: fail-fast: false matrix: environment: ["r43", "r44"] - + steps: - name: Checkout pull request branch uses: actions/checkout@v4 diff --git a/DESCRIPTION b/DESCRIPTION index 3ece6a87..87e3c40b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -62,4 +62,4 @@ LinkingTo: RcppGSL NeedsCompilation: yes VignetteBuilder: knitr -RoxygenNote: 7.3.2 +RoxygenNote: 7.3.3