diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..14159b7 --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,50 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, master] + pull_request: + branches: [main, master] + +name: R-CMD-check + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: macos-latest, r: 'release'} + - {os: windows-latest, r: 'release'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes + + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/README.Rmd b/README.Rmd index af1fbea..7144cf4 100644 --- a/README.Rmd +++ b/README.Rmd @@ -18,6 +18,7 @@ knitr::opts_chunk$set( [![pkgdown](https://github.com/rmgpanw/gtexr/actions/workflows/pkgdown.yaml/badge.svg)](https://github.com/rmgpanw/gtexr/actions/workflows/pkgdown.yaml) [![Codecov test coverage](https://codecov.io/gh/rmgpanw/gtexr/branch/main/graph/badge.svg)](https://app.codecov.io/gh/rmgpanw/gtexr?branch=main) +[![R-CMD-check](https://github.com/rmgpanw/gtexr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rmgpanw/gtexr/actions/workflows/R-CMD-check.yaml) The goal of gtexr is to provide a convenient R interface to the [GTEx Portal API V2](https://gtexportal.org/api/v2/redoc#tag/GTEx-Portal-API-Info). diff --git a/README.md b/README.md index 2f3c070..6c1f3c9 100644 --- a/README.md +++ b/README.md @@ -8,6 +8,7 @@ [![pkgdown](https://github.com/rmgpanw/gtexr/actions/workflows/pkgdown.yaml/badge.svg)](https://github.com/rmgpanw/gtexr/actions/workflows/pkgdown.yaml) [![Codecov test coverage](https://codecov.io/gh/rmgpanw/gtexr/branch/main/graph/badge.svg)](https://app.codecov.io/gh/rmgpanw/gtexr?branch=main) +[![R-CMD-check](https://github.com/rmgpanw/gtexr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rmgpanw/gtexr/actions/workflows/R-CMD-check.yaml) The goal of gtexr is to provide a convenient R interface to the [GTEx @@ -43,8 +44,7 @@ Retrieve eQTL genes for whole blood tissue: ``` r get_eqtl_genes("Whole_Blood") #> Warning: ! Total number of items (12360) exceeds maximum page size (250). -#> ℹ Try increasing `itemsPerPage`, or set this to `NULL` to return all available -#> items in one page. +#> ℹ Try increasing `itemsPerPage`. #> #> ── Paging info ───────────────────────────────────────────────────────────────── #> • numberOfPages = 50