diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 28776d4..a3ac618 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -1,14 +1,10 @@ -# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. -# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions +# 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 + branches: [main, master] pull_request: - branches: - - main - - master + branches: [main, master] name: R-CMD-check @@ -22,66 +18,32 @@ jobs: fail-fast: false matrix: config: + - {os: macos-latest, r: 'release'} - {os: windows-latest, r: 'release'} - - {os: macOS-latest, r: 'release'} - - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - #- {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - RSPM: ${{ matrix.config.rspm }} GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true - - uses: r-lib/actions/setup-pandoc@v1 - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Cache R packages - if: runner.os != 'Windows' - uses: actions/cache@v2 + - uses: r-lib/actions/setup-r-dependencies@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' - run: | - while read -r cmd - do - eval sudo $cmd - done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') - - - name: Install dependencies - run: | - remotes::install_cran("rcmdcheck") - remotes::install_cran("BiocManager") - BiocManager::install(update=TRUE, ask=FALSE) - BiocManager::install(remotes::dev_package_deps(dependencies = TRUE)[["package"]]) - remotes::install_github("satijalab/seurat-data") - shell: Rscript {0} - - - name: Check - env: - _R_CHECK_CRAN_INCOMING_REMOTE_: false - run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") - shell: Rscript {0} + extra-packages: any::rcmdcheck + needs: check - - name: Upload check results - if: failure() - uses: actions/upload-artifact@main + - uses: r-lib/actions/check-r-package@v2 with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check + upload-snapshots: true diff --git a/DESCRIPTION b/DESCRIPTION index a68aacc..2f53183 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: Canek Type: Package Title: Batch Correction of Single Cell Transcriptome Data -Version: 0.2.2 +Version: 0.2.3 Authors@R: c( person("Martin", "Loza", email = "martin.loza.lopez@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3342-2643")), diff --git a/README.Rmd b/README.Rmd index 487c911..b321048 100644 --- a/README.Rmd +++ b/README.Rmd @@ -22,7 +22,7 @@ knitr::opts_chunk$set( # Canek -[![R-CMD-check](https://github.com/MartinLoza/Canek/workflows/R-CMD-check/badge.svg)](https://github.com/MartinLoza/Canek/actions) +[![R-CMD-check](https://github.com/MartinLoza/Canek/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/MartinLoza/Canek/actions/workflows/R-CMD-check.yaml) [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/Canek)](https://cran.r-project.org/package=Canek) [![CRAN Downloads](https://cranlogs.r-pkg.org/badges/Canek)](https://cran.r-project.org/package=Canek) [![CRAN Downloads](https://cranlogs.r-pkg.org/badges/grand-total/Canek)](https://cran.r-project.org/package=Canek) diff --git a/README.md b/README.md index 26ee631..a21158a 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ -[![R-CMD-check](https://github.com/MartinLoza/Canek/workflows/R-CMD-check/badge.svg)](https://github.com/MartinLoza/Canek/actions) +[![R-CMD-check](https://github.com/MartinLoza/Canek/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/MartinLoza/Canek/actions/workflows/R-CMD-check.yaml) [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/Canek)](https://cran.r-project.org/package=Canek) [![CRAN Downloads](https://cranlogs.r-pkg.org/badges/Canek)](https://cran.r-project.org/package=Canek) @@ -102,6 +102,6 @@ If you use Canek in your research please cite our work using: Loza M, Teraguchi S, Standley D, Diez D (2022). “Unbiased integration of single cell transcriptome replicates.” *NAR Genomics and -Bioinformatics*, *4*(1), lqac022. doi: 10.1093/nargab/lqac022 (URL: -), \\>. +Bioinformatics*, *4*(1), lqac022. +, +.