diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 194dbd4..22b8e64 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -11,7 +11,7 @@ # ======================================================== # on: [push, pull_request] -name: package-build +name: R-CMD-check # ======================================================== # # Determine actions to take # @@ -28,76 +28,32 @@ jobs: - {os: windows-latest, r: 'release'} - {os: macOS-latest, r: 'release'} - {os: ubuntu-latest, r: 'release'} - - {os: ubuntu-latest, r: 'devel'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes steps: - - name: Retrieving current month - if: runner.os == 'Linux' - run: echo "CURRENT_MONTH=$(date +%m)" >> $GITHUB_ENV - - # Checking out code -------------------------------------- # - name: Checking out the repository - uses: actions/checkout@v2 + uses: actions/checkout@v3 + + - name: Setting up pandoc + uses: r-lib/actions/setup-pandoc@v2 - # Setting up environment --------------------------------- # - name: Setting up R ${{ matrix.config.r }} on ${{ matrix.config.os }} - uses: r-lib/actions/setup-r@v1 + uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true - # Installing Pandoc -------------------------------------- # - - name: Installing Pandoc - uses: r-lib/actions/setup-pandoc@v1 - - # Querying dependencies ---------------------------------- # - name: Querying dependencies - run: | - install.packages("remotes") - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - # Restoring R package cache ------------------------------ # - - name: Restoring R package cache - 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- + extra-packages: any::rcmdcheck + needs: check - # Installing system dependencies ------------------------- # - - name: Installing system dependencies - if: runner.os == 'Linux' - run: | - sudo apt-get install libcurl4-openssl-dev - while read -r cmd - do - eval sudo $cmd - done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') - - # Installing package dependencies ------------------------ # - - name: Installing package dependencies - if: ${{ env.CURRENT_MONTH < 4 || env.CURRENT_MONTH > 10 }} - run: | - remotes::install_cran(c("rcmdcheck", "BiocManager")) - BiocManager::install("GenomicRanges") - BiocManager::install("Rsamtools") - remotes::install_deps(dependencies = TRUE) - shell: Rscript {0} - - # Checking package --------------------------------------- # - name: Checking package - if: ${{ env.CURRENT_MONTH < 4 || env.CURRENT_MONTH > 10 }} - env: - _R_CHECK_CRAN_INCOMING_REMOTE_: false - run: | - options(crayon.enabled = TRUE) - rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") - shell: Rscript {0} - - # Uploading check results -------------------------------- # - - name: Uploading 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 2ce1513..557b643 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: rBAPS Title: Bayesian Analysis of Population Structure -Version: 0.0.0.9010 +Version: 0.0.0.9011 Date: 2020-11-09 Authors@R: c(