explicit use of BiocManager and remotes in R-CMD-check

          - {os: ubuntu-latest,   r: '3.4'}

    env:

      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

      R_KEEP_PKG_SOURCE: yes

          http-user-agent: ${{ matrix.config.http-user-agent }}

          use-public-rspm: true

      - uses: r-lib/actions/setup-r-dependencies@v1

        with:

          extra-packages: rcmdcheck

      - name: Install Remotes and BiocManager

      	run: |

      	  install.packages(c("remotes","BiocManager"))

      	  # set Bioc Goettingen mirror

      	  options("BioC_mirror"="https://ftp.gwdg.de/pub/misc/bioconductor")

      	shell: Rscript {0}

      - uses: r-lib/actions/check-r-package@v1

      - 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", "latest"))')

      - name: Show testthat output

        if: always()

        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true

        shell: bash

      - name: Install dependencies

        run: |

          BiocManager::install(c("BiocParallel", "GenomicRanges", "Gviz", "rtracklayer", "stageR", "tximport", "DESeq2", "GenomicFeatures"))

          remotes::install_deps(dependencies = TRUE)

          remotes::install_cran("rcmdcheck")

        shell: Rscript {0}

      - uses: r-lib/actions/check-r-package@v1

      - name: Upload check results

        if: failure()