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+## Read more about GitHub actions the features of this GitHub Actions workflow

+## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action

+##

+## For more details, check the biocthis developer notes vignette at

+## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html

+##

+## You can add this workflow to other packages using:

+## > biocthis::use_bioc_github_action()

+##

+## Using GitHub Actions exposes you to many details about how R packages are

+## compiled and installed in several operating system.s

+### If you need help, please follow the steps listed at

+## https://github.com/r-lib/actions#where-to-find-help

+##

+## If you found an issue specific to biocthis's GHA workflow, please report it

+## with the information that will make it easier for others to help you.

+## Thank you!

+

+## Acronyms:

+## * GHA: GitHub Action

+## * OS: operating system

+

+on:

+  push:

+  pull_request:

+

+name: R-CMD-check-bioc

+

+## These environment variables control whether to run GHA code later on that is

+## specific to testthat, covr, and pkgdown.

+##

+## If you need to clear the cache of packages, update the number inside

+## cache-version as discussed at https://github.com/r-lib/actions/issues/86.

+## Note that you can always run a GHA test without the cache by using the word

+## "/nocache" in the commit message.

+env:

+  has_testthat: 'true'

+  run_covr: 'true'

+  run_pkgdown: 'true'

+  has_RUnit: 'false'

+  has_BiocCheck: 'false'

+  cache-version: 'cache-v1'

+

+jobs:

+  build-check:

+    runs-on: ${{ matrix.config.os }}

+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})

+    container: ${{ matrix.config.cont }}

+    ## Environment variables unique to this job.

+

+    strategy:

+      fail-fast: false

+      matrix:

+        config:

+          - { os: ubuntu-latest, r: 'devel', bioc: '3.15', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }

+          - { os: macOS-latest, r: 'devel', bioc: '3.15'}

+          - { os: windows-latest, r: 'devel', bioc: '3.15'}

+    env:

+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

+      RSPM: ${{ matrix.config.rspm }}

+      NOT_CRAN: true

+      TZ: UTC

+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

+

+    steps:

+

+      ## Set the R library to the directory matching the

+      ## R packages cache step further below when running on Docker (Linux).

+      - name: Set R Library home on Linux

+        if: runner.os == 'Linux'

+        run: |

+          mkdir /__w/_temp/Library

+          echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile

+

+      ## Most of these steps are the same as the ones in

+      ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml

+      ## If they update their steps, we will also need to update ours.

+      - name: Checkout Repository

+        uses: actions/checkout@v2

+

+      ## R is already included in the Bioconductor docker images

+      - name: Setup R from r-lib

+        if: runner.os != 'Linux'

+        uses: r-lib/actions/setup-r@master

+        with:

+          r-version: ${{ matrix.config.r }}

+

+      ## pandoc is already included in the Bioconductor docker images

+      - name: Setup pandoc from r-lib

+        if: runner.os != 'Linux'

+        uses: r-lib/actions/setup-pandoc@master

+

+      - name: Query dependencies

+        run: |

+          install.packages('remotes')

+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)

+        shell: Rscript {0}

+

+      - name: Cache R packages

+        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"

+        uses: actions/cache@v2

+        with:

+          path: ${{ env.R_LIBS_USER }}

+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}

+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-

+

+      - name: Cache R packages on Linux

+        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "

+        uses: actions/cache@v2

+        with:

+          path: /home/runner/work/_temp/Library

+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}

+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-

+

+      - name: Install Linux system dependencies

+        if: runner.os == 'Linux'

+        run: |

+          sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')

+          echo $sysreqs

+          sudo -s eval "$sysreqs"

+

+      - name: Install macOS system dependencies

+        if: matrix.config.os == 'macOS-latest'

+        run: |

+          ## Enable installing XML from source if needed

+          brew install libxml2

+          echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV

+

+          ## Required to install magick as noted at

+          ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2

+          brew install imagemagick@6

+

+          ## For textshaping, required by ragg, and required by pkgdown

+          brew install harfbuzz fribidi

+

+          ## For installing usethis's dependency gert

+          brew install libgit2

+

+          ## required for ncdf4

+          ## brew install netcdf ## Does not work as it is compiled with gcc

+          ## Use pre-compiled libraries from https://mac.r-project.org/libs-4/

+          curl -O https://mac.r-project.org/libs-4/netcdf-4.7.4-darwin.17-x86_64.tar.gz

+          tar fvxzm netcdf-4.7.4-darwin.17-x86_64.tar.gz -C /

+          rm netcdf-4.7.4-darwin.17-x86_64.tar.gz

+          curl -O https://mac.r-project.org/libs-4/hdf5-1.12.0-darwin.17-x86_64.tar.gz

+          tar fvxzm hdf5-1.12.0-darwin.17-x86_64.tar.gz -C /

+          rm hdf5-1.12.0-darwin.17-x86_64.tar.gz

+          curl -O https://mac.r-project.org/libs-4/szip-2.1.1-darwin.17-x86_64.tar.gz

+          tar fvxzm szip-2.1.1-darwin.17-x86_64.tar.gz -C /

+          rm szip-2.1.1-darwin.17-x86_64.tar.gz

+

+      - name: Install Windows system dependencies

+        if: runner.os == 'Windows'

+        run: |

+          ## Edit below if you have any Windows system dependencies

+        shell: Rscript {0}

+

+      - name: Install BiocManager

+        run: |

+          message(paste('****', Sys.time(), 'installing BiocManager ****'))

+          remotes::install_cran("BiocManager")

+        shell: Rscript {0}

+

+      - name: Set BiocVersion

+        run: |

+          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)

+        shell: Rscript {0}

+

+      - name: Install dependencies pass 1

+        run: |

+          ## Try installing the package dependencies in steps. First the local

+          ## dependencies, then any remaining dependencies to avoid the

+          ## issues described at

+          ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html

+          ## https://github.com/r-lib/remotes/issues/296

+          ## Ideally, all dependencies should get installed in the first pass.

+

+          ## Pass #1 at installing dependencies

+          message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))

+          remotes::install_local(dependencies = TRUE, repos =

+          BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)

+

+          BiocManager::install(c("rmarkdown", "BiocStyle"))

+        continue-on-error: true

+        shell: Rscript {0}

+

+      - name: Install dependencies pass 2

+        run: |

+          ## Pass #2 at installing dependencies

+          message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))

+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)

+

+          ## Manually install packages that seem to be skipped.

+          message(paste('****', Sys.time(), 'force installation of selected packages  ****'))

+          BiocManager::install(c("faahKO"))

+          BiocManager::install("lgatto/ProtGenerics")

+          BiocManager::install("lgatto/MSnbase")

+          ## BiocManager::install("sneumann/mzR")

+          BiocManager::install("RforMassSpectrometry/Spectra")

+          BiocManager::install("RforMassSpectrometry/MsBackendMgf")

+          BiocManager::install("magick")

+

+          ## For running the checks

+          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))

+          remotes::install_cran("rcmdcheck")

+          BiocManager::install(c("BiocCheck", "DBI"))

+        shell: Rscript {0}

+

+      - name: Install BiocGenerics

+        if:  env.has_RUnit == 'true'

+        run: |

+          ## Install BiocGenerics

+          BiocManager::install("BiocGenerics")

+        shell: Rscript {0}

+

+      - name: Install covr

+        if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'

+        run: |

+          remotes::install_cran("covr")

+        shell: Rscript {0}

+

+      - name: Install pkgdown

+        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'

+        run: |

+          remotes::install_github("r-lib/pkgdown")

+        shell: Rscript {0}

+

+      - name: Session info

+        run: |

+          options(width = 100)

+          pkgs <- installed.packages()[, "Package"]

+          sessioninfo::session_info(pkgs, include_base = TRUE)

+        shell: Rscript {0}

+

+      - name: Run CMD check

+        env:

+          _R_CHECK_CRAN_INCOMING_: false

+        run: |

+          rcmdcheck::rcmdcheck(

+              args = c("--no-build-vignettes", "--no-manual", "--timings"),

+              build_args = c("--no-manual", "--no-resave-data"),

+              error_on = "warning",

+              check_dir = "check"

+          )

+        shell: Rscript {0}

+

+      ## Might need an to add this to the if:  && runner.os == 'Linux'

+      - name: Reveal testthat details

+        if:  env.has_testthat == 'true'

+        run: find . -name testthat.Rout -exec cat '{}' ';'

+

+      - name: Run RUnit tests

+        if:  env.has_RUnit == 'true'

+        run: |

+          BiocGenerics:::testPackage()

+        shell: Rscript {0}

+

+      - name: Run BiocCheck

+        if:  env.has_BiocCheck == 'true'

+        run: |

+          BiocCheck::BiocCheck(

+              dir('check', 'tar.gz$', full.names = TRUE),

+              `quit-with-status` = TRUE,

+              `no-check-R-ver` = TRUE,

+              `no-check-bioc-help` = TRUE

+          )

+        shell: Rscript {0}

+

+      - name: Test coverage

+        if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'

+        run: |

+          covr::codecov()

+        shell: Rscript {0}

+

+      - name: Install package

+        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'

+        run: R CMD INSTALL .

+

+      - name: Deploy package

+        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'

+        run: |

+          git config --local user.email "actions@github.com"

+          git config --local user.name "GitHub Actions"

+          Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"

+        shell: bash {0}

+        ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)

+        ## at least one locally before this will work. This creates the gh-pages

+        ## branch (erasing anything you haven't version controlled!) and

+        ## makes the git history recognizable by pkgdown.

+

+      - name: Upload check results

+        if: failure()

+        uses: actions/upload-artifact@master

+        with:

+          name: ${{ runner.os }}-biocversion-devel-r-devel-results

+          path: check