@@ -6,9 +6,6 @@

 ##

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

 ## > biocthis::use_bioc_github_action()

-## or

-## > usethis::use_github_action("check-bioc", "https://bit.ly/biocthis_gha", "check-bioc.yml")

-## without having to install biocthis.

 ##

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

 ## compiled and installed in several operating system.s

@@ -19,25 +16,13 @@

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

 ## Thank you!

-

-

 ## Acronyms:

 ## * GHA: GitHub Action

 ## * OS: operating system

-## Specify which branches you want this GHA to run on.

-## Bioconductor uses branches such as master (bioc-devel) and RELEASE_* like

-## RELEASE_3_10. For more details check

-## http://bioconductor.org/developers/how-to/git/

 on:

   push:

-    branches:

-      - master

-      - 'RELEASE_*'

   pull_request:

-    branches:

-      - master

-      - 'RELEASE_*'

 name: R-CMD-check-bioc

@@ -51,283 +36,58 @@ name: R-CMD-check-bioc

 env:

   has_testthat: 'true'

   run_covr: 'true'

-  run_pkgdown: 'false'

+  run_pkgdown: 'true'

   has_RUnit: 'false'

   cache-version: 'cache-v1'

 jobs:

-  ## This first job uses the GitHub repository branch name to infer what

-  ## version of Bioconductor we will be working on.

-  define-docker-info:

-    runs-on: ubuntu-latest

-    outputs:

-      imagename: ${{ steps.findinfo.outputs.imagename }}

-      biocversion: ${{ steps.findinfo.outputs.biocversion }}

-    steps:

-      - id: findinfo

-        run: |

-          ## Find what Bioconductor RELEASE branch we are working on

-          ## otherwise, assume we are working on bioc-devel.

-          if echo "$GITHUB_REF" | grep -q "RELEASE_"; then

-              biocversion="$(basename -- $GITHUB_REF)"

-          else

-              biocversion="devel"

-          fi

-          ## Define the image name and print the information

-          imagename="bioconductor/bioconductor_docker:${biocversion}"

-          echo $imagename

-          echo $biocversion

-

-          ## Save the information for the next job

-          echo "::set-output name=imagename::${imagename}"

-          echo "::set-output name=biocversion::${biocversion}"

-

-  R-CMD-check-bioc:

-    ## This job then checks the R package using the Bioconductor docker that

-    ## was defined by the previous job. This job will determine what version of

-    ## R to use for the macOS and Windows builds on the next job.

-    runs-on: ubuntu-latest

-    needs: define-docker-info

-

-    ## Name shown on the GHA log

-    name: ubuntu-latest (r-biocdocker bioc-${{ needs.define-docker-info.outputs.biocversion }})

-

-    ## Information used by the next job that will run on macOS and Windows

-    outputs:

-      rversion: ${{ steps.findrversion.outputs.rversion }}

-      biocversionnum: ${{ steps.findrversion.outputs.biocversionnum }}

-

+  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: '4.0', bioc: '3.12', cont: "bioconductor/bioconductor_docker:RELEASE_3_12", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }

+          - { os: macOS-latest, r: '4.0', bioc: '3.12'}

+          - { os: windows-latest, r: '4.0', bioc: '3.12'}

     env:

       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

-      TZ: UTC

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

       NOT_CRAN: true

+      TZ: UTC

       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

-    ## The docker container to use. Note that we link a directory on the GHA

-    ## runner to a docker directory, such that we can then cache the linked

-    ## directory. This directory will contain the R packages used.

-    container:

-      image: ${{ needs.define-docker-info.outputs.imagename }}

-      volumes:

-        - /home/runner/work/_temp/Library:/usr/local/lib/R/host-site-library

-

     steps:

-      - name: Install latest git

+

+      ## 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: |

-          ## git version provided

-          git --version

-          ## to be able to install software properties

-          sudo apt-get update -y

-          ## to be able to use add-apt-repository

-          sudo apt-get install software-properties-common -y

-          ## to use stable releases of git that are already in a PPA at

-          ## https://launchpad.net/~git-core/+archive/ubuntu/candidate

-          sudo add-apt-repository ppa:git-core/candidate -y

-          ## Update

-          sudo apt-get update -y

-          ## Upgrade git and other tools

-          sudo apt-get upgrade -y

-          ## latest git version

-          git --version

-        shell: bash {0}

-      ## Related to https://github.com/rocker-org/rocker-versioned2/issues/52

+          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.

-      - uses: actions/checkout@v2

-

-      - name: Query dependencies

-        run: |

-          install.packages('remotes')

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

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

-          remotes::install_cran("BiocManager")

-        shell: Rscript {0}

-

-      ## Find the corresponding R version based on the Bioconductor version

-      ## to use for the macOS and Windows checks by the next GHA job

-      - id: findrversion

-        name: Find Bioc and R versions

-        run: |

-          ## Find what branch we are working on

-          if echo "$GITHUB_REF" | grep -q "master"; then

-              biocversion="devel"

-          elif echo "$GITHUB_REF" | grep -q "RELEASE_"; then

-              biocversion="release"

-          fi

-

-          ## Define the R and Bioconductor version numbers

-          biocversionnum=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == '${biocversion}')[, 'Bioc']; cat(as.character(res))")

-          rversion=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == '${biocversion}')[, 'R']; cat(as.character(res))")

-

-          ## Print the results

-          echo $biocversion

-          echo $biocversionnum

-          echo $rversion

-

-          ## Save the info for the next job

-          echo "::set-output name=rversion::${rversion}"

-          echo "::set-output name=biocversionnum::${biocversionnum}"

-        shell:

-          bash {0}

-

-      - name: Cache R packages

-        if: "!contains(github.event.head_commit.message, '/nocache')"

-        uses: actions/cache@v1

-        with:

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

-          key: ${{ env.cache-version }}-${{ runner.os }}-biocdocker-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-${{ hashFiles('.github/depends.Rds') }}

-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocdocker-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-

-

-      - name: Install dependencies

-        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 ****'))

-          local_deps <- remotes::local_package_deps(dependencies = TRUE)

-          deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())

-          BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]])

-

-          ## Pass #2 at installing dependencies

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

-          deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())

-          BiocManager::install(deps$package[deps$diff != 0])

-

-          ## For running the checks

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

-          remotes::install_cran("rcmdcheck")

-          BiocManager::install("BiocCheck")

-        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: 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}

-

-      - 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: |

-          ## Install BiocGenerics

-          BiocManager::install("BiocGenerics")

-          BiocGenerics:::testPackage()

-        shell: Rscript {0}

-

-      - name: BiocCheck

-        run: |

-          ## This syntax works on Windows as well as other OS

-          ## plus it doesn't break the GHA workflow in case BiocCheck finds

-          ## an error (for example, the package is bigger than the maximum

-          ## allowed size). We want the rest of the GHA to proceed even if

-          ## there is a BiocCheck error in order to see the full output and

-          ## run the tests on all operating systems.

-          BiocCheck::BiocCheck(dir('check', 'tar.gz$', full.names = TRUE), `no-check-R-ver` = TRUE, `no-check-bioc-help` = TRUE)

-          ## For more options check http://bioconductor.org/packages/release/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html

-        shell: Rscript {0}

-

-      - name: Install covr

-        if: github.ref == 'refs/heads/master' && env.run_covr == 'true'

-        run: |

-          remotes::install_cran("covr")

-        shell: Rscript {0}

-

-      - name: Test coverage

-        if: github.ref == 'refs/heads/master' && env.run_covr == 'true'

-        run: |

-          covr::codecov()

-        shell: Rscript {0}

-

-      - name: Install pkgdown

-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true'

-        run: |

-          remotes::install_cran("pkgdown")

-        shell: Rscript {0}

-

-      - name: Install package

-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true'

-        run: R CMD INSTALL .

-

-      - name: Deploy package

-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true'

-        run: |

-          git config --local user.email "action@github.com"

-          git config --local user.name "GitHub Action"

-          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: ${{ runner.os }}-biocdocker-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-results

-          path: check

-

-  ## Run R CMD check on both macOS and Windows. You can also run the

-  ## tests on Linux outside of the Bioconductor docker environment. If you

-  ## do so, you might have to install system dependencies on Linux

-  ## Bioconductor's docker includes all the system dependencies required by

-  ## Bioconductor packages and their dependencies (which includes many CRAN

-  ## dependencies as well, thus making this workflow useful beyond Bioconductor)

-  R-CMD-check-r-lib:

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

-    needs: [define-docker-info, R-CMD-check-bioc]

-

-    name: ${{ matrix.config.os }} (r-${{ needs.R-CMD-check-bioc.outputs.rversion }} bioc-${{ needs.define-docker-info.outputs.biocversion }})

-

-    strategy:

-      fail-fast: false

-      matrix:

-        config:

-          ## Comment/Un-comment in case you also want to run other versions

-          - {os: windows-latest}

-          - {os: macOS-latest}

-          # - {os: ubuntu-16.04, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}

-

-    env:

-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

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

-      BIOCVERSIONNUM: ${{ needs.R-CMD-check-bioc.outputs.biocversionnum }}

-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

-

-    steps:

-      - uses: actions/checkout@v2

+      - 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: ${{ needs.R-CMD-check-bioc.outputs.rversion }}

+          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

@@ -337,20 +97,26 @@ jobs:

         shell: Rscript {0}

       - name: Cache R packages

-        if: "!contains(github.event.head_commit.message, '/nocache')"

-        uses: actions/cache@v1

+        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 }}-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ needs.R-CMD-check-bioc.outputs.rversion }}-bioc-${{ needs.define-docker-info.outputs.biocversion }}-${{ hashFiles('.github/depends.Rds') }}

-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ needs.R-CMD-check-bioc.outputs.rversion }}-bioc-${{ needs.define-docker-info.outputs.biocversion }}-

+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }}

+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-

+

+      - 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-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }}

+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-

       - name: Install Linux system dependencies

         if: runner.os == 'Linux'

-        env:

-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc

         run: |

-          Rscript -e "remotes::install_github('r-hub/sysreqs')"

-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")

+          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

@@ -358,12 +124,18 @@ jobs:

         run: |

           ## Enable installing XML from source if needed

           brew install libxml2

-          echo "::set-env name=XML_CONFIG::/usr/local/opt/libxml2/bin/xml2-config"

+          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

+

+          ## See if this helps get RCurl installed

+          brew uninstall curl

+

       - name: Install Windows system dependencies

         if: runner.os == 'Windows'

         run: |

@@ -378,7 +150,7 @@ jobs:

       - name: Set BiocVersion

         run: |

-          BiocManager::install(version = Sys.getenv('BIOCVERSIONNUM'), ask = FALSE)

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

         shell: Rscript {0}

       - name: Install dependencies

@@ -390,16 +162,18 @@ jobs:

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

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

+          ## Temporary for now due to https://github.com/ropensci/RefManageR/issues/79

+          remotes::install_github("ropensci/bibtex")

+          remotes::install_github("ropensci/RefManageR")

+          remotes::install_github("cboettig/knitcitations")

+

           ## Pass #1 at installing dependencies

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

-          local_deps <- remotes::local_package_deps(dependencies = TRUE)

-          deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())

-          BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]])

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

           ## Pass #2 at installing dependencies

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

-          deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())

-          BiocManager::install(deps$package[deps$diff != 0])

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

           ## For running the checks

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

@@ -407,6 +181,25 @@ jobs:

           BiocManager::install("BiocCheck")

         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_cran("pkgdown")

+        shell: Rscript {0}

+

       - name: Session info

         run: |

           options(width = 100)

@@ -414,7 +207,7 @@ jobs:

           sessioninfo::session_info(pkgs, include_base = TRUE)

         shell: Rscript {0}

-      - name: Check

+      - name: Run CMD check

         env:

           _R_CHECK_CRAN_INCOMING_: false

         run: |

@@ -426,6 +219,7 @@ jobs:

           )

         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 '{}' ';'

@@ -433,26 +227,45 @@ jobs:

       - name: Run RUnit tests

         if:  env.has_RUnit == 'true'

         run: |

-          ## Install BiocGenerics

-          BiocManager::install("BiocGenerics")

           BiocGenerics:::testPackage()

         shell: Rscript {0}

-      - name: BiocCheck

+      - name: Run BiocCheck

         run: |

-          ## This syntax works on Windows as well as other OS

-          ## plus it doesn't break the GHA workflow in case BiocCheck finds

-          ## an error (for example, the package is bigger than the maximum

-          ## allowed size). We want the rest of the GHA to proceed even if

-          ## there is a BiocCheck error in order to see the full output and

-          ## run the tests on all operating systems.

-          BiocCheck::BiocCheck(dir('check', 'tar.gz$', full.names = TRUE), `no-check-R-ver` = TRUE, `no-check-bioc-help` = TRUE)

-          ## For more options check http://bioconductor.org/packages/release/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html

+          BiocCheck::BiocCheck(

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

+              `quit-with-status` = TRUE,

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

+              `no-check-pkg-size` = 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: ${{ runner.os }}-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ needs.R-CMD-check-bioc.outputs.rversion }}-bioc-${{ needs.define-docker-info.outputs.biocversion }}-results

+          name: ${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-results

           path: check