From 1575be78b514896d82ed1ddc08d0615807cca16c Mon Sep 17 00:00:00 2001
From: Daena Rys <rysdaena8@gmail.com>
Date: Wed, 26 Jun 2024 06:51:25 +0300
Subject: [PATCH] remove old workflow

Signed-off-by: Daena Rys <rysdaena8@gmail.com>
---
 .github/workflows/check-bioc.yml | 328 -------------------------------
 1 file changed, 328 deletions(-)
 delete mode 100644 .github/workflows/check-bioc.yml

diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
deleted file mode 100644
index 717020e..0000000
--- a/.github/workflows/check-bioc.yml
+++ /dev/null
@@ -1,328 +0,0 @@
-## 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: 'false'
-  run_covr: 'false'
-  run_pkgdown: 'false'
-  has_RUnit: 'false'
-  cache-version: 'cache-v1'
-  run_docker: 'false'
-
-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: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.2', bioc: '3.16'}
-          - { os: windows-latest, r: '4.2', bioc: '3.16'}
-          ## Check https://github.com/r-lib/actions/tree/master/examples
-          ## for examples using the http-user-agent
-    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@v3
-
-      ## 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@v2
-        with:
-          r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
-
-      ## 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@v2
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-        shell: Rscript {0}
-
-      - name: Restore R package cache
-        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
-        uses: actions/cache@v3
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
-
-      - name: Cache R packages on Linux
-        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
-        uses: actions/cache@v3
-        with:
-          path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
-
-      - 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"
-          sudo apt-get install -y libcurl4-openssl-dev libglpk-dev  
-
-      - 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" >> $GITHUB_ENV
-
-          ## Required to install magick as noted at
-          ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
-          brew install imagemagick@6
-
-          ## For textshaping, required by ragg, and required by pkgdown
-          brew install harfbuzz fribidi
-
-          ## For installing usethis's dependency gert
-          brew install libgit2
-
-          ## Required for tcltk
-          brew install xquartz --cask
-
-      - name: Install Windows system dependencies
-        if: runner.os == 'Windows'
-        run: |
-          ## Edit below if you have any Windows system dependencies
-        shell: Rscript {0}
-
-      - name: Install BiocManager
-        run: |
-          message(paste('****', Sys.time(), 'installing BiocManager ****'))
-          remotes::install_cran("BiocManager")
-        shell: Rscript {0}
-
-      - name: Set BiocVersion
-        run: |
-          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
-        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.
-          install.packages("matrixStats", repos = "https://cran.rstudio.com/")
-          BiocManager::install("cran/vegan")
-          BiocManager::install("fionarhuang/TreeSummarizedExperiment")
-          BiocManager::install("stan-dev/rstantools")
-          BiocManager::install("cran/reldist")
-          BiocManager::install("cran/densEstBayes")
-
-          ## Set the repos source depending on the OS
-          ## Alternatively use https://storage.googleapis.com/bioconductor_docker/packages/
-          ## though based on https://bit.ly/bioc2021-package-binaries
-          ## the Azure link will be the main one going forward.
-          gha_repos <- if(
-              .Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin"
-          ) c(
-              "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.16/bioc",
-              BiocManager::repositories()
-              ) else BiocManager::repositories()
-
-          ## For running the checks
-          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
-          install.packages(c("rcmdcheck", "BiocCheck"), repos = gha_repos)
-
-          ## Pass #1 at installing dependencies
-          ## This pass uses AnVIL-powered fast binaries
-          ## details at https://github.com/nturaga/bioc2021-bioconductor-binaries
-          ## The speed gains only apply to the docker builds.
-          message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
-          remotes::install_local(dependencies = TRUE, repos = gha_repos, build_vignettes = FALSE, upgrade = TRUE)
-        continue-on-error: true
-        shell: Rscript {0}
-
-      - name: Install dependencies pass 2
-        run: |
-          ## Pass #2 at installing dependencies
-          ## This pass does not use AnVIL and will thus update any packages
-          ## that have seen been updated in Bioconductor
-          message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
-          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
-        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)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
-
-      - name: Run CMD check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-          DISPLAY: 99.0
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(
-              args = c("--no-manual", "--no-vignettes", "--timings"),
-              build_args = c("--no-manual", "--keep-empty-dirs", "--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
-        env:
-          DISPLAY: 99.0
-        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: Build pkgdown site
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
-        shell: Rscript {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: Install deploy dependencies
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
-        run: |
-          apt-get update && apt-get -y install rsync
-
-      - name: Deploy pkgdown site to GitHub pages
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
-        uses: JamesIves/github-pages-deploy-action@releases/v4
-        with:
-          clean: false
-          branch: gh-pages
-          folder: docs
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@master
-        with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-results
-          path: check
-
-        ## Note that DOCKER_PASSWORD is really a token for your dockerhub
-        ## account, not your actual dockerhub account password.
-        ## This comes from
-        ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html#6-add-secrets-to-github-repo
-        ## Check https://github.com/docker/build-push-action/tree/releases/v1
-        ## for more details.
-      - uses: docker/build-push-action@v1
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' "
-        with:
-          username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-          repository: microbiome/miatime
-          tag_with_ref: true
-          tag_with_sha: true
-          tags: latest