clean up

.github/alt/OS-check_alt.yaml

@@ -0,0 +1,103 @@
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+name: OS-check
+
+jobs:
+  OS-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'release'}
+          - {os: macOS-latest,   r: 'oldrel'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-16.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_TOKEN: ${{ secrets.GHTOKEN2 }}
+      GITHUB_PAT: ${{ secrets.GHTOKEN2 }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps("scRNASeq/",dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        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-
+
+      # - name: Install XQuartz on macOS
+      #   if: runner.os == 'macOS'
+      #   run: brew cask install xquartz
+
+      - name: Install System Dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y glpk-utils
+          sudo apt-get install -y libcurl4-openssl-dev
+        shell: bash {0}
+
+      - name: Install XML
+        if: runner.os == 'Windows'
+        run: |
+          install.packages("XML", type = "source")
+        shell: Rscript {0}
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps("scRNASeq/",dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+          remotes::install_cran("BiocManager")
+          BiocManager::install("rmarkdown")
+          BiocManager::install("devtools")
+          BiocManager::install("RockefellerUniversity/compileCourses",subdir="compileCourses")
+        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: Install package
+        if: github.ref == 'refs/heads/master' 
+        run: |
+          devtools::install("scRNASeq/",dependencies = TRUE,quick = TRUE)
+        shell: Rscript {0}
+
+      - name: CompileCourse
+        run: |
+          require(compileCourses)
+          compileCourses::compileSingleCourseMaterial(repo="RockefellerUniversity",subdir="scRNASeq",branch="master")
+        shell: Rscript {0}

.github/alt/compilation-check_alt.yml

@@ -0,0 +1,240 @@
+## 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()
+## 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
+### 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
+
+## 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:
+      - main
+      - 'RELEASE_*'
+  pull_request:
+    branches:
+      - main
+      - 'RELEASE_*'
+
+name: compilation-check
+
+## 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'
+  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 }}
+    steps:
+      - id: findinfo
+        run: |
+          ## Define the image name and print the information
+          imagename="bioconductor/bioconductor_docker"
+          echo $imagename
+          ## Save the information for the next job
+          echo "::set-output name=imagename::${imagename}"
+  compilation-check:
+    ## 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
+
+    ## Information used by the next job that will run on macOS and Windows
+    outputs:
+      rversion: ${{ steps.findrversion.outputs.rversion }}
+      biocversionnum: ${{ steps.findrversion.outputs.biocversionnum }}
+
+    ## Environment variables unique to this job.
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      TZ: UTC
+      NOT_CRAN: true
+      GITHUB_TOKEN: ${{ secrets.GHTOKEN2 }}
+      GITHUB_PAT: ${{ secrets.GHTOKEN2 }}
+
+    ## 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 Git
+        run: |
+          sudo apt-get update -y
+          sudo apt install make libssl-dev libghc-zlib-dev libcurl4-gnutls-dev libexpat1-dev gettext unzip -y
+          wget https://github.com/git/git/archive/v2.26.2.zip -O git.zip
+          unzip git.zip
+          cd git-*
+          make prefix=/usr all
+          sudo make prefix=/usr install
+          cd -
+          git --version
+        shell: bash {0}
+
+      - name: Install GitLFS
+        run: |
+          sudo apt-get update 
+          sudo apt-get install git-lfs
+          git lfs install
+        shell: bash {0}
+
+      - name: Install GLPK
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y glpk-utils
+        shell: bash {0}
+        ## Related to https://github.com/actions/checkout/issues/238
+      ## https://www.digitalocean.com/community/tutorials/how-to-install-git-on-ubuntu-18-04
+
+      ## 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
+        uses: actions/checkout@v2
+        with:
+          lfs: true
+      - name: Checkout LFS objects
+        run: git lfs pull
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps("scRNASeq/",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: |
+          ## 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 == 'release')[, 'Bioc']; cat(as.character(res))")
+          rversion=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == 'release')[, 'R']; cat(as.character(res))")
+          ## Print the results
+          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-release-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocdocker-biocbranch-release-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("scRNASeq/",dependencies = TRUE)
+          deps <- remotes::dev_package_deps("scRNASeq/",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("scRNASeq/",dependencies = TRUE, repos = BiocManager::repositories())
+          BiocManager::install(deps$package[deps$diff != 0])
+          ## For running the checks addiotnal cusotm packages can be added here
+          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
+          remotes::install_cran("rcmdcheck")
+          BiocManager::install("BiocCheck")
+          BiocManager::install("rmarkdown")
+          BiocManager::install("RockefellerUniversity/compileCourses",subdir="compileCourses")
+          BiocManager::install("devtools")
+          BiocManager::install("Herper")
+          devtools::install_github('satijalab/seurat-data')
+        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: Install package
+        if: github.ref == 'refs/heads/main' 
+        run: R CMD INSTALL ./scRNASeq/
+
+      - name: Session info
+        run: |
+          require(compileCourses)
+          compileCourses::compileSingleCourseMaterial(repo="RockefellerUniversity",subdir="scRNASeq",branch="main")
+        shell: Rscript {0}
+
+      - name: Move to docs
+        run: |
+          mkdir -p docs
+          rm -r r_course/*/*/*_cache
+          cp -r  r_course/* docs/
+          echo "Copied to docs"
+        shell:
+          bash {0}
+
+      - name: commit
+        run: |
+          git config --global user.email "tc.infomatics@gmail.com"
+          git config --global http.postBuffer 263112000
+          git add docs/\* r_course/\*
+          git commit -m 'Autobuild' 
+          git push origin HEAD:refs/heads/main
+      
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-biocdocker-biocbranch-release-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-results
+          path: check

.github/workflows/compilation-check.yml

@@ -206,6 +206,7 @@ jobs:
       - name: commit
         run: |
           git config --global user.email "tc.infomatics@gmail.com"
+          git config --global http.postBuffer 263112000
           git add docs/\* r_course/\*
           git commit -m 'Autobuild' 
           git push origin HEAD:refs/heads/master