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‎.github/workflows/R-CMD-check.yaml

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on:
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push:
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branches:
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- master
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pull_request:
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branches:
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- master
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name: R-CMD-check
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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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strategy:
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fail-fast: false
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matrix:
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config:
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- {os: macOS-latest, r: 'release'}
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- {os: macOS-latest, r: 'oldrel'}
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- {os: windows-latest, r: 'release'}
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- {os: ubuntu-16.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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RSPM: ${{ matrix.config.rspm }}
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GITHUB_TOKEN: ${{ secrets.GHTOKEN2 }}
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GITHUB_PAT: ${{ secrets.GHTOKEN2 }}
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@master
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with:
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r-version: ${{ matrix.config.r }}
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- uses: r-lib/actions/setup-pandoc@master
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps("MyCoursePackage/",dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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remotes::install_cran("BiocManager")
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remotes::install_cran("devtools")
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shell: Rscript {0}
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- name: Cache R packages
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if: runner.os != 'Windows'
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uses: actions/cache@v1
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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- name: Install System Dependencies
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if: runner.os == 'Linux'
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run: |
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sudo apt-get update -y
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sudo apt-get install -y glpk-utils
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sudo apt-get install -y libcurl4-openssl-dev
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shell: bash {0}
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- name: Install dependencies
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run: |
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## Try installing the package dependencies in steps. First the local
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## dependencies, then any remaining dependencies to avoid the
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## issues described at
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## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
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## https://github.com/r-lib/remotes/issues/296
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## Ideally, all dependencies should get installed in the first pass.
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## Pass #1 at installing dependencies
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message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
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local_deps <- remotes::local_package_deps("MyCoursePackage/",dependencies = TRUE)
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deps <- remotes::dev_package_deps("MyCoursePackage/",dependencies = TRUE, repos = BiocManager::repositories())
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BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]])
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## Pass #2 at installing dependencies
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message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
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deps <- remotes::dev_package_deps("MyCoursePackage/",dependencies = TRUE, repos = BiocManager::repositories())
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BiocManager::install(deps$package[deps$diff != 0])
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## For running the checks
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message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
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remotes::install_cran("rcmdcheck")
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BiocManager::install("BiocCheck")
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BiocManager::install("rmarkdown")
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BiocManager::install("RockefellerUniversity/compileCourses",subdir="compileCourses")
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BiocManager::install("RockefellerUniversity/Herper")
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shell: Rscript {0}
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- name: Session info
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run: |
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options(width = 100)
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pkgs <- installed.packages()[, "Package"]
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sessioninfo::session_info(pkgs, include_base = TRUE)
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shell: Rscript {0}
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- name: Install package
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if: github.ref == 'refs/heads/master'
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run: |
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devtools::install("MyCoursePackage/",dependencies = TRUE,quick = TRUE)
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shell: Rscript {0}
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- name: CompileCourse
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run: |
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require(compileCourses)
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compileCourses::compileSingleCourseMaterial(repo="RockefellerUniversity",subdir="MyCoursePackage",branch="master")
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shell: Rscript {0}

‎.github/workflows/selfTest.yml

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## Read more about GitHub actions the features of this GitHub Actions workflow
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## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action
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##
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## For more details, check the biocthis developer notes vignette at
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## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html
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##
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## You can add this workflow to other packages using:
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## > biocthis::use_bioc_github_action()
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## or
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## > usethis::use_github_action("check-bioc", "https://bit.ly/biocthis_gha", "check-bioc.yml")
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## without having to install biocthis.
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##
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## Using GitHub Actions exposes you to many details about how R packages are
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## compiled and installed in several operating system.s
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### If you need help, please follow the steps listed at
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## https://github.com/r-lib/actions#where-to-find-help
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##
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## If you found an issue specific to biocthis's GHA workflow, please report it
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## with the information that will make it easier for others to help you.
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## Thank you!
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## Acronyms:
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## * GHA: GitHub Action
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## * OS: operating system
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## Specify which branches you want this GHA to run on.
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## Bioconductor uses branches such as master (bioc-devel) and RELEASE_* like
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## RELEASE_3_10. For more details check
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## http://bioconductor.org/developers/how-to/git/
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on:
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push:
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branches:
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- master
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- 'RELEASE_*'
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pull_request:
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branches:
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- master
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- 'RELEASE_*'
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name: R-CMD-check-bioc
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## These environment variables control whether to run GHA code later on that is
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## specific to testthat, covr, and pkgdown.
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##
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## If you need to clear the cache of packages, update the number inside
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## cache-version as discussed at https://github.com/r-lib/actions/issues/86.
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## Note that you can always run a GHA test without the cache by using the word
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## "/nocache" in the commit message.
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env:
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has_testthat: 'true'
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run_covr: 'true'
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run_pkgdown: 'true'
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cache-version: 'cache-v1'
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jobs:
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## This first job uses the GitHub repository branch name to infer what
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## version of Bioconductor we will be working on.
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define-docker-info:
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runs-on: ubuntu-latest
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outputs:
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imagename: ${{ steps.findinfo.outputs.imagename }}
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biocversion: ${{ steps.findinfo.outputs.biocversion }}
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steps:
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- id: findinfo
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run: |
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## Find what Bioconductor RELEASE branch we are working on
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## otherwise, assume we are working on bioc-devel.
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if echo "$GITHUB_REF" | grep -q "RELEASE_"; then
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biocversion="$(basename -- $GITHUB_REF | tr '[:upper:]' '[:lower:]')"
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else
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biocversion="RELEASE_3_11"
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fi
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## Define the image name and print the information
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imagename="bioconductor/bioconductor_docker:${biocversion}"
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echo $imagename
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echo $biocversion
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## Save the information for the next job
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echo "::set-output name=imagename::${imagename}"
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echo "::set-output name=biocversion::${biocversion}"
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R-CMD-check-bioc:
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## This job then checks the R package using the Bioconductor docker that
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## was defined by the previous job. This job will determine what version of
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## R to use for the macOS and Windows builds on the next job.
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runs-on: ubuntu-latest
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needs: define-docker-info
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## Name shown on the GHA log
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name: ubuntu-latest (r-biocdocker bioc-${{ needs.define-docker-info.outputs.biocversion }})
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## Information used by the next job that will run on macOS and Windows
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outputs:
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rversion: ${{ steps.findrversion.outputs.rversion }}
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biocversionnum: ${{ steps.findrversion.outputs.biocversionnum }}
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## Environment variables unique to this job.
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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TZ: UTC
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NOT_CRAN: true
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GITHUB_TOKEN: ${{ secrets.GHTOKEN2 }}
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GITHUB_PAT: ${{ secrets.GHTOKEN2 }}
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## The docker container to use. Note that we link a directory on the GHA
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## runner to a docker directory, such that we can then cache the linked
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## directory. This directory will contain the R packages used.
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container:
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image: ${{ needs.define-docker-info.outputs.imagename }}
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volumes:
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- /home/runner/work/_temp/Library:/usr/local/lib/R/host-site-library
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steps:
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- name: Install Git
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run: |
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sudo apt-get update -y
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sudo apt install make libssl-dev libghc-zlib-dev libcurl4-gnutls-dev libexpat1-dev gettext unzip -y
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wget https://github.com/git/git/archive/v2.26.2.zip -O git.zip
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unzip git.zip
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cd git-*
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make prefix=/usr all
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sudo make prefix=/usr install
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cd -
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git --version
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shell: bash {0}
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- name: Install GLPK
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run: |
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sudo apt-get update -y
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sudo apt-get install -y glpk-utils
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shell: bash {0}
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## Related to https://github.com/actions/checkout/issues/238
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## https://www.digitalocean.com/community/tutorials/how-to-install-git-on-ubuntu-18-04
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## Most of these steps are the same as the ones in
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## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
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## If they update their steps, we will also need to update ours.
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- uses: actions/checkout@v2
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps("MyCoursePackage/",dependencies = TRUE), ".github/depends.Rds", version = 2)
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message(paste('****', Sys.time(), 'installing BiocManager ****'))
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remotes::install_cran("BiocManager")
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shell: Rscript {0}
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## Find the corresponding R version based on the Bioconductor version
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## to use for the macOS and Windows checks by the next GHA job
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- id: findrversion
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name: Find Bioc and R versions
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run: |
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## Find what branch we are working on
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if echo "$GITHUB_REF" | grep -q "master"; then
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biocversion="devel"
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elif echo "$GITHUB_REF" | grep -q "RELEASE_"; then
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biocversion="release"
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fi
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## Define the R and Bioconductor version numbers
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biocversionnum=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == '${biocversion}')[, 'Bioc']; cat(as.character(res))")
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rversion=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == '${biocversion}')[, 'R']; cat(as.character(res))")
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## Print the results
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echo $biocversion
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echo $biocversionnum
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echo $rversion
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## Save the info for the next job
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echo "::set-output name=rversion::${rversion}"
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echo "::set-output name=biocversionnum::${biocversionnum}"
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shell:
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bash {0}
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- name: Cache R packages
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if: "!contains(github.event.head_commit.message, '/nocache')"
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uses: actions/cache@v1
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with:
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path: /home/runner/work/_temp/Library
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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') }}
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restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocdocker-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-
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- name: Install dependencies
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run: |
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## Try installing the package dependencies in steps. First the local
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## dependencies, then any remaining dependencies to avoid the
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## issues described at
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## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
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## https://github.com/r-lib/remotes/issues/296
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## Ideally, all dependencies should get installed in the first pass.
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## Pass #1 at installing dependencies
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message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
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local_deps <- remotes::local_package_deps("MyCoursePackage/",dependencies = TRUE)
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deps <- remotes::dev_package_deps("MyCoursePackage/",dependencies = TRUE, repos = BiocManager::repositories())
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BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]])
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## Pass #2 at installing dependencies
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message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
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deps <- remotes::dev_package_deps("MyCoursePackage/",dependencies = TRUE, repos = BiocManager::repositories())
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BiocManager::install(deps$package[deps$diff != 0])
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## For running the checks
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message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
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remotes::install_cran("rcmdcheck")
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BiocManager::install("BiocCheck")
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BiocManager::install("rmarkdown")
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BiocManager::install("RockefellerUniversity/compileCourses",subdir="compileCourses")
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BiocManager::install("RockefellerUniversity/Herper")
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BiocManager::install("BSgenome")
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BiocManager::install("BSgenome.Mmusculus.UCSC.mm10")
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shell: Rscript {0}
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- name: Session info
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run: |
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options(width = 100)
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pkgs <- installed.packages()[, "Package"]
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sessioninfo::session_info(pkgs, include_base = TRUE)
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shell: Rscript {0}
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- name: Install package
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if: github.ref == 'refs/heads/master'
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run: R CMD INSTALL ./MyCoursePackage/
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- name: Session info
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run: |
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require(compileCourses)
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compileCourses::compileSingleCourseMaterial(repo="RockefellerUniversity",subdir="MyCoursePackage",branch="master")
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shell: Rscript {0}
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- name: Move to docs
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run: |
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mkdir -p docs
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rm -r r_course/*/*/*_cache
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cp -r r_course/* docs/
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echo "Copied to docs"
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shell:
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bash {0}
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- name: commit
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run: |
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git config --global user.email "[email protected]"
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git add docs/\* r_course/\*
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git commit -m 'Autobuild'
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git push origin HEAD:refs/heads/master
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- name: Upload check results
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if: failure()
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uses: actions/upload-artifact@master
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with:
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name: ${{ runner.os }}-biocdocker-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-results
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path: check

‎.gitignore

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.Rproj.user
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.Rhistory
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.RData
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.Ruserdata
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.DS_Store
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.gitignore

‎MyCoursePackage/.Rbuildignore

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^.*\.Rproj$
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^\.Rproj\.user$
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^appveyor\.yml$

‎MyCoursePackage/DESCRIPTION

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Package: MyCoursePackage
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Type: Package
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Title: Template Package for Courses
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Version: 0.1.1
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Author: Matt Paul and Thomas Carroll.
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Maintainer: Thomas Carroll <tc.infomatics@gmail>
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Description: This pacakge shows an example framework to build a teaching course.
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License: What license is it under?
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LazyData: TRUE
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biocViews: Training
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Depends: methods, ggplot2, rmarkdown, rio
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Suggests: knitr,
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rmarkdown,
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testthat,
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yaml
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SystemRequirements: R, RStudio
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VignetteBuilder: knitr
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RoxygenNote: 6.0.1

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