Add metric QC function #368
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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' | |
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: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" } | |
- { os: macOS-latest, r: '4.3', bioc: '3.18'} | |
- { os: windows-latest, r: '4.3', bioc: '3.18'} | |
## 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_18-r-4.3-${{ hashFiles('.github/depends.Rds') }} | |
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3- | |
- 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_18-r-4.3-${{ hashFiles('.github/depends.Rds') }} | |
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3- | |
# - 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" >> $GITHUB_ENV | |
## Required to install magick as noted at | |
## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 | |
brew install imagemagick@6 | |
## For textshaping, required by ragg, and required by pkgdown | |
brew install harfbuzz fribidi | |
## For installing usethis's dependency gert | |
brew install libgit2 | |
## Required for tcltk | |
brew install xquartz --cask | |
- name: Install Windows system dependencies | |
if: runner.os == 'Windows' | |
run: | | |
## Edit below if you have any Windows system dependencies | |
shell: Rscript {0} | |
- name: Install BiocManager | |
run: | | |
message(paste('****', Sys.time(), 'installing BiocManager ****')) | |
remotes::install_cran("BiocManager") | |
shell: Rscript {0} | |
- name: Set BiocVersion | |
run: | | |
BiocManager::install(version = "${{ 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. | |
## For running the checks | |
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) | |
install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories()) | |
## 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) | |
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 = 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/devel' && env.run_covr == 'true' && runner.os == 'Linux' | |
run: | | |
remotes::install_cran("covr") | |
shell: Rscript {0} | |
- name: Install pkgdown | |
if: github.ref == 'refs/heads/devel' && 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 = "error", | |
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, | |
`no-check-coding-practices` = TRUE | |
) | |
shell: Rscript {0} | |
- name: Test coverage | |
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' | |
run: | | |
covr::codecov() | |
shell: Rscript {0} | |
- name: Install package | |
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | |
run: R CMD INSTALL . | |
- name: Build pkgdown site | |
if: github.ref == 'refs/heads/devel' && 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/devel' && 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/devel' && 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: ${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-results | |
path: check | |
## Code adapted from | |
## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92 | |
docker-build-and-push: | |
runs-on: ubuntu-latest | |
needs: build-check | |
steps: | |
- name: Checkout Repository | |
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | |
uses: actions/checkout@v3 | |
- name: Register repo name | |
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | |
id: reg_repo_name | |
run: | | |
echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV | |
- name: Set up QEMU | |
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | |
uses: docker/setup-qemu-action@v2 | |
- name: Set up Docker Buildx | |
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | |
uses: docker/setup-buildx-action@v2 | |
- name: Login to Docker Hub | |
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | |
uses: docker/login-action@v2 | |
with: | |
username: ${{ secrets.DOCKERHUB_USERNAME }} | |
password: ${{ secrets.DOCKERHUB_TOKEN }} | |
## Note that DOCKERHUB_TOKEN is really a token for your dockerhub | |
## account, not your actual dockerhub account password. You can get it | |
## from https://hub.docker.com/settings/security. | |
## Check https://github.com/docker/build-push-action/tree/v4.0.0 | |
## for more details. | |
## Alternatively, try checking | |
## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html. | |
- name: Build and Push Docker | |
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()" | |
uses: docker/build-push-action@v4 | |
with: | |
context: . | |
push: true | |
tags: > | |
${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest, | |
${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel |