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build_book_bioc_docker.yml
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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-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:
cache-version: 'cache-v1'
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: '4.1', bioc: '3.13', cont: "bioconductor/bioconductor_docker:RELEASE_3_13", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
- { os: macOS-latest, r: '4.1', bioc: '3.13'}
- { os: windows-latest, r: '4.1', bioc: '3.13'}
## 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_13-r-4.1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_13-r-4.1-
- 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_13-r-4.1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_13-r-4.1-
# - 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: Session info
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}
- name: Build website
run: |
bookdown::render_book("index.Rmd")
system("touch _book/.nojekyll")
shell: Rscript {0}
- name: Install deploy dependencies
if: runner.os == 'Linux'
run: |
apt-get update && apt-get -y install rsync
- name: Deploy 🚀
if: runner.os == 'Linux'
uses: JamesIves/github-pages-deploy-action@4.1.4
with:
branch: gh-pages # The branch the action should deploy to.
folder: _book # The folder the action should deploy.