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build-book-release.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:
branches:
- master
pull_request:
branches:
- master
name: build-book-release
## 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'
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', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
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
- name: Checkout Repository
uses: actions/checkout@v2
- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
shell: Rscript {0}
- name: Cache R packages
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
uses: actions/cache@v1
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-
- name: Install BiocManager
run: |
message(paste('****', Sys.time(), 'installing BiocManager ****'))
remotes::install_cran("BiocManager")
shell: Rscript {0}
- name: Set BiocVersion
run: |
BiocManager::install(version = "3.17", ask = FALSE)
shell: Rscript {0}
- name: Cache R packages on Linux
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
uses: actions/cache@v1
with:
path: /home/runner/work/_temp/Library
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-
- name: Install Linux system dependencies
if: runner.os == 'Linux'
env:
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
run: |
Rscript -e "remotes::install_github('r-hub/sysreqs')"
sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
sudo -s eval "$sysreqs"
sudo apt-get install -y libcurl4-openssl-dev libglpk-dev
- name: Install bookdown
if: github.ref == 'refs/heads/master' && runner.os == 'Linux'
run: |
remotes::install_cran("bookdown")
shell: Rscript {0}
- 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.
BiocManager::install("LTLA/bluster")
## 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, force=TRUE)
## 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 = FALSE, 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: Bookdown Deploy Preparation
if: github.ref == 'refs/heads/master' && runner.os == 'Linux'
run: |
git config --global user.email "action@github.com"
git config --global user.name "GitHub Action"
git config --global --add safe.directory /__w/OMA/OMA
git fetch --all
commit=$(git --work-tree=../ rev-parse --verify --short HEAD)
git worktree add --track -B gh-pages docs origin/gh-pages
- name: Bookdown
if: runner.os == 'Linux'
run: |
Rscript -e 'bookdown::render_book("index.Rmd", "bookdown::gitbook")'
- uses: r-lib/actions/setup-tinytex@v2
- name: Bookdown pdf
if: runner.os == 'Linux'
run: |
Rscript -e 'tinytex::reinstall_tinytex()'
Rscript -e 'install.packages("webshot")'
Rscript -e 'webshot::install_phantomjs()'
Rscript -e 'bookdown::render_book("index.Rmd", "bookdown::pdf_book")'
- name: Bookdown Deploy
if: github.ref == 'refs/heads/master' && runner.os == 'Linux'
run: |
cd docs
git add -A .
git commit --allow-empty -m "Build book @$(git rev-parse --short HEAD)"
git push --force origin HEAD:gh-pages
cd ..
- name: Upload check results
if: runner.os == 'Linux' && failure()
uses: actions/upload-artifact@master
with:
name: ${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-results
path: docs