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check-bioc.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-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'
cache-version: 'cache-v3'
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: 'next', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
## Dockers for macOS and Windows can't handle r: 'next' at this stage
# - { os: macOS-latest, r: 'next', bioc: 'devel'}
# - { os: windows-latest, r: 'next', bioc: 'devel'}
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 }}
## 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: Cache R packages
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-devel-r-next-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-next-
- 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-devel-r-next-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-next-
- 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" >> $GITHUB_ENV
## Required to install magick as noted at
## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
brew install imagemagick@6
## For textshaping, required by ragg, and required by pkgdown
brew install harfbuzz fribidi
## For installing usethis's dependency gert
brew install libgit2
- name: Install Windows system dependencies
if: runner.os == 'Windows'
run: |
## Edit below if you have any Windows system dependencies
shell: Rscript {0}
- name: Install BiocManager
run: |
message(paste('****', Sys.time(), 'installing BiocManager ****'))
remotes::install_cran("BiocManager")
shell: Rscript {0}
- name: Set BiocVersion
run: |
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
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.
## 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 = TRUE, 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)
## For running the checks
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
remotes::install_cran("rcmdcheck")
BiocManager::install("BiocCheck")
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
run: |
rcmdcheck::rcmdcheck(
args = c("--no-build-vignettes", "--no-manual", "--timings"),
build_args = c("--no-manual", "--no-resave-data"),
error_on = "warning",
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 BiocCheck
if: env.run_BiocCheck == 'true'
run: |
BiocCheck::BiocCheck(
dir('check', 'tar.gz$', full.names = TRUE),
`quit-with-status` = TRUE,
`no-check-R-ver` = TRUE,
`no-check-bioc-help` = 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: Deploy package
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
git config --global user.email "[email protected]"
git config --global user.name "GitHub Actions"
git config --global --add safe.directory /__w/ngsReports/ngsReports
Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
shell: bash {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: Upload check results
if: failure()
uses: actions/upload-artifact@master
with:
name: ${{ runner.os }}-biocversion-devel-r-next-results
path: check