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check-bioc.yml
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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.
env:
has_testthat: 'true'
run_covr: 'true'
run_pkgdown: 'true'
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 }}
strategy:
fail-fast: false
matrix:
config:
- { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", 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:
- 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@v3
- 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 }}
- 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_14-r-4.1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-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_14-r-4.1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-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 BiocManager
run: |
message(paste('****', Sys.time(), 'installing BiocManager ****'))
remotes::install_cran("BiocManager")
shell: Rscript {0}
- name: Set BiocVersion
run: |
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
shell: Rscript {0}
- name: Install dependencies pass 1
run: |
## Try installing the package dependencies in steps. First the local
## dependencies, then any remaining dependencies to avoid the
## issues described at
## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
## https://github.com/r-lib/remotes/issues/296
## Ideally, all dependencies should get installed in the first pass.
## Set the repos source depending on the OS
## Alternatively use https://storage.googleapis.com/bioconductor_docker/packages/
## though based on https://bit.ly/bioc2021-package-binaries
## the Azure link will be the main one going forward.
gha_repos <- if(
.Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin"
) c(
"AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.14/bioc",
BiocManager::repositories()
) else BiocManager::repositories()
## For running the checks
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
install.packages(c("rcmdcheck", "BiocCheck"), repos = gha_repos)
## Pass #1 at installing dependencies
## This pass uses AnVIL-powered fast binaries
## details at https://github.com/nturaga/bioc2021-bioconductor-binaries
## The speed gains only apply to the docker builds.
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
remotes::install_local(dependencies = TRUE, repos = gha_repos, build_vignettes = FALSE, upgrade = TRUE)
continue-on-error: true
shell: Rscript {0}
- name: Install dependencies pass 2
run: |
## Pass #2 at installing dependencies
## This pass does not use AnVIL and will thus update any packages
## that have seen been updated in Bioconductor
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/master' && env.run_covr == 'true' && runner.os == 'Linux'
run: |
remotes::install_cran("covr")
shell: Rscript {0}
- name: Install pkgdown
if: github.ref == 'refs/heads/master' && 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 = "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 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$', full.names = TRUE),
`quit-with-status` = FALSE,
`no-check-R-ver` = TRUE,
`no-check-bioc-help` = TRUE
)
shell: Rscript {0}
- name: Test coverage
if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
run: |
covr::codecov()
shell: Rscript {0}
- name: Install package
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: R CMD INSTALL .
- name: Get R package info
if: runner.os == 'Linux'
run: |
#### DockerHub repos must be lowercase (,,) ####
name=$(grep '^Package:' DESCRIPTION | cut -d\ -f2)
echo "packageNameOrig=${name}" >> $GITHUB_ENV
echo $name
version=$(grep Version DESCRIPTION | grep -o "[0-9.]\+")
echo "packageVersion=${version}" >> $GITHUB_ENV
echo $version
shell: bash {0}
- name: Build and deploy pkgdown site
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
git config --global --add safe.directory /__w/${{env.packageNameOrig}}/${{env.packageNameOrig}}
git config --local user.name "$GITHUB_ACTOR"
git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
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-RELEASE_3_14-r-4.1-results
path: check