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Updated NEWS file and package maintainer :' #175

Updated NEWS file and package maintainer :'

Updated NEWS file and package maintainer :' #175

Workflow file for this run

## 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()
## or
## > usethis::use_github_action("check-bioc", "https://bit.ly/biocthis_gha", "check-bioc.yml")
## without having to install biocthis.
##
## Using GitHub Actions exposes you to many details about how R packages are
## compiled and installed in several operating systems.
## 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:
- devel
- 'RELEASE_*'
pull_request:
branches:
- devel
- 'RELEASE_*'
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: 'false'
run_covr: 'true'
run_pkgdown: 'false'
has_RUnit: 'true'
cache-version: 'cache-v1'
jobs:
## This first job uses the GitHub repository branch name to infer what
## version of Bioconductor we will be working on.
define-docker-info:
runs-on: ubuntu-latest
outputs:
imagename: ${{ steps.findinfo.outputs.imagename }}
biocversion: ${{ steps.findinfo.outputs.biocversion }}
steps:
- id: findinfo
run: |
## Find what Bioconductor RELEASE branch we are working on
## otherwise, assume we are working on bioc-devel.
if echo "$GITHUB_REF" | grep -q "RELEASE_"; then
biocversion="$(basename -- $GITHUB_REF | tr '[:upper:]' '[:lower:]')"
else
biocversion="devel"
fi
## Define the image name and print the information
imagename="bioconductor/bioconductor_docker:${biocversion}"
echo $imagename
echo $biocversion
## Save the information for the next job
echo "::set-output name=imagename::${imagename}"
echo "::set-output name=biocversion::${biocversion}"
R-CMD-check-bioc:
## This job then checks the R package using the Bioconductor docker that
## was defined by the previous job. This job will determine what version of
## R to use for the macOS and Windows builds on the next job.
runs-on: ubuntu-latest
needs: define-docker-info
## Name shown on the GHA log
name: ubuntu-latest (r-biocdocker bioc-${{ needs.define-docker-info.outputs.biocversion }})
## Information used by the next job that will run on macOS and Windows
outputs:
rversion: ${{ steps.findrversion.outputs.rversion }}
biocversionnum: ${{ steps.findrversion.outputs.biocversionnum }}
## Environment variables unique to this job.
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
TZ: UTC
NOT_CRAN: true
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
## The docker container to use. Note that we link a directory on the GHA
## runner to a docker directory, such that we can then cache the linked
## directory. This directory will contain the R packages used.
container:
image: ${{ needs.define-docker-info.outputs.imagename }}
volumes:
- /home/runner/work/_temp/Library:/usr/local/lib/R/host-site-library
steps:
- name: Install latest git
run: |
## git version provided
git --version
## to be able to install software properties
sudo apt-get update -y
## to be able to use add-apt-repository
sudo apt-get install software-properties-common -y
## to use stable releases of git that are already in a PPA at
## https://launchpad.net/~git-core/+archive/ubuntu/candidate
sudo add-apt-repository ppa:git-core/candidate -y
## Update
sudo apt-get update -y
## Upgrade git and other tools
sudo apt-get upgrade -y
## latest git version
git --version
shell: bash {0}
## Most of these steps are the same as the ones in
## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
## If they update their steps, we will also need to update ours.
- uses: actions/checkout@v2
- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
message(paste('****', Sys.time(), 'installing BiocManager ****'))
remotes::install_cran("BiocManager")
shell: Rscript {0}
## Find the corresponding R version based on the Bioconductor version
## to use for the macOS and Windows checks by the next GHA job
- id: findrversion
name: Find Bioc and R versions
run: |
## Find what branch we are working on
if echo "$GITHUB_REF" | grep -q "devel"; then
biocversion="devel"
elif echo "$GITHUB_REF" | grep -q "RELEASE_"; then
biocversion="release"
fi
## Define the R and Bioconductor version numbers
biocversionnum=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == '${biocversion}')[, 'Bioc']; cat(as.character(res))")
rversion=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == '${biocversion}')[, 'R']; cat(as.character(res))")
## Print the results
echo $biocversion
echo $biocversionnum
echo $rversion
## Save the info for the next job
echo "::set-output name=rversion::${rversion}"
echo "::set-output name=biocversionnum::${biocversionnum}"
shell:
bash {0}
- name: Cache R packages
if: "!contains(github.event.head_commit.message, '/nocache')"
uses: actions/cache@v1
with:
path: /home/runner/work/_temp/Library
key: ${{ env.cache-version }}-${{ runner.os }}-biocdocker-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocdocker-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-
- name: Install dependencies
run: |
## Try installing the package dependencies in steps. First the local
## dependencies, then any remaining dependencies to avoid the
## issues described at
## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
## https://github.com/r-lib/remotes/issues/296
## Ideally, all dependencies should get installed in the first pass.
## Pass #1 at installing dependencies
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
local_deps <- remotes::local_package_deps(dependencies = TRUE)
deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]])
## Pass #2 at installing dependencies
message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
BiocManager::install(deps$package[deps$diff != 0])
## For running the checks
message(paste('****', Sys.time(), 'installing rcmdcheck ****'))
remotes::install_cran("rcmdcheck")
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: 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 = "error",
check_dir = "check"
)
shell: Rscript {0}
- 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: |
## Install BiocGenerics
BiocManager::install("BiocGenerics")
## Install the package itself, otherwise BiocGenerics:::testPackage() doesn't find it
install.packages(".", repos=NULL)
BiocGenerics:::testPackage()
shell: Rscript {0}
- name: Install covr
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true'
run: |
remotes::install_cran("covr")
shell: Rscript {0}
- name: Test coverage
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true'
run: |
covr::codecov()
shell: Rscript {0}
- name: Install pkgdown
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true'
run: |
remotes::install_github("r-lib/pkgdown")
shell: Rscript {0}
- name: Install package
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true'
run: R CMD INSTALL .
- name: Deploy package
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true'
run: |
git config --local user.email "[email protected]"
git config --local user.name "GitHub Action"
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: ${{ runner.os }}-biocdocker-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-results
path: check