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build_site_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: '4.0', bioc: '3.12', cont: "bioconductor/bioconductor_docker:RELEASE_3_12", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
#- { os: macOS-latest, r: '4.0', bioc: '3.12'}
#- { os: windows-latest, r: '4.0', bioc: '3.12'}
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: Cache R packages
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
uses: actions/cache@v2
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-
- 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_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
- 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
run: |
## Temporary for now due to https://github.com/ropensci/RefManageR/issues/79
remotes::install_github("ropensci/bibtex")
remotes::install_github("ropensci/RefManageR")
remotes::install_github("cboettig/knitcitations")
## For building the website & getting the R session info
## Edit as necessary with other packages in the future
BiocManager::install(c(
"rmarkdown",
"sessioninfo",
"BiocStyle",
"clusterProfiler",
"edgeR",
"getopt",
"here",
"LieberInstitute/jaffelab",
"knitcitations",
"limma",
"org.Hs.eg.db",
"pheatmap",
"RColorBrewer",
"recount",
"SummarizedExperiment",
"tidyr",
"VariantAnnotation",
"statmod",
"usethis",
"iSEE",
"ggplot2",
"plotly",
"ExploreModelMatrix",
"enrichplot",
"ggnewscale"
))
tinytex::install_tinytex()
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: |
rmarkdown::render_site()
system("touch docs/.nojekyll")
shell: Rscript {0}
- name: Install deploy dependencies
run: |
apt-get update && apt-get -y install rsync
- name: Deploy 🚀
uses: JamesIves/github-pages-deploy-action@releases/v4
with:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
BRANCH: gh-pages # The branch the action should deploy to.
FOLDER: docs # The folder the action should deploy.