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Merge branch 'devel' into check_time_update #298

Merge branch 'devel' into check_time_update

Merge branch 'devel' into check_time_update #298

Workflow file for this run

on:
push:
pull_request:
branches:
- devel
name: build_deploy
jobs:
build_deploy:
runs-on: ubuntu-latest
container: bioconductor/bioconductor_docker:devel
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- name: Check out repo
uses: actions/checkout@v3
- name: apt-get update
run: |
apt-get update -y
- name: Set up pandoc
uses: r-lib/actions/setup-pandoc@v2
- name: Install TinyTeX
run: |
install.packages('tinytex')
tinytex::install_tinytex()
shell: Rscript {0}
- name: Install dependencies
run: |
install.packages(c('remotes', 'BiocManager'))
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories())
BiocManager::install(update = TRUE, ask = FALSE, Ncpus = 2L)
shell: Rscript {0}
- name: Session info
run: |
install.packages('sessioninfo')
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}
# - name: Render book (git)
# run: |
# bookdown::render_book('index.Rmd', 'bookdown::gitbook')
# shell: Rscript {0}
# - name: Render book (pdf)
# run: |
# bookdown::render_book('index.Rmd', 'bookdown::pdf_book')
# shell: Rscript {0}
# - name: Render book (epub)
# run: |
# bookdown::render_book('index.Rmd', 'bookdown::epub_book')
# shell: Rscript {0}
- name: Render book (bs4_book)
run: |
bookdown::render_book('index.Rmd', 'bookdown::bs4_book')
shell: Rscript {0}
- name: Copy docs/ subdirectory to book
run: |
cp -R docs _book/
# deploy needs rsync? Seems so.
- name: Install deploy dependencies
if: github.event_name == 'push' && github.ref == 'refs/heads/devel'
run: |
apt-get update && apt-get -y install rsync
- name: Deploy 🚀
if: github.event_name == 'push' && github.ref == 'refs/heads/devel'
uses: JamesIves/[email protected]
with:
ACCESS_TOKEN: ${{ secrets.ACCESS_TOKEN }}
BRANCH: gh-pages
FOLDER: _book