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build.yml
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# This workflow uses actions that are not certified by GitHub.
# They are provided by a third-party and are governed by
# separate terms of service, privacy policy, and support
# documentation.
#
name: build
on:
push:
branches: [ release, master ]
pull_request:
branches: [ release, master ]
workflow_dispatch:
jobs:
build:
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.r }})
strategy:
fail-fast: false
matrix:
r: ['release', 'devel']
config:
- {os: windows-latest, suffix: 'zip'}
- {os: macOS-latest, suffix: 'tgz'}
- {os: ubuntu-16.04, suffix: 'tar.gz', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
isMaster:
- ${{ contains(github.ref, 'master') }}
exclude:
- isMaster: false
r: devel
- isMaster: true
r: release
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}
steps:
- uses: actions/checkout@v2
- name: Set up R ${{ matrix.r }}
uses: r-lib/actions/setup-r@v1
with:
r-version: ${{ matrix.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}
- uses: r-lib/actions/setup-pandoc@v1
- uses: r-lib/actions/setup-tinytex@v1
- run: tlmgr --version
- name: add more tex pkgs
run: |
install.packages('tinytex')
tinytex:::install_yihui_pkgs()
shell: Rscript {0}
- name: set token for cytoinstaller(and remotes) to increase github API rate limit
env:
SUPER_SECRET: ${{ secrets.CYTOINSTALLER_TOKEN }}
run: echo "GITHUB_TOKEN=$SUPER_SECRET" >> $GITHUB_ENV
- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
shell: Rscript {0}
- name: Get bioc ver
run: echo "bioc_ver=$(Rscript -e 'writeLines(as.character(remotes::bioc_version()))')" >> $GITHUB_ENV
shell: bash
- name: Cache R packages
if: runner.os != 'Windows'
uses: actions/cache@v2
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
- name: check bioc ver
run: echo $bioc_ver
shell: bash
- name: Install system dependencies
if: runner.os == 'Linux'
run: |
while read -r cmd
do
eval sudo $cmd
done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "16.04"))')
sudo apt-get install -y libcurl4-openssl-dev
- name: Install system dependencies (mac)
if: runner.os == 'macOS'
run: |
brew install libgit2
- name: Install dependencies
run: |
remotes::install_cran(c("rcmdcheck", "devtools"))
remotes::install_github("RGLab/cytoinstaller")
cytoinstaller::cyto_install_deps(dependencies = TRUE)
shell: Rscript {0}
- name: check rate limit
run: |
gh::gh("GET /rate_limit")$resources$core$remaining
shell: Rscript {0}
- name: Check
env:
_R_CHECK_CRAN_INCOMING_REMOTE_: false
run: rcmdcheck::rcmdcheck(args = c("--no-manual"), check_dir = "check")
shell: Rscript {0}
- name: Upload check results
if: failure()
uses: actions/upload-artifact@main
with:
name: ${{ runner.os }}-r${{ matrix.config.r }}-results
path: check
- name: build src pkg
if: runner.os == 'Linux'
run: devtools::build()
shell: Rscript {0}
- name: build bin pkg
if: runner.os != 'Linux'
run: devtools::build(binary = TRUE)
shell: Rscript {0}
- name: Upload Release Asset
uses: svenstaro/upload-release-action@v2
with:
repo_token: ${{ secrets.GITHUB_TOKEN }}
file: '../*.${{ matrix.config.suffix }}'
file_glob: true
tag: bioc_${{ env.bioc_ver}}
overwrite: true
body: ""