Update gs_cyto_data<- to support replacement with flowSet objects. (#… #41
Workflow file for this run
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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 ] | |
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@master | |
with: | |
r-version: ${{ matrix.r }} | |
http-user-agent: ${{ matrix.config.http-user-agent }} | |
- uses: r-lib/actions/setup-pandoc@v1 | |
# - 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 $cmd | |
done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "16.04"))') | |
sudo apt-get install -y libcurl4-openssl-dev | |
- name: Install dependencies | |
run: | | |
remotes::install_deps(dependencies = TRUE) | |
remotes::install_cran(c("rcmdcheck", "devtools")) | |
# remotes::install_github("RGLab/cytoinstaller") | |
# cytoinstaller::cyto_install_deps(dependencies = TRUE) | |
shell: Rscript {0} | |
# - name: check rate limit | |
# run: | | |
# gh::gh("GET /rate_limit")$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: "This is my release text" |