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Merge pull request #28 from massonix/lady_ghagha
Lady ghagha
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^inst/scripts/HCATonsilDataRNA$ | ||
^inst/scripts/rna_raw_data$ | ||
^inst/scripts/cite_raw_data$ | ||
^\.github$ |
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on: | ||
push: | ||
pull_request: | ||
branches: | ||
- devel | ||
schedule: | ||
- cron: '0 8 * * 5' | ||
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name: R-CMD-check | ||
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jobs: | ||
R-CMD-check: | ||
runs-on: ${{ matrix.config.os }} | ||
container: ${{ matrix.config.image }} | ||
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name: ${{ matrix.config.os }} (${{ matrix.config.bioc }} - ${{ matrix.config.image }}) | ||
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strategy: | ||
fail-fast: false | ||
matrix: | ||
config: | ||
- { os: windows-latest, bioc: 'devel'} | ||
- { os: macOS-latest, bioc: 'devel', curlConfigPath: '/usr/bin/'} | ||
- { os: ubuntu-latest, bioc: 'devel'} | ||
- { os: ubuntu-latest, image: 'bioconductor/bioconductor_docker:devel'} | ||
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env: | ||
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
CRAN: ${{ matrix.config.cran }} | ||
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
CURL_CONFIG: ${{ matrix.config.curlConfigPath }}curl-config | ||
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steps: | ||
- name: Check out repo | ||
uses: actions/checkout@v2 | ||
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- name: Set up R and install BiocManager | ||
uses: grimbough/bioc-actions/setup-bioc@v1 | ||
if: matrix.config.image == null | ||
with: | ||
bioc-version: ${{ matrix.config.bioc }} | ||
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- name: Set up pandoc | ||
uses: r-lib/actions/setup-pandoc@v2 | ||
if: matrix.config.image == null | ||
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- name: Install remotes | ||
run: | | ||
install.packages('remotes') | ||
shell: Rscript {0} | ||
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- name: Query dependencies | ||
run: | | ||
saveRDS(remotes::dev_package_deps(dependencies = TRUE, repos = c(getOption('repos'), BiocManager::repositories())), 'depends.Rds', version = 2) | ||
shell: Rscript {0} | ||
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- name: Cache R packages | ||
if: runner.os != 'Windows' && matrix.config.image == null | ||
uses: actions/cache@v1 | ||
with: | ||
path: ${{ env.R_LIBS_USER }} | ||
key: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }} | ||
restore-keys: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}- | ||
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- name: Install system dependencies | ||
if: runner.os == 'Linux' | ||
env: | ||
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | ||
run: | | ||
Rscript -e "remotes::install_github('r-hub/sysreqs')" | ||
sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") | ||
sudo -s eval "$sysreqs" | ||
sudo apt-get update && sudo apt-get -y install libcurl4-openssl-dev libglpk-dev libharfbuzz-dev libfribidi-dev | ||
- name: Install system dependencies (macOS) | ||
if: runner.os == 'macOS' | ||
run: | | ||
brew install cairo | ||
brew install --cask xquartz | ||
brew install harfbuzz | ||
brew install fribidi | ||
brew install fftw | ||
- name: Install dependencies | ||
run: | | ||
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]], Ncpu = 2L) | ||
remotes::install_cran('rcmdcheck', Ncpu = 2L) | ||
shell: Rscript {0} | ||
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- name: Session info | ||
run: | | ||
options(width = 100) | ||
pkgs <- installed.packages()[, "Package"] | ||
sessioninfo::session_info(pkgs, include_base = TRUE) | ||
shell: Rscript {0} | ||
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- name: Build, Install, Check | ||
uses: grimbough/bioc-actions/build-install-check@v1 | ||
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- name: Run BiocCheck | ||
uses: grimbough/bioc-actions/run-BiocCheck@v1 | ||
with: | ||
arguments: '--no-check-bioc-views --no-check-bioc-help' | ||
error-on: 'error' | ||
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- name: Show testthat output | ||
if: always() | ||
run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | ||
shell: bash | ||
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- name: Upload check results | ||
if: failure() | ||
uses: actions/upload-artifact@master | ||
with: | ||
name: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-results | ||
path: check | ||
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- name: Test coverage | ||
if: matrix.config.os == 'macOS-latest' | ||
run: | | ||
install.packages("covr") | ||
covr::codecov(token = "${{secrets.CODECOV_TOKEN}}") | ||
shell: Rscript {0} |
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