Merge pull request #1080 from drieslab/suite_dev #236
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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
name: R-CMD-check | |
on: | |
push: | |
branches: | |
- 'suite' | |
- 'suite_dev' | |
permissions: | |
contents: read | |
jobs: | |
R-CMD-check: | |
env: | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
runs-on: ${{ matrix.config.os }} | |
name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
strategy: | |
fail-fast: false | |
matrix: | |
config: # matrix of system runners to run workflow on | |
- {os: macOS-latest, r: 'release'} | |
- {os: windows-latest, r: 'release'} | |
# - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} | |
- {os: ubuntu-latest, r: 'release'} | |
- {os: ubuntu-latest, r: 'oldrel-1'} | |
steps: | |
- name: Remove vignettes dir | |
run: rm -rf 'vignettes/' | |
shell: bash | |
- name: Checkout repo for workflow access | |
uses: actions/checkout@v4 | |
- name: Set up R environment | |
uses: r-lib/actions/setup-r@v2 | |
with: | |
r-version: ${{ matrix.config.r }} | |
http-user-agent: ${{ matrix.config.http-user-agent }} | |
use-public-rspm: true | |
- name: Set up dependencies (general) | |
uses: r-lib/actions/setup-r-dependencies@v2 | |
env: | |
_R_CHECK_FORCE_SUGGESTS: false | |
_R_CHECK_RD_XREFS: false | |
with: | |
dependencies: '"hard"' # do not use suggested dependencies | |
install-pandoc: false | |
extra-packages: | | |
any::rcmdcheck | |
any::testthat | |
any::hdf5r | |
any::rlang | |
any::R.utils | |
any::remotes | |
any::spdep | |
any::future.apply | |
github::drieslab/GiottoData | |
- name: Test python env install | |
run: | | |
if (!GiottoClass::checkGiottoEnvironment()) { | |
GiottoClass::installGiottoEnvironment() | |
} | |
reticulate::py_list_packages(envname = "giotto_env") | |
shell: Rscript {0} | |
- name: Run R CMD check | |
uses: r-lib/actions/check-r-package@v2 | |
with: | |
upload-snapshots: true | |
error-on: '"error"' # workflow errors on error only, can change to include warnings | |
# show testthat output for ease of access | |
- name: Show testthat output | |
if: always() | |
run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
shell: bash |