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Merge pull request #1080 from drieslab/suite_dev #236

Merge pull request #1080 from drieslab/suite_dev

Merge pull request #1080 from drieslab/suite_dev #236

Workflow file for this run

# 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