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Update workflows #178

Workflow file for this run

on:
push:
branches-ignore:
- mac-conda
pull_request:
branches:
- devel
name: R-CMD-check
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
jobs:
R-CMD-check:
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.bioc-version }})
strategy:
fail-fast: false
matrix:
config:
- { os: windows-2022, bioc-version: 'devel', Ncpus: 4}
- { os: macOS-13, bioc-version: 'devel', Ncpus: 4}
- { os: macOS-14, bioc-version: 'devel', Ncpus: 3}
- { os: ubuntu-20.04, bioc-version: 'devel', Ncpus: 4, system-libs: 'libcurl4-gnutls-dev libaec-dev'}
- { os: ubuntu-22.04, bioc-version: 'devel', Ncpus: 4, system-libs: 'libcurl4-openssl-dev'}
steps:
- name: Configure git
run: |
git config --global core.autocrlf false
- name: Install Linux system libraries
if: ${{ runner.os == 'Linux' }}
run: |
sudo apt-get update && sudo apt-get install ${{ matrix.config.system-libs }}
- name: Install Mac system libraries
if: ${{ matrix.config.os == 'macOS-latest' }}
run: |
source("https://mac.R-project.org/bin/install.R")
install.libs("openssl")
shell: Rscript {0}
- uses: actions/checkout@v4
- name: Setup R and Bioconductor
uses: grimbough/bioc-actions/setup-bioc@v1
with:
bioc-version: ${{ matrix.config.bioc-version }}
bioc-mirror: https://ftp.gwdg.de/pub/misc/bioconductor
Ncpus: ${{ matrix.config.Ncpus }}
- uses: r-lib/actions/setup-pandoc@v2
- name: Install dependencies
uses: r-lib/actions/setup-r-dependencies@v2
with:
## install BiocCheck here so it is cached
extra-packages: |
bioc::BiocCheck
- name: Bioc - Build, Install, Check
id: build-install-check
uses: grimbough/bioc-actions/build-install-check@v1
- name: Run BiocCheck
uses: grimbough/bioc-actions/run-BiocCheck@v1
with:
error-on: 'never'
arguments: '--no-check-bioc-help'
- name: Session info
run: |
sessionInfo()
shell: Rscript {0}
- name: Upload check results
if: always()
uses: actions/upload-artifact@v4
with:
name: ${{ matrix.config.os }}-results
path: ${{ steps.build-install-check.outputs.check-dir }}
- name: Upload check results
if: ${{ failure() }}
uses: actions/upload-artifact@v4
with:
name: ${{ matrix.config.os }}-${{ matrix.config.r }}-hdf5_config.log
path: check/*.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/config.log