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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
on:
push:
branches: [dev]
pull_request:
branches: [dev]
name: R-CMD-check.yaml
permissions: read-all
jobs:
R-CMD-check:
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
strategy:
fail-fast: false
matrix:
config:
- {os: macos-latest, r: 'release'}
- {os: windows-latest, r: 'release'}
- {os: ubuntu-latest, r: 'release'}
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_KEEP_PKG_SOURCE: yes
steps:
- uses: actions/checkout@v4
- uses: r-lib/actions/setup-pandoc@v2
- 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: Install reticulate
run: |
Rscript -e "install.packages('reticulate')"
- name: Create miniconda
run: |
Rscript -e "reticulate::install_miniconda()"
Rscript -e "reticulate::conda_install(packages = 'scipy')"
- name: Install pak
run: |
Rscript -e "install.packages('pak')"
- name: Install remotes
run: |
Rscript -e "install.packages('remotes')"
- name: Install GiottoUtils
run: |
Rscript -e "remotes::install_github('drieslab/GiottoUtils@dev')"
- name: Install GiottoData
run: |
Rscript -e "remotes::install_github('drieslab/GiottoData')"
- name: Install rcmdcheck
run: |
Rscript -e "install.packages('rcmdcheck')"
- name: Install knitr
run: |
Rscript -e "install.packages('knitr')"
- name: Install rmarkdown
run: |
Rscript -e "install.packages('rmarkdown')"
- name: Install testthat
run: |
Rscript -e "install.packages('testthat')"
- name: Install BiocCheck
run: |
Rscript -e "install.packages('BiocManager')"
Rscript -e "BiocManager::install('BiocCheck')"
- name: Install dbscan
run: |
Rscript -e "BiocManager::install('dbscan')"
- name: Install deldir
run: |
Rscript -e "BiocManager::install('deldir')"
- name: Install igraph
run: |
Rscript -e "BiocManager::install('igraph')"
- name: Install magick
run: |
Rscript -e "BiocManager::install('magick')"
- name: Install matrixStats
run: |
Rscript -e "BiocManager::install('matrixStats')"
- name: Install sp
run: |
Rscript -e "BiocManager::install('sp')"
- name: Install terra
run: |
Rscript -e "BiocManager::install('terra')"
- name: Install scattermore
run: |
Rscript -e "install.packages('scattermore')"
- name: Install exactextractr
run: |
Rscript -e "install.packages('exactextractr')"
- name: Install future.apply
run: |
Rscript -e "BiocManager::install('future.apply')"
- name: Install stars
run: |
Rscript -e "BiocManager::install('stars')"
- name: Install qs
run: |
Rscript -e "BiocManager::install('qs')"
- name: Install RTriangle
run: |
Rscript -e "BiocManager::install('RTriangle')"
- name: Install geometry
run: |
Rscript -e "BiocManager::install('geometry')"
- name: Install Seurat
run: |
Rscript -e "BiocManager::install('Seurat')"
- name: Install chihaya
run: |
Rscript -e "BiocManager::install('chihaya')"
- name: Install DelayedArray
run: |
Rscript -e "BiocManager::install('DelayedArray')"
- name: Install DelayedMatrixStats
run: |
Rscript -e "BiocManager::install('DelayedMatrixStats')"
- name: Install HDF5Array
run: |
Rscript -e "BiocManager::install('HDF5Array')"
- name: Install rgl
run: |
Rscript -e "BiocManager::install('rgl')"
- name: Install rhdf5
run: |
Rscript -e "BiocManager::install('rhdf5')"
- name: Install S4Vectors
run: |
Rscript -e "BiocManager::install('S4Vectors')"
- name: Install ScaledMatrix
run: |
Rscript -e "BiocManager::install('ScaledMatrix')"
- name: Install SingleCellExperiment
run: |
Rscript -e "BiocManager::install('SingleCellExperiment')"
- name: Install SpatialExperiment
run: |
Rscript -e "BiocManager::install('SpatialExperiment')"
- name: Install STexampleData
run: |
Rscript -e "BiocManager::install('STexampleData')"
- name: Install SummarizedExperiment
run: |
Rscript -e "BiocManager::install('SummarizedExperiment')"
- name: Run BiocCheck
run: |
Rscript -e "BiocCheck::BiocCheck()"
- name: Run rcmdcheck
run: |
Rscript -e "rcmdcheck::rcmdcheck()"