Ubuntu_setup.yml

# Workflow is triggered on label and check installation on various operating systems
# This action is adapted from https://github.com/t4d-gmbh/stubbed_versioning
name: Ubuntu Install

on:
  push:
    branches:
      - "main"

env:
  BRANCH: ${{ github.head_ref || github.ref_name }}

permissions:
  packages: read
  contents: write
  pull-requests: write
  repository-projects: write

jobs:
  setup-and-install:
    runs-on: ubuntu-latest
    name: ubuntu-latest R release
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes

    steps:

      - name: Update and upgrade
        run: |
          sudo apt-get update && sudo apt-get upgrade

      - name: install R
        run: |
          sudo apt-get -y install r-base

      - name: fixing folder perms for local lib
        run: |
          sudo chown root:adm -R /usr/lib/R
          sudo chmod g+w -R /usr/lib/R
          sudo chown root:adm -R /usr/local/lib/R
          sudo chmod g+w -R /usr/local/lib/R

      - name: install config and build dependencies
        run: |
          sudo apt-get -y install libcurl4-openssl-dev  # needed for pak

      - name: install pak
        run: |
          install.packages('pak', repos=c(CRAN="https://cran.r-project.org"))
        shell: Rscript {0}

      # - name: install from CRAN with pak
      #   run: |
      #     pak::pkg_install('abn', dependencies=TRUE)
      #     library('abn')
      #   shell: Rscript {0}

      - name: temporal workaround for ragg
        run: |
          pak::pak("r-lib/ragg")
        shell: Rscript {0}

      - name: pak install from GitHub
        run: |
          pak::repo_add(INLA = "https://inla.r-inla-download.org/R/stable/")
          pak::pkg_install("furrer-lab/abn@${{ env.BRANCH }}", dependencies=TRUE)
          library('abn')
        shell: Rscript {0}

      - name: fetch the repository from GitHub
        uses: actions/checkout@v4

      - name: deactivate the renv
        run: |
            renv::deactivate()
        shell: Rscript {0}

      - name: install from source
        run: |
            pak::local_install(dependencies=TRUE)
        shell: Rscript {0}