Fedora_setup_pak.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: Fedora Install

on:
  push:
    branches:
      - "main"
      - "117-elaborate-if-inla-jags-and-gsl-can-be-installed-via-systemrequirements"

env:
  JAGS: '4.3.2'
  BUILD_LOC: "./build"
  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
    container:
      image: "fedora:latest"
    name: fedora-latest R release
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes
    steps:
      - name: prepare fedora
        run: |
          dnf -y install wget
          dnf -y install gcc
          dnf -y install gcc-c++
          dnf -y install gfortran
          dnf -y install lapack*  # is needed on fedora server
          dnf -y install blas*
          dnf -y install atlas*

      - name: install R
        run: |
          dnf -y install R

      - name: install config and build dependencies
        run: |
          dnf -y install libcurl-devel  # needef for pak

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

      - name: install JAGS
        run: |
          wget -O /tmp/jags.tar.gz https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-${{ env.JAGS }}.tar.gz/download
          cd /tmp
          tar -xf jags.tar.gz
          cd /tmp/JAGS-${{ env.JAGS }} 
          ./configure --libdir=/usr/local/lib64
          make
          make install

      - name: assert runtime linkage
        run: |
          echo "/usr/local/lib64" > /etc/ld.so.conf.d/jags.conf
          /sbin/ldconfig

      - name: install rjags
        run: |
            install.packages("rjags", configure.args="--enable-rpath", repos=c(CRAN="https://cran.r-project.org"))
            library("rjags")
        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}

      - name: run the tests
        run: |
            pak::pak('r-lib/testthat')
            testthat::test_local(path='tests', load_package='none')
        shell: Rscript {0}