install with pak (and thus sysdeps) #3
Workflow file for this run
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| # 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: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - name: prepare fedora | |
| run: | | |
| dnf -y install wget | |
| dnf -y install gcc | |
| dnf -y install gcc-c++ | |
| dnf -y install gfortran | |
| dnf -y install lapack* # is needed on fedora server | |
| dnf -y install blas* | |
| dnf -y install atlas* | |
| - name: install R | |
| run: | | |
| dnf -y install R | |
| - name: install config and build dependencies | |
| run: | | |
| dnf -y install pkg-config | |
| dnf -y install cmake | |
| dnf -y install R-devtools | |
| - name: install GSL | |
| run: | | |
| dnf -y install gsl-devel | |
| - name: install JAGS | |
| run: | | |
| wget -O /tmp/jags.tar.gz https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-${{ env.JAGS }}.tar.gz/download | |
| cd /tmp | |
| tar -xf jags.tar.gz | |
| cd /tmp/JAGS-${{ env.JAGS }} | |
| ./configure --libdir=/usr/local/lib64 | |
| make | |
| make install | |
| - name: assert runtime linkage | |
| run: | | |
| echo "/usr/local/lib64" > /etc/ld.so.conf.d/jags.conf | |
| /sbin/ldconfig | |
| - name: install rjags | |
| run: | | |
| install.packages("rjags", configure.args="--enable-rpath", repos=c(CRAN="https://cran.r-project.org")) | |
| library("rjags") | |
| shell: Rscript {0} | |
| - name: installing dependencies from BiocManager | |
| run: | | |
| if (!requireNamespace("BiocManager", quietly = TRUE)) | |
| install.packages("BiocManager", repos=c(CRAN="https://cran.r-project.org")) | |
| BiocManager::install("Rgraphviz") | |
| BiocManager::install("graph") | |
| shell: Rscript {0} | |
| - name: pak install from GitHub | |
| run: | | |
| pak::pkg_install("furrer-lab/abn@${{ env.BRANCH }}") | |
| 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} | |