Detailed installation instructions #42
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: Ubuntu Install | |
| on: | |
| pull_request: | |
| types: [ labeled ] | |
| env: | |
| LABEL_CHECK: 'ubuntuInstall::check' | |
| LABEL_SUCCESS: 'ubuntuInstall::passed' | |
| LABEL_FAILURE: 'ubuntuInstall::failed' | |
| JAGS: '4.3.2' | |
| BUILD_LOC: "./build" | |
| permissions: | |
| packages: read | |
| contents: write | |
| pull-requests: write | |
| repository-projects: write | |
| jobs: | |
| setup-and-install: | |
| runs-on: ubuntu-latest | |
| if: ${{ github.event.label.name == 'ubuntuInstall::check' }} | |
| name: ubuntu-latest (${{ matrix.config.r }}) | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {r: 'release'} | |
| # - {r: '4.1',} | |
| # - {r: 'devel', http-user-agent: 'release'} | |
| # - {r: 'oldrel-1',} | |
| # - {r: 'oldrel-2',} | |
| # - {r: 'oldrel-3',} | |
| steps: | |
| - name: install R | |
| run: | | |
| sudo apt-get -y install r-base | |
| - name: install config and build dependencies | |
| run: | | |
| sudo apt-get -y install pkg-config | |
| sudo apt-get -y install cmake | |
| sudo apt-get -y install r-cran-devtools | |
| - 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: update R packages | |
| run: | | |
| update.packages(ask = FALSE, checkBuilt = TRUE) | |
| shell: Rscript {0} | |
| - name: install GSL | |
| run: | | |
| sudo apt-get -y install libgsl-dev | |
| - name: install JAGS | |
| run: | | |
| sudo apt-get -y install jags | |
| - 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: install INLA dependencies | |
| run: | | |
| sudo apt-get install -y --no-install-recommends libudunits2-dev | |
| sudo apt -y install libcurl4-openssl-dev # rCurl for (for INLA) | |
| sudo apt-get -y install libssl-dev # s2 package | |
| sudo apt-get -y install libproj-dev # sf package | |
| sudo apt-get -y install libgeos-dev # terra package | |
| sudo apt-get -y install libgdal-dev # terra package | |
| - name: install INLA | |
| run: | | |
| install.packages("INLA", repos = c(CRAN = "https://cran.r-project.org", INLA = "https://inla.r-inla-download.org/R/stable"), dep = TRUE) | |
| 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: install from CRAN | |
| run: | | |
| install.packages('abn', repos=c(CRAN="https://cran.r-project.org")) | |
| library('abn') | |
| shell: Rscript {0} | |
| - name: install from GitHub | |
| run: | | |
| devtools::install_github("furrer-lab/abn", ref="detailed-installation-instructions", dependencies=c("Depends", "Imports", "LinkingTo"), local=FALSE) | |
| 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} | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: install from source | |
| run: | | |
| devtools::install_deps(pkg = '.', dependencies = TRUE, upgrade='never') | |
| devtools::build(pkg = '.', path = '${{ env.BUILD_LOC }}/abn.tar.gz') | |
| install.packages('${{ env.BUILD_LOC }}/abn.tar.gz', repos=NULL, type="source") | |
| shell: Rscript {0} | |
| report_Ubuntu_setup: | |
| if: ${{ (success() || failure()) }} | |
| needs: | |
| - setup-and-install | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| repository-projects: write | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| OWNER: ${{ github.repository_owner }} | |
| REPO: ${{ github.event.repository.name }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Check if on demand tasks succeeded | |
| run: | | |
| gh pr edit ${{ env.EVENT }} --remove-label ${{ env.LABEL_CHECK }} --repo ${{ env.OWNER }}/${{ env.REPO }} | |
| if [ ${{ needs.setup-and-install.result }} == "success" ]; then | |
| gh pr edit ${{ env.EVENT }} --remove-label ${{ env.LABEL_FAILURE }} --repo ${{ env.OWNER }}/${{ env.REPO }} | |
| gh pr edit ${{ env.EVENT }} --add-label ${{ env.LABEL_SUCCESS }} --repo ${{ env.OWNER }}/${{ env.REPO }} | |
| echo "### ${{ github.event.label.url }} passed! :rocket:" >> $GITHUB_STEP_SUMMARY | |
| exit 0 | |
| elif [ ${{ needs.setup-and-install.result }} == "failure" ]; then | |
| gh pr edit ${{ env.EVENT }} --remove-label ${{ env.LABEL_SUCCESS }} --repo ${{ env.OWNER }}/${{ env.REPO }} | |
| gh pr edit ${{ env.EVENT }} --add-label ${{ env.LABEL_FAILURE }} --repo ${{ env.OWNER }}/${{ env.REPO }} | |
| echo "### ${{ github.event.label.url }} failed!" >> $GITHUB_STEP_SUMMARY | |
| exit 1 | |
| else | |
| gh pr edit ${{ env.EVENT }} --add-label ${{ env.LABEL_CHECK }} --repo ${{ env.OWNER }}/${{ env.REPO }} | |
| echo "On demand task outcome was ${{ needs.setup-and-installoutcome }}" | |
| fi | |
| shell: bash | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| EVENT: ${{ github.event.number }} # This is either the issue or pr |