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add specific sysreqs for INLA installation (#139)
* add specific sysreqs for INLA installation * run on this dev branch * add udunits2 for fedora * check the package to verify if INLA is installed * we do not need to test the CRAN here * run checks on HEAD of the branch * no need to install from source * try without gsl install (old DESC file) * only update devtools - for speed * Revert "only update devtools - for speed" This reverts commit c05b5f9. * update only needed packages * go back to updating all * installing from source + checks * adding openssl as sysdep * adding curl as sysdep * trying INLA install via sysreq on Ubuntu * trying INLA install via sysreq Fedora * trying INLA install via sysreq Windows * running checks at the end * runnin on dev - to revert * upgrading ubuntu floavors * simpler dependency statemnt (incl. suggests) * also checks on macOS * adding the shlib_openmp_clfags to pkg_libs * addressing warning from checks * bump R6 to dependency so it is installed on cueck_built * include macos for testing * only fail on error * rely on rcmdcheck * removing prev. absent dep again * fix in build args param * adding sf as dependency (>fmesher>INLA) * ingore vignettes * losing Matrix req that requires R > 4.4.0 * remove dev running condition * install with pak (and thus sysdeps) * install curl for pak * separate step for pak install * including optional deps (i.e. also Suggests) * reverting dep for Matrix * adding INLA repo * cleaning up * try again with adding INLA repo * removing version pinning for Matrix * rely on sysdeps for fedora * ditch biocm specialy install * adding jags as sysdep (for ubuntu) * setup on Ubuntu with pak * removing dev running cond * now with pak * update might not be needed with pak * also adding libcurl for pak install * Case sensitivity * expicitely loading data * since tests run isolated - load package first * pak based setup on Fedora * adding Macos pak setup * better output for testthat * Windows setup with pak * updated instructions for Linux based systems * updated instructions for Linux based systems * formatting * adapting instructions for Mac&Windows * adaptig installing f GH * completing with pak install * adpted installation instructions for pak * cleaning up * keep only intallation steps * renaming * adapting setup batches * cleaning up * corrected naming * typo * completing from source install --------- Co-authored-by: Jonas I. Liechti <[email protected]>
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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 | ||
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| on: | ||
| push: | ||
| branches: | ||
| - "main" | ||
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| env: | ||
| BRANCH: ${{ github.head_ref || github.ref_name }} | ||
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| permissions: | ||
| packages: read | ||
| contents: write | ||
| pull-requests: write | ||
| repository-projects: write | ||
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| jobs: | ||
| setup-and-install: | ||
| runs-on: ubuntu-latest | ||
| name: ubuntu-latest R release | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| R_KEEP_PKG_SOURCE: yes | ||
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| steps: | ||
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| - name: Update and upgrade | ||
| run: | | ||
| sudo apt-get update && sudo apt-get upgrade | ||
| - name: install R | ||
| run: | | ||
| sudo apt-get -y install r-base | ||
| - name: fixing folder perms for local lib | ||
| run: | | ||
| sudo chown root:adm -R /usr/lib/R | ||
| sudo chmod g+w -R /usr/lib/R | ||
| sudo chown root:adm -R /usr/local/lib/R | ||
| sudo chmod g+w -R /usr/local/lib/R | ||
| - name: install config and build dependencies | ||
| run: | | ||
| sudo apt-get -y install libcurl4-openssl-dev # needed for pak | ||
| - name: install pak | ||
| run: | | ||
| install.packages('pak', repos=c(CRAN="https://cran.r-project.org")) | ||
| shell: Rscript {0} | ||
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| # - name: install from CRAN with pak | ||
| # run: | | ||
| # pak::pkg_install('abn', dependencies=TRUE) | ||
| # library('abn') | ||
| # shell: Rscript {0} | ||
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| - name: pak install from GitHub | ||
| run: | | ||
| pak::repo_add(INLA = "https://inla.r-inla-download.org/R/stable/") | ||
| pak::pkg_install("furrer-lab/abn@${{ env.BRANCH }}", dependencies=TRUE) | ||
| library('abn') | ||
| shell: Rscript {0} | ||
|
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| - name: fetch the repository from GitHub | ||
| uses: actions/checkout@v4 | ||
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| - name: deactivate the renv | ||
| run: | | ||
| renv::deactivate() | ||
| shell: Rscript {0} | ||
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| - name: install from source | ||
| run: | | ||
| pak::local_install(dependencies=TRUE) | ||
| shell: Rscript {0} |
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