-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
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 <j-i-l@t4d.ch>
- Loading branch information
1 parent
4279bc3
commit 49f0a6d
Showing
8 changed files
with
319 additions
and
541 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,77 @@ | ||
| # 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: ${{ secrets.GITHUB_TOKEN }} | ||
| R_KEEP_PKG_SOURCE: yes | ||
|
|
||
| steps: | ||
|
|
||
| - name: Update and upgrade | ||
| run: | | ||
| sudo apt-get update && sudo apt-get upgrade | ||
| - name: install R | ||
| run: | | ||
| sudo apt-get -y install r-base | ||
| - name: fixing folder perms for local lib | ||
| run: | | ||
| sudo chown root:adm -R /usr/lib/R | ||
| sudo chmod g+w -R /usr/lib/R | ||
| sudo chown root:adm -R /usr/local/lib/R | ||
| sudo chmod g+w -R /usr/local/lib/R | ||
| - name: install config and build dependencies | ||
| run: | | ||
| sudo apt-get -y install libcurl4-openssl-dev # needed for pak | ||
| - name: install pak | ||
| run: | | ||
| install.packages('pak', repos=c(CRAN="https://cran.r-project.org")) | ||
| shell: Rscript {0} | ||
|
|
||
| # - name: install from CRAN with pak | ||
| # run: | | ||
| # pak::pkg_install('abn', dependencies=TRUE) | ||
| # library('abn') | ||
| # shell: Rscript {0} | ||
|
|
||
| - name: pak install from GitHub | ||
| run: | | ||
| pak::repo_add(INLA = "https://inla.r-inla-download.org/R/stable/") | ||
| pak::pkg_install("furrer-lab/abn@${{ 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} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file was deleted.
Oops, something went wrong.
Oops, something went wrong.