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matteodelucchij-i-l
matteodelucchi
and
j-i-l
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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 <j-i-l@t4d.ch>
1 parent 4279bc3 commit 49f0a6d

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.github/workflows/onlabel_Fedora_setup.yml renamed to .github/workflows/Fedora_setup.yml

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- name: install config and build dependencies
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run: |
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dnf -y install pkg-config
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dnf -y install cmake
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dnf -y install R-devtools
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dnf -y install libcurl-devel # needed for pak
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- name: install GSL
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- name: install pak
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run: |
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dnf -y install gsl-devel
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install.packages('pak', repos=c(CRAN="https://cran.r-project.org"))
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shell: Rscript {0}
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- name: install JAGS
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run: |
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library("rjags")
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shell: Rscript {0}
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- name: install INLA dependencies
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run: |
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dnf -y install udunits2-devel
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dnf -y install libcurl-devel # rCurls package (for INLA)
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dnf -y install openssl-devel # s2 package
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dnf -y install libjpeg-devel # jpeg package
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dnf -y install proj-devel # sf package
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dnf -y install geos-devel # sf package
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dnf -y install gdal-devel # terra package
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- name: install INLA
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run: |
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install.packages("INLA", repos = c(CRAN = "https://cran.r-project.org", INLA = "https://inla.r-inla-download.org/R/stable"), dep = TRUE)
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shell: Rscript {0}
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- name: installing dependencies from BiocManager
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run: |
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if (!requireNamespace("BiocManager", quietly = TRUE))
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install.packages("BiocManager", repos=c(CRAN="https://cran.r-project.org"))
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BiocManager::install("Rgraphviz")
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BiocManager::install("graph")
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shell: Rscript {0}
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- name: install from CRAN
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run: |
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install.packages('abn', repos=c(CRAN="https://cran.r-project.org"))
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library('abn')
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shell: Rscript {0}
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# - name: install from CRAN with pak
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# run: |
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# pak::pkg_install('abn', dependencies=TRUE)
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# library('abn')
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# shell: Rscript {0}
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- name: install from GitHub
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- name: pak install from GitHub
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run: |
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devtools::install_github("furrer-lab/abn", ref="${{ env.BRANCH }}", dependencies=c("Depends", "Imports", "LinkingTo"), local=FALSE)
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pak::repo_add(INLA = "https://inla.r-inla-download.org/R/stable/")
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pak::pkg_install("furrer-lab/abn@${{ env.BRANCH }}", dependencies=TRUE)
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library('abn')
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shell: Rscript {0}
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- name: install from source
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run: |
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devtools::install_deps(pkg = '.', dependencies = TRUE, upgrade='never', repos=c(CRAN="https://cran.r-project.org"))
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devtools::build(pkg = '.', path = '${{ env.BUILD_LOC }}/abn.tar.gz', vignettes = FALSE)
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install.packages('${{ env.BUILD_LOC }}/abn.tar.gz', repos=NULL, type="source")
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pak::local_install(dependencies=TRUE)
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shell: Rscript {0}

.github/workflows/onlabel_Macos_setup.yml renamed to .github/workflows/Macos_setup.yml

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run: |
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brew install jags
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- name: install rjags
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run: |
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install.packages("rjags", type="source", repos=c(CRAN="https://cran.r-project.org"))
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library("rjags")
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shell: Rscript {0}
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# - name: install rjags
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# run: |
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# install.packages("rjags", type="source", repos=c(CRAN="https://cran.r-project.org"))
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# library("rjags")
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# shell: Rscript {0}
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- name: install INLA dependencies
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run: |
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install.packages("INLA", repos = c(CRAN = "https://cran.r-project.org", INLA = "https://inla.r-inla-download.org/R/stable"), dep = TRUE)
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shell: Rscript {0}
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- name: installing dependencies from BiocManager
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- name: install pak
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run: |
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if (!requireNamespace("BiocManager", quietly = TRUE))
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install.packages("BiocManager", repos=c(CRAN="https://cran.r-project.org"))
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BiocManager::install("Rgraphviz")
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BiocManager::install("graph")
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install.packages('pak', repos=c(CRAN="https://cran.r-project.org"))
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shell: Rscript {0}
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- name: install from CRAN
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run: |
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install.packages('abn', repos=c(CRAN="https://cran.r-project.org"))
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library('abn')
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shell: Rscript {0}
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# - name: install from CRAN with pak
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# run: |
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# pak::pkg_install('abn', dependencies=TRUE)
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# library('abn')
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# shell: Rscript {0}
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- name: install from GitHub
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- name: pak install from GitHub
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run: |
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devtools::install_github("furrer-lab/abn", ref="${{ env.BRANCH }}", dependencies=c("Depends", "Imports", "LinkingTo"), local=FALSE)
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pak::repo_add(INLA = "https://inla.r-inla-download.org/R/stable/")
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pak::pkg_install("furrer-lab/abn@${{ env.BRANCH }}", dependencies=TRUE)
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library('abn')
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shell: Rscript {0}
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- name: install from source
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run: |
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devtools::install_deps(pkg = '.', dependencies = TRUE, upgrade='never', repos=c(CRAN="https://cran.r-project.org"))
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devtools::build(pkg = '.', path = '${{ env.BUILD_LOC }}/abn.tar.gz', vignettes = FALSE)
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install.packages('${{ env.BUILD_LOC }}/abn.tar.gz', repos=NULL, type="source")
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pak::local_install(dependencies=TRUE)
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shell: Rscript {0}

‎.github/workflows/Ubuntu_setup.yml‎

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# Workflow is triggered on label and check installation on various operating systems
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# This action is adapted from https://github.com/t4d-gmbh/stubbed_versioning
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name: Ubuntu Install
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on:
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push:
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branches:
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- "main"
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env:
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BRANCH: ${{ github.head_ref || github.ref_name }}
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permissions:
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packages: read
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contents: write
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pull-requests: write
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repository-projects: write
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jobs:
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setup-and-install:
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runs-on: ubuntu-latest
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name: ubuntu-latest R release
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- name: Update and upgrade
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run: |
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sudo apt-get update && sudo apt-get upgrade
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- name: install R
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run: |
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sudo apt-get -y install r-base
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- name: fixing folder perms for local lib
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run: |
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sudo chown root:adm -R /usr/lib/R
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sudo chmod g+w -R /usr/lib/R
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sudo chown root:adm -R /usr/local/lib/R
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sudo chmod g+w -R /usr/local/lib/R
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- name: install config and build dependencies
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run: |
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sudo apt-get -y install libcurl4-openssl-dev # needed for pak
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- name: install pak
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run: |
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install.packages('pak', repos=c(CRAN="https://cran.r-project.org"))
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shell: Rscript {0}
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# - name: install from CRAN with pak
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# run: |
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# pak::pkg_install('abn', dependencies=TRUE)
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# library('abn')
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# shell: Rscript {0}
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- name: pak install from GitHub
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run: |
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pak::repo_add(INLA = "https://inla.r-inla-download.org/R/stable/")
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pak::pkg_install("furrer-lab/abn@${{ env.BRANCH }}", dependencies=TRUE)
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library('abn')
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shell: Rscript {0}
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- name: fetch the repository from GitHub
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uses: actions/checkout@v4
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- name: deactivate the renv
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run: |
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renv::deactivate()
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shell: Rscript {0}
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- name: install from source
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run: |
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pak::local_install(dependencies=TRUE)
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shell: Rscript {0}

.github/workflows/onlabel_Windows_setup.yml renamed to .github/workflows/Windows_setup.yml

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R_KEEP_PKG_SOURCE: yes
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steps:
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- name: prepare windows
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- name: install pak
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run: |
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install.packages("devtools", repos=c(CRAN="https://cran.r-project.org"))
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install.packages('pak', repos=c(CRAN="https://cran.r-project.org"))
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shell: Rscript {0}
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- name: install GSL
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library("rjags")
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shell: Rscript {0}
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- name: install INLA
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run: |
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install.packages("INLA", repos = c(CRAN = "https://cran.r-project.org", INLA = "https://inla.r-inla-download.org/R/stable"), dep = TRUE)
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shell: Rscript {0}
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- name: installing dependencies from BiocManager
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run: |
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if (!requireNamespace("BiocManager", quietly = TRUE))
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install.packages("BiocManager", repos=c(CRAN="https://cran.r-project.org"))
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BiocManager::install("Rgraphviz")
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BiocManager::install("graph")
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shell: Rscript {0}
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- name: install from CRAN
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run: |
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install.packages('abn', repos=c(CRAN="https://cran.r-project.org"))
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library('abn')
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shell: Rscript {0}
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# - name: install from CRAN with pak
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# run: |
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# pak::pkg_install('abn', dependencies=TRUE)
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# library('abn')
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# shell: Rscript {0}
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- name: install from GitHub
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- name: pak install from GitHub
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run: |
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devtools::install_github("furrer-lab/abn", ref="${{ env.BRANCH }}", dependencies=c("Depends", "Imports", "LinkingTo"), local=FALSE)
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pak::repo_add(INLA = "https://inla.r-inla-download.org/R/stable/")
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pak::pkg_install("furrer-lab/abn@${{ env.BRANCH }}", dependencies=TRUE)
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library('abn')
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shell: Rscript {0}
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- name: install from source
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run: |
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devtools::install_deps(pkg = '.', dependencies = TRUE, upgrade='never', repos=c(CRAN="https://cran.r-project.org"))
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devtools::build(pkg = '.', path = '${{ env.BUILD_LOC }}/abn.tar.gz', vignettes = FALSE)
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install.packages('${{ env.BUILD_LOC }}/abn.tar.gz', repos=NULL, type="source")
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pak::local_install(dependencies=TRUE)
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shell: Rscript {0}
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- name: run the tests
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run: |
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pak::pak('r-lib/testthat')
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library("abn")
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testthat::test_local(path='tests', load_package='none')
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shell: Rscript {0}

‎.github/workflows/onlabel_Ubuntu_setup.yml‎

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