add specific sysreqs for INLA installation

.github/workflows/onlabel_Fedora_setup.yml → .github/workflows/Fedora_setup.yml

@@ -44,13 +44,12 @@ jobs:
 
       - name: install config and build dependencies
         run: |
-          dnf -y install pkg-config
-          dnf -y install cmake
-          dnf -y install R-devtools
+          dnf -y install libcurl-devel  # needed for pak
 
-      - name: install GSL
+      - name: install pak
         run: |
-          dnf -y install gsl-devel
+          install.packages('pak', repos=c(CRAN="https://cran.r-project.org"))
+        shell: Rscript {0}
 
       - name: install JAGS
         run: |
@@ -73,38 +72,16 @@ jobs:
             library("rjags")
         shell: Rscript {0}
 
-      - name: install INLA dependencies
-        run: |
-          dnf -y install udunits2-devel
-          dnf -y install libcurl-devel  # rCurls package (for INLA)
-          dnf -y install openssl-devel  # s2 package
-          dnf -y install libjpeg-devel  # jpeg package
-          dnf -y install proj-devel     # sf package
-          dnf -y install geos-devel     # sf package
-          dnf -y install gdal-devel     # 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 CRAN with pak
+      #   run: |
+      #     pak::pkg_install('abn', dependencies=TRUE)
+      #     library('abn')
+      #   shell: Rscript {0}
 
-      - name: install from GitHub
+      - name: pak install from GitHub
         run: |
-          devtools::install_github("furrer-lab/abn", ref="${{ env.BRANCH }}", dependencies=c("Depends", "Imports", "LinkingTo"), local=FALSE)
+          pak::repo_add(INLA = "https://inla.r-inla-download.org/R/stable/")
+          pak::pkg_install("furrer-lab/abn@${{ env.BRANCH }}", dependencies=TRUE)
           library('abn')
         shell: Rscript {0}
 
@@ -118,7 +95,5 @@ jobs:
 
       - name: install from source
         run: |
-            devtools::install_deps(pkg = '.', dependencies = TRUE, upgrade='never', repos=c(CRAN="https://cran.r-project.org"))
-            devtools::build(pkg = '.', path = '${{ env.BUILD_LOC }}/abn.tar.gz', vignettes = FALSE)
-            install.packages('${{ env.BUILD_LOC }}/abn.tar.gz', repos=NULL, type="source")
+            pak::local_install(dependencies=TRUE)
         shell: Rscript {0}

.github/workflows/onlabel_Macos_setup.yml → .github/workflows/Macos_setup.yml

@@ -39,11 +39,11 @@ jobs:
         run: |
           brew install jags
 
-      - name: install rjags
-        run: |
-            install.packages("rjags", type="source", repos=c(CRAN="https://cran.r-project.org"))
-            library("rjags")
-        shell: Rscript {0}
+      # - name: install rjags
+      #   run: |
+      #       install.packages("rjags", type="source", repos=c(CRAN="https://cran.r-project.org"))
+      #       library("rjags")
+      #   shell: Rscript {0}
 
       - name: install INLA dependencies
         run: |
@@ -58,23 +58,21 @@ jobs:
             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
+      - name: install pak
         run: |
-          if (!requireNamespace("BiocManager", quietly = TRUE))
-              install.packages("BiocManager", repos=c(CRAN="https://cran.r-project.org"))
-          BiocManager::install("Rgraphviz")
-          BiocManager::install("graph")
+          install.packages('pak', repos=c(CRAN="https://cran.r-project.org"))
         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 CRAN with pak
+      #   run: |
+      #     pak::pkg_install('abn', dependencies=TRUE)
+      #     library('abn')
+      #   shell: Rscript {0}
 
-      - name: install from GitHub
+      - name: pak install from GitHub
         run: |
-          devtools::install_github("furrer-lab/abn", ref="${{ env.BRANCH }}", dependencies=c("Depends", "Imports", "LinkingTo"), local=FALSE)
+          pak::repo_add(INLA = "https://inla.r-inla-download.org/R/stable/")
+          pak::pkg_install("furrer-lab/abn@${{ env.BRANCH }}", dependencies=TRUE)
           library('abn')
         shell: Rscript {0}
 
@@ -88,7 +86,5 @@ jobs:
 
       - name: install from source
         run: |
-            devtools::install_deps(pkg = '.', dependencies = TRUE, upgrade='never', repos=c(CRAN="https://cran.r-project.org"))
-            devtools::build(pkg = '.', path = '${{ env.BUILD_LOC }}/abn.tar.gz', vignettes = FALSE)
-            install.packages('${{ env.BUILD_LOC }}/abn.tar.gz', repos=NULL, type="source")
+            pak::local_install(dependencies=TRUE)
         shell: Rscript {0}

.github/workflows/Ubuntu_setup.yml

@@ -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}

.github/workflows/onlabel_Windows_setup.yml → .github/workflows/Windows_setup.yml

@@ -29,9 +29,9 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
     steps:
 
-      - name: prepare windows
+      - name: install pak
         run: |
-            install.packages("devtools", repos=c(CRAN="https://cran.r-project.org"))
+          install.packages('pak', repos=c(CRAN="https://cran.r-project.org"))
         shell: Rscript {0}
 
       - name: install GSL
@@ -55,28 +55,16 @@ jobs:
             library("rjags")
         shell: Rscript {0}
 
-      - 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 CRAN with pak
+      #   run: |
+      #     pak::pkg_install('abn', dependencies=TRUE)
+      #     library('abn')
+      #   shell: Rscript {0}
 
-      - name: install from GitHub
+      - name: pak install from GitHub
         run: |
-          devtools::install_github("furrer-lab/abn", ref="${{ env.BRANCH }}", dependencies=c("Depends", "Imports", "LinkingTo"), local=FALSE)
+          pak::repo_add(INLA = "https://inla.r-inla-download.org/R/stable/")
+          pak::pkg_install("furrer-lab/abn@${{ env.BRANCH }}", dependencies=TRUE)
           library('abn')
         shell: Rscript {0}
 
@@ -90,7 +78,12 @@ jobs:
 
       - name: install from source
         run: |
-            devtools::install_deps(pkg = '.', dependencies = TRUE, upgrade='never', repos=c(CRAN="https://cran.r-project.org"))
-            devtools::build(pkg = '.', path = '${{ env.BUILD_LOC }}/abn.tar.gz', vignettes = FALSE)
-            install.packages('${{ env.BUILD_LOC }}/abn.tar.gz', repos=NULL, type="source")
+            pak::local_install(dependencies=TRUE)
+        shell: Rscript {0}
+
+      - name: run the tests
+        run: |
+            pak::pak('r-lib/testthat')
+            library("abn")
+            testthat::test_local(path='tests', load_package='none')
         shell: Rscript {0}