Fix: detailed installation instructions (#126)

* on label install check mac & windows

* fixing running condition

* installing dependencies for macos

* try installing gsl package

* dedicated window pipeline

* fixing os parameter

* dedicated macos workflow

* Revert "try installing gsl package"

This reverts commit b6678f5.

* minor label formatting

* fixing container declaration

* installing jags

* adding jags path

* trying again with install

* installing rjags providing Jags home

* try with silent mode fore setup exe'

* adding more R versions

* install INLA

* renaming workflow

* debugging - show gls configs

* fixing to always report

* create configure file with autoconf

* installing automake

* debugging - gsl path

* providing flags for clang/gcc as well

* debugging - check jags location

* try to detect the paths for jags

* passing the args to Makevars

* better test

* debugging

* unconditional try

* debugging

* separate install of rjags

* simplify

* working with only configure.ac file

* providing jags paths does not help

* started with Fedora installation workflow

* started with restructuring installation section

* adding installing ... sections

* workflow to Fedora

* in a container it is

* installing missing tools

* specify mirror

* missing gfortran and deps

* wip on README

* fixing INLA installation mirror

* more details on jags

* adding mirrors

* Info about GSL

* fixing installation command

* done with extre installation steps

* harmonizing structure

* fixing gsl download

* providig mirror

* separately install rjags

* install R-devtools

* adding BiocManager deps

* fixing testthat call

* installing INLA separately

* fixing name

* intalling R on macos

* test without cmake

* getting the tests and run testthat

* properly handling renv

* attempt to link (r)jags

* intalling alos Suggests

* fixing path to jags.pc

* installing Suggests

* also install rjags explicitly

* install pkg-config for rjags

* working config on fedora server

* try with the pkg-config path

* without specifying type

* debugging

* fixed R script run

* check runtime linkage

* better highlighting

* debugging

* provide path to jags library

* try without pkg_config_path

* details about fedora and jags

* including entropy package

* to revert - test with actual version

* run autoconf before installing from source

* started with prereq part

* started with macos prereqs

* separate location for build and test

* Ubuntu installation workflow

* Ubuntu based workflow

* debugging folder permisssions

* allow adm group to write to /usr/local/lib

* install dependencies

* completing installing from ... parts

* formatting

* specify which dependencies

* identical testing workflow

* fixing pkg root

* adding dependencies for testing

* adding udunits for INLA #125

* typeo

* adiding curl dev for inla dep.

* installing INLA dependencies

* try to avoid version check issue in devtools

* installing openssl heasders

* installing openssl dev

* fixing package name

* first make dir writeable

* macos install gdal for s2>fmesher>INLA

* installing gdal for INLA

* fixing folder perms for R site-library

* jpeg headers for INLA dependency

* includig gdal headers for INLA

* adding gdal headers for INLA

* adding testthat again

* try install avoiding useing local .o and .so

* testing the install via CRAN

* bouncing moments dependency

* fixing typeo

* proj headers for sf>fmesher>INLA

* adding proj headers for INLA

* adding configure built with configure.ac - see #127

* specify mirror for CRAN install

* adding some more info to configure

* fixing typeo

* uniform naming

* loading library

* cleaning up windows workflow

* cleaning up macos workflow

* cleaning up fedora workflow

* cleaning up ubuntu workflow

* installing geos headers for INLA

* installing geos>terra>INLA

* corrected comment

* building from source

* how to install from source

* adding pandoc to build from source

* do not build vignettes

* fixing devtools info for mac +

* do not build vignettes

* specify repos

* ditch the matrix

* using autoreconf

* removing virtual env setup for now (is untested)

* only claim what we really tested

* minor completion by adding mirror

* adding install status badges

* minor formatting

* running on specific branch

* more structure in INLA part

* test headers

* formatting dropdowns as headers

* properly set targeted branch

* minor formatting

* adding rjags install for ubunut

* fixing typos

* fixing #129 - typo

* better indentation

* fixing some permissions for fedora

* simply ignore the installation issue for html docs

.github/workflows/onlabel_CRAN_checks.yml

@@ -87,10 +87,9 @@ jobs:
         run: |
             renv::deactivate()
         shell: Rscript {0}
-      - name: Change permissions of configure
+      - name: Configure ABN for installation
         run: |
-            chmod +x configure
-        shell: bash
+          autoreconf
       - name: Install package dependencies
         run: |
             devtools::install_deps(pkg = '.', dependencies = TRUE, upgrade='never')

.github/workflows/onlabel_Fedora_setup.yml

@@ -0,0 +1,164 @@
+# 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: Fedora Install
+
+on:
+  pull_request:
+    types: [ labeled ]
+
+env:
+  LABEL_CHECK: 'fedoraInstall::check'
+  LABEL_SUCCESS: 'fedoraInstall::passed'
+  LABEL_FAILURE: 'fedoraInstall::failed'
+  JAGS: '4.3.2'
+  BUILD_LOC: "./build"
+  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
+    container:
+      image: "fedora:latest"
+    if: ${{ github.event.label.name == 'fedoraInstall::check' }}
+    name: fedora-latest R release
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - name: prepare fedora
+        run: |
+          dnf -y install wget
+          dnf -y install gcc
+          dnf -y install gcc-c++
+          dnf -y install gfortran
+          dnf -y install lapack*  # is needed on fedora server
+          dnf -y install blas*
+          dnf -y install atlas*
+
+      - name: install R
+        run: |
+          dnf -y install R
+
+      - name: install config and build dependencies
+        run: |
+          dnf -y install pkg-config
+          dnf -y install cmake
+          dnf -y install R-devtools
+
+      - name: install GSL
+        run: |
+          dnf -y install gsl-devel
+
+      - name: install JAGS
+        run: |
+          wget -O /tmp/jags.tar.gz https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-${{ env.JAGS }}.tar.gz/download
+          cd /tmp
+          tar -xf jags.tar.gz
+          cd /tmp/JAGS-${{ env.JAGS }} 
+          ./configure --libdir=/usr/local/lib64
+          make
+          make install
+
+      - name: assert runtime linkage
+        run: |
+          echo "/usr/local/lib64" > /etc/ld.so.conf.d/jags.conf
+          /sbin/ldconfig
+
+      - name: install rjags
+        run: |
+            install.packages("rjags", configure.args="--enable-rpath", repos=c(CRAN="https://cran.r-project.org"))
+            library("rjags")
+        shell: Rscript {0}
+
+      - name: install INLA dependencies
+        run: |
+          dnf -y install udunits2-devel
+          dnf -y install libcurl-devel  # rCurls package (for INLA)
+          dnf -y install openssl-devel  # s2 package
+          dnf -y install libjpeg-devel  # jpeg package
+          dnf -y install proj-devel     # sf package
+          dnf -y install geos-devel     # sf package
+          dnf -y install gdal-devel     # terra package
+
+      - name: install INLA
+        run: |
+            install.packages("INLA", repos = c(CRAN = "https://cran.r-project.org", INLA = "https://inla.r-inla-download.org/R/stable"), dep = TRUE)
+        shell: Rscript {0}
+
+      - name: installing dependencies from BiocManager
+        run: |
+          if (!requireNamespace("BiocManager", quietly = TRUE))
+              install.packages("BiocManager", repos=c(CRAN="https://cran.r-project.org"))
+          BiocManager::install("Rgraphviz")
+          BiocManager::install("graph")
+        shell: Rscript {0}
+
+      - name: install from CRAN
+        run: |
+          install.packages('abn', repos=c(CRAN="https://cran.r-project.org"))
+          library('abn')
+        shell: Rscript {0}
+
+      - name: install from GitHub
+        run: |
+          devtools::install_github("furrer-lab/abn", ref="${{ env.BRANCH }}", 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}
+
+      - 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")
+        shell: Rscript {0}
+
+  report_Fedora_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

.github/workflows/onlabel_Macos_setup.yml

@@ -0,0 +1,134 @@
+# 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: Macos Install
+
+on:
+  pull_request:
+    types: [ labeled ]
+
+env:
+  LABEL_CHECK: 'macosInstall::check'
+  LABEL_SUCCESS: 'macosInstall::passed'
+  LABEL_FAILURE: 'macosInstall::failed'
+  BUILD_LOC: "./build"
+  BRANCH: ${{ github.head_ref || github.ref_name }}
+
+permissions:
+  packages: read
+  contents: write
+  pull-requests: write
+  repository-projects: write
+
+jobs:
+  setup-and-install:
+    if: ${{ github.event.label.name == 'macosInstall::check' }}
+    name: macos-latest R release
+    runs-on: macos-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - name: prepare macos
+        run: |
+          brew install R
+          brew install pkg-config
+          brew install automake  # needed to run autoconf
+
+      - name: install GSL
+        run: |
+          brew install gsl
+
+      - name: install JAGS
+        run: |
+          brew install jags
+
+      - name: install rjags
+        run: |
+            install.packages("rjags", type="source", repos=c(CRAN="https://cran.r-project.org"))
+            library("rjags")
+        shell: Rscript {0}
+
+      - name: install INLA dependencies
+        run: |
+          brew install udunits 
+          brew install [email protected]  # s2 package
+          brew install gdal  # installs geos as dependency
+                             # for s2 fmesher terra)
+          brew install proj  # sf package
+
+      - name: install INLA
+        run: |
+            install.packages("INLA", repos = c(CRAN = "https://cran.r-project.org", INLA = "https://inla.r-inla-download.org/R/stable"), dep = TRUE)
+        shell: Rscript {0}
+
+      - name: installing dependencies from BiocManager
+        run: |
+          if (!requireNamespace("BiocManager", quietly = TRUE))
+              install.packages("BiocManager", repos=c(CRAN="https://cran.r-project.org"))
+          BiocManager::install("Rgraphviz")
+          BiocManager::install("graph")
+        shell: Rscript {0}
+
+      - name: install from CRAN
+        run: |
+          install.packages('abn', repos=c(CRAN="https://cran.r-project.org"))
+          library('abn')
+        shell: Rscript {0}
+
+      - name: install from GitHub
+        run: |
+          devtools::install_github("furrer-lab/abn", ref="${{ env.BRANCH }}", 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}
+
+      - 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")
+        shell: Rscript {0}
+
+  report_Macos_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-install.outcome }}"
+          fi
+        shell: bash
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          EVENT: ${{ github.event.number }}  # This is either the issue or pr