R4.2 update

FBartos · Mar 13, 2023 · 4c77b00 · 4c77b00
1 parent d7febd9
commit 4c77b00
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,3 +1,5 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
 on:
   push:
     branches:
@@ -22,84 +24,64 @@ jobs:
       fail-fast: false
       matrix:
         config:
-        #  - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-        #  - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: ubuntu-20.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: 'devel',   rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", http-user-agent: "R/4.1.0 (ubuntu-20.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
+        #  - {os: macOS-11.6.2,   r: 'release'} # the release C++ version does not compile properly
 
     env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: false
-      NOT_CRAN: true
 
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v1
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v1
 
       - name: Query dependencies
         run: |
           install.packages('remotes')
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
 
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v1
+      - name: Restore R package cache
+        uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-r-${{ matrix.config.r }}-3-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-3-
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
 
-      - name: Set path for RTools 4.0
-        if: runner.os == 'Windows'
-        run: echo "C:/rtools40/usr/bin;C:/rtools40/mingw64/bin" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
-
-      - name: Install most Windows system dependencies
-        if: runner.os == 'Windows'
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
         run: |
-          pacman -Syu mingw-w64-x86_64-make --noconfirm
-          g++ --version
-          Get-Command g++ | Select-Object -ExpandProperty Definition
-          mingw32-make --version
-          Get-Command mingw32-make | Select-Object -ExpandProperty Definition
-          (New-Object System.Net.WebClient).DownloadFile('https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Windows/JAGS-4.3.1.exe', 'C:\JAGS-4.3.1.exe')
-        shell: powershell
-
-      - name: Install JAGS on Windows
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install JAGS (windows-latest)
         if: runner.os == 'Windows'
-        run: C:\JAGS-4.3.1.exe /S
+        run: |
+          curl.exe -o wjags.exe --url https://deac-fra.dl.sourceforge.net/project/mcmc-jags/JAGS/4.x/Windows/JAGS-4.3.1.exe
+          wjags.exe /S
+          del wjags.exe
         shell: cmd
 
-      - name: Install Linux system dependencies
-        if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-        run: |
-          sudo apt-get install -y libglpk-dev
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
-          sudo -s apt-get install jags
-          sudo -s apt-get install libv8-dev
-          sudo -s apt-get install libnode-dev
-          sudo -s apt-get install libcurl4-openssl-dev
-
-      - name: Install Mac system dependencies
+      - name: Install JAGS (macOS-latest)
         if: runner.os == 'macOS'
-        run: |
-          brew install jags
-          brew install libgit2
-          
+        run : |
+          rm '/usr/local/bin/gfortran'
+          brew install automake jags
+
       - name: Install dependencies
         run: |
-          remotes::install_deps(dependencies = TRUE, type = ifelse(tolower(Sys.info()["sysname"]) == "linux", "source", "binary"))
+          remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 
@@ -108,6 +90,7 @@ jobs:
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
         run: |
+          options(crayon.enabled = TRUE)
           rcmdcheck::rcmdcheck(
             args        = c("--no-manual", "--as-cran", "--ignore-vignettes"),
             build_args  = c("--no-build-vignettes"),
@@ -122,12 +105,14 @@ jobs:
           JAGS_ROOT: "/c/progra~1/JAGS/JAGS-4.3.1"
           JAGS_MAJOR_VERSION: 4
         run: |
+          options(crayon.enabled = TRUE)
           rcmdcheck::rcmdcheck(
             args        = c("--no-manual", "--as-cran", "--ignore-vignettes"),
             build_args  = c("--no-build-vignettes"),
             error_on    = "warning",
             check_dir   = "check")
-        shell: Rscript {0}"
+        shell: Rscript {0}
+
 
       - name: Upload check results
         if: failure()

diff --git a/.github/workflows/R-CMD-tests.yaml b/.github/workflows/R-CMD-tests.yaml
@@ -24,96 +24,71 @@ jobs:
       fail-fast: false
       matrix:
         config:
-        #  - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-        #  - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: ubuntu-20.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+        #  - {os: macOS-11.6.2,   r: 'release'} # the release C++ version does not compile properly
 
     env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      NOT_CRAN: true
 
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v1
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v1
 
       - name: Query dependencies
         run: |
           install.packages('remotes')
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
 
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v1
+      - name: Restore R package cache
+        uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-r-${{ matrix.config.r }}-3-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-3-
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
 
-      - name: Set path for RTools 4.0
-        if: runner.os == 'Windows'
-        run: echo "C:/rtools40/usr/bin;C:/rtools40/mingw64/bin" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8
-
-      - name: Install most Windows system dependencies
-        if: runner.os == 'Windows'
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
         run: |
-          pacman -Syu mingw-w64-x86_64-make --noconfirm
-          g++ --version
-          Get-Command g++ | Select-Object -ExpandProperty Definition
-          mingw32-make --version
-          Get-Command mingw32-make | Select-Object -ExpandProperty Definition
-          (New-Object System.Net.WebClient).DownloadFile('https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Windows/JAGS-4.3.1.exe', 'C:\JAGS-4.3.1.exe')
-        shell: powershell
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
 
-      - name: Install JAGS on Windows
+      - name: Install JAGS (windows-latest)
         if: runner.os == 'Windows'
-        run: C:\JAGS-4.3.1.exe /S
-        shell: cmd
-
-      - name: Install Linux system dependencies
-        if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
         run: |
-          sudo apt-get install -y libglpk-dev
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
-          sudo -s apt-get install jags
-          sudo -s apt-get install libv8-dev
-          sudo -s apt-get install libnode-dev
-          sudo -s apt-get install libcurl4-openssl-dev
+          curl.exe -o wjags.exe --url https://deac-fra.dl.sourceforge.net/project/mcmc-jags/JAGS/4.x/Windows/JAGS-4.3.1.exe
+          wjags.exe /S
+          del wjags.exe
+        shell: cmd
 
-      - name: Install Mac system dependencies
+      - name: Install JAGS (macOS-latest)
         if: runner.os == 'macOS'
+        run : |
+          rm '/usr/local/bin/gfortran'
+          brew install automake jags
+
+      - name: Install and test RoBSA (non-Windows)
+        if: runner.os != 'Windows'
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
         run: |
-          brew install jags
-          brew install libgit2
-          
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE, type = ifelse(tolower(Sys.info()["sysname"]) == "linux", "source", "binary"))
+          remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
           install.packages("devtools")
           install.packages("testthat")
           install.packages("vdiffr")
           devtools::install()
-        shell: Rscript {0}
-
-      - name: Install and test RoBSA (non-Windows)
-        if: runner.os != 'Windows'
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run:
           library(vdiffr)
           library(testthat)
           devtools::test()
@@ -125,7 +100,13 @@ jobs:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
           JAGS_ROOT: "/c/progra~1/JAGS/JAGS-4.3.1"
           JAGS_MAJOR_VERSION: 4
-        run:
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+          install.packages("devtools")
+          install.packages("testthat")
+          install.packages("vdiffr")
+          devtools::install()
           library(vdiffr)
           library(testthat)
           devtools::test()

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: ubuntu-latest,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -62,7 +62,7 @@ jobs:
       - name: Install JAGS (windows-latest)
         if: runner.os == 'Windows'
         run: |
-          curl.exe -o wjags.exe --url https://deac-fra.dl.sourceforge.net/project/mcmc-jags/JAGS/4.x/Windows/JAGS-4.2.0-Rtools33.exe
+          curl.exe -o wjags.exe --url https://deac-fra.dl.sourceforge.net/project/mcmc-jags/JAGS/4.x/Windows/JAGS-4.3.1.exe
           wjags.exe /S
           del wjags.exe
         shell: cmd
@@ -77,8 +77,6 @@ jobs:
         run: |
           remotes::install_deps(dependencies = TRUE)
           install.packages("pkgdown")
-          #remotes::install_version("BayesTools", "0.2.10")
-          remotes::install_github("FBartos/[email protected]")
         shell: Rscript {0}
 
       - name: Install package