updates (#14)

* update deps
* fix badges
* modernize ga workflows
* fix urls
* update to fix checks on CRAN's Fedora system
* update to c++14
* update cran comments
* update news
* deprecate raster package
* use sf and terra packages
* update data
* update citation format

.Rbuildignore

@@ -18,7 +18,5 @@ cran-comments.md
 _pkgdown.yml
 README.Rmd
 spell.log
-^extdata*
-^inst/extdata*
 Rplots.pdf
 ^\.github$

.github/workflows/R-CMD-check-fedora.yaml

@@ -0,0 +1,125 @@
+# 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: workflow_dispatch
+
+name: Fedora
+
+env:
+  OMP_THREAD_LIMIT: 2
+  KMP_DEVICE_THREAD_LIMIT: 2
+  _R_CHECK_SUGGESTS_ONLY_: true
+  _R_CHECK_NO_RECOMMENDED_: true
+  _R_CHECK_DOC_SIZES2_: true
+  _R_CHECK_DEPRECATED_DEFUNCT_: true
+  _R_CHECK_SCREEN_DEVICE_: warn
+  _R_CHECK_REPLACING_IMPORTS_: true
+  _R_CHECK_TOPLEVEL_FILES_: true
+  _R_CHECK_DOT_FIRSTLIB_: true
+  _R_CHECK_RD_LINE_WIDTHS_: true
+  _R_CHECK_S3_METHODS_NOT_REGISTERED_: true
+  _R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_: true
+  _R_CHECK_CODE_USAGE_WITH_ONLY_BASE_ATTACHED_: true
+  _R_CHECK_NATIVE_ROUTINE_REGISTRATION_: true
+  _R_CHECK_FF_CALLS_: registration
+  _R_CHECK_PRAGMAS_: true
+  _R_CHECK_COMPILATION_FLAGS_: true
+  _R_CHECK_R_DEPENDS_: true
+  _R_CHECK_PACKAGES_USED_IN_TESTS_USE_SUBDIRS_: true
+  _R_CHECK_SHLIB_OPENMP_FLAGS_: true
+  _R_CHECK_BROWSER_NONINTERACTIVE_: true
+  _R_CHECK_CODE_ASSIGN_TO_GLOBALENV_: true
+  _R_CHECK_CODE_DATA_INTO_GLOBALENV_: true
+  _R_CHECK_PKG_SIZES_: true
+  _R_CHECK_LIMIT_CORES_: true
+  _R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_: true
+  _R_CHECK_AUTOCONF_: true
+  _R_CHECK_THINGS_IN_CHECK_DIR_: true
+  _R_CHECK_THINGS_IN_TEMP_DIR_: true
+  _R_CHECK_THINGS_IN_TEMP_DIR_EXCLUDE_: "^ompi"
+  _R_CHECK_BASHISMS_: true
+  _R_CHECK_ORPHANED_: true
+  _R_CHECK_DEPENDS_ONLY_DATA_: true
+  _R_CHECK_XREFS_PKGS_ARE_DECLARED_: true
+  _R_CHECK_MATRIX_DATA_: true
+  _R_CHECK_RD_VALIDATE_RD2HTML_: true
+  _R_CHECK_RD_MATH_RENDERING_: true
+
+jobs:
+  R-CMD-check:
+    name: Fedora (devel)
+
+    runs-on: ubuntu-latest
+
+    container:
+      image: docker://rhub/fedora-clang-devel:latest
+      options: --user root
+      env:
+        _R_REMOTES_NO_ERRORS_FROM_WARNINGS_: true
+        _R_CHECK_FORCE_SUGGESTS_: false
+        _R_CHECK_TIMINGS_: 10
+        _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        _R_CHECK_LIMIT_CORES_: true
+        _R_CHECK_LICENSE_: true
+        OMP_THREAD_LIMIT: 2
+        KMP_DEVICE_THREAD_LIMIT: 2
+        KMP_TEAMS_THREAD_LIMIT: 2
+        KMP_ALL_THREADS: 2
+        NOT_CRAN: true
+        GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+        CI: true
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Setup path
+        run: |
+          echo "/opt/R-devel/bin" >> $GITHUB_PATH
+
+      - name: Install system dependencies
+        run: |
+          echo $PATH
+          dnf install -y \
+            mpfr-devel \
+            automake \
+            fftw-devel \
+            gmp-devel \
+            openssl-devel \
+            zlib-devel \
+            pandoc \
+            geos-devel \
+            make \
+            gdal \
+            libxml2-devel \
+            cmake \
+            proj-devel \
+            sqlite-devel \
+            gdal-devel \
+            libicu-devel \
+            udunits2-devel \
+            coin-or-SYMPHONY-devel \
+            git-all
+
+      - name: Install dependencies
+        run: |
+          options(repos = "https://cloud.r-project.org/")
+          install.packages("remotes")
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Session information
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        run: |
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-build-vignettes"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash

.github/workflows/R-CMD-check-macos.yaml

@@ -12,7 +12,7 @@ on:
       - main
       - master
 
-name: Mac OSX
+name: macOS
 
 jobs:
   R-CMD-check:
@@ -33,46 +33,37 @@ jobs:
       _R_CHECK_CRAN_INCOMING_REMOTE_: false
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       CI: true
-      ## rgl R package environmental variables
-      RGL_USE_NULL: true
-      SDKROOT: /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-      DISPLAY: ":99"
 
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
-        with:
-          r-version: ${{ matrix.config.r }}
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - 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@v2
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
 
       - name: Install system dependencies
-        if: runner.os == 'macOS'
         run: |
-          brew install --cask xquartz
+          brew install automake
+          brew install gdal
 
-      - name: Install dependencies
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 1
+          extra-packages: |
+            any::rcmdcheck
+            gurobi=?ignore
+          needs: |
+            check
+            coverage
+
+      - name: Install spatial R packages
         run: |
-          options("install.packages.compile.from.source" = "never")
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          remotes::install_cran("covr")
+          options(repos = "https://cloud.r-project.org/")
+          install.packages("sf")
+          install.packages("terra")
         shell: Rscript {0}
 
       - name: Session information
@@ -82,19 +73,11 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - name: Check
-        run: |
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-build-vignettes"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
 
       - name: Show testthat output
         if: always()
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check

.github/workflows/R-CMD-check-ubuntu.yaml

@@ -38,43 +38,40 @@ jobs:
       CI: true
 
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v1
-        with:
-          r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: actions/checkout@v2
 
-      - 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}
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-2-
+          r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
 
       - name: Install system dependencies
-        if: runner.os == 'Linux'
         run: |
-          sudo apt-get -y install libcurl4-openssl-dev
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+          sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
+          sudo apt update
+          sudo apt-get install \
+            libgdal-dev libgeos-dev libproj-dev \
+            libudunits2-dev libharfbuzz-dev libfribidi-dev
 
-      - name: Install dependencies
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 1
+          extra-packages: |
+            any::covr
+            any::rcmdcheck
+            gurobi=?ignore
+          needs: |
+            check
+            coverage
+
+      - name: Install spatial R packages
         run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          remotes::install_cran("covr")
+          options(repos = "https://cloud.r-project.org/")
+          install.packages("sf")
+          install.packages("terra")
         shell: Rscript {0}
 
       - name: Session information
@@ -84,22 +81,15 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - name: Set environmental variables for package checks
+      - name: Environmental variables
         if: matrix.config.pkgs == 'depends only'
         run: |
           echo "_R_CHECK_DEPENDS_ONLY_=true" >> $GITHUB_ENV
 
-      - name: Check
-        run: |
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-build-vignettes"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          args: 'c("--no-manual", "--as-cran", "--no-build-vignettes")'
+          upload-snapshots: true
 
       - name: Show testthat output
         if: always()