fix ci + package manual entry (PR #16)

* update ci * package manual entry
prioritizr · Jul 8, 2024 · df31a5f · df31a5f
1 parent 087ad2b
commit df31a5f
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diff --git a/.github/workflows/R-CMD-check-ubuntu.yaml b/.github/workflows/R-CMD-check-ubuntu.yaml
@@ -38,45 +38,42 @@ jobs:
       NOT_CRAN: true
 
     steps:
+      # configure git to prevent it from automatically converting line-endings
+      # this is important to avoid WARNINGS during CRAN checks
+      # that are false-positives, see:
+      # https://msmith.de/2020/03/12/r-cmd-check-github-actions.html
+      - name: Configure git
+        run: git config --global core.autocrlf false
+
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
+      - name: Install system 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}
+          sudo apt-get install libnlopt-dev coinor-libsymphony-dev
 
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@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-
-
-      - name: Install system dependencies
-        run: |
-          sudo apt-get -y install \
-            libcurl4-openssl-dev coinor-libsymphony-dev coinor-libcbc-dev coinor-libclp-dev \
-            libudunits2-dev libgdal-dev libgeos-dev libproj-dev libglpk-dev
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
+          cache-version: 4
+          extra-packages: |
+            any::rcmdcheck
+            any::remotes
+            any::XML
+            any::covr
+          needs: |
+            check
+
+      - name: Install spatial R packages
         run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          remotes::install_cran("covr")
-          remotes::install_cran("urlchecker", force = TRUE)
+          options(repos = "https://cloud.r-project.org/")
+          install.packages("sf")
+          install.packages("terra")
         shell: Rscript {0}
 
       - name: Session information
@@ -91,17 +88,9 @@ jobs:
         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
+          upload-snapshots: true
 
       - name: Show testthat output
         if: always()

diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml
@@ -36,46 +36,39 @@ jobs:
       NOT_CRAN: true
 
     steps:
+      # configure git to prevent it from automatically converting line-endings
+      # this is important to avoid WARNINGS during CRAN checks
+      # that are false-positives, see:
+      # https://msmith.de/2020/03/12/r-cmd-check-github-actions.html
+      - name: Configure git
+        run: git config --global core.autocrlf false
+
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
 
-      - 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-dependencies@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-
-
-      - name: Install system dependencies
-        run: |
-          sudo apt-get -y install \
-            libcurl4-openssl-dev coinor-libsymphony-dev coinor-libcbc-dev coinor-libclp-dev \
-            libudunits2-dev libgdal-dev libgeos-dev libproj-dev libglpk-dev
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+          cache-version: 4
+          extra-packages: |
+            any::rcmdcheck
+            any::remotes
+            any::XML
+            any::covr
+            any::urlchecker
+          needs: |
+            check
 
-      - name: Install dependencies
+      - name: Install spatial R packages
         run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          remotes::install_cran("covr")
-          remotes::install_bioc("lpsymphony")
-          remotes::install_cran("urlchecker")
+          options(repos = "https://cloud.r-project.org/")
+          install.packages("sf")
+          install.packages("terra")
         shell: Rscript {0}
 
       - name: Session information
@@ -85,19 +78,16 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - name: Set environmental variables for package checks
-        if: matrix.config.pkgs == 'depends only'
-        run: |
-          echo "_R_CHECK_DEPENDS_ONLY_=true" >> $GITHUB_ENV
-
       - name: Check URLs
         if: runner.os == 'Linux' && matrix.config.r == 'release'
         run: |
           result <- urlchecker::url_check()
+          result <- result[result$Message != "OK", , drop = FALSE]
           result <- result[result$URL != "https://www.bcassessment.ca/", , drop = FALSE]
           result <- result[!startsWith(result$URL, "https://doi.org/"), , drop = FALSE]
           if (nrow(result) > 0) {
             print(result)
+            print(str(result))
             stop("Invalid URLs detected")
           }
         shell: Rscript {0}
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: prioritizrdata
 Type: Package
-Version: 0.3.2.1
+Version: 0.3.2.2
 Title: Conservation Planning Datasets
 Description: Conservation planning datasets for learning how to use the
     'prioritizr' package <https://CRAN.R-project.org/package=prioritizr>.
@@ -21,7 +21,7 @@ Authors@R:
       person(c('Peter'), 'Arcese',
         email='[email protected]', role = c('aut'),
         comment = c(ORCID = '0000-0002-8097-482X')),
-      person(c('Joseph'), 'Bennett',
+      person(c('Joseph', 'R'), 'Bennett',
         email='[email protected]', role = c('aut'),
         comment = c(ORCID = '0000-0002-3901-9513')),
       person(c('Hugh', 'P'), 'Possingham',
@@ -44,7 +44,7 @@ Language: en-US
 URL: https://prioritizr.github.io/prioritizrdata/,
     https://github.com/prioritizr/prioritizrdata
 BugReports: https://github.com/prioritizr/prioritizrdata/issues
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Collate:
     'package.R'
     'salt_data.R'

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# prioritizrdata 0.3.2.2
+
+- Update package manual entry.
+
 # prioritizrdata 0.3.2.1
 
 - Fix aliasing for package manual entry (#14).

diff --git a/R/package.R b/R/package.R
@@ -25,6 +25,7 @@
 #' @name prioritizrdata
 #' @docType package
 #' @aliases prioritizrdata-package
+"_PACKAGE"
 NULL
 
 # avoid false positive NOTES

diff --git a/README.md b/README.md
@@ -60,6 +60,6 @@ publications. To cite the latest official version, please use:
 Alternatively, to cite the latest development version, please use:
 
 > Hanson JO, Schuster R, Morrell N, Strimas-Mackey M, Watts ME, Arcese
-> P, Bennett J, Possingham HP (2023). prioritizrdata: Conservation
-> Planning Datasets. R package version 0.3.2.1. Available at
+> P, Bennett J, Possingham HP (2024). prioritizrdata: Conservation
+> Planning Datasets. R package version 0.3.2.2. Available at
 > <https://github.com/prioritizr/prioritizrdata>.
diff --git a/docs/404.html b/docs/404.html