Clean up documentation, configuration, and CI following S2 version update

.Rbuildignore

@@ -16,3 +16,4 @@
 ^tools/dist$
 ^compile_commands\.json$
 ^\.cache$
+^docker-compose\.yml$

.github/workflows/check-standard.yaml → .github/workflows/R-CMD-check.yaml

@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
@@ -8,19 +8,42 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
+  # Check MacOS first before embarking on the full check matrix
+  test:
+    runs-on: macos-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: r-lib/actions/setup-r@v2
+      - name: Install Abseil (MacOS)
+        run: brew install abseil
+      - name: Install minimal dependencies
+        run: |
+          R -e 'install.packages(c("wk", "Rcpp", "bit64", "testthat"))'
+      - name: Install
+        run: |
+          R CMD INSTALL .
+      - name: Test
+        run: |
+          R -e 'testthat::test_local()'
+
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
 
+    needs:
+      - test
+
     strategy:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
           # TODO: Solve Abseil linking issue on R 4.0 and R 4.1/Windows
           # - {os: windows-latest, r: '4.1'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: '4.2'}
           - {os: windows-latest, r: '4.3'}
           - {os: windows-latest, r: 'release'}
@@ -33,7 +56,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -43,25 +66,27 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
+      - name: Install Abseil (MacOS)
+        if: matrix.config.os == 'macos-latest'
+        run: |
+          brew install abseil
+
+      - name: Set Makevars (Ubuntu)
+        if: matrix.config.os == 'ubuntu-latest'
+        run: |
+          mkdir ~/.R && echo "MAKEFLAGS = -j$(nproc)" > ~/.R/Makevars
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
       - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
 
       - name: Show install output
         if: always()
         run: find check -name '00install.out*' -exec cat '{}' \; || true
         shell: bash
-
-      - 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/pkgdown.yaml

@@ -11,6 +11,8 @@ on:
 
 name: pkgdown
 
+permissions: read-all
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
@@ -19,8 +21,10 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -39,7 +43,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@4.1.4
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/test-coverage.yaml

@@ -1,5 +1,3 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
-# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
     branches: [main, master]
@@ -8,19 +6,25 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
+      - name: Install Abseil (Ubuntu)
+        run: |
+          sudo apt-get update && sudo apt-get install -y libabsl-dev
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: covr

DESCRIPTION

@@ -25,7 +25,7 @@ License: Apache License (== 2.0)
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 SystemRequirements: OpenSSL >= 1.0.1, Abseil >= 20230802.0
 LinkingTo:
     Rcpp,

README.Rmd

@@ -16,15 +16,15 @@ knitr::opts_chunk$set(
 # s2
 
 <!-- badges: start -->
-![R-CMD-check](https://github.com/r-spatial/s2/workflows/R-CMD-check/badge.svg)
-[![codecov](https://codecov.io/gh/r-spatial/s2/branch/master/graph/badge.svg)](https://app.codecov.io/gh/r-spatial/s2)
+[![R-CMD-check](https://github.com/r-spatial/s2/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/r-spatial/s2/actions/workflows/R-CMD-check.yaml)
+[![codecov](https://codecov.io/gh/r-spatial/s2/branch/main/graph/badge.svg)](https://app.codecov.io/gh/r-spatial/s2)
 [![CRAN](http://www.r-pkg.org/badges/version/s2)](https://cran.r-project.org/package=s2)
 [![Downloads](http://cranlogs.r-pkg.org/badges/s2?color=brightgreen)](https://www.r-pkg.org/pkg/s2)
 <!-- badges: end -->
 
 The s2 R package provides bindings to Google's [S2Geometry](http://s2geometry.io) library. The package exposes an API similar to Google's [BigQuery Geography API](https://cloud.google.com/bigquery/docs/reference/standard-sql/geography_functions), whose functions also operate on spherical geometries. Package [sf](https://cran.r-project.org/package=sf) uses this package by default for nearly all its geometrical operations on objects with ellipsoidal (unprojected) coordinates; in cases where it doesn't, such as `st_relate()`, it emits a warning.
 
-This package is a complete rewrite of an earlier CRAN package s2 with versions up 
+This package is a complete rewrite of an earlier CRAN package s2 with versions up
 to 0.4-2, for which the sources are found [here](https://github.com/spatstat/s2/).
 
 ## Installation
@@ -42,6 +42,14 @@ And the development version from [GitHub](https://github.com/) with:
 remotes::install_github("r-spatial/s2")
 ```
 
+The S2 package requires [Abseil]() and OpenSSL. You can install these using a system package manager on most platforms:
+
+- Windows: Both OpenSSL and Abseil are available from RTools since R 4.3
+- MacOS: `brew install openssl abseil`
+- Debian/Ubuntu: `apt-get install libssl-dev libabsl-dev`
+- Fedora: `dnf install openssl-devel abseil-cpp-devel`
+- Alpine: `apk add abseil-cpp`
+
 ## Example
 
 The s2 package provides geometry transformers and predicates similar to those found in [GEOS](https://trac.osgeo.org/geos/), except instead of assuming a planar geometry, s2's functions work in latitude and longitude and assume a spherical geometry:
@@ -63,9 +71,9 @@ The [sf package](https://r-spatial.github.io/sf/) uses s2 for geographic coordin
 library(dplyr)
 library(sf)
 
-nc_s2 <- read_sf(system.file("shape/nc.shp", package = "sf")) %>% 
-  mutate(geometry = as_s2_geography(geometry)) %>% 
-  as_tibble() %>% 
+nc_s2 <- read_sf(system.file("shape/nc.shp", package = "sf")) %>%
+  mutate(geometry = as_s2_geography(geometry)) %>%
+  as_tibble() %>%
   select(NAME, geometry)
 
 nc_s2
@@ -74,7 +82,7 @@ nc_s2
 Use accessors to extract information about geometries:
 
 ```{r}
-nc_s2 %>% 
+nc_s2 %>%
   mutate(
     area = s2_area(geometry),
     perimeter = s2_perimeter(geometry)
@@ -84,29 +92,29 @@ nc_s2 %>%
 Use predicates to subset vectors:
 
 ```{r}
-nc_s2 %>% 
+nc_s2 %>%
   filter(s2_contains(geometry, "POINT (-80.9313 35.6196)"))
 ```
 
 Use transformers to create new geometries:
 
 ```{r}
-nc_s2 %>% 
+nc_s2 %>%
   mutate(geometry = s2_boundary(geometry))
 ```
 
 Finally, use the WKB or WKT exporters to export to sf or some other package:
 
 ```{r}
-nc_s2 %>% 
-  mutate(geometry = st_as_sfc(s2_as_binary(geometry))) %>% 
+nc_s2 %>%
+  mutate(geometry = st_as_sfc(s2_as_binary(geometry))) %>%
   st_as_sf()
 ```
 
 ## Acknowledgment
 
-This project gratefully acknowledges financial [support](https://www.r-consortium.org/projects) from the
+This project gratefully acknowledges financial [support](https://www.r-consortium.org/) from the
 
-<a href="https://www.r-consortium.org/projects">
+<a href="https://www.r-consortium.org/">
 <img src="man/figures/rc300.png" width="300" />
 </a>

README.md

@@ -5,8 +5,8 @@
 
 <!-- badges: start -->
 
-![R-CMD-check](https://github.com/r-spatial/s2/workflows/R-CMD-check/badge.svg)
-[![codecov](https://codecov.io/gh/r-spatial/s2/branch/master/graph/badge.svg)](https://app.codecov.io/gh/r-spatial/s2)
+[![R-CMD-check](https://github.com/r-spatial/s2/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/r-spatial/s2/actions/workflows/R-CMD-check.yaml)
+[![codecov](https://codecov.io/gh/r-spatial/s2/branch/main/graph/badge.svg)](https://app.codecov.io/gh/r-spatial/s2)
 [![CRAN](http://www.r-pkg.org/badges/version/s2)](https://cran.r-project.org/package=s2)
 [![Downloads](http://cranlogs.r-pkg.org/badges/s2?color=brightgreen)](https://www.r-pkg.org/pkg/s2)
 <!-- badges: end -->
@@ -41,6 +41,15 @@ And the development version from [GitHub](https://github.com/) with:
 remotes::install_github("r-spatial/s2")
 ```
 
+The S2 package requires [Abseil]() and OpenSSL. You can install these
+using a system package manager on most platforms:
+
+- Windows: Both OpenSSL and Abseil are available from RTools since R 4.3
+- MacOS: `brew install openssl abseil`
+- Debian/Ubuntu: `apt-get install libssl-dev libabsl-dev`
+- Fedora: `dnf install openssl-devel abseil-cpp-devel`
+- Alpine: `apk add abseil-cpp`
+
 ## Example
 
 The s2 package provides geometry transformers and predicates similar to
@@ -69,9 +78,9 @@ using `as_s2_geography()`:
 library(dplyr)
 library(sf)
 
-nc_s2 <- read_sf(system.file("shape/nc.shp", package = "sf")) %>% 
-  mutate(geometry = as_s2_geography(geometry)) %>% 
-  as_tibble() %>% 
+nc_s2 <- read_sf(system.file("shape/nc.shp", package = "sf")) %>%
+  mutate(geometry = as_s2_geography(geometry)) %>%
+  as_tibble() %>%
   select(NAME, geometry)
 
 nc_s2
@@ -88,13 +97,13 @@ nc_s2
 #>  8 Gates       POLYGON ((-76.46035 36.3738976, -76.5024643 36.4522858, -76.4983…
 #>  9 Warren      POLYGON ((-78.1347198 36.2365837, -78.1096268 36.2135086, -78.05…
 #> 10 Stokes      POLYGON ((-80.0240555 36.5450249, -80.0480957 36.5471344, -80.43…
-#> # … with 90 more rows
+#> # ℹ 90 more rows
 ```
 
 Use accessors to extract information about geometries:
 
 ``` r
-nc_s2 %>% 
+nc_s2 %>%
   mutate(
     area = s2_area(geometry),
     perimeter = s2_perimeter(geometry)
@@ -112,13 +121,13 @@ nc_s2 %>%
 #>  8 Gates       POLYGON ((-76.46035 36.3738976, -76.5024643 36.… 9.03e8   123170.
 #>  9 Warren      POLYGON ((-78.1347198 36.2365837, -78.1096268 3… 1.18e9   141073.
 #> 10 Stokes      POLYGON ((-80.0240555 36.5450249, -80.0480957 3… 1.23e9   140583.
-#> # … with 90 more rows
+#> # ℹ 90 more rows
 ```
 
 Use predicates to subset vectors:
 
 ``` r
-nc_s2 %>% 
+nc_s2 %>%
   filter(s2_contains(geometry, "POINT (-80.9313 35.6196)"))
 #> # A tibble: 1 × 2
 #>   NAME    geometry                                                              
@@ -129,7 +138,7 @@ nc_s2 %>%
 Use transformers to create new geometries:
 
 ``` r
-nc_s2 %>% 
+nc_s2 %>%
   mutate(geometry = s2_boundary(geometry))
 #> # A tibble: 100 × 2
 #>    NAME        geometry                                                         
@@ -144,15 +153,15 @@ nc_s2 %>%
 #>  8 Gates       LINESTRING (-76.46035 36.3738976, -76.5024643 36.4522858, -76.49…
 #>  9 Warren      LINESTRING (-78.1347198 36.2365837, -78.1096268 36.2135086, -78.…
 #> 10 Stokes      LINESTRING (-80.0240555 36.5450249, -80.0480957 36.5471344, -80.…
-#> # … with 90 more rows
+#> # ℹ 90 more rows
 ```
 
 Finally, use the WKB or WKT exporters to export to sf or some other
 package:
 
 ``` r
-nc_s2 %>% 
-  mutate(geometry = st_as_sfc(s2_as_binary(geometry))) %>% 
+nc_s2 %>%
+  mutate(geometry = st_as_sfc(s2_as_binary(geometry))) %>%
   st_as_sf()
 #> Simple feature collection with 100 features and 1 field
 #> Geometry type: GEOMETRY
@@ -172,13 +181,13 @@ nc_s2 %>%
 #>  8 Gates       POLYGON ((-76.46035 36.3739, -76.50246 36.45229, -76.49834 36.50…
 #>  9 Warren      POLYGON ((-78.13472 36.23658, -78.10963 36.21351, -78.05835 36.2…
 #> 10 Stokes      POLYGON ((-80.02406 36.54502, -80.0481 36.54713, -80.43531 36.55…
-#> # … with 90 more rows
+#> # ℹ 90 more rows
 ```
 
 ## Acknowledgment
 
 This project gratefully acknowledges financial
-[support](https://www.r-consortium.org/projects) from the
+[support](https://www.r-consortium.org/) from the
 
-<a href="https://www.r-consortium.org/projects">
+<a href="https://www.r-consortium.org/">
 <img src="man/figures/rc300.png" width="300" /> </a>