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

…date (#263) This PR: Cleans up the configure script to remove pathways that are no longer supported. Basically, pkg-config is required now (because resolving the linking order of the absl static libraries is absolutely insane without it). It also improves the error messages for various types of failures, although probably not all of them. Adds Docker images and a docker compose setup to ensure that the compile + test works based on the install instructions for various linux setups. Notably, it makes sure that it effectively uses system Abseil where available (e.g., debian testing, fedora >= 39, alpine), and that it does not use system Abseil of an insufficient version (e.g., all current Ubuntu, Fedora 36). Improves the CI jobs to effectively use system Abseil where possible (basically just MacOS). I added a bit of a "pre-check" job that, if it fails, will prevent the other long-running jobs from kicking off. This should give relatively rapid feedback for the feature development + test cycle (and not significantly delay changes related to the build). This PR does not fix R 4.0 and R 4.1 on Windows yet (battle for another day).
r-spatial · Oct 11, 2024 · b495b0d · b495b0d
1 parent ece75d4
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -16,3 +16,4 @@
 ^tools/dist$
 ^compile_commands\.json$
 ^\.cache$
+^docker-compose\.yml$
diff --git a/.github/workflows/check-standard.yaml → .github/workflows/R-CMD-check.yaml b/.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
diff --git a/.github/workflows/pkgdown.yaml b/.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

diff --git a/.github/workflows/test-coverage.yaml b/.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

diff --git a/DESCRIPTION b/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,

diff --git a/README.Rmd b/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>
diff --git a/README.md b/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>