Merge branch 'dev' of https://github.com/ipeaGIT/r5r into dev

# Conflicts: # .github/workflows/R-CMD-check.yaml
ipeaGIT · Oct 21, 2024 · 19758b4 · 19758b4
2 parents ea8d8f4 + 64db9c9
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diff --git a/.github/workflows/R-CMD-check-CRAN.yaml b/.github/workflows/R-CMD-check-CRAN.yaml
@@ -1,25 +1,19 @@
-# 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:
     paths:
       - r-package/**
     branches:
-      - main
       - master
-      - dev
   pull_request:
     paths:
       - r-package/**
     branches:
-      - main
       - master
-      - dev
 
-name: R-CMD-check-as-CRAN
+name: check_as_cran
 
 jobs:
-  R-CMD-check:
+  check_as_cran:
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -28,63 +22,80 @@ jobs:
       fail-fast: false
       matrix:
         config:
-        - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+        - {os: ubuntu-22.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@v2
+        id: install-r
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Query dependencies
+      - name: Install pak and 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")
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
         shell: Rscript {0}
         working-directory: r-package
 
-      - name: Cache R packages
+      - name: Restore R package cache
         uses: actions/cache@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-
+          path: |
+            ${{ env.R_LIBS_USER }}/*
+            !${{ env.R_LIBS_USER }}/pak
+          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
+          restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
 
-      - name: Install system dependencies
+      - name: Install system dependencies (Linux)
+        if: runner.os == 'Linux'
         run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+          pak::local_system_requirements(execute = TRUE)
+          pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
+        shell: Rscript {0}
         working-directory: r-package
 
       - name: Install dependencies
         run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
+          pak::local_install_dev_deps(upgrade = TRUE)
+          pak::pkg_install("rcmdcheck")
+        shell: Rscript {0}
+        working-directory: r-package
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
         working-directory: r-package
 
       - name: Check
         env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+          _R_CHECK_CRAN_INCOMING_: false
           NOT_CRAN: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
         working-directory: r-package
 
+      - 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
+          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
           path: check
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -5,14 +5,12 @@ on:
     paths:
       - r-package/**
     branches:
-      - main
       - master
       - dev
   pull_request:
     paths:
       - r-package/**
     branches:
-      - main
       - master
       - dev
 
@@ -31,7 +29,6 @@ jobs:
         - {os: windows-latest, r: 'release'}
         - {os: windows-latest, r: 'oldrel'}
         - {os: macOS-latest, r: 'release'}
-        - {os: macOS-latest, r: 'oldrel'}
         - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
         - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
         - {os: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
@@ -42,19 +39,22 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Java setup
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v2
         with:
+          distribution: 'temurin'
           java-version: '21'
-          java-package: jdk
 
       - name: Query dependencies
         run: |
@@ -74,36 +74,22 @@ jobs:
 
       - name: Install system dependencies (Linux)
         if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+        run: brew install gdal proj
         working-directory: r-package
 
-      - name: Install system dependencies (MacOS)
-        if: runner.os == 'macOS'
-        run: |
-          brew install pkg-config gdal proj geos
+      - name: Install macOS system dependencies
+        if: runner.os == 'macos'
+        run: brew install gdal proj
         working-directory: r-package
 
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-        working-directory: r-package
 
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
         working-directory: r-package
 
-      - 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
+
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -3,6 +3,7 @@ on:
     paths:
       - r-package/**
       - README.md
+      - .github/workflows/pkgdown.yaml
     branches:
       - master
 
@@ -20,6 +21,12 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
+      - name: Java setup
+        uses: actions/setup-java@v1
+        with:
+          java-version: '21'
+          java-package: jdk
+
       - name: Query dependencies
         run: |
           install.packages('remotes')

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -24,7 +24,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
       - uses: r-lib/actions/setup-pandoc@v1
 

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # r5r: Rapid Realistic Routing with R5 in R <img align="right" src="r-package/man/figures/r5r_blue.png" alt="logo" width="180">
 
 [![CRAN/METACRAN Version](https://www.r-pkg.org/badges/version/r5r)](https://CRAN.R-project.org/package=r5r)
-[![CRAN/METACRAN Total downloads](http://cranlogs.r-pkg.org/badges/grand-total/r5r?color=blue)](https://CRAN.R-project.org/package=r5r)
+[![CRAN/METACRAN Total downloads](https://cranlogs.r-pkg.org/badges/grand-total/r5r?color=blue)](https://CRAN.R-project.org/package=r5r)
 [![R build status](https://github.com/ipeaGIT/r5r/workflows/R-CMD-check/badge.svg)](https://github.com/ipeaGIT/r5r/actions)
 [![Codecov test coverage](https://codecov.io/gh/ipeaGIT/r5r/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ipeaGIT/r5r?branch=master)
 [![Lifecycle: maturing](https://lifecycle.r-lib.org/articles/figures/lifecycle-maturing.svg)](https://lifecycle.r-lib.org/articles/stages.html)
@@ -27,29 +27,28 @@ This repository contains the `R` code (r-package folder) and the Java code
 You can install `r5r`:
 
 ```R
-# From CRAN
-  install.packages("r5r")
-  library(r5r)
+# from CRAN
+install.packages("r5r")
 
-# or use the development version with latest features
-  utils::remove.packages('r5r')
-  devtools::install_github("ipeaGIT/r5r", subdir = "r-package")
-  library(r5r)
+# dev version with latest features
+utils::remove.packages('r5r')
+devtools::install_github("ipeaGIT/r5r", subdir = "r-package")
 
 ```
 
-Please bear in mind that you need to have *Java SE Development Kit 21* installed 
-on your computer to use `r5r`. No worries, you don't have to pay for it. The jdk 
-21 is freely available from the options below:
-- [OpenJDK](https://jdk.java.net/java-se-ri/21)
-- [Oracle](https://docs.oracle.com/en/java/javase/21/install/index.html)
+Please bear in mind that you need to have *Java Development Kit (JDK) 21* installed on your computer to use `r5r`. No worries, you don't have to pay for it. There are numerous open-source JDK implementations, any of which should work with `r5r`. If you don't already have a preferred JDK, we recommend [Adoptium/Eclipse Temurin](https://adoptium.net/). Other open-source JDK implementations include [Amazon Corretto](https://aws.amazon.com/corretto/), and [Oracle OpenJDK](https://jdk.java.net/21/). You only need to install one JDK.
 
-If you don't know what version of Java you have installed on your computer, you 
-can check it by running this on R console.
+The easiest way to install JDK is using the new [{rJavaEnv}](https://www.ekotov.pro/rJavaEnv/) package in R:
 
 ```R
-rJava::.jinit()
-rJava::.jcall("java.lang.System", "S", "getProperty", "java.version")
+# install.packages('rJavaEnv')
+
+# check version of Java currently installed (if any) 
+rJavaEnv::java_check_version_rjava()
+
+# install Java 21
+rJavaEnv::java_quick_install(version = 21)
+
 ```
 
 ## Usage
@@ -146,11 +145,12 @@ and Open Street Map networks of Porto Alegre (Brazil). Three steps are required
 use `r5r`, as follows.
 
 ```R
-# allocate RAM memory to Java
+# allocate RAM memory to Java **before** loading the {r5r} library
 options(java.parameters = "-Xmx2G")
 
-# 1) build transport network, pointing to the path where OSM and GTFS data are stored
 library(r5r)
+
+# 1) build transport network, pointing to the path where OSM and GTFS data are stored
 path <- system.file("extdata/poa", package = "r5r")
 r5r_core <- setup_r5(data_path = path, verbose = FALSE)
 

diff --git a/java-r5rcore/.idea/artifacts/r5r_1_1_0_jar.xml b/java-r5rcore/.idea/artifacts/r5r_1_1_0_jar.xml
diff --git a/java-r5rcore/.idea/misc.xml b/java-r5rcore/.idea/misc.xml
diff --git a/java-r5rcore/.vscode/settings.json b/java-r5rcore/.vscode/settings.json
@@ -0,0 +1,3 @@
+{
+    "java.configuration.updateBuildConfiguration": "interactive"
+}