test simplified github r cmd actions workflow

ncsu-landscape-dynamics · Sep 15, 2023 · 7ba47ed · 7ba47ed
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,12 +1,10 @@
-# 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
+# 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:
-    branches:
-      - main
+    branches: [main]
   pull_request:
-    branches:
-      - main
+    branches: [main]
 
 name: R-CMD-check
 
@@ -20,86 +18,31 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      RENV_CI_CACHE_VERSION_LINUX: 1
-      RENV_CI_CACHE_VERSION_MACOS: 1
-      RENV_CI_CACHE_VERSION_WINDOWS: 1
-      USE_CXX1X: TRUE
-      USE_CXX11: TRUE
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: ${{ matrix.config.r }}
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
-        with:
-          pandoc-version: '2.7.3'
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-        run: |
-          # install spatial dependencies
-          sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
-          sudo apt update
-          sudo apt install \
-            libudunits2-dev \
-            libgdal-dev \
-            libgeos-dev \
-            libproj-dev \
-            libharfbuzz-dev \
-            libfribidi-dev
 
-      - name: Install system dependencies
-        if: runner.os == 'macOS'
-        run: |
-          # install spatial dependencies
-          brew install pkg-config gdal proj geos harfbuzz fribidi
-          export LDFLAGS="-L/usr/local/opt/libpq/lib"
-          export CPPFLAGS="-I/usr/local/opt/libpq/include"
-
-      - name: Install renv
-        shell: Rscript {0}
-        run: |
-          install.packages("renv")
-
-      - uses: actions/cache@v2
-        if: startsWith(runner.os, 'Linux')
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ~/.local/share/renv
-          key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-renv-
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: actions/cache@v2
-        if: startsWith(runner.os, 'macOS')
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ~/Library/Application Support/renv
-          key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-renv-
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: actions/cache@v2
-        if: startsWith(runner.os, 'Windows')
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          path: ~\AppData\Local\renv
-          key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-renv-
-
-      - name: Restore packages
-        shell: Rscript {0}
-        run: |
-          renv::restore()
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--no-multiarch"), error_on = "warning")
+          upload-snapshots: true
diff --git a/R/calibrate.R b/R/calibrate.R
@@ -796,7 +796,7 @@ calibrate <- function(infected_years_file,
               mean(c(median(parameters_test[, 16], na.rm = TRUE), config$quantity)) - 0.02
             config$allocation_threshold <-
               mean(c(median(parameters_test[, 17], na.rm = TRUE), config$allocation)) - 0.02
-            config$configuration_threshold<-
+            config$configuration_threshold <-
               mean(c(median(parameters_test[, 18], na.rm = TRUE), config$configuration_dis)) - 0.02
             ## reset starting point of parameters kept and acceptance rate
             parameters_kept <- matrix(ncol = 18, nrow = config$num_particles)
@@ -814,7 +814,7 @@ calibrate <- function(infected_years_file,
             config$mcc_threshold <- median(parameters_kept[, 15], na.rm = TRUE)
             config$quantity_threshold <- median(parameters_kept[, 16], na.rm = TRUE)
             config$allocation_threshold <- median(parameters_kept[, 17], na.rm = TRUE)
-            config$configuration_threshold<- median(parameters_kept[, 18], na.rm = TRUE)
+            config$configuration_threshold <- median(parameters_kept[, 18], na.rm = TRUE)
             ## reset starting point of parameters kept and acceptance rate
             parameters_kept <- matrix(ncol = 18, nrow = config$num_particles)
             parameters_test <- matrix(ncol = 18, nrow = 200)
@@ -855,7 +855,7 @@ calibrate <- function(infected_years_file,
       config$mcc_threshold <- median(parameters_kept[start_index:end_index, 15])
       config$quantity_threshold <- median(parameters_kept[start_index:end_index, 16])
       config$allocation_threshold <- median(parameters_kept[start_index:end_index, 17])
-      config$configuration_threshold<- median(parameters_kept[start_index:end_index, 18])
+      config$configuration_threshold <- median(parameters_kept[start_index:end_index, 18])
       config$current_bin <- config$current_bin + 1
     }