try fixing CMD check

FBartos · May 23, 2024 · c27190d · c27190d
1 parent 3d8454b
commit c27190d
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Showing 2 changed files with 52 additions and 45 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -16,60 +16,68 @@ name: R-CMD-check
 
 jobs:
   R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    runs-on: ${{ matrix.os }}
+    name: ${{ matrix.os }} (R ${{ matrix.r }})
 
     strategy:
       fail-fast: false
       matrix:
-        config:
-          - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest,   r: 'release'}
-          - {os: ubuntu-latest,  r: 'release'}
+        r: ['4.3.3']
+        os: [ubuntu-latest, macOS-latest, windows-latest]
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
+      R_REMOTES_UPGRADE: never
+      VDIFFR_RUN_TESTS: true
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      _R_CHECK_LENGTH_1_CONDITION_: TRUE #deprecated from R 4.2.0
+      _R_CHECK_MATRIX_DATA_: TRUE # only works from R 4.2.0 onwards
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v2
+          r-version: ${{ matrix.r }}
 
-      - name: Query dependencies
+      - name: Install system dependencies on macOS
+        if: runner.os == 'macOS'
         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: 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-
-
-      - name: Install system dependencies
+          # see https://github.com/orgs/Homebrew/discussions/4612
+          unset HOMEBREW_NO_INSTALL_FROM_API
+          brew update
+          brew install --cask xquartz
+          brew install libarchive
+        shell: bash
+
+      - name: Install system dependencies on macOS specific to R devel
+        if: runner.os == 'macOS' && matrix.r == 'devel'
+        run: |
+          # ragg                                          requires harfbuzz fribidi
+          # The dependencies of the two R packages below are required for compiling from source on Ubuntu, but macOS seems fine without them
+          # credentials   (dependency of usethis)         requires libgit2
+          # curl          (dependency of usethis)         requires openssl
+          
+          brew install harfbuzz fribidi libgit2 openssl curl
+        shell: bash
+
+      - name: Install system dependencies on linux
         if: runner.os == 'Linux'
         run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          sudo apt-get install libcurl4-openssl-dev
+          # ragg                                          requires libharfbuzz-dev libfribidi-dev 
+          # credentials   (dependency of usethis)         requires libgit2-dev
+          # curl          (dependency of usethis)         requires libcurl4-openssl-dev
+          # libicu   (dependency of igraph or stringi...) requires libicu libicu-dev
+
+          sudo apt install libharfbuzz-dev libfribidi-dev libgit2-dev libcurl4-openssl-dev libicu*
+        shell: bash
 
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
-
+        
       - name: Check
         if: runner.os != 'Windows'
         env:
@@ -96,7 +104,6 @@ jobs:
             check_dir   = "check")
         shell: Rscript {0}
 
-
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@main

diff --git a/tests/testthat/test-zcurve.R b/tests/testthat/test-zcurve.R
@@ -59,8 +59,8 @@ test_that("z-curve EM can be fitted and reproduces OSC results", {
     ))
 
   # plot
-  expect_doppelganger("z-curve EM", function()plot(fit.EM, main = "OSC (with EM)", annotation = TRUE, CI = TRUE))
-  expect_doppelganger("z-curve EM (ggplot)", suppressWarnings(plot(fit.EM, main = "OSC (with EM)", annotation = TRUE, CI = TRUE, plot_type = "ggplot")))
+  vdiffr::expect_doppelganger("z-curve EM", function()plot(fit.EM, main = "OSC (with EM)", annotation = TRUE, CI = TRUE))
+  vdiffr::expect_doppelganger("z-curve EM (ggplot)", suppressWarnings(plot(fit.EM, main = "OSC (with EM)", annotation = TRUE, CI = TRUE, plot_type = "ggplot")))
 
 })
 test_that("z-curve KD2 can be fitted and reproduces OSC results", {
@@ -100,8 +100,8 @@ test_that("z-curve KD2 can be fitted and reproduces OSC results", {
     ))
 
   # plot
-  expect_doppelganger("z-curve KD2", function()plot(fit.KD2))
-  expect_doppelganger("z-curve KD2 (ggplot)", plot(fit.KD2, plot_type = "ggplot"))
+  vdiffr::expect_doppelganger("z-curve KD2", function()plot(fit.KD2))
+  vdiffr::expect_doppelganger("z-curve KD2 (ggplot)", plot(fit.KD2, plot_type = "ggplot"))
 
 })
 test_that("z-curve EM censoring works", {
@@ -132,8 +132,8 @@ test_that("z-curve EM censoring works", {
     ))
 
   # plot
-  expect_doppelganger("z-curve mixed EM", function()plot(fit.mixed, CI = TRUE))
-  expect_doppelganger("z-curve mixed EM (ggplot)", plot(fit.mixed, CI = TRUE, plot_type = "ggplot"))
+  vdiffr::expect_doppelganger("z-curve mixed EM", function()plot(fit.mixed, CI = TRUE))
+  vdiffr::expect_doppelganger("z-curve mixed EM (ggplot)", plot(fit.mixed, CI = TRUE, plot_type = "ggplot"))
 
 
   # censoring only
@@ -157,8 +157,8 @@ test_that("z-curve EM censoring works", {
     ))
 
   # plot
-  expect_doppelganger("z-curve cens EM", function()plot(fit.cens, CI = TRUE))
-  expect_doppelganger("z-curve cens EM (ggplot)", plot(fit.cens, CI = TRUE, plot_type = "ggplot"))
+  vdiffr::expect_doppelganger("z-curve cens EM", function()plot(fit.cens, CI = TRUE))
+  vdiffr::expect_doppelganger("z-curve cens EM (ggplot)", plot(fit.cens, CI = TRUE, plot_type = "ggplot"))
 })
 test_that("z-curve clustered works", {
 
@@ -204,7 +204,7 @@ test_that("z-curve clustered works", {
       "Q = -238.11, 95% CI[-269.95, -219.12]"  
     ))
 
-  expect_doppelganger("z-curve clustered rounded", function(){
+  vdiffr::expect_doppelganger("z-curve clustered rounded", function(){
     oldpar <- graphics::par(no.readonly = TRUE)
     on.exit(graphics::par(mfrow = oldpar[["mfrow"]]))
     par(mfrow = c(1, 2))
@@ -251,7 +251,7 @@ test_that("z-curve clustered works", {
       "Q = -201.69, 95% CI[-219.18, -185.82]" 
     ))
 
-  expect_doppelganger("z-curve clustered precise", function(){
+  vdiffr::expect_doppelganger("z-curve clustered precise", function(){
     oldpar <- graphics::par(no.readonly = TRUE)
     on.exit(graphics::par(mfrow = oldpar[["mfrow"]]))
     par(mfrow = c(1, 2))
@@ -298,14 +298,14 @@ test_that("z-curve clustered works", {
       "Q = -321.39, 95% CI[-361.78, -298.20]"  
     ))
 
-  expect_doppelganger("z-curve clustered mixed", function(){
+  vdiffr::expect_doppelganger("z-curve clustered mixed", function(){
     oldpar <- graphics::par(no.readonly = TRUE)
     on.exit(graphics::par(mfrow = oldpar[["mfrow"]]))
     par(mfrow = c(1, 2))
     plot(fitb)
     plot(fitw)
   })
 
-  expect_doppelganger("z-curve clustered mixed (ggplot-1)", plot(fitb, plot_type = "ggplot"))
-  expect_doppelganger("z-curve clustered mixed (ggplot-2)", plot(fitw, plot_type = "ggplot"))
+  vdiffr::expect_doppelganger("z-curve clustered mixed (ggplot-1)", plot(fitb, plot_type = "ggplot"))
+  vdiffr::expect_doppelganger("z-curve clustered mixed (ggplot-2)", plot(fitw, plot_type = "ggplot"))
 })