add r cmd pipeline

.Rbuildignore

@@ -5,3 +5,4 @@
 ^doc$
 ^Meta$
 ^\.github$
+.lintr

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,52 @@
+# 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]
+  pull_request:
+    branches: [main]
+
+name: R-CMD-check
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - 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-r-dependencies@v2
+        with:
+          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")'

.gitignore

@@ -8,3 +8,6 @@ renv
 .DS_Store
 doc
 .Rproj.user
+PathwaySpace.Rcheck
+..Rcheck
+*.tar.gz

README.md

@@ -1,5 +1,7 @@
 ### PathwaySpace: Spatial projection of network signals along geodesic paths
-
+  <!-- badges: start -->
+  [![R-CMD-check](https://github.com/sysbiolab/PathwaySpace/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/sysbiolab/PathwaySpace/actions/workflows/R-CMD-check.yaml)
+  <!-- badges: end -->
 *PathwaySpace* is an R package that creates landscape images from graphs containing vertices (nodes), edges (lines), and a signal associated with the vertices. The package processes the signal using a convolution algorithm that considers the graph's topology to project the signal on a 2D space. 
 
 *PathwaySpace* could have various applications, such as visualizing network data in a graphical format that highlights the relationships and signal strengths between vertices. 

tests/testthat/test-plotImageSpace.R

@@ -17,8 +17,7 @@ test_that("Execution test of circularProjection", {
   pspace_toy <- buildPathwaySpace(toy_graph, mar = 0.2, verbose = FALSE)
   pspace_projection <- circularProjection(pspace_toy, knn = 1, pdist = 0.4, verbose = FALSE)
   # pspace_plot <- plotImageSpace(pspace_projection, marks = TRUE, verbose = FALSE)
-
-  plotImageSpace(pspace_projection, marks = c("n3","n4"), theme = "th2")
+  # print(class(pspace_plot))
 
   expect_equal(class(pspace_projection@gxyz), c("matrix", "array"))
 })