mas

Author: esiegel

.github/workflows/lint-project.yaml

@@ -22,11 +22,17 @@ jobs:
           use-public-rspm: true
 
       - name: Install lintr
-        run: install.packages("lintr")
+        run: |
+          install.packages("lintr")
+          install.packages("devtools")
         shell: Rscript {0}
 
+      # we must use devtools::load_all to all lintr to not consider
+      # all of the internal non exported functions as non declared globals
       - name: Lint root directory
-        run: lintr::lint_dir()
+        run: |
+          devtools::load_all()
+          lintr::lint_dir()
         shell: Rscript {0}
         env:
           LINTR_ERROR_ON_LINT: true

tests/testthat/test-hdf5.R

@@ -46,9 +46,9 @@ test_that("can create hdf5", {
   expect_equal(hdf5r::readDataSet(tool), "loupeR")
 
   extra <- hdf5r::openGroup(metadata, "extra")
-  loupeR_seurat_version <- hdf5r::openLocation(extra, "loupeR_seurat_version")
-  val <- hdf5r::readDataSet(loupeR_seurat_version)
-  expect(!is.null(hdf5r::readDataSet(loupeR_seurat_version)), "extra field is missing")
+  louper_seurat_version <- hdf5r::openLocation(extra, "loupeR_seurat_version")
+  val <- hdf5r::readDataSet(louper_seurat_version)
+  expect(!is.null(hdf5r::readDataSet(louper_seurat_version)), "extra field is missing")
 })
 
 test_that("can create hdf5 custom feature ids", {