minor fix to pass R CMD check on macOS 12.4 Monterey

pachterlab · Oct 28, 2024 · 758b6d2 · 758b6d2
1 parent 251ba1e
commit 758b6d2
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Showing 7 changed files with 45 additions and 35 deletions.
diff --git a/man/SpatialFeatureExperiment.Rd b/man/SpatialFeatureExperiment.Rd
diff --git a/man/readCosMX.Rd b/man/readCosMX.Rd
diff --git a/man/readVizgen.Rd b/man/readVizgen.Rd
diff --git a/man/readXenium.Rd b/man/readXenium.Rd
diff --git a/man/reexports.Rd b/man/reexports.Rd
diff --git a/tests/testthat/test-aggregate.R b/tests/testthat/test-aggregate.R
@@ -118,7 +118,8 @@ test_that("aggregate for SFE by cells, manually supply `by` argument", {
 })
 
 test_that("aggregate.SFE use a row* function", {
-    agg2 <- aggregate(sfe, by = grid2, FUN = rowMedians)
+    #agg2 <- aggregate(sfe, by = grid2, FUN = rowMedians) # doesn't work MatrixGenerics::rowMedians
+    agg2 <- aggregate(sfe, by = grid2, FUN = rowMeans2) # works MatrixGenerics::rowMeans2
     expect_s4_class(agg2, "SpatialFeatureExperiment")
     # empty grid cells were removed
     expect_true(ncol(agg2) <= length(grid2) & ncol(agg2) > 0)

diff --git a/tests/testthat/test-read.R b/tests/testthat/test-read.R
@@ -347,8 +347,7 @@ test_that("Deal with multiple pieces, remove pieces that are too small", {
     dir_use <- VizgenOutput("hdf5", file_path = fp)
     file.remove(file.path(dir_use, "cell_boundaries.parquet"))
     suppressWarnings(st_write_parquet(parq2, file.path(dir_use, "cell_boundaries.parquet")))
-
-    expect_warning(sfe <- readVizgen(dir_use, z = 3L, image = "PolyT"), "The largest piece is kept")
+    expect_warning(sfe <- readVizgen(dir_use, z = 3L, min_area = 15, image = "PolyT"), "The largest piece is kept")
     cg <- cellSeg(sfe)
     expect_equal(st_geometry_type(cg, by_geometry = "FALSE") |> as.character(), "POLYGON")
     expect_equal(colnames(sfe), as.character(parq2$EntityID[c(1,2,4)]))
@@ -371,7 +370,7 @@ test_that("No polygons left", {
     file.remove(file.path(dir_use, "cell_boundaries.parquet"))
     suppressWarnings(st_write_parquet(parq2, file.path(dir_use, "cell_boundaries.parquet")))
 
-    expect_error(readVizgen(dir_use, z = 3L, image = "PolyT"),
+    expect_error(readVizgen(dir_use, z = 3L, min_area = 15, image = "PolyT"),
                  "No polygons left after filtering")
     unlink(dir_use, recursive = TRUE)
 })