R CMD check issues

R/reexports.R

@@ -4,12 +4,11 @@
 #' so you don't have to separately attach those packages to use these functions.
 #'
 #' @name reexports
-#' @inheritParams SummarizedExperiment::colData
-#' @inheritParams SingleCellExperiment::reducedDim
-#' @inheritParams SpatialExperiment::getImg
 #' @inheritParams SummarizedExperiment::`colData<-`
-#' @inheritParams SingleCellExperiment::counts
 #' @inheritParams SummarizedExperiment::rowData
+#' @param object A \code{SingleCellExperiment} object, which includes SFE.
+#' @param type Name or numeric index to indicate which \code{reducedDim} to get,
+#' such as "PCA". By default the first item in \code{reducedDims}.
 NULL
 
 #' @rdname reexports

tests/testthat/test-formatTxSpots.R

@@ -130,7 +130,7 @@ test_that("Error message when Parquet driver is unavailable", {
     fn <- XeniumOutput("v2", file_path = file.path(fp, "xenium_test"))
     expect_error(fn_tx <- formatTxTech(fn, tech = "Xenium", flip = TRUE, return = FALSE,
                                        file_out = file.path(fn, "tx_spots.parquet")),
-                 "GDAL Parquet driver is required to selectively read genes")
+                 "GDAL Parquet driver is required")
     unlink(fn, recursive = TRUE)
 })
 
@@ -152,6 +152,7 @@ test_that("Add a subset of spots", {
 })
 
 test_that("Add subset of spots, multiple files in tx spots output", {
+    skip_if_not(gdalParquetAvailable())
     fp <- tempdir()
     dir_use <- CosMXOutput(file_path = file.path(fp, "cosmx_test"))