Fixes to pass CHECK.

ArtifactDB · Nov 28, 2023 · 7905e71 · 7905e71
1 parent 50b11b6
commit 7905e71
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Showing 6 changed files with 12 additions and 2 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -16,10 +16,12 @@ Imports:
     BiocGenerics,
     S4Vectors,
     DelayedArray (>= 0.27.2),
+    S4Arrays,
     SparseArray,
     rhdf5,
     HDF5Array,
-    Matrix
+    Matrix,
+    Rcpp
 Suggests:
     testthat,
     knitr,

diff --git a/R/readArray.R b/R/readArray.R
@@ -31,6 +31,8 @@
 #' readArray(dir)
 #' 
 #' @export
+#' @aliases
+#' loadArray
 #' @importFrom HDF5Array HDF5Array
 #' @importFrom DelayedArray type<-
 readArray <- function(path, array.output.type=NULL, ...) {

diff --git a/R/saveDelayedArray.R b/R/saveDelayedArray.R
@@ -21,6 +21,9 @@
 #' list.files(dir)
 #'
 #' @name saveDelayedArray
+#' @aliases 
+#' stageObject,DelayedArray-method
+#' stageObject,DelayedMatrix-method
 NULL
 
 #' @export

diff --git a/man/readArray.Rd b/man/readArray.Rd
diff --git a/man/saveDelayedArray.Rd b/man/saveDelayedArray.Rd
diff --git a/tests/testthat/test-SparseMatrix.R b/tests/testthat/test-SparseMatrix.R
@@ -148,7 +148,7 @@ test_that("fallback to large integer types for indices works correctly", {
         x[100000,20] <- 99 # making sure there's a value at the bottom-right so that we check the index correctly.
 
         if (i == 2) {
-            x <- t(x)
+            x <- Matrix::t(x)
             x <- as(x, "RsparseMatrix")
         } else if (i == 3) {
             x <- as(x, "SVT_SparseMatrix")