From 7905e7125a9c6b65eb687bfbc29a6dafa3abe0b4 Mon Sep 17 00:00:00 2001
From: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: Tue, 28 Nov 2023 09:23:49 -0800
Subject: [PATCH] Fixes to pass CHECK.

---
 DESCRIPTION                        | 4 +++-
 R/readArray.R                      | 2 ++
 R/saveDelayedArray.R               | 3 +++
 man/readArray.Rd                   | 1 +
 man/saveDelayedArray.Rd            | 2 ++
 tests/testthat/test-SparseMatrix.R | 2 +-
 6 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f2fa7c8..2ee8150 100644
--- 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
index 772b706..9aeb7c0 100644
--- 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
index b326341..0cc5051 100644
--- 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
index 24773ae..d5027c5 100644
--- a/man/readArray.Rd
+++ b/man/readArray.Rd
@@ -2,6 +2,7 @@
 % Please edit documentation in R/readArray.R
 \name{readArray}
 \alias{readArray}
+\alias{loadArray}
 \title{Read a dense array from disk}
 \usage{
 readArray(path, array.output.type = NULL, ...)
diff --git a/man/saveDelayedArray.Rd b/man/saveDelayedArray.Rd
index aaf3686..1d341df 100644
--- a/man/saveDelayedArray.Rd
+++ b/man/saveDelayedArray.Rd
@@ -2,6 +2,8 @@
 % Please edit documentation in R/saveDelayedArray.R
 \name{saveDelayedArray}
 \alias{saveDelayedArray}
+\alias{stageObject,DelayedArray-method}
+\alias{stageObject,DelayedMatrix-method}
 \alias{saveObject,DelayedArray-method}
 \title{Save DelayedArrays to disk}
 \usage{
diff --git a/tests/testthat/test-SparseMatrix.R b/tests/testthat/test-SparseMatrix.R
index 1a3708b..0df067d 100644
--- 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")