From 1e757c656c13033945006eefa8e3542ea5e94d61 Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Tue, 17 Mar 2026 22:46:13 +0100
Subject: [PATCH] switch from Rarr to ZarrArray

---
 DESCRIPTION        | 5 +++--
 NAMESPACE          | 2 +-
 R/ImageArray.R     | 2 +-
 R/LabelArray.R     | 2 +-
 R/read.R           | 5 ++---
 man/ImageArray.Rd  | 2 +-
 man/LabelArray.Rd  | 2 +-
 man/SpatialData.Rd | 8 ++++----
 8 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b09a82f..add5c00 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -43,7 +43,7 @@ Imports:
     jsonlite,
     Matrix,
     methods,
-    Rarr,
+    ZarrArray,
     RBGL,
     reticulate,
     sf,
@@ -70,7 +70,8 @@ Remotes:
     keller-mark/pizzarr,
     keller-mark/anndataR@spatialdata,
     HelenaLC/SpatialData.data,
-    HelenaLC/SpatialData.plot
+    HelenaLC/SpatialData.plot,
+    Bioconductor/ZarrArray
 biocViews: 
     DataImport, 
     DataRepresentation, 
diff --git a/NAMESPACE b/NAMESPACE
index 2f78dff..a090f83 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -91,7 +91,6 @@ importFrom(Matrix,rowSums)
 importFrom(Matrix,sparseVector)
 importFrom(Matrix,t)
 importFrom(RBGL,sp.between)
-importFrom(Rarr,ZarrArray)
 importFrom(S4Arrays,as.array.Array)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,coolcat)
@@ -107,6 +106,7 @@ importFrom(SingleCellExperiment,int_metadata)
 importFrom(SummarizedExperiment,"colData<-")
 importFrom(SummarizedExperiment,assay)
 importFrom(SummarizedExperiment,colData)
+importFrom(ZarrArray,ZarrArray)
 importFrom(arrow,open_dataset)
 importFrom(basilisk,BasiliskEnvironment)
 importFrom(basilisk,basiliskRun)
diff --git a/R/ImageArray.R b/R/ImageArray.R
index c54901e..583fb21 100644
--- a/R/ImageArray.R
+++ b/R/ImageArray.R
@@ -2,7 +2,7 @@
 #' @title The `ImageArray` class
 #' 
 #' @param x \code{ImageArray}
-#' @param data list of \code{\link[Rarr]{ZarrArray}}s
+#' @param data list of \code{\link[ZarrArray]{ZarrArray}}s
 #' @param meta \code{\link{Zattrs}}
 #' @param metadata optional list of arbitrary 
 #'   content describing the overall object.
diff --git a/R/LabelArray.R b/R/LabelArray.R
index 64ed3f6..519fc7c 100644
--- a/R/LabelArray.R
+++ b/R/LabelArray.R
@@ -14,7 +14,7 @@
 #' }
 #'
 #' @param x \code{LabelArray}
-#' @param data list of \code{\link[Rarr]{ZarrArray}}s
+#' @param data list of \code{\link[ZarrArray]{ZarrArray}}s
 #' @param meta \code{\link{Zattrs}}
 #' @param metadata optional list of arbitrary 
 #'   content describing the overall object.
diff --git a/R/read.R b/R/read.R
index 11f03dc..de5e960 100644
--- a/R/read.R
+++ b/R/read.R
@@ -69,15 +69,15 @@ allp = c("zarr==3.1.5", "spatialdata==0.7.0", "spatialdata_io==0.6.0",
 #' (x <- readSpatialData(base))
 NULL
 
+#' @importFrom ZarrArray ZarrArray
 readsdlayer <- function(x, ...) {
   md <- fromJSON(file.path(x, ".zattrs"))
   ps <- .get_multiscales_dataset_paths(md)
-  list(array = lapply(ps, \(.) ZarrArray(file.path(x, as.character(.)))), 
+  list(array = lapply(ps, \(.) ZarrArray::ZarrArray(file.path(x, as.character(.)))), 
        md = md)
 }
 
 #' @rdname readSpatialData
-#' @importFrom Rarr ZarrArray
 #' @importFrom jsonlite fromJSON
 #' @export
 readImage <- function(x, ...) {
@@ -86,7 +86,6 @@ readImage <- function(x, ...) {
 }
 
 #' @rdname readSpatialData
-#' @importFrom Rarr ZarrArray
 #' @importFrom jsonlite fromJSON
 #' @export
 readLabel <- function(x, ...) {
diff --git a/man/ImageArray.Rd b/man/ImageArray.Rd
index 85160a3..96c1b35 100644
--- a/man/ImageArray.Rd
+++ b/man/ImageArray.Rd
@@ -17,7 +17,7 @@ ImageArray(data = list(), meta = Zattrs(), metadata = list(), ...)
 \S4method{[}{ImageArray,ANY,ANY,ANY}(x, i, j, k, ..., drop = FALSE)
 }
 \arguments{
-\item{data}{list of \code{\link[Rarr]{ZarrArray}}s}
+\item{data}{list of \code{\link[ZarrArray]{ZarrArray}}s}
 
 \item{meta}{\code{\link{Zattrs}}}
 
diff --git a/man/LabelArray.Rd b/man/LabelArray.Rd
index 44f557f..2d9c7f1 100644
--- a/man/LabelArray.Rd
+++ b/man/LabelArray.Rd
@@ -10,7 +10,7 @@ LabelArray(data = array(), meta = Zattrs(), metadata = list(), ...)
 \S4method{[}{LabelArray,ANY,ANY,ANY}(x, i, j, ..., drop = FALSE)
 }
 \arguments{
-\item{data}{list of \code{\link[Rarr]{ZarrArray}}s}
+\item{data}{list of \code{\link[ZarrArray]{ZarrArray}}s}
 
 \item{meta}{\code{\link{Zattrs}}}
 
diff --git a/man/SpatialData.Rd b/man/SpatialData.Rd
index 9521d85..e760cfd 100644
--- a/man/SpatialData.Rd
+++ b/man/SpatialData.Rd
@@ -50,8 +50,8 @@
 \alias{element,SpatialData,ANY,numeric-method}
 \alias{element,SpatialData,ANY,missing-method}
 \alias{element,SpatialData,ANY,ANY-method}
-\alias{[[<-,SpatialData,numeric,ANY,ANY-method}
-\alias{[[<-,SpatialData,character,ANY,ANY-method}
+\alias{[[<-,SpatialData,numeric,ANY-method}
+\alias{[[<-,SpatialData,character,ANY-method}
 \title{The `SpatialData` class}
 \usage{
 SpatialData(images, labels, points, shapes, tables)
@@ -88,9 +88,9 @@ SpatialData(images, labels, points, shapes, tables)
 
 \S4method{element}{SpatialData,ANY,ANY}(x, i, j)
 
-\S4method{[[}{SpatialData,numeric,ANY,ANY}(x, i) <- value
+\S4method{[[}{SpatialData,numeric,ANY}(x, i) <- value
 
-\S4method{[[}{SpatialData,character,ANY,ANY}(x, i) <- value
+\S4method{[[}{SpatialData,character,ANY}(x, i) <- value
 }
 \arguments{
 \item{images}{list of \code{\link{ImageArray}}s}