diff --git a/DESCRIPTION b/DESCRIPTION index 2394c6d..d462a41 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -59,7 +59,6 @@ Imports: dplyr, duckspatial, EBImage, - geoarrow, graph, Matrix, methods, diff --git a/NAMESPACE b/NAMESPACE index 3c84afb..f22eb4a 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -112,7 +112,6 @@ exportMethods(tableNames) exportMethods(tables) exportMethods(transform) exportMethods(translation) -import(geoarrow) importFrom(BiocGenerics,as.data.frame) importFrom(BiocGenerics,colnames) importFrom(BiocGenerics,combine) diff --git a/R/read.R b/R/read.R index 30228f5..48250e5 100644 --- a/R/read.R +++ b/R/read.R @@ -90,7 +90,6 @@ readPoint <- function(x, ...) { #' @rdname readSpatialData #' @importFrom Rarr read_zarr_attributes #' @importFrom duckspatial ddbs_open_dataset -#' @import geoarrow #' @export readShape <- function(x, ...) { md <- read_zarr_attributes(x) diff --git a/R/tables.R b/R/tables.R index a6c857d..c58b10b 100644 --- a/R/tables.R +++ b/R/tables.R @@ -149,6 +149,7 @@ setMethod("getTable", c("SpatialData", "character"), \(x, i, j, assay=1, drop=TR #' @export setMethod("setTable", c("SpatialData", "ANY"), \(x, i, ..., name=NULL, rk="rk", ik="ik") .invalid_i()) +# TODO: should this comment be removed ? # it seems pull below dispatches to arrow, and a warning on as_vector was being produced #' @rdname table-utils #' @importFrom methods as diff --git a/README.md b/README.md index 73fe312..76906ad 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,7 @@ For more details on the framework, see [Marconato et al. (2024)](https://doi.org ## Key features - Out-of-memory handling of images and labels using `ZarrArray` (via the [Rarr](https://bioconductor.org/packages/Rarr) package). -- Points and shapes are managed using [arrow](https://cran.r-project.org/package=arrow) or [duckdb](https://cran.r-project.org/package=duckdb)-backed tables. +- Points and shapes are managed using [duckdb](https://cran.r-project.org/package=duckdb)-backed tables. - Functional annotations (e.g., gene expression) are represented as `SingleCellExperiment` objects, integrated via [anndataR](https://bioconductor.org/packages/anndataR). - A system for mapping data across multiple coordinate spaces, including support for transformation graphs.