Temporarily re-admit as.data.frame=TRUE in tiledb_array() (#752)

* Temporarily re-admit `as.data.frame=TRUE` in tiledb_array()

* Update NEWS.md [ci skip]

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tiledb
 Type: Package
-Version: 0.29.0.6
+Version: 0.29.0.7
 Title: Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays
 Authors@R: c(person("TileDB, Inc.", role = c("aut", "cph")),
   person("Dirk", "Eddelbuettel", email = "dirk@tiledb.com", role = "cre"))

NEWS.md

@@ -24,6 +24,9 @@
 
 * Boolean arguments `as.data.frame`, `as.matrix` and `as.array` to the `tiledb_array()` accessor, deprecated in release 0.20.0 in July 2023 in favor of the more general `return_as="..."` form, have been removed. (#751)
 
+## Deprecation
+
+* As BioConductor package \pkg{TileDBArray} still relies on `as.data.frame` it was temporarily re-admitted as an argument. It is expected to be removed following the upcoming 3.20 release of BioConducto.r (#752)
 
 
 # tiledb 0.29.0

R/TileDBArray.R

@@ -133,6 +133,9 @@ setClass("tiledb_array",
 #' \code{/dev/shm}) for writing out results buffers (for internal use / testing)
 #' @param buffers An optional list with full pathnames of shared memory buffers to read data from
 #' @param ctx optional tiledb_ctx
+#' @param as.data.frame An optional deprecated alternative to \code{return_as="data.frame"} which has
+#' been deprecated and removed, but is still used in one BioConductor package; this argument will be removed
+#' once the updated package has been released.
 #' @return tiledb_array object
 #' @importFrom spdl set_level
 #' @export
@@ -156,7 +159,8 @@ tiledb_array <- function(uri,
                          sil = list(),
                          dumpbuffers = character(),
                          buffers = list(),
-                         ctx = tiledb_get_context()) {
+                         ctx = tiledb_get_context(),
+                         as.data.frame = FALSE) {
   stopifnot("Argument 'ctx' must be a tiledb_ctx object" = is(ctx, "tiledb_ctx"),
             "Argument 'uri' must be a string scalar" = !missing(uri) && is.scalar(uri, "character"),
             "Argument 'matrix' (for 'return_as') cannot be selected for sparse arrays" =
@@ -170,6 +174,12 @@ tiledb_array <- function(uri,
     array_xptr <- libtiledb_array_open(ctx@ptr, uri, query_type)
   }
 
+  if (as.data.frame) {
+      ## accommodating TileDBArray prior to BioConductor 3.20
+      .Deprecated(old="as.data.frame", new=r"(return_as="data.frame")")
+      return_as <- "data.frame"
+  }
+
   if (length(timestamp_start) > 0) {
       libtiledb_array_set_open_timestamp_start(array_xptr, timestamp_start)
   }