diff --git a/DESCRIPTION b/DESCRIPTION index a9e72424d4..8a6554b123 100644 --- a/DESCRIPTION +++ b/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")) diff --git a/NEWS.md b/NEWS.md index 0ecda8a7f0..088ce5ce36 100644 --- a/NEWS.md +++ b/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 diff --git a/R/TileDBArray.R b/R/TileDBArray.R index 87b5c0130b..4db3f7217c 100644 --- a/R/TileDBArray.R +++ b/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) } diff --git a/man/tiledb_array.Rd b/man/tiledb_array.Rd index 21b31d1876..5b2668a9ed 100644 --- a/man/tiledb_array.Rd +++ b/man/tiledb_array.Rd @@ -27,7 +27,8 @@ tiledb_array( sil = list(), dumpbuffers = character(), buffers = list(), - ctx = tiledb_get_context() + ctx = tiledb_get_context(), + as.data.frame = FALSE ) tiledb_dense(...) @@ -99,6 +100,10 @@ parsed.} \item{ctx}{optional tiledb_ctx} +\item{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.} + \item{...}{Used as a pass-through for \code{tiledb_dense} and \code{tiledb_sparse} aliasing} }