eddelbuettel
commented
4 years ago That is related to #156.
One can for now suppress this via the diff below (and re-running roxygen2::roxygenize() of course. In my experience it also does not appear to happen with 2.0.8 but only with dev. I should get to a proper fix in the next few days.
modified R/Config.R
@@ -40,15 +40,16 @@ tiledb_config.from_ptr <- function(ptr) {
#' @param config (optonal) character vector of config parameter names, values
#' @return `tiledb_config` object
#' @examples
#' \dontshow{ctx <- tiledb_ctx(limitTileDBCores())}
+#' \dontrun{
#' cfg <- tiledb_config()
#' cfg["sm.tile_cache_size"]
#'
#' # set tile cache size to custom value
#' cfg <- tiledb_config(c("sm.tile_cache_size" = "100"))
#' cfg["sm.tile_cache_size"]
-#'
+#' }
#' @importFrom methods new
#' @export tiledb_config
tiledb_config <- function(config = NA_character_) {
if (!is.na(config)) {
@@ -99,15 +100,16 @@ setMethod("[", "tiledb_config",
#' @param value value to set, will be converted into a stringa
#' @return updated `tiledb_config` object
#' @examples
#' \dontshow{ctx <- tiledb_ctx(limitTileDBCores())}
+#' \dontrun{
#' cfg <- tiledb_config()
#' cfg["sm.tile_cache_size"]
#'
#' # set tile cache size to custom value
#' cfg["sm.tile_cache_size"] <- 100
#' cfg["sm.tile_cache_size"]
-#'
+#' }
#' @aliases [<-,tiledb_config
#' @aliases [<-,tiledb_config-method
#' @aliases [<-,tiledb_config,ANY,tiledb_config-method
#' @aliases [<-,tiledb_config,ANY,ANY,tiledb_config-method
@@ -149,14 +151,15 @@ setMethod("show", signature(object = "tiledb_config"),
#' @param path The path to config file to be created
#' @return path to created config file
#' @examples
#' \dontshow{ctx <- tiledb_ctx(limitTileDBCores())}
+#' \dontrun{
#' tmp <- tempfile()
#' cfg <- tiledb_config(c("sm.tile_cache_size" = "10"))
#' pth <- tiledb_config_save(cfg, tmp)
#'
#' cat(readLines(pth), sep = "\n")
-#'
+#' }
#' @export
tiledb_config_save <- function(config, path) {
stopifnot(class(config) == "tiledb_config")
stopifnot(typeof(path) == "character")
@@ -167,14 +170,15 @@ tiledb_config_save <- function(config, path) {
#'
#' @param path path to the config file
#' @examples
#' \dontshow{ctx <- tiledb_ctx(limitTileDBCores())}
+#' \dontrun{
#' tmp <- tempfile()
#' cfg <- tiledb_config(c("sm.tile_cache_size" = "10"))
#' pth <- tiledb_config_save(cfg, tmp)
#' cfg <- tiledb_config_load(pth)
#' cfg["sm.tile_cache_size"]
-#'
+#' }
#' @export
tiledb_config_load <- function(path) {
stopifnot(typeof(path) == "character")
ptr <- libtiledb_config_load_from_file(path)
modified R/Ctx.R
@@ -69,14 +69,15 @@ setContext <- function(ctx) tiledb_set_context(ctx)
#' @param cached (optional) logical switch to force new creation
#' @return `tiledb_ctx` object
#' @examples
#' \dontshow{ctx <- tiledb_ctx(limitTileDBCores())}
+#' \dontrun{
#' # default configuration
#' ctx <- tiledb_ctx()
#'
#' # optionally set config parameters
#' ctx <- tiledb_ctx(c("sm.tile_cache_size" = "100"))
-#'
+#' }
#' @importFrom methods new
#' @importFrom methods is
#' @export tiledb_ctx
tiledb_ctx <- function(config = NULL, cached = TRUE) {
@@ -119,12 +120,13 @@ setGeneric("config", function(object, ...) {
#' @param object tiledb_ctx object
#' @return `tiledb_config` object associated with the `tiledb_ctx` instance
#' @examples
#' \dontshow{ctx <- tiledb_ctx(limitTileDBCores())}
+#' \dontrun{
#' ctx <- tiledb_ctx(c("sm.tile_cache_size" = "10"))
#' cfg <- config(ctx)
#' cfg["sm.tile_cache_size"]
-#'
+#' }
#' @export
setMethod("config", signature(object = "tiledb_ctx"),
function(object = tiledb_get_context()) {
ptr <- libtiledb_ctx_config(object@ptr)
@@ -159,11 +161,12 @@ tiledb_is_supported_fs <- function(scheme, object = tiledb_get_context()) {
#' @param key string
#' @param value string
#' @examples
#' \dontshow{ctx <- tiledb_ctx(limitTileDBCores())}
+#' \dontrun{
#' ctx <- tiledb_ctx(c("sm.tile_cache_size" = "10"))
#' cfg <- tiledb_ctx_set_tag(ctx, "tag", "value")
-#'
+#' }
#' @export
tiledb_ctx_set_tag <- function(object, key, value) {
stopifnot(is(object, "tiledb_ctx"))
return(libtiledb_ctx_set_tag(object@ptr, key, value))
jeroen
ihnorton
Running CMD check hangs after running the examples or tests (probably during
gc()cleanup). I suspect something in your finalizers in causing the process to freeze on exit, preventing R from quitting.This happens with TileDB 2.0.8 both in 32-bit and 64-bit.