docs: fix typos

DESCRIPTION

@@ -36,5 +36,5 @@ LinkingTo: Rcpp, RcppInt64, nanoarrow
 Suggests: tinytest, simplermarkdown, curl, bit64, Matrix, palmerpenguins, nycflights13, data.table, tibble, arrow
 VignetteBuilder: simplermarkdown
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
 Encoding: UTF-8
+Config/roxygen2/version: 8.1.0

NAMESPACE

@@ -413,20 +413,24 @@ exportMethods(tile_order)
 exportMethods(tiledb_ndim)
 import(nanotime)
 importFrom(Rcpp,sourceCpp)
-importFrom(methods,.hasSlot)
-importFrom(methods,as)
-importFrom(methods,is)
-importFrom(methods,new)
-importFrom(methods,setClass)
-importFrom(methods,setGeneric)
-importFrom(methods,setMethod)
-importFrom(methods,slot)
-importFrom(methods,validObject)
+importFrom(methods,
+  .hasSlot,
+  as,
+  is,
+  new,
+  setClass,
+  setGeneric,
+  setMethod,
+  slot,
+  validObject
+)
 importFrom(nanoarrow,as_nanoarrow_array)
 importFrom(spdl,set_level)
 importFrom(stats,na.omit)
-importFrom(utils,head)
-importFrom(utils,packageVersion)
-importFrom(utils,read.table)
-importFrom(utils,tail)
+importFrom(utils,
+  head,
+  packageVersion,
+  read.table,
+  tail
+)
 useDynLib(tiledb, .registration = TRUE)

R/Array.R

@@ -183,7 +183,7 @@ tiledb_array_is_homogeneous <- function(arr) {
 ##' Check for Heterogeneous Domain
 ##'
 ##' @param arr A TileDB Array object
-##' @return A boolean indicating if the array has heterogenous domains
+##' @return A boolean indicating if the array has heterogeneous domains
 ##' @export
 tiledb_array_is_heterogeneous <- function(arr) {
   stopifnot("The 'arr' argument must be a tiledb_array object" = .isArray(arr))

R/ArrowIO.R

@@ -42,7 +42,7 @@ tiledb_query_export_buffer <- function(query, name, ctx = tiledb_get_context())
 ##' Import to Query Buffer from Pair of Arrow IO Pointers
 ##'
 ##' This function imports to the named buffer for a \sQuote{WRITE} query
-##' from two Arrow exerternal pointers.
+##' from two Arrow external pointers.
 ##' @param query A TileDB Query object
 ##' @param name A character variable identifying the buffer
 ##' @param nanoarrowptr A \code{nanoarrow} object (which is an external pointer to an Arrow Array

R/Config.R

@@ -214,7 +214,7 @@ as.vector.tiledb_config <- function(x, mode = "any") {
 #'
 #' @param x A `tiledb_config` object
 #' @param ... Extra parameter for method signature, currently unused.
-#' @return a data.frame wth parameter, value columns
+#' @return a data.frame with parameter, value columns
 #' @examples
 #' cfg <- tiledb_config()
 #' as.data.frame(cfg)

R/Ctx.R

@@ -142,7 +142,7 @@ setMethod(
 
 #' Query if a TileDB backend is supported
 #'
-#' The scheme corresponds to the URI scheme for TileDB resouces.
+#' The scheme corresponds to the URI scheme for TileDB resources.
 #'
 #' Ex:
 #'  * `{file}:///path/to/file`

R/CurrentDomain.R

@@ -43,7 +43,7 @@ setClass("tiledb_current_domain",
 #' @export
 tiledb_current_domain <- function(ctx = tiledb_get_context()) {
   stopifnot(
-    "The first argment must be a TileDB Ctx object" = is(ctx, "tiledb_ctx"),
+    "The first argument must be a TileDB Ctx object" = is(ctx, "tiledb_ctx"),
     "This function needs TileDB 2.25.0 or later" = tiledb_version(TRUE) >= "2.25.0"
   )
   ptr <- libtiledb_current_domain_create(ctx@ptr)
@@ -57,7 +57,7 @@ tiledb_current_domain <- function(ctx = tiledb_get_context()) {
 #' @export
 tiledb_current_domain_get_type <- function(cd) {
   stopifnot(
-    "The first argment must be a TileDB CurrentDomain object" =
+    "The first argument must be a TileDB CurrentDomain object" =
       is(cd, "tiledb_current_domain"),
     "This function needs TileDB 2.25.0 or later" = tiledb_version(TRUE) >= "2.25.0"
   )
@@ -72,7 +72,7 @@ tiledb_current_domain_get_type <- function(cd) {
 #' @export
 tiledb_current_domain_set_ndrectangle <- function(cd, ndr) {
   stopifnot(
-    "The first argment must be a TileDB CurrentDomain object" =
+    "The first argument must be a TileDB CurrentDomain object" =
       is(cd, "tiledb_current_domain"),
     "The second argument must be a TileDB NDRectangle object" = is(ndr, "tiledb_ndrectangle"),
     "This function needs TileDB 2.25.0 or later" = tiledb_version(TRUE) >= "2.25.0"
@@ -88,7 +88,7 @@ tiledb_current_domain_set_ndrectangle <- function(cd, ndr) {
 #' @export
 tiledb_current_domain_get_ndrectangle <- function(cd) {
   stopifnot(
-    "The first argment must be a TileDB CurrentDomain object" =
+    "The first argument must be a TileDB CurrentDomain object" =
       is(cd, "tiledb_current_domain"),
     "This function needs TileDB 2.25.0 or later" = tiledb_version(TRUE) >= "2.25.0"
   )
@@ -103,7 +103,7 @@ tiledb_current_domain_get_ndrectangle <- function(cd) {
 #' @export
 tiledb_current_domain_is_empty <- function(cd) {
   stopifnot(
-    "The first argment must be a TileDB CurrentDomain object" =
+    "The first argument must be a TileDB CurrentDomain object" =
       is(cd, "tiledb_current_domain"),
     "This function needs TileDB 2.25.0 or later" = tiledb_version(TRUE) >= "2.25.0"
   )

R/DataFrame.R

@@ -62,7 +62,7 @@
 ##' writing to the newly-created array) and \sQuote{append} (to only append to an already existing
 ##' array).
 ##' @param filter_list A named list specifying filter choices per column, default is an empty
-##' \code{list} object. This argument applies for all named arguments and the matchin dimensions
+##' \code{list} object. This argument applies for all named arguments and the matching dimensions
 ##' or attributes. The \code{filter} argument still applies for all unnamed arguments.
 ##' @param coords_filters A character vector with filters for coordinates, default is \code{ZSTD}.
 ##' @param offsets_filters A character vector with filters for coordinates, default is \code{ZSTD}.
@@ -83,16 +83,16 @@
 ##' all.equal(as.matrix(iris), as.matrix(newdf))	# also strips attribute
 ##' @export
 fromDataFrame <- function(
-  obj, 
-  uri, 
-  col_index = NULL, 
-  sparse = TRUE, 
+  obj,
+  uri,
+  col_index = NULL,
+  sparse = TRUE,
   allows_dups = sparse,
   cell_order = "COL_MAJOR",
   tile_order = "COL_MAJOR",
   filter = "ZSTD",
-  capacity = 10000L, 
-  tile_domain = NULL, 
+  capacity = 10000L,
+  tile_domain = NULL,
   tile_extent = NULL,
   mode = c("ingest", "schema_only", "append"),
   filter_list = NULL,

R/Filestore.R

@@ -101,7 +101,7 @@ tiledb_filestore_buffer_import <- function(filestore_uri, buf, bytes, ctx = tile
 ##' Export from a TileDB Filestore to a character variable
 ##'
 ##' @param filestore_uri Character with an TileDB Array Schema URI
-##' @param offset (optional) Numeric variable with offset from beginnig, default is zero
+##' @param offset (optional) Numeric variable with offset from beginning, default is zero
 ##' @param bytes (optional) Numeric variable with number of bytes to read, default is zero
 ##' @param ctx (optional) A TileDB Ctx object; if not supplied the default
 ##' context object is retrieved

R/Metadata.R

@@ -25,7 +25,7 @@
 ##' @param arr A TileDB Array object
 ##' @param key A character value describing a metadata key
 ##' @return A logical value indicating if the given key exists in the
-##'   metdata of the given array
+##'   metadata of the given array
 ##' @export
 tiledb_has_metadata <- function(arr, key) {
   stopifnot(

R/NDRectangle.R

@@ -46,7 +46,7 @@ setClass("tiledb_ndrectangle",
 tiledb_ndrectangle <- function(dom, ctx = tiledb_get_context()) {
   stopifnot(
     "The first argument must be a TileDB Domain object" = is(dom, "tiledb_domain"),
-    "The second argment must be a TileDB Ctx object" = is(ctx, "tiledb_ctx"),
+    "The second argument must be a TileDB Ctx object" = is(ctx, "tiledb_ctx"),
     "This function needs TileDB 2.25.0 or later" = tiledb_version(TRUE) >= "2.25.0"
   )
   ptr <- libtiledb_ndrectangle_create(ctx@ptr, dom@ptr)

R/Profile.R

@@ -92,8 +92,8 @@ tiledb_profile_dir <- function(profile) {
 #' @export
 tiledb_profile_set_param <- function(profile, param, value) {
   stopifnot(`The 'profile' argument must be a tiledb_profile object` = is(profile, "tiledb_profile"))
-  stopifnot(`The 'param' arugment must have character type` = is.character(param))
-  stopifnot(`The 'value' arugment must have character type` = is.character(value))
+  stopifnot(`The 'param' argument must have character type` = is.character(param))
+  stopifnot(`The 'value' argument must have character type` = is.character(value))
   libtiledb_profile_set_param(profile@ptr, param, value)
   return(invisible(NULL))
 }
@@ -106,7 +106,7 @@ tiledb_profile_set_param <- function(profile, param, value) {
 #' @export
 tiledb_profile_get_param <- function(profile, param) {
   stopifnot(`The 'profile' argument must be a tiledb_profile object` = is(profile, "tiledb_profile"))
-  stopifnot(`The 'param' arugment must have character type` = is.character(param))
+  stopifnot(`The 'param' argument must have character type` = is.character(param))
   value <- libtiledb_profile_get_param(profile@ptr, param)
   return(value)
 }

R/Query.R

@@ -74,7 +74,7 @@ tiledb_query_type <- function(query) {
 #' @return The modified query object, invisibly
 #' @export
 tiledb_query_set_layout <- function(
-  query, 
+  query,
   layout = c(
     "COL_MAJOR", "ROW_MAJOR",
     "GLOBAL_ORDER", "UNORDERED"
@@ -165,8 +165,8 @@ tiledb_query_create_buffer_ptr_char <- function(query, varvec) {
 #' @return An external pointer to the allocated buffer object
 #' @export
 tiledb_query_alloc_buffer_ptr_char <- function(
-  sizeoffsets, 
-  sizedata, 
+  sizeoffsets,
+  sizedata,
   nullable = FALSE
 ) {
   stopifnot(
@@ -221,15 +221,15 @@ tiledb_query_set_buffer_ptr_char <- function(query, attr, bufptr) {
 #' @param ncells A number of elements (not bytes)
 #' @param nullable Optional boolean parameter indicating whether missing values
 #' are allowed (for which another column is allocated), default is FALSE
-#' @param varnum Option intgeter parameter for the number of elemements per variable,
+#' @param varnum Option integer parameter for the number of elements per variable,
 #' default is one
 #' @return An external pointer to the allocated buffer object
 #' @export
 tiledb_query_buffer_alloc_ptr <- function(
-  query, 
-  datatype, 
-  ncells, 
-  nullable = FALSE, 
+  query,
+  datatype,
+  ncells,
+  nullable = FALSE,
   varnum = 1
 ) {
   stopifnot(
@@ -303,7 +303,7 @@ tiledb_query_get_buffer_ptr <- function(bufptr) {
 #' @return An R object as resulting from the query
 #' @export
 tiledb_query_get_buffer_char <- function(
-  bufptr, 
+  bufptr,
   sizeoffsets = 0,
   sizestring = 0
 ) {
@@ -410,8 +410,8 @@ tiledb_query_result_buffer_elements <- function(query, attr) {
 #' @seealso tiledb_query_result_buffer_elements
 #' @export
 tiledb_query_result_buffer_elements_vec <- function(
-  query, 
-  attr, 
+  query,
+  attr,
   nullable = FALSE
 ) {
   stopifnot(
@@ -433,10 +433,10 @@ tiledb_query_result_buffer_elements_vec <- function(
 #' @return The query object, invisibly
 #' @export
 tiledb_query_add_range <- function(
-  query, 
-  schema, 
-  attr, lowval, 
-  highval, 
+  query,
+  schema,
+  attr, lowval,
+  highval,
   stride = NULL
 ) {
   stopifnot(
@@ -465,11 +465,11 @@ tiledb_query_add_range <- function(
 #' @return The query object, invisibly
 #' @export
 tiledb_query_add_range_with_type <- function(
-  query, 
-  idx, 
-  datatype, 
-  lowval, 
-  highval, 
+  query,
+  idx,
+  datatype,
+  lowval,
+  highval,
   stride = NULL
 ) {
   stopifnot(
@@ -517,7 +517,7 @@ tiledb_query_get_fragment_uri <- function(query, idx) {
 #' Retrieve the timestamp range for a given Query Fragment
 #'
 #' This function is only applicable to \sQuote{WRITE} queries. The time resolution in
-#' TileDB is millseconds since the epoch so an R \code{Datetime} vector is returned.
+#' TileDB is milliseconds since the epoch so an R \code{Datetime} vector is returned.
 #' @param query A TileDB Query object
 #' @param idx An integer (or numeric) index ranging from zero to the number of fragments minus 1
 #' @return A two-element datetime vector with the start and end time of the fragment write.
@@ -686,7 +686,7 @@ tiledb_query_ctx <- function(query) {
 ##' @return The value of the aggregation
 ##' @export
 tiledb_query_apply_aggregate <- function(
-  query, 
+  query,
   attrname,
   operation = c("Count", "NullCount", "Min", "Max", "Mean",  "Sum"),
   nullable = TRUE

R/QueryCondition.R

@@ -302,7 +302,7 @@ parse_query_condition <- function(expr, ta = NULL, debug = FALSE, strict = TRUE,
 #' @param use_enum A boolean to set (if TRUE) or unset (if FALSE) enumeration use
 #' @param ctx (optional) A TileDB Ctx object; if not supplied the default
 #' context object is retrieved
-#' @return Nothing is retuned, the function is invoked for the side effect
+#' @return Nothing is returned, the function is invoked for the side effect
 #' @export
 tiledb_query_condition_set_use_enumeration <- function(qc, use_enum, ctx = tiledb_get_context()) {
   stopifnot(

R/TileDBArray.R

@@ -52,7 +52,7 @@
 #' conversion, permitted values are \sQuote{asis} (default, returning a list
 #' of columns), \sQuote{array}, \sQuote{matrix},\sQuote{data.frame},
 #' \sQuote{data.table} \sQuote{tibble}, \sQuote{arrow_table} or \sQuote{arrow}
-#' (where the last two are synomyms); note that \sQuote{data.table},
+#' (where the last two are synonyms); note that \sQuote{data.table},
 #' \sQuote{tibble} and \sQuote{arrow} require the respective packages
 #' to be installed.
 #' @slot query_statistics A logical value, defaults to \sQuote{FALSE}; if
@@ -125,10 +125,10 @@ setClass(
 #' default uninitialized without a condition; this functionality requires
 #' TileDB 2.3.0 or later
 #' @param timestamp_start optional A POSIXct Datetime value determining the
-#' inclusive time point at which the array is to be openened. No fragments
+#' inclusive time point at which the array is to be opened. No fragments
 #' written earlier will be considered.
 #' @param timestamp_end optional A POSIXct Datetime value determining the
-#' inclusive time point until which the array is to be openened. No fragments
+#' inclusive time point until which the array is to be opened. No fragments
 #' written earlier later be considered.
 #' @param return_as optional A character value with the desired
 #' \code{tiledb_array} conversion, permitted values are \sQuote{asis} (default,
@@ -500,7 +500,7 @@ setValidity("tiledb_array", function(object) {
 
 #' Returns a TileDB array, allowing for specific subset ranges.
 #'
-#' Heterogenous domains are supported, including timestamps and characters.
+#' Heterogeneous domains are supported, including timestamps and characters.
 #'
 #' This function may still still change; the current implementation should be
 #' considered as an initial draft.
@@ -1429,10 +1429,10 @@ setMethod(
           }
         } else {
           if (length(tstamp) > 0) {
-            spdl::debug("['[<-'] openning for WRITE at {}", tstamp)
+            spdl::debug("['[<-'] opening for WRITE at {}", tstamp)
             arrptr <- libtiledb_array_open_at(ctx@ptr, uri, "WRITE", tstamp)
           } else {
-            spdl::debug("['[<-'] openning for WRITE")
+            spdl::debug("['[<-'] opening for WRITE")
             arrptr <- libtiledb_array_open(ctx@ptr, uri, "WRITE")
           }
         }
@@ -1818,7 +1818,7 @@ setMethod("query_layout", signature = "tiledb_array", function(object) object@qu
 #'
 #' @param value A character variable for the query layout. Permitted values
 #' are \dQuote{ROW_MAJOR}, \dQuote{COL_MAJOR}, \dQuote{GLOBAL_ORDER}, or
-#' \dQuote{UNORDERD}.
+#' \dQuote{UNORDERED}.
 #' @return The modified \code{tiledb_array} array object
 #' @export
 setReplaceMethod(
@@ -2359,7 +2359,7 @@ setGeneric("tdb_filter", function(x, ...) standardGeneric("tdb_filter"))
 #'
 #' @param x A tiledb_array object as first argument, permitting piping
 #' @param ... One or more expressions that are parsed as query_condition objects
-#' @param strict A boolean toogle to, if set, errors if a non-existing attribute
+#' @param strict A boolean toggle to, if set, errors if a non-existing attribute
 #' is selected or filtered on, defaults to 'TRUE'; if 'FALSE' a warning is shown
 #' by execution proceeds.
 #' @return The tiledb_array object, permitting piping