diff --git a/DESCRIPTION b/DESCRIPTION index f572d22d1c..890b9d9801 100644 --- a/DESCRIPTION +++ b/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 diff --git a/NAMESPACE b/NAMESPACE index 112555b22f..cc3f9f5aec 100644 --- a/NAMESPACE +++ b/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) diff --git a/R/Array.R b/R/Array.R index 8e4edf44fe..6a778d0ccd 100644 --- a/R/Array.R +++ b/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)) diff --git a/R/ArrowIO.R b/R/ArrowIO.R index a4c095f817..00a825b166 100644 --- a/R/ArrowIO.R +++ b/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 diff --git a/R/Config.R b/R/Config.R index 01329b4cb9..967f1dc1d8 100644 --- a/R/Config.R +++ b/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) diff --git a/R/Ctx.R b/R/Ctx.R index 3765e4befc..8a79361a48 100644 --- a/R/Ctx.R +++ b/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` diff --git a/R/CurrentDomain.R b/R/CurrentDomain.R index a617219b5a..10f176298c 100644 --- a/R/CurrentDomain.R +++ b/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" ) diff --git a/R/DataFrame.R b/R/DataFrame.R index c443385b5c..4ba2a1a23a 100644 --- a/R/DataFrame.R +++ b/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, diff --git a/R/Filestore.R b/R/Filestore.R index 4f35350022..966b555318 100644 --- a/R/Filestore.R +++ b/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 diff --git a/R/Metadata.R b/R/Metadata.R index c9feaa8ca4..92327fd8f8 100644 --- a/R/Metadata.R +++ b/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( diff --git a/R/NDRectangle.R b/R/NDRectangle.R index a01076bd8c..e348201c64 100644 --- a/R/NDRectangle.R +++ b/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) diff --git a/R/Profile.R b/R/Profile.R index b1539b9600..776cbf32c2 100644 --- a/R/Profile.R +++ b/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) } diff --git a/R/Query.R b/R/Query.R index 7c532204a3..a80929e1c2 100644 --- a/R/Query.R +++ b/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 diff --git a/R/QueryCondition.R b/R/QueryCondition.R index 6eef7d32df..591647403f 100644 --- a/R/QueryCondition.R +++ b/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( diff --git a/R/TileDBArray.R b/R/TileDBArray.R index dcf37d0da7..439afb6bda 100644 --- a/R/TileDBArray.R +++ b/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 diff --git a/R/VFS.R b/R/VFS.R index 2aab1a8f51..35454dd799 100644 --- a/R/VFS.R +++ b/R/VFS.R @@ -153,7 +153,7 @@ tiledb_vfs_empty_bucket <- function(uri, vfs = tiledb_get_vfs()) { #' Create a VFS Directory #' -#' @param uri Character variable with a URI describing a diretory path +#' @param uri Character variable with a URI describing a directory path #' @param vfs A TileDB VFS object; default is to use a cached value. #' @return The uri value of the created directory #' @export @@ -167,7 +167,7 @@ tiledb_vfs_create_dir <- function(uri, vfs = tiledb_get_vfs()) { #' Test for VFS Directory #' -#' @param uri Character variable with a URI describing a diretory path +#' @param uri Character variable with a URI describing a directory path #' @param vfs A TileDB VFS object; default is to use a cached value. #' @return A boolean value indicating if it is a directory #' @export @@ -181,7 +181,7 @@ tiledb_vfs_is_dir <- function(uri, vfs = tiledb_get_vfs()) { #' Remove a VFS Directory #' -#' @param uri Character variable with a URI describing a diretory path +#' @param uri Character variable with a URI describing a directory path #' @param vfs A TileDB VFS object; default is to use a cached value. #' @return The uri value of the removed directory #' @export @@ -320,7 +320,7 @@ tiledb_set_vfs <- function(vfs) { #' @return A TileDB VFS Filehandle object (as an external pointer) #' @export tiledb_vfs_open <- function( - binfile, + binfile, mode = c("READ", "WRITE", "APPEND"), vfs = tiledb_get_vfs(), ctx = tiledb_get_context() @@ -336,7 +336,7 @@ tiledb_vfs_open <- function( #' Close a TileDB VFS Filehandle #' -#' @param fh A TileDB VFS Filehandle external pointer as returned from +#' @param fh A TileDB VFS Filehandle external pointer as returned from #' \code{tiledb_vfs_open} #' @param ctx (optional) A TileDB Ctx object #' @return The result of the close operation is returned. @@ -351,7 +351,7 @@ tiledb_vfs_close <- function(fh, ctx = tiledb_get_context()) { #' Sync a TileDB VFS Filehandle #' -#' @param fh A TileDB VFS Filehandle external pointer as returned from +#' @param fh A TileDB VFS Filehandle external pointer as returned from #' \code{tiledb_vfs_open} #' @param ctx (optional) A TileDB Ctx object #' @return The result of the sync operation is returned. @@ -366,12 +366,12 @@ tiledb_vfs_sync <- function(fh, ctx = tiledb_get_context()) { #' Write to a TileDB VFS Filehandle #' -#' This interface currently defaults to using an integer vector. This is suitable -#' for R objects as the raw vector result from serialization can be mapped easily -#' to an integer vector. It is also possible to \code{memcpy} to the contiguous +#' This interface currently defaults to using an integer vector. This is suitable +#' for R objects as the raw vector result from serialization can be mapped easily +#' to an integer vector. It is also possible to \code{memcpy} to the contiguous #' memory of an integer vector should other (non-R) data be transferred. -#' -#' @param fh A TileDB VFS Filehandle external pointer as returned from +#' +#' @param fh A TileDB VFS Filehandle external pointer as returned from #' \code{tiledb_vfs_open} #' @param vec An integer vector of content to be written #' @param ctx (optional) A TileDB Ctx object @@ -388,14 +388,14 @@ tiledb_vfs_write <- function(fh, vec, ctx = tiledb_get_context()) { #' Read from a TileDB VFS Filehandle #' -#' This interface currently defaults to reading an integer vector. This is -#' suitable for R objects as a raw vector used for (de)serialization can be -#' mapped easily to an integer vector. It is also possible to \code{memcpy} to -#' the contiguous memory of an integer vector should other (non-R) data +#' This interface currently defaults to reading an integer vector. This is +#' suitable for R objects as a raw vector used for (de)serialization can be +#' mapped easily to an integer vector. It is also possible to \code{memcpy} to +#' the contiguous memory of an integer vector should other (non-R) data #' be transferred. -#' @param fh A TileDB VFS Filehandle external pointer as returned from +#' @param fh A TileDB VFS Filehandle external pointer as returned from #' \code{tiledb_vfs_open} -#' @param offset A scalar value with the byte offset from the beginning of the +#' @param offset A scalar value with the byte offset from the beginning of the #' file with a of zero. #' @param nbytes A scalar value with the number of bytes to be read. #' @param ctx (optional) A TileDB Ctx object @@ -540,13 +540,13 @@ tiledb_vfs_copy_dir <- function(dir, uri, vfs = tiledb_get_vfs()) { #' This functionality is currently limited to S3 URIs. #' #' @param uri Character variable with a URI describing a file path -#' @param vfs (optiona) A TileDB VFS object; default is to use a cached value. +#' @param vfs (optional) A TileDB VFS object; default is to use a cached value. #' @param ctx (optional) A TileDB Ctx object #' @return A data.frame object with two columns for the full path and the object #' size in bytes #' @export tiledb_vfs_ls_recursive <- function( - uri, + uri, vfs = tiledb_get_vfs(), ctx = tiledb_get_context() ) { diff --git a/R/Version.R b/R/Version.R index 6734c57466..d8c61fd23c 100644 --- a/R/Version.R +++ b/R/Version.R @@ -22,7 +22,7 @@ #' The version of the libtiledb library #' -#' @param compact Logical value indicating wheter a compact +#' @param compact Logical value indicating whether a compact #' \code{package_version} object should be returned #' @return An named int vector c(major, minor, patch), or if select, #' a \code{package_version} object diff --git a/inst/notebooks/datetimes.Rmd b/inst/notebooks/datetimes.Rmd index f4e9ffb128..cc481839f9 100644 --- a/inst/notebooks/datetimes.Rmd +++ b/inst/notebooks/datetimes.Rmd @@ -18,7 +18,8 @@ Sys.setenv("TZ"="UTC") ## Overview -TileDB supports a wide range of date and time types as shown in the [documention for + +TileDB supports a wide range of date and time types as shown in the [documentation for Datetimes][doc_datetimes]. The supported range of dates and times correspond to the dates and times supported by the Python diff --git a/man/as.data.frame.tiledb_config.Rd b/man/as.data.frame.tiledb_config.Rd index 69559c5200..f824d45b62 100644 --- a/man/as.data.frame.tiledb_config.Rd +++ b/man/as.data.frame.tiledb_config.Rd @@ -12,7 +12,7 @@ \item{...}{Extra parameter for method signature, currently unused.} } \value{ -a data.frame wth parameter, value columns +a data.frame with parameter, value columns } \description{ Convert a TileDB Config object to \code{data.frame} diff --git a/man/fromDataFrame.Rd b/man/fromDataFrame.Rd index 50e75b4c94..066f8f0ce7 100644 --- a/man/fromDataFrame.Rd +++ b/man/fromDataFrame.Rd @@ -65,7 +65,7 @@ writing to the newly-created array) and \sQuote{append} (to only append to an al array).} \item{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.} \item{coords_filters}{A character vector with filters for coordinates, default is \code{ZSTD}.} diff --git a/man/query_layout-set-tiledb_array-method.Rd b/man/query_layout-set-tiledb_array-method.Rd index daa113bf7d..b3175ce7bc 100644 --- a/man/query_layout-set-tiledb_array-method.Rd +++ b/man/query_layout-set-tiledb_array-method.Rd @@ -14,7 +14,7 @@ query_layout(x) <- value \item{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}.} } \value{ The modified \code{tiledb_array} array object diff --git a/man/sub-tiledb_array-ANY-method.Rd b/man/sub-tiledb_array-ANY-method.Rd index 3b5c6266f2..cc60f40f1c 100644 --- a/man/sub-tiledb_array-ANY-method.Rd +++ b/man/sub-tiledb_array-ANY-method.Rd @@ -30,7 +30,7 @@ currently unused.} The resulting elements in the selected format } \description{ -Heterogenous domains are supported, including timestamps and characters. +Heterogeneous domains are supported, including timestamps and characters. } \details{ This function may still still change; the current implementation should be diff --git a/man/tdb_filter-tiledb_array-method.Rd b/man/tdb_filter-tiledb_array-method.Rd index d465cd56f2..cc387084a3 100644 --- a/man/tdb_filter-tiledb_array-method.Rd +++ b/man/tdb_filter-tiledb_array-method.Rd @@ -11,7 +11,7 @@ \item{...}{One or more expressions that are parsed as query_condition objects} -\item{strict}{A boolean toogle to, if set, errors if a non-existing attribute +\item{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.} } diff --git a/man/tiledb_array-class.Rd b/man/tiledb_array-class.Rd index 770fec15ae..9abfc8f5a8 100644 --- a/man/tiledb_array-class.Rd +++ b/man/tiledb_array-class.Rd @@ -50,7 +50,7 @@ interval start} 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.} diff --git a/man/tiledb_array.Rd b/man/tiledb_array.Rd index 11928910c3..d779b019d7 100644 --- a/man/tiledb_array.Rd +++ b/man/tiledb_array.Rd @@ -71,11 +71,11 @@ default uninitialized without a condition; this functionality requires TileDB 2.3.0 or later} \item{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.} \item{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.} \item{return_as}{optional A character value with the desired diff --git a/man/tiledb_array_is_heterogeneous.Rd b/man/tiledb_array_is_heterogeneous.Rd index c05e1e9d5a..fa6b22e4c8 100644 --- a/man/tiledb_array_is_heterogeneous.Rd +++ b/man/tiledb_array_is_heterogeneous.Rd @@ -10,7 +10,7 @@ tiledb_array_is_heterogeneous(arr) \item{arr}{A TileDB Array object} } \value{ -A boolean indicating if the array has heterogenous domains +A boolean indicating if the array has heterogeneous domains } \description{ Check for Heterogeneous Domain diff --git a/man/tiledb_filestore_buffer_export.Rd b/man/tiledb_filestore_buffer_export.Rd index 2e0535c0c4..39e3823b28 100644 --- a/man/tiledb_filestore_buffer_export.Rd +++ b/man/tiledb_filestore_buffer_export.Rd @@ -14,7 +14,7 @@ tiledb_filestore_buffer_export( \arguments{ \item{filestore_uri}{Character with an TileDB Array Schema URI} -\item{offset}{(optional) Numeric variable with offset from beginnig, default is zero} +\item{offset}{(optional) Numeric variable with offset from beginning, default is zero} \item{bytes}{(optional) Numeric variable with number of bytes to read, default is zero} diff --git a/man/tiledb_has_metadata.Rd b/man/tiledb_has_metadata.Rd index 6c9569389b..d0430232e6 100644 --- a/man/tiledb_has_metadata.Rd +++ b/man/tiledb_has_metadata.Rd @@ -13,7 +13,7 @@ tiledb_has_metadata(arr, key) } \value{ A logical value indicating if the given key exists in the -metdata of the given array +metadata of the given array } \description{ Test if TileDB Array has Metadata diff --git a/man/tiledb_is_supported_fs.Rd b/man/tiledb_is_supported_fs.Rd index bd4da11883..b6769e89d4 100644 --- a/man/tiledb_is_supported_fs.Rd +++ b/man/tiledb_is_supported_fs.Rd @@ -15,7 +15,7 @@ tiledb_is_supported_fs(scheme, object = tiledb_get_context()) TRUE if tiledb backend is supported, FALSE otherwise } \description{ -The scheme corresponds to the URI scheme for TileDB resouces. +The scheme corresponds to the URI scheme for TileDB resources. } \details{ Ex: diff --git a/man/tiledb_query_buffer_alloc_ptr.Rd b/man/tiledb_query_buffer_alloc_ptr.Rd index 883c493e78..d9c373486c 100644 --- a/man/tiledb_query_buffer_alloc_ptr.Rd +++ b/man/tiledb_query_buffer_alloc_ptr.Rd @@ -22,7 +22,7 @@ tiledb_query_buffer_alloc_ptr( \item{nullable}{Optional boolean parameter indicating whether missing values are allowed (for which another column is allocated), default is FALSE} -\item{varnum}{Option intgeter parameter for the number of elemements per variable, +\item{varnum}{Option integer parameter for the number of elements per variable, default is one} } \value{ diff --git a/man/tiledb_query_condition_set_use_enumeration.Rd b/man/tiledb_query_condition_set_use_enumeration.Rd index f815008a30..7dd08fb940 100644 --- a/man/tiledb_query_condition_set_use_enumeration.Rd +++ b/man/tiledb_query_condition_set_use_enumeration.Rd @@ -19,7 +19,7 @@ tiledb_query_condition_set_use_enumeration( context object is retrieved} } \value{ -Nothing is retuned, the function is invoked for the side effect +Nothing is returned, the function is invoked for the side effect } \description{ Set a boolean toggle to signal use of enumeration in query condition (TileDB 2.17 or later) diff --git a/man/tiledb_query_get_fragment_timestamp_range.Rd b/man/tiledb_query_get_fragment_timestamp_range.Rd index fbb4017828..aee69e732b 100644 --- a/man/tiledb_query_get_fragment_timestamp_range.Rd +++ b/man/tiledb_query_get_fragment_timestamp_range.Rd @@ -16,5 +16,5 @@ A two-element datetime vector with the start and end time of the fragment write. } \description{ 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. } diff --git a/man/tiledb_query_import_buffer.Rd b/man/tiledb_query_import_buffer.Rd index 0d38fa40ed..47b2a1e5f6 100644 --- a/man/tiledb_query_import_buffer.Rd +++ b/man/tiledb_query_import_buffer.Rd @@ -26,5 +26,5 @@ The update Query external pointer is returned } \description{ This function imports to the named buffer for a \sQuote{WRITE} query -from two Arrow exerternal pointers. +from two Arrow external pointers. } diff --git a/man/tiledb_version.Rd b/man/tiledb_version.Rd index 3fb0874140..7fe8e64abd 100644 --- a/man/tiledb_version.Rd +++ b/man/tiledb_version.Rd @@ -7,7 +7,7 @@ tiledb_version(compact = FALSE) } \arguments{ -\item{compact}{Logical value indicating wheter a compact +\item{compact}{Logical value indicating whether a compact \code{package_version} object should be returned} } \value{ diff --git a/man/tiledb_vfs_create_dir.Rd b/man/tiledb_vfs_create_dir.Rd index 57e19befe4..2d3175d27b 100644 --- a/man/tiledb_vfs_create_dir.Rd +++ b/man/tiledb_vfs_create_dir.Rd @@ -7,7 +7,7 @@ tiledb_vfs_create_dir(uri, vfs = tiledb_get_vfs()) } \arguments{ -\item{uri}{Character variable with a URI describing a diretory path} +\item{uri}{Character variable with a URI describing a directory path} \item{vfs}{A TileDB VFS object; default is to use a cached value.} } diff --git a/man/tiledb_vfs_is_dir.Rd b/man/tiledb_vfs_is_dir.Rd index f860ddb765..ae4eb7b6c9 100644 --- a/man/tiledb_vfs_is_dir.Rd +++ b/man/tiledb_vfs_is_dir.Rd @@ -7,7 +7,7 @@ tiledb_vfs_is_dir(uri, vfs = tiledb_get_vfs()) } \arguments{ -\item{uri}{Character variable with a URI describing a diretory path} +\item{uri}{Character variable with a URI describing a directory path} \item{vfs}{A TileDB VFS object; default is to use a cached value.} } diff --git a/man/tiledb_vfs_ls_recursive.Rd b/man/tiledb_vfs_ls_recursive.Rd index eddeb84480..4def73da52 100644 --- a/man/tiledb_vfs_ls_recursive.Rd +++ b/man/tiledb_vfs_ls_recursive.Rd @@ -13,7 +13,7 @@ tiledb_vfs_ls_recursive( \arguments{ \item{uri}{Character variable with a URI describing a file path} -\item{vfs}{(optiona) A TileDB VFS object; default is to use a cached value.} +\item{vfs}{(optional) A TileDB VFS object; default is to use a cached value.} \item{ctx}{(optional) A TileDB Ctx object} } diff --git a/man/tiledb_vfs_remove_dir.Rd b/man/tiledb_vfs_remove_dir.Rd index 21a5187018..cb4571689c 100644 --- a/man/tiledb_vfs_remove_dir.Rd +++ b/man/tiledb_vfs_remove_dir.Rd @@ -7,7 +7,7 @@ tiledb_vfs_remove_dir(uri, vfs = tiledb_get_vfs()) } \arguments{ -\item{uri}{Character variable with a URI describing a diretory path} +\item{uri}{Character variable with a URI describing a directory path} \item{vfs}{A TileDB VFS object; default is to use a cached value.} } diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml index a72c4303e2..c95c013a74 100644 --- a/pkgdown/_pkgdown.yml +++ b/pkgdown/_pkgdown.yml @@ -117,7 +117,7 @@ reference: - matches("array_consolidate") - matches("array_vacuum") - title: MetaData - desc: arrray metadata functionality + desc: array metadata functionality contents: - matches("metadata") - title: Stats diff --git a/src/deprecation.cpp b/src/deprecation.cpp index 97a8f962f8..45536c95d3 100644 --- a/src/deprecation.cpp +++ b/src/deprecation.cpp @@ -53,7 +53,7 @@ _string_to_tiledb_encryption_type_t(std::string encstr) { int rc = tiledb_encryption_type_from_str(encstr.c_str(), &enc); if (rc == TILEDB_OK) return enc; - Rcpp::stop("Unknow TileDB encryption type '%s'", encstr.c_str()); + Rcpp::stop("Unknown TileDB encryption type '%s'", encstr.c_str()); } // Deprecated in Core April 2024, removed July 2024 diff --git a/src/libtiledb.cpp b/src/libtiledb.cpp index 01ea2080dc..d8e9b3b226 100644 --- a/src/libtiledb.cpp +++ b/src/libtiledb.cpp @@ -844,7 +844,7 @@ XPtr libtiledb_dim(XPtr ctx, std::array _domain = {domain_vec[0], domain_vec[1]}; Rcpp::NumericVector ext(tile_extent); if (!isInteger64(ext)) { - Rcpp::stop("tile exent for INT64 domain must be an integer64 type in R"); + Rcpp::stop("tile extent for INT64 domain must be an integer64 type in R"); } int64_t _tile_extent = fromInteger64(ext[0]); auto dim = new tiledb::Dimension(tiledb::Dimension::create( @@ -867,7 +867,7 @@ XPtr libtiledb_dim(XPtr ctx, static_cast(domain_vec[1])}; Rcpp::NumericVector ext(tile_extent); if (!isInteger64(ext)) { - Rcpp::stop("tile exent for UINT64 domain must be an integer64 type in R"); + Rcpp::stop("tile extent for UINT64 domain must be an integer64 type in R"); } uint64_t _tile_extent = static_cast(fromInteger64(ext[0])); auto dim = new tiledb::Dimension(tiledb::Dimension::create( @@ -1381,7 +1381,7 @@ double _domain_datatype_time_scale_factor(tiledb_datatype_t dtype) { case TILEDB_DATETIME_AS: return 1e-9; default: - Rcpp::stop("Unsupport datatype (%d)", dtype); + Rcpp::stop("Unsupported datatype (%d)", dtype); } return R_NaReal; // not reached } @@ -2081,7 +2081,7 @@ int libtiledb_array_schema_get_capacity(XPtr schema) { check_xptr_tag(schema); uint64_t cap = schema->capacity(); if (cap > std::numeric_limits::max()) { - Rcpp::stop("Overflow on schema capcity at '%ld'", cap); + Rcpp::stop("Overflow on schema capacity at '%ld'", cap); } return static_cast(cap); } @@ -5995,4 +5995,3 @@ void libtiledb_profile_save(XPtr profile) { std::string libtiledb_profile_dump(XPtr profile) { return profile->dump(); } - diff --git a/vignettes/data-ingestion-from-sql.Rmd b/vignettes/data-ingestion-from-sql.Rmd index 54290d10a4..e40c1f105c 100644 --- a/vignettes/data-ingestion-from-sql.Rmd +++ b/vignettes/data-ingestion-from-sql.Rmd @@ -152,7 +152,7 @@ The [TileDB R Tutorial at useR! 2021](https://dirk.eddelbuettel.com/papers/useR2021_tiledb_tutorial.pdf) contained a worked example of writing *much* larger data set in chunks. The process is very similar to the simple example we showed here -- and -in addition requires a suffient domain range for the dimension along +in addition requires a sufficient domain range for the dimension along with a (sequential or parallel) loop of reading chunks and writing them to TileDB. diff --git a/vignettes/documentation.Rmd b/vignettes/documentation.Rmd index 702d4eb826..8df7ee3743 100644 --- a/vignettes/documentation.Rmd +++ b/vignettes/documentation.Rmd @@ -111,7 +111,7 @@ library(tiledb) # Create dimension dim <- tiledb_dim("dim1", c(1L, 4L), 2L, "INT32") -# String dimenions: no values for domain and extent +# String dimensions: no values for domain and extent strdim <- tiledb_dim("dim2", NULL, NULL, "ASCII") ``` @@ -575,7 +575,7 @@ sch <- schema(uri) # get an encrypted scheme directory from storage, enc_key is the AES-256 key sch <- schema(uri, enc_key) -# get a schema from an already openened array +# get a schema from an already opened array # using a sparse array example, works the same for dense arrays array_name <- urisparse A <- tiledb_array(uri = array_name, is.sparse = TRUE) @@ -1016,7 +1016,7 @@ uri <- "" # Consolidate with default configuration array_consolidate(uri) -# Alteratively, create and pass a configuration object +# Alternatively, create and pass a configuration object cfg <- tiledb_config() cfg["sm.consolidation.steps"] <- "3" cfg["sm.consolidation.mode"] <- "fragments" @@ -1032,7 +1032,7 @@ uri <- "" # Vacuum with default configuration array_vacuum(uri) -# Alteratively, create and pass a configuration object +# Alternatively, create and pass a configuration object cfg <- tiledb_config() cfg["sm.vacuum.mode"] <- "fragments" array_vacuum(uri, cfg) diff --git a/vignettes/installation-options.Rmd b/vignettes/installation-options.Rmd index bb569702cb..11db524456 100644 --- a/vignettes/installation-options.Rmd +++ b/vignettes/installation-options.Rmd @@ -22,7 +22,7 @@ package. The TileDB R package is released via the Comprehensive R Archive Network, or CRAN. CRAN generally provides binaries for the two most -widely operating systems, Windows and macOS. So issueing the command +widely operating systems, Windows and macOS. So issuing the command ``` r install.packages("tiledb")