From 8c50c7204db625f3b1a202e1022135b0b6c650e6 Mon Sep 17 00:00:00 2001 From: Constantinos Giachalis Date: Thu, 16 Oct 2025 16:21:02 +0300 Subject: [PATCH 1/9] Fix docs Ctx.R --- R/Ctx.R | 4 ++-- man/tiledb_set_context.Rd | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/R/Ctx.R b/R/Ctx.R index 3765e4befc..89bd1c8020 100644 --- a/R/Ctx.R +++ b/R/Ctx.R @@ -1,6 +1,6 @@ # MIT License # -# Copyright (c) 2017-2023 TileDB Inc. +# Copyright (c) 2017-2025 TileDB Inc. # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -55,7 +55,7 @@ getContext <- function() tiledb_get_context() #' #' @param ctx A TileDB context object #' @return NULL, invisibly. The function is invoked for the side-effect of -#' storing the VFS object. +#' storing the Ctx object. #' @export tiledb_set_context <- function(ctx) { stopifnot(`The 'ctx' argument must be a tiledb_ctx object` = is(ctx, "tiledb_ctx")) diff --git a/man/tiledb_set_context.Rd b/man/tiledb_set_context.Rd index 8933d7de52..77fe0279df 100644 --- a/man/tiledb_set_context.Rd +++ b/man/tiledb_set_context.Rd @@ -11,7 +11,7 @@ tiledb_set_context(ctx) } \value{ NULL, invisibly. The function is invoked for the side-effect of -storing the VFS object. +storing the Ctx object. } \description{ Store a TileDB context object in the package cache From 8105cb58d160993a492987f45e87a9db0bc41a36 Mon Sep 17 00:00:00 2001 From: Constantinos Giachalis Date: Thu, 16 Oct 2025 16:21:44 +0300 Subject: [PATCH 2/9] Fix docs Group.R --- R/Group.R | 5 +++-- man/tiledb_group_has_metadata.Rd | 3 ++- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/R/Group.R b/R/Group.R index a10c953288..8d712d84a5 100644 --- a/R/Group.R +++ b/R/Group.R @@ -1,6 +1,6 @@ # MIT License # -# Copyright (c) 2022-2024 TileDB Inc. +# Copyright (c) 2022-2025 TileDB Inc. # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -262,7 +262,8 @@ tiledb_group_get_metadata <- function(grp, key) { ##' \code{tiledb_group()} ##' @param key A character value with they index under which the ##' data will be written -##' @return A boolean value indicating with the object is present +##' @return A logical value indicating if the given key exists in the +##' metadata of the given group ##' @export tiledb_group_has_metadata <- function(grp, key) { stopifnot( diff --git a/man/tiledb_group_has_metadata.Rd b/man/tiledb_group_has_metadata.Rd index 0b2ce3c59d..039358a3f0 100644 --- a/man/tiledb_group_has_metadata.Rd +++ b/man/tiledb_group_has_metadata.Rd @@ -14,7 +14,8 @@ tiledb_group_has_metadata(grp, key) data will be written} } \value{ -A boolean value indicating with the object is present +A logical value indicating if the given key exists in the +metadata of the given group } \description{ Checks for Metadata in a TileDB Group From d94113a85c93bc61dd365bf01fe03796fd910825 Mon Sep 17 00:00:00 2001 From: Constantinos Giachalis Date: Thu, 16 Oct 2025 16:22:36 +0300 Subject: [PATCH 3/9] Fix docs Metadata.R --- R/Metadata.R | 4 ++-- man/tiledb_has_metadata.Rd | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/R/Metadata.R b/R/Metadata.R index c9feaa8ca4..c9794f57df 100644 --- a/R/Metadata.R +++ b/R/Metadata.R @@ -1,6 +1,6 @@ # MIT License # -# Copyright (c) 2017-2023 TileDB Inc. +# Copyright (c) 2017-2025 TileDB Inc. # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -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/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 From 370676bd93c015ed5db67179eedce44e9e6478aa Mon Sep 17 00:00:00 2001 From: Constantinos Giachalis Date: Thu, 16 Oct 2025 16:23:23 +0300 Subject: [PATCH 4/9] Fix docs VFS.R --- R/VFS.R | 38 ++++++++++++++++++------------------ man/tiledb_vfs_is_bucket.Rd | 2 +- man/tiledb_vfs_is_dir.Rd | 2 +- man/tiledb_vfs_remove_dir.Rd | 2 +- 4 files changed, 22 insertions(+), 22 deletions(-) diff --git a/R/VFS.R b/R/VFS.R index 2aab1a8f51..375ab628c5 100644 --- a/R/VFS.R +++ b/R/VFS.R @@ -1,6 +1,6 @@ # MIT License # -# Copyright (c) 2017-2024 TileDB Inc. +# Copyright (c) 2017-2025 TileDB Inc. # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -102,7 +102,7 @@ tiledb_vfs_remove_bucket <- function(uri, vfs = tiledb_get_vfs()) { #' cfg["vfs.s3.region"] <- "us-west-1" #' ctx <- tiledb_ctx(cfg) #' vfs <- tiledb_vfs() -#' tiledb_vfs_is_bucket(vfs, "s3://tiledb-public-us-west-1/test-array-4x4") +#' tiledb_vfs_is_bucket("s3://tiledb-public-us-west-1/test-array-4x4", vfs = vfs) #' } tiledb_vfs_is_bucket <- function(uri, vfs = tiledb_get_vfs()) { stopifnot( @@ -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 @@ -546,7 +546,7 @@ tiledb_vfs_copy_dir <- function(dir, uri, vfs = tiledb_get_vfs()) { #' size in bytes #' @export tiledb_vfs_ls_recursive <- function( - uri, + uri, vfs = tiledb_get_vfs(), ctx = tiledb_get_context() ) { diff --git a/man/tiledb_vfs_is_bucket.Rd b/man/tiledb_vfs_is_bucket.Rd index 249e8aa1b6..53fe2b17cf 100644 --- a/man/tiledb_vfs_is_bucket.Rd +++ b/man/tiledb_vfs_is_bucket.Rd @@ -26,6 +26,6 @@ cfg <- tiledb_config() cfg["vfs.s3.region"] <- "us-west-1" ctx <- tiledb_ctx(cfg) vfs <- tiledb_vfs() -tiledb_vfs_is_bucket(vfs, "s3://tiledb-public-us-west-1/test-array-4x4") +tiledb_vfs_is_bucket("s3://tiledb-public-us-west-1/test-array-4x4", vfs = vfs) } } 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_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.} } From 405fa0a7b4b3b7a5c17fcc375ff6ef6f34e9e498 Mon Sep 17 00:00:00 2001 From: Constantinos Giachalis Date: Thu, 16 Oct 2025 16:25:02 +0300 Subject: [PATCH 5/9] Fix docs Query.R --- R/Query.R | 62 +++++++++---------- man/query_layout-set-tiledb_array-method.Rd | 2 +- man/tiledb_query.Rd | 8 +-- man/tiledb_query_apply_aggregate.Rd | 4 +- man/tiledb_query_buffer_alloc_ptr.Rd | 2 +- man/tiledb_query_result_buffer_elements.Rd | 2 +- ...tiledb_query_result_buffer_elements_vec.Rd | 2 +- man/tiledb_query_set_buffer.Rd | 2 +- man/tiledb_query_set_subarray.Rd | 2 +- man/tiledb_query_type.Rd | 2 +- 10 files changed, 44 insertions(+), 44 deletions(-) diff --git a/R/Query.R b/R/Query.R index 7c532204a3..6828182d92 100644 --- a/R/Query.R +++ b/R/Query.R @@ -1,6 +1,6 @@ # MIT License # -# Copyright (c) 2017-2024 TileDB Inc. +# Copyright (c) 2017-2025 TileDB Inc. # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -31,13 +31,13 @@ setClass("tiledb_query", ## could add arr of type 'ANY' (using shortcut to not have to deal with collate order) ## if array was needed for query object -#' Creates a 'tiledb_query' object +#' Creates a `tiledb_query` object #' #' @param array A TileDB Array object #' @param type A character value that must be one of 'READ', 'WRITE', or -#' 'DELETE' (for TileDB >= 2.12.0) +#' 'DELETE', 'MODIFY_EXCLUSIVE' (for TileDB >= 2.12.0) #' @param ctx (optional) A TileDB Ctx object -#' @return 'tiledb_query' object +#' @return A `tiledb_query` object #' @export tiledb_query tiledb_query <- function( array, @@ -59,7 +59,7 @@ tiledb_query <- function( #' Return TileDB Query type #' #' @param query A TileDB Query object -#' @return A character value, either 'READ' or 'WRITE' +#' @return A character value, either 'READ', 'WRITE', 'DELETE' or 'MODIFY_EXCLUSIVE' #' @export tiledb_query_type <- function(query) { stopifnot(`Argument 'query' must be a tiledb_query object` = is(query, "tiledb_query")) @@ -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" @@ -99,7 +99,7 @@ tiledb_query_get_layout <- function(query) { #' Set subarray for TileDB Query object #' #' @param query A TileDB Query object -#' @param subarray A subarry vector object +#' @param subarray A subarray vector object #' @param type An optional type as a character, if missing type is #' inferred from the vector. #' @return The modified query object, invisibly @@ -123,7 +123,7 @@ tiledb_query_set_subarray <- function(query, subarray, type) { #' @param query A TileDB Query object #' @param attr A character value containing the attribute #' @param buffer A vector providing the query buffer -#' @return The modified query object, invisisibly +#' @return The modified query object, invisibly #' @export tiledb_query_set_buffer <- function(query, attr, buffer) { stopifnot( @@ -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 Optional 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 ) { @@ -378,7 +378,7 @@ tiledb_query_status <- function(query) { #' @param attr A character value containing the attribute #' @return A integer with the number of elements in the results buffer #' for the given attribute -#' @seealso tiledb_query_result_buffer_elements_vec +#' @seealso [tiledb_query_result_buffer_elements_vec] #' @export tiledb_query_result_buffer_elements <- function(query, attr) { stopifnot( @@ -407,11 +407,11 @@ tiledb_query_result_buffer_elements <- function(query, attr) { #' for fixed-size attribute or dimensions), the number elements in the results #' buffer for the given attribute, and (if nullable) a third element with the validity #' buffer size. -#' @seealso tiledb_query_result_buffer_elements +#' @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( @@ -677,7 +677,7 @@ tiledb_query_ctx <- function(query) { # query@arr # } -##' Run an aggregate oprtation on the given query attribute +##' Run an aggregate operation on the given query attribute ##' ##' @param query A TileDB Query object ##' @param attrname The name of an attribute @@ -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/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/tiledb_query.Rd b/man/tiledb_query.Rd index 6f132a1900..f41ae77c93 100644 --- a/man/tiledb_query.Rd +++ b/man/tiledb_query.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/Query.R \name{tiledb_query} \alias{tiledb_query} -\title{Creates a 'tiledb_query' object} +\title{Creates a \code{tiledb_query} object} \usage{ tiledb_query( array, @@ -19,13 +19,13 @@ tiledb_query( \item{array}{A TileDB Array object} \item{type}{A character value that must be one of 'READ', 'WRITE', or -'DELETE' (for TileDB >= 2.12.0)} +'DELETE', 'MODIFY_EXCLUSIVE' (for TileDB >= 2.12.0)} \item{ctx}{(optional) A TileDB Ctx object} } \value{ -'tiledb_query' object +A \code{tiledb_query} object } \description{ -Creates a 'tiledb_query' object +Creates a \code{tiledb_query} object } diff --git a/man/tiledb_query_apply_aggregate.Rd b/man/tiledb_query_apply_aggregate.Rd index b2e4daa4df..3a9688d64b 100644 --- a/man/tiledb_query_apply_aggregate.Rd +++ b/man/tiledb_query_apply_aggregate.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/Query.R \name{tiledb_query_apply_aggregate} \alias{tiledb_query_apply_aggregate} -\title{Run an aggregate oprtation on the given query attribute} +\title{Run an aggregate operation on the given query attribute} \usage{ tiledb_query_apply_aggregate( query, @@ -24,5 +24,5 @@ tiledb_query_apply_aggregate( The value of the aggregation } \description{ -Run an aggregate oprtation on the given query attribute +Run an aggregate operation on the given query attribute } diff --git a/man/tiledb_query_buffer_alloc_ptr.Rd b/man/tiledb_query_buffer_alloc_ptr.Rd index 883c493e78..b621c6b651 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}{Optional integer parameter for the number of elements per variable, default is one} } \value{ diff --git a/man/tiledb_query_result_buffer_elements.Rd b/man/tiledb_query_result_buffer_elements.Rd index 92d8754b42..348d4cf0b6 100644 --- a/man/tiledb_query_result_buffer_elements.Rd +++ b/man/tiledb_query_result_buffer_elements.Rd @@ -28,5 +28,5 @@ As this function was first made available when only a scalar (corresponding to the second result) was returned, we still return that value. } \seealso{ -tiledb_query_result_buffer_elements_vec +\link{tiledb_query_result_buffer_elements_vec} } diff --git a/man/tiledb_query_result_buffer_elements_vec.Rd b/man/tiledb_query_result_buffer_elements_vec.Rd index b0de33b139..81cfabd9e6 100644 --- a/man/tiledb_query_result_buffer_elements_vec.Rd +++ b/man/tiledb_query_result_buffer_elements_vec.Rd @@ -31,5 +31,5 @@ In the case of a nullable attribute, a third element is returned with the size o the validity buffer. } \seealso{ -tiledb_query_result_buffer_elements +\link{tiledb_query_result_buffer_elements} } diff --git a/man/tiledb_query_set_buffer.Rd b/man/tiledb_query_set_buffer.Rd index 9c9500eece..1d5e1e3d56 100644 --- a/man/tiledb_query_set_buffer.Rd +++ b/man/tiledb_query_set_buffer.Rd @@ -14,7 +14,7 @@ tiledb_query_set_buffer(query, attr, buffer) \item{buffer}{A vector providing the query buffer} } \value{ -The modified query object, invisisibly +The modified query object, invisibly } \description{ This function allocates query buffers directly from R vectors in diff --git a/man/tiledb_query_set_subarray.Rd b/man/tiledb_query_set_subarray.Rd index 8cabef8986..977a448ba9 100644 --- a/man/tiledb_query_set_subarray.Rd +++ b/man/tiledb_query_set_subarray.Rd @@ -9,7 +9,7 @@ tiledb_query_set_subarray(query, subarray, type) \arguments{ \item{query}{A TileDB Query object} -\item{subarray}{A subarry vector object} +\item{subarray}{A subarray vector object} \item{type}{An optional type as a character, if missing type is inferred from the vector.} diff --git a/man/tiledb_query_type.Rd b/man/tiledb_query_type.Rd index 5f4a2ae067..8149485e18 100644 --- a/man/tiledb_query_type.Rd +++ b/man/tiledb_query_type.Rd @@ -10,7 +10,7 @@ tiledb_query_type(query) \item{query}{A TileDB Query object} } \value{ -A character value, either 'READ' or 'WRITE' +A character value, either 'READ', 'WRITE', 'DELETE' or 'MODIFY_EXCLUSIVE' } \description{ Return TileDB Query type From 9cc43b32f501aea53fbfc99be3f842c27c9b9320 Mon Sep 17 00:00:00 2001 From: Constantinos Giachalis Date: Thu, 16 Oct 2025 16:25:31 +0300 Subject: [PATCH 6/9] Fix docs TileDBArray.R --- R/TileDBArray.R | 18 +++++++++--------- man/sub-tiledb_array-ANY-method.Rd | 4 ++-- man/subset-tiledb_array-ANY-ANY-ANY-method.Rd | 2 +- man/tiledb_array-class.Rd | 4 ++-- man/tiledb_array.Rd | 4 ++-- 5 files changed, 16 insertions(+), 16 deletions(-) diff --git a/R/TileDBArray.R b/R/TileDBArray.R index 4cf16d7850..f027a3d8c1 100644 --- a/R/TileDBArray.R +++ b/R/TileDBArray.R @@ -1,6 +1,6 @@ # MIT License # -# Copyright (c) 2017-2024 TileDB Inc. +# Copyright (c) 2017-2025 TileDB Inc. # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -28,7 +28,7 @@ #' based on a refactored implementation utilising newer TileDB features. #' #' @slot ctx A TileDB context object -#' @slot uri A character despription with the array URI +#' @slot uri A character description with the array URI #' @slot is.sparse A logical value whether the array is sparse or not #' @slot attrs A character vector to select particular column #' \sQuote{attributes}; default is an empty character vector implying @@ -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, @@ -502,9 +502,9 @@ setValidity("tiledb_array", function(object) { #' #' Heterogenous domains are supported, including timestamps and characters. #' -#' This function may still still change; the current implementation should be +#' This function may still change; the current implementation should be #' considered as an initial draft. -#' @param x tiledb_array object +#' @param x A `tiledb_array` object. #' @param i optional row index expression which can be a list in which case #' minimum and maximum of each list element determine a range; multiple list #' elements can be used to supply multiple ranges. @@ -1253,7 +1253,7 @@ setMethod( #' as part of the left-hand side object, or as part of the data.frame #' provided appropriate column names. #' -#' This function may still still change; the current implementation should be +#' This function may still change; the current implementation should be #' considered as an initial draft. #' @param x sparse or dense TileDB array object #' @param i parameter row index @@ -1819,7 +1819,7 @@ 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( diff --git a/man/sub-tiledb_array-ANY-method.Rd b/man/sub-tiledb_array-ANY-method.Rd index 3b5c6266f2..ee8904a249 100644 --- a/man/sub-tiledb_array-ANY-method.Rd +++ b/man/sub-tiledb_array-ANY-method.Rd @@ -11,7 +11,7 @@ \S4method{[}{tiledb_array,ANY}(x, i, j, ..., drop = FALSE) } \arguments{ -\item{x}{tiledb_array object} +\item{x}{A \code{tiledb_array} object.} \item{i}{optional row index expression which can be a list in which case minimum and maximum of each list element determine a range; multiple list @@ -33,6 +33,6 @@ The resulting elements in the selected format Heterogenous domains are supported, including timestamps and characters. } \details{ -This function may still still change; the current implementation should be +This function may still change; the current implementation should be considered as an initial draft. } diff --git a/man/subset-tiledb_array-ANY-ANY-ANY-method.Rd b/man/subset-tiledb_array-ANY-ANY-ANY-method.Rd index 189c785faa..f74b5f6f14 100644 --- a/man/subset-tiledb_array-ANY-ANY-ANY-method.Rd +++ b/man/subset-tiledb_array-ANY-ANY-ANY-method.Rd @@ -33,7 +33,7 @@ For sparse matrices, row and column indices can either be supplied as part of the left-hand side object, or as part of the data.frame provided appropriate column names. -This function may still still change; the current implementation should be +This function may still change; the current implementation should be considered as an initial draft. } \examples{ diff --git a/man/tiledb_array-class.Rd b/man/tiledb_array-class.Rd index 770fec15ae..2c856077a9 100644 --- a/man/tiledb_array-class.Rd +++ b/man/tiledb_array-class.Rd @@ -14,7 +14,7 @@ based on a refactored implementation utilising newer TileDB features. \describe{ \item{\code{ctx}}{A TileDB context object} -\item{\code{uri}}{A character despription with the array URI} +\item{\code{uri}}{A character description with the array URI} \item{\code{is.sparse}}{A logical value whether the array is sparse or not} @@ -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 From b2f9eef51cad4a77e94d4ec509b690dd5f6d66c0 Mon Sep 17 00:00:00 2001 From: Constantinos Giachalis Date: Tue, 21 Oct 2025 13:34:41 +0300 Subject: [PATCH 7/9] Fix docs TileDBArray.R (v2) --- R/TileDBArray.R | 2 +- man/query_layout-tiledb_array-method.Rd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/TileDBArray.R b/R/TileDBArray.R index f027a3d8c1..d1c045a099 100644 --- a/R/TileDBArray.R +++ b/R/TileDBArray.R @@ -1803,7 +1803,7 @@ setGeneric( #' Retrieve query_layout values for the array #' #' A \code{tiledb_array} object can have a corresponding query with a given -#' layout given layout. This methods returns the selection value for +#' layout. This method returns the selection value for #' \sQuote{query_layout} as a character value. #' @param object A \code{tiledb_array} object #' @return A character value describing the query layout diff --git a/man/query_layout-tiledb_array-method.Rd b/man/query_layout-tiledb_array-method.Rd index e23775351d..25508d27ee 100644 --- a/man/query_layout-tiledb_array-method.Rd +++ b/man/query_layout-tiledb_array-method.Rd @@ -17,6 +17,6 @@ A character value describing the query layout } \description{ A \code{tiledb_array} object can have a corresponding query with a given -layout given layout. This methods returns the selection value for +layout. This method returns the selection value for \sQuote{query_layout} as a character value. } From 542098faa345c2da29561e1816d271f5b858b9c4 Mon Sep 17 00:00:00 2001 From: Constantinos Giachalis Date: Wed, 3 Dec 2025 17:18:47 +0200 Subject: [PATCH 8/9] Fix docs ArraySchema.R --- R/ArraySchema.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/ArraySchema.R b/R/ArraySchema.R index 4114fc3956..b25c5a60a1 100644 --- a/R/ArraySchema.R +++ b/R/ArraySchema.R @@ -95,7 +95,7 @@ tiledb_array_schema <- function( } # make it a list so that lapply works below stopifnot( "length of 'attrs' cannot be zero" = length(attrs) > 0, - "'attrs' must be a list of one or tiled_attr objects" = all(vapply(attrs, is_attr, logical(1))) + "'attrs' must be a list of one or tiledb_attr objects" = all(vapply(attrs, is_attr, logical(1))) ) } else { attrs <- NULL From 55fcad7e9f0df44883e28798a026f2a61bfdbf4a Mon Sep 17 00:00:00 2001 From: Constantinos Giachalis Date: Sun, 14 Dec 2025 11:24:58 +0200 Subject: [PATCH 9/9] Fix docs Group.R (v2) --- R/Group.R | 4 ++-- man/tiledb_group.Rd | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/Group.R b/R/Group.R index 8d712d84a5..d4d7a6674d 100644 --- a/R/Group.R +++ b/R/Group.R @@ -37,8 +37,8 @@ setClass("tiledb_group", #' \dQuote{READ} or \dQuote{WRITE} #' @param ctx (optional) A TileDB Context object; if not supplied the default #' context object is retrieved -#' @param cfg (optional) A TileConfig object -#' @return A 'group' object +#' @param cfg (optional) A TileDB Config object +#' @return A TileDB Group object #' @export tiledb_group <- function( uri, diff --git a/man/tiledb_group.Rd b/man/tiledb_group.Rd index 8953d08148..cf4fd9da68 100644 --- a/man/tiledb_group.Rd +++ b/man/tiledb_group.Rd @@ -20,10 +20,10 @@ tiledb_group( \item{ctx}{(optional) A TileDB Context object; if not supplied the default context object is retrieved} -\item{cfg}{(optional) A TileConfig object} +\item{cfg}{(optional) A TileDB Config object} } \value{ -A 'group' object +A TileDB Group object } \description{ Creates a 'tiledb_group' object