diff --git a/man/as.vector.tiledb_config.Rd b/man/as.vector.tiledb_config.Rd index 16a3f05765..b9ff4875d2 100644 --- a/man/as.vector.tiledb_config.Rd +++ b/man/as.vector.tiledb_config.Rd @@ -18,7 +18,9 @@ a character vector of config parameter names, values Convert a \code{tiledb_config} object to a R vector } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} cfg <- tiledb_config() as.vector(cfg) diff --git a/man/attrs-tiledb_array_schema-ANY-method.Rd b/man/attrs-tiledb_array_schema-ANY-method.Rd index 8892124f79..b80dbfb037 100644 --- a/man/attrs-tiledb_array_schema-ANY-method.Rd +++ b/man/attrs-tiledb_array_schema-ANY-method.Rd @@ -20,10 +20,14 @@ a list of tiledb_attr objects Returns a list of all \code{tiledb_attr} objects associated with the \code{tiledb_array_schema} } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 10L), type = "INT32"))) -sch <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a1", type = "INT32"), - tiledb_attr("a2", type = "FLOAT64"))) +sch <- tiledb_array_schema(dom, attrs = c( + tiledb_attr("a1", type = "INT32"), + tiledb_attr("a2", type = "FLOAT64") +)) attrs(sch) lapply(attrs(sch), datatype) diff --git a/man/attrs-tiledb_array_schema-character-method.Rd b/man/attrs-tiledb_array_schema-character-method.Rd index 59cde6eec7..d70292735c 100644 --- a/man/attrs-tiledb_array_schema-character-method.Rd +++ b/man/attrs-tiledb_array_schema-character-method.Rd @@ -20,10 +20,14 @@ a \code{tiledb_attr} object Returns a \code{tiledb_attr} object associated with the \code{tiledb_array_schema} with a given name. } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 10L), type = "INT32"))) -sch <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a1", type = "INT32"), - tiledb_attr("a2", type = "FLOAT64"))) +sch <- tiledb_array_schema(dom, attrs = c( + tiledb_attr("a1", type = "INT32"), + tiledb_attr("a2", type = "FLOAT64") +)) attrs(sch, "a2") } diff --git a/man/attrs-tiledb_array_schema-numeric-method.Rd b/man/attrs-tiledb_array_schema-numeric-method.Rd index 60fbe917a4..6531e644fc 100644 --- a/man/attrs-tiledb_array_schema-numeric-method.Rd +++ b/man/attrs-tiledb_array_schema-numeric-method.Rd @@ -20,10 +20,14 @@ a \code{tiledb_attr} object The attribute index is defined by the order the attributes were defined in the schema } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 10L), type = "INT32"))) -sch <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a1", type = "INT32"), - tiledb_attr("a2", type = "FLOAT64"))) +sch <- tiledb_array_schema(dom, attrs = c( + tiledb_attr("a1", type = "INT32"), + tiledb_attr("a2", type = "FLOAT64") +)) attrs(sch, 2) } diff --git a/man/config-tiledb_ctx-method.Rd b/man/config-tiledb_ctx-method.Rd index e6d23bbf9f..9546a68d19 100644 --- a/man/config-tiledb_ctx-method.Rd +++ b/man/config-tiledb_ctx-method.Rd @@ -16,7 +16,9 @@ Retrieve the \code{tiledb_config} object from the \code{tiledb_ctx} } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} ctx <- tiledb_ctx(c("sm.tile_cache_size" = "10")) cfg <- config(ctx) cfg["sm.tile_cache_size"] diff --git a/man/datatype-tiledb_dim-method.Rd b/man/datatype-tiledb_dim-method.Rd index 66d5c7436e..278e4408ee 100644 --- a/man/datatype-tiledb_dim-method.Rd +++ b/man/datatype-tiledb_dim-method.Rd @@ -16,7 +16,9 @@ tiledb datatype string Return the \code{tiledb_dim} datatype } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} d1 <- tiledb_dim("d1", domain = c(5L, 10L), tile = 2L, type = "INT32") datatype(d1) diff --git a/man/datatype-tiledb_domain-method.Rd b/man/datatype-tiledb_domain-method.Rd index 11395ac6fd..e96073e520 100644 --- a/man/datatype-tiledb_domain-method.Rd +++ b/man/datatype-tiledb_domain-method.Rd @@ -16,7 +16,9 @@ tiledb_domain type string Returns the tiledb_domain TileDB type string } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 100L), type = "INT32"))) datatype(dom) dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(0.5, 100.0), type = "FLOAT64"))) diff --git a/man/dim.tiledb_array_schema.Rd b/man/dim.tiledb_array_schema.Rd index 2b3d8fdc24..f1e2153c5b 100644 --- a/man/dim.tiledb_array_schema.Rd +++ b/man/dim.tiledb_array_schema.Rd @@ -16,10 +16,14 @@ a dimension vector Only valid for integral (integer) domains } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 10L), type = "INT32"))) -sch <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a1", type = "INT32"), - tiledb_attr("a2", type = "FLOAT64"))) +sch <- tiledb_array_schema(dom, attrs = c( + tiledb_attr("a1", type = "INT32"), + tiledb_attr("a2", type = "FLOAT64") +)) dim(sch) } diff --git a/man/dim.tiledb_dim.Rd b/man/dim.tiledb_dim.Rd index 420f08b07a..25d263489f 100644 --- a/man/dim.tiledb_dim.Rd +++ b/man/dim.tiledb_dim.Rd @@ -16,7 +16,9 @@ a vector of the tile_dim domain type, of the dim domain dimension (extent) Retrieves the dimension of the tiledb_dim domain } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} d1 <- tiledb_dim("d1", c(1L, 10L), 5L) dim(d1) diff --git a/man/dim.tiledb_domain.Rd b/man/dim.tiledb_domain.Rd index 5f5ba904bc..0ff154d8ab 100644 --- a/man/dim.tiledb_domain.Rd +++ b/man/dim.tiledb_domain.Rd @@ -16,9 +16,13 @@ dimension vector Only valid for integral (integer) domains } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} -dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 100L), type = "INT32"), - tiledb_dim("d2", c(1L, 100L), type = "INT32"))) +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} +dom <- tiledb_domain(dims = c( + tiledb_dim("d1", c(1L, 100L), type = "INT32"), + tiledb_dim("d2", c(1L, 100L), type = "INT32") +)) dim(dom) } diff --git a/man/dimensions-tiledb_array_schema-method.Rd b/man/dimensions-tiledb_array_schema-method.Rd index d503cd3218..39a6cd0f67 100644 --- a/man/dimensions-tiledb_array_schema-method.Rd +++ b/man/dimensions-tiledb_array_schema-method.Rd @@ -16,9 +16,13 @@ a list of tiledb_dim objects Returns a list of \code{tiledb_dim} objects associated with the \code{tiledb_array_schema} } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} -dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 100L), type = "INT32"), - tiledb_dim("d2", c(1L, 50L), type = "INT32"))) +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} +dom <- tiledb_domain(dims = c( + tiledb_dim("d1", c(1L, 100L), type = "INT32"), + tiledb_dim("d2", c(1L, 50L), type = "INT32") +)) sch <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a1", type = "INT32"))) dimensions(dom) diff --git a/man/dimensions-tiledb_domain-method.Rd b/man/dimensions-tiledb_domain-method.Rd index 95167d6d13..1f0938d091 100644 --- a/man/dimensions-tiledb_domain-method.Rd +++ b/man/dimensions-tiledb_domain-method.Rd @@ -16,9 +16,13 @@ a list of tiledb_dim Returns a list of the tiledb_domain dimension objects } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} -dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 100L), type = "INT32"), - tiledb_dim("d2", c(1L, 50L), type = "INT32"))) +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} +dom <- tiledb_domain(dims = c( + tiledb_dim("d1", c(1L, 100L), type = "INT32"), + tiledb_dim("d2", c(1L, 50L), type = "INT32") +)) dimensions(dom) lapply(dimensions(dom), name) diff --git a/man/domain-tiledb_array_schema-method.Rd b/man/domain-tiledb_array_schema-method.Rd index 144c76ed1c..3a235d6818 100644 --- a/man/domain-tiledb_array_schema-method.Rd +++ b/man/domain-tiledb_array_schema-method.Rd @@ -13,7 +13,9 @@ Returns the \code{tiledb_domain} object associated with a given \code{tiledb_array_schema} } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 10L), type = "INT32"))) sch <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a1", type = "INT32"))) domain(sch) diff --git a/man/domain-tiledb_dim-method.Rd b/man/domain-tiledb_dim-method.Rd index 34285e64a6..15cfaa3a56 100644 --- a/man/domain-tiledb_dim-method.Rd +++ b/man/domain-tiledb_dim-method.Rd @@ -16,7 +16,9 @@ a vector of (lb, ub) inclusive domain of the dimension Return the \code{tiledb_dim} domain } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} d1 <- tiledb_dim("d1", domain = c(5L, 10L)) domain(d1) diff --git a/man/filter_list-tiledb_attr-method.Rd b/man/filter_list-tiledb_attr-method.Rd index 843b36e3bf..4a7767a1e6 100644 --- a/man/filter_list-tiledb_attr-method.Rd +++ b/man/filter_list-tiledb_attr-method.Rd @@ -16,8 +16,10 @@ a tiledb_filter_list object Returns the TileDB Filter List object associated with the given TileDB Attribute } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} -attr <- tiledb_attr(type = "INT32", filter_list=tiledb_filter_list(list(tiledb_filter("ZSTD")))) +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} +attr <- tiledb_attr(type = "INT32", filter_list = tiledb_filter_list(list(tiledb_filter("ZSTD")))) filter_list(attr) } diff --git a/man/is.anonymous.Rd b/man/is.anonymous.Rd index c274716e56..f670f4eabf 100644 --- a/man/is.anonymous.Rd +++ b/man/is.anonymous.Rd @@ -19,7 +19,9 @@ TRUE or FALSE A TileDB attribute is anonymous if no name/label is defined } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} a1 <- tiledb_attr("a1", type = "FLOAT64") is.anonymous(a1) diff --git a/man/is.anonymous.tiledb_dim.Rd b/man/is.anonymous.tiledb_dim.Rd index 22952cd426..1f619b2eb6 100644 --- a/man/is.anonymous.tiledb_dim.Rd +++ b/man/is.anonymous.tiledb_dim.Rd @@ -16,7 +16,9 @@ TRUE or FALSE A TileDB dimension is anonymous if no name/label is defined } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} d1 <- tiledb_dim("d1", c(1L, 10L), 10L) is.anonymous(d1) diff --git a/man/is.integral-tiledb_domain-method.Rd b/man/is.integral-tiledb_domain-method.Rd index fe959b511a..4e32473a33 100644 --- a/man/is.integral-tiledb_domain-method.Rd +++ b/man/is.integral-tiledb_domain-method.Rd @@ -16,7 +16,9 @@ TRUE if the domain is an integral domain, else FALSE Returns TRUE is tiledb_domain is an integral (integer) domain } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 100L), type = "INT32"))) is.integral(dom) dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(0.5, 100.0), type = "FLOAT64"))) diff --git a/man/name-tiledb_attr-method.Rd b/man/name-tiledb_attr-method.Rd index 3b517465ce..f006b7a867 100644 --- a/man/name-tiledb_attr-method.Rd +++ b/man/name-tiledb_attr-method.Rd @@ -16,7 +16,9 @@ string name, empty string if the attribute is anonymous Return the \code{tiledb_attr} name } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} a1 <- tiledb_attr("a1", type = "INT32") name(a1) diff --git a/man/name-tiledb_dim-method.Rd b/man/name-tiledb_dim-method.Rd index 5746496328..05163bb11f 100644 --- a/man/name-tiledb_dim-method.Rd +++ b/man/name-tiledb_dim-method.Rd @@ -16,7 +16,9 @@ string name, empty string if the dimension is anonymous Return the \code{tiledb_dim} name } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} d1 <- tiledb_dim("d1", c(1L, 10L)) name(d1) diff --git a/man/nfilters-tiledb_filter_list-method.Rd b/man/nfilters-tiledb_filter_list-method.Rd index b68515ca99..9c2b997ef4 100644 --- a/man/nfilters-tiledb_filter_list-method.Rd +++ b/man/nfilters-tiledb_filter_list-method.Rd @@ -16,7 +16,9 @@ integer number of filters Returns the filter_list's number of filters } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} flt <- tiledb_filter("ZSTD") tiledb_filter_set_option(flt, "COMPRESSION_LEVEL", 5) filter_list <- tiledb_filter_list(c(flt)) diff --git a/man/parse_query_condition.Rd b/man/parse_query_condition.Rd index 57afae023c..b0c619b423 100644 --- a/man/parse_query_condition.Rd +++ b/man/parse_query_condition.Rd @@ -45,12 +45,16 @@ the data type is difficult to guess. Also, when using the \code{"\%in\%"} or \co the argument is mandatory. } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} \dontrun{ -uri <- "mem://airquality" # change to on-disk for persistence -fromDataFrame(airquality, uri, col_index=c("Month", "Day")) # dense array +uri <- "mem://airquality" # change to on-disk for persistence +fromDataFrame(airquality, uri, col_index = c("Month", "Day")) # dense array ## query condition on dense array requires extended=FALSE -tiledb_array(uri, return_as="data.frame", extended=FALSE, - query_condition=parse_query_condition(Temp > 90))[] +tiledb_array(uri, + return_as = "data.frame", extended = FALSE, + query_condition = parse_query_condition(Temp > 90) +)[] } } diff --git a/man/show-tiledb_config-method.Rd b/man/show-tiledb_config-method.Rd index 14097091b7..d4c889d9bc 100644 --- a/man/show-tiledb_config-method.Rd +++ b/man/show-tiledb_config-method.Rd @@ -13,7 +13,9 @@ Prints the config object to STDOUT } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} cfg <- tiledb_config() show(cfg) } diff --git a/man/sub-tiledb_config-ANY-method.Rd b/man/sub-tiledb_config-ANY-method.Rd index 71c40d009f..6f8531345c 100644 --- a/man/sub-tiledb_config-ANY-method.Rd +++ b/man/sub-tiledb_config-ANY-method.Rd @@ -28,7 +28,9 @@ a config string value if parameter exists, else NA Gets a config parameter value } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} cfg <- tiledb_config() cfg["sm.tile_cache_size"] cfg["does_not_exist"] diff --git a/man/sub-tiledb_filter_list-ANY-method.Rd b/man/sub-tiledb_filter_list-ANY-method.Rd index 4348249696..6fe405f4a4 100644 --- a/man/sub-tiledb_filter_list-ANY-method.Rd +++ b/man/sub-tiledb_filter_list-ANY-method.Rd @@ -28,7 +28,9 @@ object tiledb_filter Returns the filter at given index } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} flt <- tiledb_filter("ZSTD") tiledb_filter_set_option(flt, "COMPRESSION_LEVEL", 5) filter_list <- tiledb_filter_list(c(flt)) diff --git a/man/subset-tiledb_array-ANY-ANY-ANY-method.Rd b/man/subset-tiledb_array-ANY-ANY-ANY-method.Rd index c9681b6c55..4e8de8e616 100644 --- a/man/subset-tiledb_array-ANY-ANY-ANY-method.Rd +++ b/man/subset-tiledb_array-ANY-ANY-ANY-method.Rd @@ -37,15 +37,17 @@ This function may still still change; the current implementation should be considered as an initial draft. } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} \dontrun{ -uri <- "quickstart_sparse" ## as created by the other example -arr <- tiledb_array(uri) ## open array -df <- arr[] ## read current content +uri <- "quickstart_sparse" ## as created by the other example +arr <- tiledb_array(uri) ## open array +df <- arr[] ## read current content ## First approach: matching data.frame with appriate row and column -newdf <- data.frame(rows=c(1,2,2), cols=c(1,3,4), a=df$a+100) +newdf <- data.frame(rows = c(1, 2, 2), cols = c(1, 3, 4), a = df$a + 100) ## Second approach: supply indices explicitly -arr[c(1,2), c(1,3)] <- c(42,43) ## two values -arr[2, 4] <- 88 ## or just one +arr[c(1, 2), c(1, 3)] <- c(42, 43) ## two values +arr[2, 4] <- 88 ## or just one } } diff --git a/man/subset-tiledb_config-ANY-ANY-ANY-method.Rd b/man/subset-tiledb_config-ANY-ANY-ANY-method.Rd index 637bdfa33f..3b3685e6ba 100644 --- a/man/subset-tiledb_config-ANY-ANY-ANY-method.Rd +++ b/man/subset-tiledb_config-ANY-ANY-ANY-method.Rd @@ -26,7 +26,9 @@ updated \code{tiledb_config} object Sets a config parameter value } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} cfg <- tiledb_config() cfg["sm.tile_cache_size"] diff --git a/man/tile-tiledb_dim-method.Rd b/man/tile-tiledb_dim-method.Rd index a2721fc48e..3789607e96 100644 --- a/man/tile-tiledb_dim-method.Rd +++ b/man/tile-tiledb_dim-method.Rd @@ -16,7 +16,9 @@ a scalar tile extent Return the \code{tiledb_dim} tile extent } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} d1 <- tiledb_dim("d1", domain = c(5L, 10L), tile = 2L) tile(d1) diff --git a/man/tiledb_array_create.Rd b/man/tiledb_array_create.Rd index 2233f8d821..eb795e0fa3 100644 --- a/man/tiledb_array_create.Rd +++ b/man/tiledb_array_create.Rd @@ -18,7 +18,9 @@ in case the array should be encryption.} Creates a new TileDB array given an input schema. } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} \dontrun{ pth <- tempdir() dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 10L), type = "INT32"))) diff --git a/man/tiledb_array_open.Rd b/man/tiledb_array_open.Rd index 7eb50eecf8..be57540dee 100644 --- a/man/tiledb_array_open.Rd +++ b/man/tiledb_array_open.Rd @@ -6,8 +6,12 @@ \usage{ tiledb_array_open( arr, - type = if (tiledb_version(TRUE) >= "2.12.0") c("READ", "WRITE", "DELETE", - "MODIFY_EXCLUSIVE") else c("READ", "WRITE") + type = if (tiledb_version(TRUE) >= "2.12.0") { + c("READ", "WRITE", "DELETE", + "MODIFY_EXCLUSIVE") + } else { + c("READ", "WRITE") + } ) } \arguments{ diff --git a/man/tiledb_array_schema.Rd b/man/tiledb_array_schema.Rd index b6aea7c851..72a05baa85 100644 --- a/man/tiledb_array_schema.Rd +++ b/man/tiledb_array_schema.Rd @@ -48,15 +48,21 @@ tiledb_array_schema( Constructs a \code{tiledb_array_schema} object } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} schema <- tiledb_array_schema( - dom = tiledb_domain( - dims = c(tiledb_dim("rows", c(1L, 4L), 4L, "INT32"), - tiledb_dim("cols", c(1L, 4L), 4L, "INT32"))), - attrs = c(tiledb_attr("a", type = "INT32")), - cell_order = "COL_MAJOR", - tile_order = "COL_MAJOR", - sparse = FALSE) + dom = tiledb_domain( + dims = c( + tiledb_dim("rows", c(1L, 4L), 4L, "INT32"), + tiledb_dim("cols", c(1L, 4L), 4L, "INT32") + ) + ), + attrs = c(tiledb_attr("a", type = "INT32")), + cell_order = "COL_MAJOR", + tile_order = "COL_MAJOR", + sparse = FALSE +) schema } diff --git a/man/tiledb_attr.Rd b/man/tiledb_attr.Rd index 6332e06451..ae8f0358b5 100644 --- a/man/tiledb_attr.Rd +++ b/man/tiledb_attr.Rd @@ -38,10 +38,14 @@ values} Constructs a \code{tiledb_attr} object } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} flt <- tiledb_filter_list(list(tiledb_filter("GZIP"))) -attr <- tiledb_attr(name = "a1", type = "INT32", - filter_list = flt) +attr <- tiledb_attr( + name = "a1", type = "INT32", + filter_list = flt +) attr } diff --git a/man/tiledb_attribute_get_cell_val_num.Rd b/man/tiledb_attribute_get_cell_val_num.Rd index 24ea8c2cf0..7a139afd0e 100644 --- a/man/tiledb_attribute_get_cell_val_num.Rd +++ b/man/tiledb_attribute_get_cell_val_num.Rd @@ -22,7 +22,9 @@ integer number of cells Return the number of scalar values per attribute cell } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} a1 <- tiledb_attr("a1", type = "FLOAT64", ncells = 1) cell_val_num(a1) } diff --git a/man/tiledb_config.Rd b/man/tiledb_config.Rd index c42d5e77c4..d49d28b211 100644 --- a/man/tiledb_config.Rd +++ b/man/tiledb_config.Rd @@ -21,7 +21,9 @@ of the of the \code{tiledb_ctx} object. Examples for this are create a context object, and \code{cfg <- config(ctx)} to retrieve it. } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} cfg <- tiledb_config() cfg["sm.tile_cache_size"] diff --git a/man/tiledb_config_as_built_json.Rd b/man/tiledb_config_as_built_json.Rd index 5d78bb7bdd..4bb03b763a 100644 --- a/man/tiledb_config_as_built_json.Rd +++ b/man/tiledb_config_as_built_json.Rd @@ -13,8 +13,9 @@ The JSON string containing 'AsBuilt' information Return the 'AsBuilt' JSON string } \examples{ -if (tiledb_version(TRUE) > "2.17") - txt <- tiledb::tiledb_config_as_built_json() +if (tiledb_version(TRUE) > "2.17") { + txt <- tiledb::tiledb_config_as_built_json() +} ## now eg either one of ## sapply(jsonlite::fromJSON(txt)$as_built$parameters$storage_backends, \(x) x[[1]]) ## sapply(RcppSimdJson::fparse(txt)$as_built$parameters$storage_backends, \(x) x[[1]]) diff --git a/man/tiledb_config_load.Rd b/man/tiledb_config_load.Rd index ffdc296b2b..1fc998f959 100644 --- a/man/tiledb_config_load.Rd +++ b/man/tiledb_config_load.Rd @@ -13,7 +13,9 @@ tiledb_config_load(path) Load a saved \code{tiledb_config} file from disk } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} tmp <- tempfile() cfg <- tiledb_config(c("sm.tile_cache_size" = "10")) pth <- tiledb_config_save(cfg, tmp) diff --git a/man/tiledb_config_save.Rd b/man/tiledb_config_save.Rd index 365e3968e7..158000da24 100644 --- a/man/tiledb_config_save.Rd +++ b/man/tiledb_config_save.Rd @@ -18,7 +18,9 @@ path to created config file Save a \code{tiledb_config} object ot a local text file } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} tmp <- tempfile() cfg <- tiledb_config(c("sm.tile_cache_size" = "10")) pth <- tiledb_config_save(cfg, tmp) diff --git a/man/tiledb_ctx.Rd b/man/tiledb_ctx.Rd index 4670b81356..3e7eed3085 100644 --- a/man/tiledb_ctx.Rd +++ b/man/tiledb_ctx.Rd @@ -18,7 +18,9 @@ tiledb_ctx(config = NULL, cached = TRUE) Creates a \code{tiledb_ctx} object } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} # default configuration ctx <- tiledb_ctx() diff --git a/man/tiledb_ctx_set_tag.Rd b/man/tiledb_ctx_set_tag.Rd index ec1ec5ba9d..587d3fe33e 100644 --- a/man/tiledb_ctx_set_tag.Rd +++ b/man/tiledb_ctx_set_tag.Rd @@ -17,7 +17,9 @@ tiledb_ctx_set_tag(object, key, value) Sets a string:string "tag" on the Ctx } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} ctx <- tiledb_ctx(c("sm.tile_cache_size" = "10")) cfg <- tiledb_ctx_set_tag(ctx, "tag", "value") diff --git a/man/tiledb_current_domain.Rd b/man/tiledb_current_domain.Rd index 510fc84788..0d2cf33f2c 100644 --- a/man/tiledb_current_domain.Rd +++ b/man/tiledb_current_domain.Rd @@ -16,9 +16,11 @@ The \code{tiledb_current_domain} object Creates a \code{tiledb_current_domain} object } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} if (tiledb_version(TRUE) >= "2.25.0") { - cd <-tiledb_current_domain() + cd <- tiledb_current_domain() } } diff --git a/man/tiledb_dim.Rd b/man/tiledb_dim.Rd index 0df5f01968..f8908c1904 100644 --- a/man/tiledb_dim.Rd +++ b/man/tiledb_dim.Rd @@ -37,7 +37,9 @@ is no filter} Constructs a \code{tiledb_dim} object } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} tiledb_dim(name = "d1", domain = c(1L, 10L), tile = 5L, type = "INT32") } diff --git a/man/tiledb_domain.Rd b/man/tiledb_domain.Rd index 91221add36..fee1726f06 100644 --- a/man/tiledb_domain.Rd +++ b/man/tiledb_domain.Rd @@ -18,7 +18,11 @@ tiledb_domain All \code{tiledb_dim} must be of the same TileDB type. } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} -dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 100L), type = "INT32"), - tiledb_dim("d2", c(1L, 50L), type = "INT32"))) +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} +dom <- tiledb_domain(dims = c( + tiledb_dim("d1", c(1L, 100L), type = "INT32"), + tiledb_dim("d2", c(1L, 50L), type = "INT32") +)) } diff --git a/man/tiledb_filter.Rd b/man/tiledb_filter.Rd index 1a1a74f128..4c8761be48 100644 --- a/man/tiledb_filter.Rd +++ b/man/tiledb_filter.Rd @@ -40,7 +40,9 @@ Valid compression options vary depending on the filter used, consult the TileDB docs for more information. } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} tiledb_filter("ZSTD") } diff --git a/man/tiledb_filter_get_option.Rd b/man/tiledb_filter_get_option.Rd index 5bb9b59b82..b410e0de4b 100644 --- a/man/tiledb_filter_get_option.Rd +++ b/man/tiledb_filter_get_option.Rd @@ -18,9 +18,11 @@ Integer value Returns the filter's option } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} c <- tiledb_filter("ZSTD") -tiledb_filter_set_option(c,"COMPRESSION_LEVEL", 5) +tiledb_filter_set_option(c, "COMPRESSION_LEVEL", 5) tiledb_filter_get_option(c, "COMPRESSION_LEVEL") } diff --git a/man/tiledb_filter_list.Rd b/man/tiledb_filter_list.Rd index 6e8b314507..a17bd1ca5b 100644 --- a/man/tiledb_filter_list.Rd +++ b/man/tiledb_filter_list.Rd @@ -18,7 +18,9 @@ tiledb_filter_list object Constructs a \code{tiledb_filter_list} object } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} flt <- tiledb_filter("ZSTD") tiledb_filter_set_option(flt, "COMPRESSION_LEVEL", 5) filter_list <- tiledb_filter_list(c(flt)) diff --git a/man/tiledb_filter_list_get_max_chunk_size.Rd b/man/tiledb_filter_list_get_max_chunk_size.Rd index e930664e8b..d5fb8f0dda 100644 --- a/man/tiledb_filter_list_get_max_chunk_size.Rd +++ b/man/tiledb_filter_list_get_max_chunk_size.Rd @@ -22,7 +22,9 @@ integer max_chunk_size Returns the filter_list's max_chunk_size } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} flt <- tiledb_filter("ZSTD") tiledb_filter_set_option(flt, "COMPRESSION_LEVEL", 5) filter_list <- tiledb_filter_list(c(flt)) diff --git a/man/tiledb_filter_list_set_max_chunk_size.Rd b/man/tiledb_filter_list_set_max_chunk_size.Rd index cac45bc55f..976e6def94 100644 --- a/man/tiledb_filter_list_set_max_chunk_size.Rd +++ b/man/tiledb_filter_list_set_max_chunk_size.Rd @@ -21,7 +21,9 @@ tiledb_filter_list_set_max_chunk_size(object, value) Set the filter_list's max_chunk_size } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} flt <- tiledb_filter("ZSTD") tiledb_filter_set_option(flt, "COMPRESSION_LEVEL", 5) filter_list <- tiledb_filter_list(c(flt)) diff --git a/man/tiledb_filter_set_option.Rd b/man/tiledb_filter_set_option.Rd index ffa6ff1105..7c7bbea6bc 100644 --- a/man/tiledb_filter_set_option.Rd +++ b/man/tiledb_filter_set_option.Rd @@ -20,8 +20,10 @@ The modified filter object is returned. Set the option for a filter } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} c <- tiledb_filter("ZSTD") -tiledb_filter_set_option(c,"COMPRESSION_LEVEL", 5) +tiledb_filter_set_option(c, "COMPRESSION_LEVEL", 5) tiledb_filter_get_option(c, "COMPRESSION_LEVEL") } diff --git a/man/tiledb_filter_type.Rd b/man/tiledb_filter_type.Rd index 064e1ba3f7..7998edd5a9 100644 --- a/man/tiledb_filter_type.Rd +++ b/man/tiledb_filter_type.Rd @@ -16,7 +16,9 @@ TileDB filter type string Returns the type of the filter used } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} c <- tiledb_filter("ZSTD") tiledb_filter_type(c) diff --git a/man/tiledb_group_create.Rd b/man/tiledb_group_create.Rd index f1df01aa33..abe1bcff0b 100644 --- a/man/tiledb_group_create.Rd +++ b/man/tiledb_group_create.Rd @@ -19,7 +19,9 @@ The uri path, invisibly Create a TileDB Group at the given path } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} \dontrun{ pth <- tempdir() tiledb_group_create(pth) diff --git a/man/tiledb_is_supported_fs.Rd b/man/tiledb_is_supported_fs.Rd index 10cad11b2a..bd4da11883 100644 --- a/man/tiledb_is_supported_fs.Rd +++ b/man/tiledb_is_supported_fs.Rd @@ -26,7 +26,9 @@ Ex: } } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} tiledb_is_supported_fs("file") tiledb_is_supported_fs("s3") diff --git a/man/tiledb_ndim-tiledb_array_schema-method.Rd b/man/tiledb_ndim-tiledb_array_schema-method.Rd index c79256ef75..f264a982af 100644 --- a/man/tiledb_ndim-tiledb_array_schema-method.Rd +++ b/man/tiledb_ndim-tiledb_array_schema-method.Rd @@ -16,10 +16,14 @@ integer number of dimensions Return the number of dimensions associated with the \code{tiledb_array_schema} } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 10L), type = "INT32"))) -sch <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a1", type = "INT32"), - tiledb_attr("a2", type = "FLOAT64"))) +sch <- tiledb_array_schema(dom, attrs = c( + tiledb_attr("a1", type = "INT32"), + tiledb_attr("a2", type = "FLOAT64") +)) tiledb_ndim(sch) } diff --git a/man/tiledb_ndim-tiledb_dim-method.Rd b/man/tiledb_ndim-tiledb_dim-method.Rd index 60536de16c..a1827b7cc9 100644 --- a/man/tiledb_ndim-tiledb_dim-method.Rd +++ b/man/tiledb_ndim-tiledb_dim-method.Rd @@ -16,7 +16,9 @@ Returns the number of dimensions for a tiledb domain object } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} d1 <- tiledb_dim("d1", c(1L, 10L), 10L) tiledb_ndim(d1) diff --git a/man/tiledb_ndim-tiledb_domain-method.Rd b/man/tiledb_ndim-tiledb_domain-method.Rd index d492646d18..492eef0192 100644 --- a/man/tiledb_ndim-tiledb_domain-method.Rd +++ b/man/tiledb_ndim-tiledb_domain-method.Rd @@ -16,11 +16,15 @@ integer number of dimensions Returns the number of dimensions of the \code{tiledb_domain} } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(0.5, 100.0), type = "FLOAT64"))) tiledb_ndim(dom) -dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(0.5, 100.0), type = "FLOAT64"), - tiledb_dim("d2", c(0.5, 100.0), type = "FLOAT64"))) +dom <- tiledb_domain(dims = c( + tiledb_dim("d1", c(0.5, 100.0), type = "FLOAT64"), + tiledb_dim("d2", c(0.5, 100.0), type = "FLOAT64") +)) tiledb_ndim(dom) } diff --git a/man/tiledb_ndrectangle.Rd b/man/tiledb_ndrectangle.Rd index d2e2bfd5d5..51f21e691e 100644 --- a/man/tiledb_ndrectangle.Rd +++ b/man/tiledb_ndrectangle.Rd @@ -18,10 +18,12 @@ The \code{tiledb_ndrectangle} object Creates a \code{tiledb_ndrectangle} object } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} if (tiledb_version(TRUE) >= "2.25.0") { - dom <-tiledb_domain(dim = tiledb_dim("d1", c(1L, 100L), type = "INT32")) - ndr <- tiledb_ndrectangle(dom) + dom <- tiledb_domain(dim = tiledb_dim("d1", c(1L, 100L), type = "INT32")) + ndr <- tiledb_ndrectangle(dom) } } diff --git a/man/tiledb_ndrectangle_datatype.Rd b/man/tiledb_ndrectangle_datatype.Rd index 3ab10ee233..265727b9ac 100644 --- a/man/tiledb_ndrectangle_datatype.Rd +++ b/man/tiledb_ndrectangle_datatype.Rd @@ -18,10 +18,12 @@ The \code{tiledb_ndrectangle} dimension datatype as a character Get the datatype of a named \code{tiledb_ndrectangle} dimension } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} if (tiledb_version(TRUE) >= "2.26.0") { - dom <- tiledb_domain(dim = tiledb_dim("d1", c(1L, 100L), type = "INT32")) - ndr <- tiledb_ndrectangle(dom) - tiledb_ndrectangle_datatype(ndr, "d1") + dom <- tiledb_domain(dim = tiledb_dim("d1", c(1L, 100L), type = "INT32")) + ndr <- tiledb_ndrectangle(dom) + tiledb_ndrectangle_datatype(ndr, "d1") } } diff --git a/man/tiledb_ndrectangle_datatype_by_ind.Rd b/man/tiledb_ndrectangle_datatype_by_ind.Rd index 9dc0156bd6..e32603be25 100644 --- a/man/tiledb_ndrectangle_datatype_by_ind.Rd +++ b/man/tiledb_ndrectangle_datatype_by_ind.Rd @@ -18,10 +18,12 @@ The \code{tiledb_ndrectangle} dimension datatype as a character Get the datatype of a \code{tiledb_ndrectangle} dimension by index } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} if (tiledb_version(TRUE) >= "2.26.0") { - dom <- tiledb_domain(dim = tiledb_dim("d1", c(1L, 100L), type = "INT32")) - ndr <- tiledb_ndrectangle(dom) - tiledb_ndrectangle_datatype_by_ind(ndr, 0) + dom <- tiledb_domain(dim = tiledb_dim("d1", c(1L, 100L), type = "INT32")) + ndr <- tiledb_ndrectangle(dom) + tiledb_ndrectangle_datatype_by_ind(ndr, 0) } } diff --git a/man/tiledb_ndrectangle_dim_num.Rd b/man/tiledb_ndrectangle_dim_num.Rd index 4963985af9..35b36a2c01 100644 --- a/man/tiledb_ndrectangle_dim_num.Rd +++ b/man/tiledb_ndrectangle_dim_num.Rd @@ -16,10 +16,12 @@ The number of dimentiones for the \code{tiledb_ndrectangle} Get the number of dimensions for \code{tiledb_ndrectangle} object } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} if (tiledb_version(TRUE) >= "2.26.0") { - dom <- tiledb_domain(dim = tiledb_dim("d1", c(1L, 100L), type = "INT32")) - ndr <- tiledb_ndrectangle(dom) - tiledb_ndrectangle_dim_num(ndr) + dom <- tiledb_domain(dim = tiledb_dim("d1", c(1L, 100L), type = "INT32")) + ndr <- tiledb_ndrectangle(dom) + tiledb_ndrectangle_dim_num(ndr) } } diff --git a/man/tiledb_ndrectangle_get_range.Rd b/man/tiledb_ndrectangle_get_range.Rd index 71e0510015..e07389095b 100644 --- a/man/tiledb_ndrectangle_get_range.Rd +++ b/man/tiledb_ndrectangle_get_range.Rd @@ -18,11 +18,13 @@ The \code{tiledb_ndrectangle} range as a two-element vector Get a range from a \code{tiledb_ndrectangle} object } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} if (tiledb_version(TRUE) >= "2.26.0") { - dom <- tiledb_domain(dim = tiledb_dim("d1", c(1L, 100L), type = "INT32")) - ndr <- tiledb_ndrectangle(dom) - ndr <- tiledb_ndrectangle_set_range(ndr, "d1", 50, 500) - tiledb_ndrectangle_get_range(ndr, "d1") + dom <- tiledb_domain(dim = tiledb_dim("d1", c(1L, 100L), type = "INT32")) + ndr <- tiledb_ndrectangle(dom) + ndr <- tiledb_ndrectangle_set_range(ndr, "d1", 50, 500) + tiledb_ndrectangle_get_range(ndr, "d1") } } diff --git a/man/tiledb_ndrectangle_set_range.Rd b/man/tiledb_ndrectangle_set_range.Rd index 613b9c4efd..e7bd38f533 100644 --- a/man/tiledb_ndrectangle_set_range.Rd +++ b/man/tiledb_ndrectangle_set_range.Rd @@ -26,10 +26,12 @@ string dimensions. Set a range on a \code{tiledb_ndrectangle} object } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} if (tiledb_version(TRUE) >= "2.26.0") { - dom <-tiledb_domain(dim = tiledb_dim("d1", c(1L, 100L), type = "INT32")) - ndr <- tiledb_ndrectangle(dom) - ndr <- tiledb_ndrectangle_set_range(ndr, "d1", 50, 500) + dom <- tiledb_domain(dim = tiledb_dim("d1", c(1L, 100L), type = "INT32")) + ndr <- tiledb_ndrectangle(dom) + ndr <- tiledb_ndrectangle_set_range(ndr, "d1", 50, 500) } } diff --git a/man/tiledb_query.Rd b/man/tiledb_query.Rd index d44ddc16e3..6f132a1900 100644 --- a/man/tiledb_query.Rd +++ b/man/tiledb_query.Rd @@ -6,8 +6,12 @@ \usage{ tiledb_query( array, - type = if (tiledb_version(TRUE) >= "2.12.0") c("READ", "WRITE", "DELETE", - "MODIFY_EXCLUSIVE") else c("READ", "WRITE"), + type = if (tiledb_version(TRUE) >= "2.12.0") { + c("READ", "WRITE", "DELETE", + "MODIFY_EXCLUSIVE") + } else { + c("READ", "WRITE") + }, ctx = tiledb_get_context() ) } diff --git a/man/tiledb_stats_dump.Rd b/man/tiledb_stats_dump.Rd index 1e0fd562a5..c2a986c8ac 100644 --- a/man/tiledb_stats_dump.Rd +++ b/man/tiledb_stats_dump.Rd @@ -14,7 +14,9 @@ if the empty string is passed then the result is displayed on stdout.} Dumps internal TileDB statistics to file or stdout } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} pth <- tempfile() tiledb_stats_dump(pth) cat(readLines(pth)[1:10], sep = "\n") diff --git a/man/tiledb_stats_raw_dump.Rd b/man/tiledb_stats_raw_dump.Rd index 87fb7b1d1d..ef279fbaab 100644 --- a/man/tiledb_stats_raw_dump.Rd +++ b/man/tiledb_stats_raw_dump.Rd @@ -10,7 +10,9 @@ tiledb_stats_raw_dump() This function requires TileDB Embedded 2.0.3 or later. } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} txt <- tiledb_stats_raw_dump() cat(txt, "\n") } diff --git a/man/tiledb_version.Rd b/man/tiledb_version.Rd index ee12bf6f98..3fb0874140 100644 --- a/man/tiledb_version.Rd +++ b/man/tiledb_version.Rd @@ -18,7 +18,9 @@ a \code{package_version} object The version of the libtiledb library } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} tiledb_version() tiledb_version(compact = TRUE) } diff --git a/man/tiledb_vfs.Rd b/man/tiledb_vfs.Rd index 061c5b045b..29c36a9d18 100644 --- a/man/tiledb_vfs.Rd +++ b/man/tiledb_vfs.Rd @@ -18,7 +18,9 @@ The \code{tiledb_vfs} object Creates a \code{tiledb_vfs} object } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} # default configuration vfs <- tiledb_vfs() diff --git a/man/tiledb_vfs_is_bucket.Rd b/man/tiledb_vfs_is_bucket.Rd index ca672cde78..249e8aa1b6 100644 --- a/man/tiledb_vfs_is_bucket.Rd +++ b/man/tiledb_vfs_is_bucket.Rd @@ -18,7 +18,9 @@ A boolean value indicating if it is a valid bucket Check for VFS Bucket } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} \dontrun{ cfg <- tiledb_config() cfg["vfs.s3.region"] <- "us-west-1" diff --git a/man/tiledb_vfs_is_empty_bucket.Rd b/man/tiledb_vfs_is_empty_bucket.Rd index 0b89af0c8b..38582646c5 100644 --- a/man/tiledb_vfs_is_empty_bucket.Rd +++ b/man/tiledb_vfs_is_empty_bucket.Rd @@ -18,7 +18,9 @@ A boolean value indicating if it is an empty bucket Check for empty VFS Bucket } \examples{ -\dontshow{ctx <- tiledb_ctx(limitTileDBCores())} +\dontshow{ +ctx <- tiledb_ctx(limitTileDBCores()) +} \dontrun{ cfg <- tiledb_config() cfg["vfs.s3.region"] <- "us-west-1"