Mark three return preference arguments to tiledb_array as deprecated

R/DataFrame.R

@@ -76,7 +76,7 @@
 ##' ## turn factor into character
 ##' irisdf <- within(iris, Species <- as.character(Species))
 ##' fromDataFrame(irisdf, uri)
-##' arr <- tiledb_array(uri, as.data.frame=TRUE, sparse=FALSE)
+##' arr <- tiledb_array(uri, return_as="data.frame", sparse=FALSE)
 ##' newdf <- arr[]
 ##' all.equal(iris, newdf)
 ##' }
@@ -265,7 +265,7 @@ fromDataFrame <- function(obj, uri, col_index=NULL, sparse=TRUE, allows_dups=spa
   if (dir.exists(uri)) unlink(uri, recursive=TRUE)
   fromDataFrame(obj, uri)
 
-  df <- tiledb_array(uri, as.data.frame=TRUE)
+  df <- tiledb_array(uri, return_as="data.frame")
   df[]
 }
 
@@ -292,7 +292,7 @@ fromDataFrame <- function(obj, uri, col_index=NULL, sparse=TRUE, allows_dups=spa
   }
   fromDataFrame(bkdf, uri)
 
-  arr <- tiledb_array(uri, as.data.frame = TRUE)
+  arr <- tiledb_array(uri, return_as="data.frame")
   newdf <- arr[]
   invisible(newdf)
 }
@@ -305,7 +305,7 @@ fromDataFrame <- function(obj, uri, col_index=NULL, sparse=TRUE, allows_dups=spa
   fromDataFrame(df, uri)
   cat("Data written\n")
 
-  arr <- tiledb_array(uri, as.data.frame = TRUE)
+  arr <- tiledb_array(uri, return_as="data.frame")
   newdf <- arr[]
   invisible(newdf)
 }

R/SparseMatrix.R

@@ -112,7 +112,7 @@ fromSparseMatrix <- function(obj,
 toSparseMatrix <- function(uri) {
     stopifnot(`Argument 'uri' must be character` = is.character(uri))
 
-    arr <- tiledb_array(uri, as.data.frame=TRUE, query_layout="UNORDERED")
+    arr <- tiledb_array(uri, return_as="data.frame", query_layout="UNORDERED")
     obj <- arr[]
 
     dimnm <- list(NULL, NULL)        # by default no dimnames

R/TileDBArray.R

@@ -182,6 +182,11 @@ tiledb_array <- function(uri,
     array_xptr <- libtiledb_array_open(ctx@ptr, uri, query_type)
   }
 
+  ## Deprecated July 2023, to removed by July 2024 or later
+  if (as.data.frame) .Deprecated(old="as.data.frame", new=r"(return_as="data.frame")")
+  if (as.matrix) .Deprecated(old="as.matrix", new=r"(return_as="matrix")")
+  if (as.array) .Deprecated(old="as.array", new=r"(return_as="array")")
+
   if (length(timestamp_start) > 0) {
       libtiledb_array_set_open_timestamp_start(array_xptr, timestamp_start)
   }

inst/tinytest/test_arrowio.R

@@ -73,7 +73,7 @@ tiledb_query_set_layout(qry, "UNORDERED")
 tiledb_query_submit(qry)
 tiledb_query_finalize(qry)
 
-#arr <- tiledb_array(tmp, as.data.frame=TRUE)
+#arr <- tiledb_array(tmp, return_as="data.frame")
 #print(arr[])
 
 
@@ -162,7 +162,7 @@ tiledb_query_set_layout(qry, "UNORDERED")
 tiledb_query_submit(qry)
 tiledb_query_finalize(qry)
 
-arr <- tiledb_array(tmp, as.data.frame=TRUE)
+arr <- tiledb_array(tmp, return_as="data.frame")
 df <- arr[]
 
 for (i in 1:10) {

inst/tinytest/test_attr.R

@@ -142,7 +142,7 @@ attrib <- c(tiledb_attr("year",  type = "DATETIME_YEAR"),  # year
 schema <- tiledb_array_schema(domain, attrib, sparse=TRUE)
 res <- tiledb_array_create(uri, schema)
 
-arr <- tiledb_array(uri, as.data.frame=TRUE)
+arr <- tiledb_array(uri, return_as="data.frame")
 
 dvec <- 1:3
 data <- data.frame(row = dvec,
@@ -162,7 +162,7 @@ data <- data.frame(row = dvec,
                    )
 
 arr[] <- data
-arr2 <- tiledb_array(uri, as.data.frame=TRUE)
+arr2 <- tiledb_array(uri, return_as="data.frame")
 readdata <- arr2[]
 expect_true(all.equal(data, readdata, check.attributes=FALSE))
 
@@ -217,7 +217,7 @@ df <- data.frame(row     =  1:10,
 arr <- tiledb_array(uri)
 arr[] <- df
 
-newarr <- tiledb_array(uri, as.data.frame=TRUE)
+newarr <- tiledb_array(uri, return_as="data.frame")
 chk <- newarr[]
 expect_equal(df[,1:10], chk[,1:10])
 expect_equivalent(as.numeric(df[,11]), chk[,11]) # we currently return uint64_t as numeric

inst/tinytest/test_dataframe.R

@@ -16,7 +16,7 @@ if (tiledb_version(TRUE) < "2.7.0") exit_file("Needs TileDB 2.7.* or later")
 
 fromDataFrame(irisdf, uri)
 
-arr <- tiledb_array(uri, as.data.frame=TRUE)
+arr <- tiledb_array(uri, return_as="data.frame")
 newdf <- arr[]
 #if (getRversion() >= '4.0.0') newdf$Species <- as.factor(newdf$Species)
 if (getRversion() <  '4.0.0') newdf$Species <- as.character(newdf$Species)
@@ -29,7 +29,7 @@ expect_equal(irisdf, newdf[,-1])
 
 
 ## test attrs subselection
-arr <- tiledb_array(uri, as.data.frame=TRUE, extended=FALSE,
+arr <- tiledb_array(uri, return_as="data.frame", extended=FALSE,
                     attrs = c("Petal.Length", "Petal.Width"))
 newdf <- arr[]
 expect_equivalent(iris[, c("Petal.Length", "Petal.Width")], newdf) # skip attribute
@@ -58,7 +58,7 @@ df <- data.frame(char=c("abc", "def", "g", "hijk"),
 
 fromDataFrame(df, uri)
 
-arr <- tiledb_array(uri, as.data.frame=TRUE)
+arr <- tiledb_array(uri, return_as="data.frame")
 newdf <- arr[]
 
 ## result comes back as factor by default
@@ -78,7 +78,7 @@ df <- data.frame(index=sort(sample(1:1000, rows)),
                  vals=rnorm(rows) * 100,
                  stringsAsFactors=FALSE)
 fromDataFrame(df, uri)
-arr <- tiledb_array(uri, as.data.frame=TRUE)
+arr <- tiledb_array(uri, return_as="data.frame")
 chk <- arr[]
 if (getRversion() < '4.0.0') chk$chars <- as.character(chk$chars)
 expect_equal(df, chk[,-1])              # omit first col which is added
@@ -87,7 +87,7 @@ if (tiledb_version(TRUE) < "2.1.0") exit_file("Remaining tests require TileDB 2.
 
 if (dir.exists(uri)) unlink(uri, recursive=TRUE)
 fromDataFrame(df, uri, col_index=1)
-arr <- tiledb_array(uri, as.data.frame=TRUE)
+arr <- tiledb_array(uri, return_as="data.frame")
 chk <- arr[]
 if (getRversion() < '4.0.0') chk$chars <- as.character(chk$chars)
 expect_equal(df[,2], na.omit(chk)[,2])  # compare column by column
@@ -96,7 +96,7 @@ expect_equal(df[,3], na.omit(chk)[,3])
 
 if (dir.exists(uri)) unlink(uri, recursive=TRUE)
 fromDataFrame(df, uri, col_index="index")
-arr <- tiledb_array(uri, as.data.frame=TRUE)
+arr <- tiledb_array(uri, return_as="data.frame")
 chk <- arr[]
 if (getRversion() < '4.0.0') chk$chars <- as.character(chk$chars)
 expect_equal(df[,2], na.omit(chk)[,2])  # compare column by column
@@ -108,7 +108,7 @@ df <- data.frame(chars=olddf$chars,
                  val=olddf$vals)
 if (dir.exists(uri)) unlink(uri, recursive=TRUE)
 fromDataFrame(df, uri)
-arr <- tiledb_array(uri, as.data.frame=TRUE)
+arr <- tiledb_array(uri, return_as="data.frame")
 chk <- arr[]
 if (getRversion() < '4.0.0') {
     df$chars <- as.character(df$chars)
@@ -118,15 +118,15 @@ expect_equal(df, chk[,-1])              # omit first col which is added
 
 if (dir.exists(uri)) unlink(uri, recursive=TRUE)
 fromDataFrame(df, uri, col_index=2)
-arr <- tiledb_array(uri, as.data.frame=TRUE)
+arr <- tiledb_array(uri, return_as="data.frame")
 chk <- arr[]
 if (getRversion() < '4.0.0') chk$chars <- as.character(chk$chars)
 expect_equal(df[,1], na.omit(chk)[,2])  # compare column by column
 expect_equal(df[,3], na.omit(chk)[,3])
 
 if (dir.exists(uri)) unlink(uri, recursive=TRUE)
 fromDataFrame(df, uri, col_index="index")
-arr <- tiledb_array(uri, as.data.frame=TRUE)
+arr <- tiledb_array(uri, return_as="data.frame")
 chk <- arr[]
 if (getRversion() < '4.0.0') chk$chars <- as.character(chk$chars)
 expect_equal(df[,1], na.omit(chk)[,2])  # compare column by column
@@ -155,13 +155,13 @@ df <- data.frame(time=round(Sys.time(), "secs") + trunc(cumsum(runif(nobs)*3600)
 if (dir.exists(uri)) unlink(uri, recursive=TRUE)
 fromDataFrame(df, uri, sparse=TRUE)
 
-chk <- tiledb_array(uri, as.data.frame=TRUE, extended=FALSE)
+chk <- tiledb_array(uri, return_as="data.frame", extended=FALSE)
 expect_equivalent(df, chk[])            # skip attribute
 
 for (i in seq_len(dim(df)[2])) {
     if (dir.exists(uri)) unlink(uri, recursive=TRUE)
     fromDataFrame(df, uri, sparse=TRUE, col_index=i)
-    chk <- tiledb_array(uri, as.data.frame=TRUE)
+    chk <- tiledb_array(uri, return_as="data.frame")
     expect_equal(df, chk[][,colnames(df)]) 		# index col comes first so need re-order
 }
 
@@ -181,7 +181,7 @@ df <- data.frame(time = round(Sys.time(), "secs") + trunc(cumsum(runif(nobs)*360
 if (dir.exists(uri)) unlink(uri, recursive=TRUE)
 fromDataFrame(df, uri, sparse=TRUE)
 
-chk <- tiledb_array(uri, as.data.frame=TRUE, extended=FALSE)
+chk <- tiledb_array(uri, return_as="data.frame", extended=FALSE)
 newdf <- chk[]
 if (getRversion() < '4.0.0') newdf$txt <- as.character(newdf$txt)
 expect_equivalent(df, newdf)            # skip attribute
@@ -190,7 +190,7 @@ expect_equivalent(df, newdf)            # skip attribute
 for (i in seq_len(dim(df)[2])) {
     if (dir.exists(uri)) unlink(uri, recursive=TRUE)
     fromDataFrame(df, uri, sparse=TRUE, col_index=i)
-    chk <- tiledb_array(uri, as.data.frame=TRUE)
+    chk <- tiledb_array(uri, return_as="data.frame")
     newdf <- chk[]
     if (getRversion() < '4.0.0') newdf$txt <- as.character(newdf$txt)
     expect_equal(df, newdf[, colnames(df)])
@@ -201,14 +201,14 @@ combinations <- list(c(1,2), c(1,3), c(2,4), c(3,5), c(4,5), c(2,3,4))
 for (comb in combinations) {
     if (dir.exists(uri)) unlink(uri, recursive=TRUE)
     fromDataFrame(df, uri, sparse=TRUE, col_index=comb) # by index
-    chk <- tiledb_array(uri, as.data.frame=TRUE)
+    chk <- tiledb_array(uri, return_as="data.frame")
     newdf <- chk[]
     if (getRversion() < '4.0.0') newdf$txt <- as.character(newdf$txt)
     expect_equal(df, newdf[][, colnames(df)])
 
     if (dir.exists(uri)) unlink(uri, recursive=TRUE)
     fromDataFrame(df, uri, sparse=TRUE, col_index=colnames(df)[comb]) # by name
-    chk <- tiledb_array(uri, as.data.frame=TRUE)
+    chk <- tiledb_array(uri, return_as="data.frame")
     newdf <- chk[]
     if (getRversion() < '4.0.0') newdf$txt <- as.character(newdf$txt)
     expect_equal(df, newdf[, colnames(df)])
@@ -223,7 +223,7 @@ dat <- data.frame(A=1:10,
 dat[3,1] <- NA
 dat[4,3] <- NA
 fromDataFrame(dat, uri)
-chk <- tiledb_array(uri, as.data.frame=TRUE)
+chk <- tiledb_array(uri, return_as="data.frame")
 val <- chk[][,-1]  # omit added rows
 if (getRversion() < '4.0.0') {
     dat$B <- as.character(dat$B)
@@ -239,7 +239,7 @@ D <- data.frame(sample=paste(LETTERS[1:N], as.character(sort(trunc(runif(N, 100,
                 stringsAsFactors=FALSE)
 uri <- tempfile()
 fromDataFrame(D, uri, col_index=1, sparse=TRUE)
-arr <- tiledb_array(uri, as.data.frame=TRUE)
+arr <- tiledb_array(uri, return_as="data.frame")
 chk <- arr[]
 if (getRversion() < '4.0.0') {
     chk$sample <- as.character(chk$sample)
@@ -260,7 +260,7 @@ expect_error(fromDataFrame(df, uri, col_index=1, sparse=TRUE, allows_dups=FALSE)
 uri <- tempfile()
 expect_silent(arr <- fromDataFrame(df, uri, col_index=1, sparse=TRUE, allows_dups=TRUE))
 
-arr <- tiledb_array(uri, as.data.frame=TRUE)
+arr <- tiledb_array(uri, return_as="data.frame")
 chk <- arr[]
 if (getRversion() <  '4.0.0') chk$char <- as.character(chk$char)
 expect_equivalent(df, chk)              # skip attribute

inst/tinytest/test_dim.R

@@ -163,7 +163,7 @@ for (dtype in dimtypes) {
     schema <- tiledb_array_schema(domain, attrib, sparse=TRUE)
     tiledb_array_create(uri, schema)
 
-    arr <- tiledb_array(uri, as.data.frame=TRUE)
+    arr <- tiledb_array(uri, return_as="data.frame")
     dvec <- switch(dtype,
                    "ASCII"   = LETTERS[1:5],
                    "INT8"    =,
@@ -195,7 +195,7 @@ for (dtype in dimtypes) {
     data <- data.frame(row = dvec, attr = avec, stringsAsFactors=FALSE)
     arr[] <- data
 
-    arr2 <- tiledb_array(uri, as.data.frame=TRUE)
+    arr2 <- tiledb_array(uri, return_as="data.frame")
     readdata <- arr2[]
     if (dtype == "ASCII" && getRversion() < '4.0.0') readdata$row <- as.character(readdata$row)
     if (dtype == "UINT64") readdata[,1] <- as.integer64(readdata[,1])  # return doubles here
@@ -212,7 +212,7 @@ for (dtype in dimtypes) {
     }
 
     ## subset tests
-    arr3 <- tiledb_array(uri, as.data.frame=TRUE)
+    arr3 <- tiledb_array(uri, return_as="data.frame")
     if (dtype %in% c("DATETIME_YEAR", "DATETIME_MONTH", "DATETIME_WEEK", "DATETIME_DAY")) {
         scaleDate <- function(val, dtype) {
             val <- switch(dtype,
@@ -331,7 +331,7 @@ for (dtype in dimtypes) {
     schema <- tiledb_array_schema(domain, attrib, sparse=TRUE)
     tiledb_array_create(uri, schema)
 
-    arr <- tiledb_array(uri, as.data.frame=TRUE)
+    arr <- tiledb_array(uri, return_as="data.frame")
     dvec <- switch(dtype,
                    "ASCII"   = LETTERS[1:5],
                    "INT8"    =,
@@ -363,7 +363,7 @@ for (dtype in dimtypes) {
     data <- data.frame(row = dvec, attr = avec, stringsAsFactors=FALSE)
     arr[] <- data
 
-    ## arr2 <- tiledb_array(uri, as.data.frame=TRUE)
+    ## arr2 <- tiledb_array(uri, return_as="data.frame")
     ## readdata <- arr2[]
     ## if (dtype == "ASCII" && getRversion() < '4.0.0') readdata$row <- as.character(readdata$row)
     ## if (dtype == "UINT64") readdata[,1] <- as.integer64(readdata[,1])  # return doubles here
@@ -380,7 +380,7 @@ for (dtype in dimtypes) {
     ## }
 
     ## subset tests
-    arr3 <- tiledb_array(uri, as.data.frame=TRUE)
+    arr3 <- tiledb_array(uri, return_as="data.frame")
     if (dtype %in% c("DATETIME_YEAR", "DATETIME_MONTH", "DATETIME_WEEK", "DATETIME_DAY")) {
         scaleDate <- function(val, dtype) {
             val <- switch(dtype,

inst/tinytest/test_dimsubset.R

@@ -78,7 +78,7 @@ log_info("re-arranged list object made")
 arr[] <- newlst
 log_info("array written")
 
-newarr <- tiledb_array(tmp, as.data.frame=TRUE, query_layout="UNORDERED")
+newarr <- tiledb_array(tmp, return_as="data.frame", query_layout="UNORDERED")
 dat <- newarr[]
 log_info("array read")
 expect_equal(nrow(dat), nrow(flights))
@@ -97,15 +97,15 @@ expect_equal(unique(dat$origin), "JFK")
 expect_equal(unique(dat$dest), "BOS")
 
 ## same via selected_points
-newarr <- tiledb_array(tmp, as.data.frame=TRUE, query_layout="UNORDERED",
+newarr <- tiledb_array(tmp, return_as="data.frame", query_layout="UNORDERED",
                        selected_points= list("AA", "JFK", "BOS", NULL))
 dat <- newarr[]
 expect_equal(unique(dat$carrier), "AA")
 expect_equal(unique(dat$origin), "JFK")
 expect_equal(unique(dat$dest), "BOS")
 
 ## test named lists with one element
-newarr <- tiledb_array(tmp, as.data.frame=TRUE, query_layout="UNORDERED")
+newarr <- tiledb_array(tmp, return_as="data.frame", query_layout="UNORDERED")
 selected_ranges(newarr) <- list(carrier = cbind("AA","AA"))
 dat <- newarr[]
 expect_equal(unique(dat$carrier), "AA")

inst/tinytest/test_metadata.R

@@ -19,8 +19,7 @@ unlink_and_create_simple <- function(tmp) {
   sch <- tiledb_array_schema(dom, c(a1, a2), sparse=TRUE)
   tiledb_array_create(tmp, sch)
 
-  #arr <- tiledb_sparse(tmp, as.data.frame=FALSE)
-  arr <- tiledb_array(tmp, as.data.frame=FALSE)
+  arr <- tiledb_array(tmp, return_as="asis")
 
   if (tiledb:::libtiledb_array_is_open(arr@ptr)) {
       tiledb_array_close(arr)
@@ -44,8 +43,7 @@ unlink_and_create_ptr <- function(tmp) {
 
   arr <- tiledb_array_open(arr, "READ")
   ##return(arrR)
-  #arr <- tiledb_sparse(tmp, as.data.frame=FALSE)
-  arr <- tiledb_array(tmp, as.data.frame=FALSE)
+  arr <- tiledb_array(tmp, return_as="asis")
 }
 
 close_and_reopen <- function(arr, txt) {

inst/tinytest/test_query.R

@@ -239,7 +239,7 @@ cfg <- tiledb_config()
 cfg["sm.memory_budget"] <- "16"
 cfg["sm.memory_budget_var"] <- "32"
 ctx <- tiledb_ctx(cfg)
-array <- tiledb_array(tmp, as.data.frame=TRUE)
+array <- tiledb_array(tmp, return_as="data.frame")
 
 if (packageVersion("tiledb") <= "0.11.0") expect_warning(res <- array[]) # newer versions loop, no warning