Use the latest rhdf5 to avoid NA-related warnings on read.

No more need for a blanket suppressMessages to keep H5Dread quiet.

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: alabaster.base
 Title: Save Bioconductor Objects To File
-Version: 1.3.22
-Date: 2024-03-08
+Version: 1.3.23
+Date: 2024-03-13
 Authors@R: person("Aaron", "Lun", role=c("aut", "cre"), email="[email protected]")
 License: MIT + file LICENSE
 Description: 
@@ -14,7 +14,7 @@ Imports:
     methods,
     utils,
     S4Vectors,
-    rhdf5 (>= 2.47.1),
+    rhdf5 (>= 2.47.6),
     jsonlite,
     jsonvalidate,
     Rcpp

R/hdf5.R

@@ -132,7 +132,7 @@ h5_read_vector <- function(handle, name, check=FALSE, default=NULL, bit64convers
 
     dhandle <- H5Dopen(handle, name)
     on.exit(H5Dclose(dhandle), add=TRUE, after=FALSE)
-    output <- suppressMessages(H5Dread(dhandle, bit64conversion=bit64conversion, drop=TRUE))
+    output <- H5Dread(dhandle, bit64conversion=bit64conversion, drop=TRUE)
 
     if (is.raw(output)) {
         storage.mode(output) <- "integer"

R/readAtomicVector.R

@@ -34,7 +34,7 @@ readAtomicVector <- function(path, metadata, ...) {
 
     vhandle <- H5Dopen(ghandle, "values")
     on.exit(H5Dclose(vhandle), add=TRUE, after=FALSE)
-    contents <- suppressMessages(H5Dread(vhandle, drop=TRUE))
+    contents <- H5Dread(vhandle, drop=TRUE)
     missing.placeholder <- h5_read_attribute(vhandle, missingPlaceholderName, check=TRUE, default=NULL)
 
     contents <- h5_cast(contents, expected.type=expected.type, missing.placeholder=missing.placeholder)

R/readBaseFactor.R

@@ -45,7 +45,7 @@ readBaseFactor <- function(path, metadata, ...) {
 .simple_read_codes <- function(handle, name="codes") {
     chandle <- H5Dopen(handle, name)
     on.exit(H5Dclose(chandle), add=TRUE, after=FALSE)
-    codes <- suppressMessages(H5Dread(chandle, drop=TRUE))
+    codes <- H5Dread(chandle, drop=TRUE)
     missing.placeholder <- h5_read_attribute(chandle, missingPlaceholderName, check=TRUE, default=NULL)
     codes <- h5_cast(codes, expected.type="integer", missing.placeholder=missing.placeholder)
     codes + 1L

R/readDataFrame.R

@@ -70,7 +70,7 @@ readDataFrame <- function(path, metadata, ...) {
                 columns[[col]] <- local({
                     colhandle <- H5Dopen(gdhandle, expected)
                     on.exit(H5Dclose(colhandle), add=TRUE, after=FALSE)
-                    contents <- suppressMessages(H5Dread(colhandle, drop=TRUE))
+                    contents <- H5Dread(colhandle, drop=TRUE)
 
                     missing.placeholder <- h5_read_attribute(colhandle, missingPlaceholderName, check=TRUE, default=NULL)
                     contents <- h5_cast(contents, expected.type=type, missing.placeholder=missing.placeholder)