diff --git a/DESCRIPTION b/DESCRIPTION index c824be6..a25529a 100644 --- a/DESCRIPTION +++ b/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="infinite.monkeys.with.keyboards@gmail.com") License: MIT + file LICENSE Description: @@ -14,7 +14,7 @@ Imports: methods, utils, S4Vectors, - rhdf5 (>= 2.47.1), + rhdf5 (>= 2.47.6), jsonlite, jsonvalidate, Rcpp diff --git a/R/hdf5.R b/R/hdf5.R index 8b40d30..97a4a0c 100644 --- a/R/hdf5.R +++ b/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" diff --git a/R/readAtomicVector.R b/R/readAtomicVector.R index 811bf6b..0ed7719 100644 --- a/R/readAtomicVector.R +++ b/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) diff --git a/R/readBaseFactor.R b/R/readBaseFactor.R index 3dfc86d..d890ad1 100644 --- a/R/readBaseFactor.R +++ b/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 diff --git a/R/readDataFrame.R b/R/readDataFrame.R index f14cb9f..c7b703e 100644 --- a/R/readDataFrame.R +++ b/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)