New Upstream Release - r-bioc-hdf5array
Ready changes
Summary
Merged new upstream version: 1.28.1 (was: 1.26.0).
Diff
diff --git a/DESCRIPTION b/DESCRIPTION
index bd0c599..6426743 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -14,15 +14,15 @@ biocViews: Infrastructure, DataRepresentation, DataImport, Sequencing,
ImmunoOncology
URL: https://bioconductor.org/packages/HDF5Array
BugReports: https://github.com/Bioconductor/HDF5Array/issues
-Version: 1.26.0
+Version: 1.28.1
License: Artistic-2.0
Encoding: UTF-8
Author: Hervé Pagès
Maintainer: Hervé Pagès <hpages.on.github@gmail.com>
-Depends: R (>= 3.4), methods, DelayedArray (>= 0.15.16), rhdf5 (>=
+Depends: R (>= 3.4), methods, DelayedArray (>= 0.26.1), rhdf5 (>=
2.31.6)
Imports: utils, stats, tools, Matrix, rhdf5filters, BiocGenerics (>=
- 0.31.5), S4Vectors, IRanges
+ 0.31.5), S4Vectors, IRanges, S4Arrays (>= 1.0.1)
LinkingTo: S4Vectors (>= 0.27.13), Rhdf5lib
SystemRequirements: GNU make
Suggests: BiocParallel, GenomicRanges, SummarizedExperiment (>=
@@ -39,9 +39,9 @@ Collate: utils.R H5File-class.R h5ls.R H5DSetDescriptor-class.R
H5ADMatrix-class.R TENxMatrixSeed-class.R TENxMatrix-class.R
writeTENxMatrix.R zzz.R
git_url: https://git.bioconductor.org/packages/HDF5Array
-git_branch: RELEASE_3_16
-git_last_commit: 38b7bd6
-git_last_commit_date: 2022-11-01
-Date/Publication: 2022-11-01
+git_branch: RELEASE_3_17
+git_last_commit: 90e4bef
+git_last_commit_date: 2023-04-30
+Date/Publication: 2023-05-01
NeedsCompilation: yes
-Packaged: 2022-11-01 21:44:25 UTC; biocbuild
+Packaged: 2023-05-01 20:57:04 UTC; biocbuild
diff --git a/NAMESPACE b/NAMESPACE
index 74608d6..7f82d6b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -15,6 +15,7 @@ import(rhdf5)
import(BiocGenerics)
import(S4Vectors)
import(IRanges)
+import(S4Arrays)
import(DelayedArray)
@@ -88,11 +89,13 @@ exportMethods(
## Methods for generics defined in the BiocGenerics package:
path, "path<-", type, updateObject,
+ ## Methods for generics defined in the S4Arrays package:
+ extract_array, is_sparse, "is_sparse<-",
+
## Methods for generics defined in the DelayedArray package:
- extract_array,
- sparsity, is_sparse, "is_sparse<-", extract_sparse_array,
- read_sparse_block, write_block,
- matrixClass, DelayedArray, chunkdim,
+ chunkdim, write_block,
+ sparsity, extract_sparse_array, read_sparse_block,
+ matrixClass, DelayedArray,
close
)
diff --git a/NEWS b/NEWS
index 01cbc86..45e8aee 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,9 @@
+CHANGES IN VERSION 1.28.0
+-------------------------
+
+- No changes in this version.
+
+
CHANGES IN VERSION 1.26.0
-------------------------
diff --git a/R/H5ADMatrixSeed-class.R b/R/H5ADMatrixSeed-class.R
index c40e1f7..0c9e0ab 100644
--- a/R/H5ADMatrixSeed-class.R
+++ b/R/H5ADMatrixSeed-class.R
@@ -25,7 +25,7 @@ setClass("CSR_H5ADMatrixSeed",
### We overwrite the method for HDF5ArraySeed objects with a method that
### accesses the slot, not the file.
setMethod("dimnames", "Dense_H5ADMatrixSeed",
- function(x) DelayedArray:::simplify_NULL_dimnames(x@dimnames)
+ function(x) S4Arrays:::simplify_NULL_dimnames(x@dimnames)
)
diff --git a/R/H5File-class.R b/R/H5File-class.R
index 7ad6f1e..842c4a9 100644
--- a/R/H5File-class.R
+++ b/R/H5File-class.R
@@ -91,7 +91,7 @@
if (use.rhdf5) {
fid <- .ID_to_H5IdComponent(ID)
- rhdf5:::H5Fclose(fid)
+ rhdf5::H5Fclose(fid)
} else {
.Call2("C_h5closefile", ID, PACKAGE="HDF5Array")
}
diff --git a/R/H5SparseMatrixSeed-class.R b/R/H5SparseMatrixSeed-class.R
index 6383011..3aa6aad 100644
--- a/R/H5SparseMatrixSeed-class.R
+++ b/R/H5SparseMatrixSeed-class.R
@@ -108,7 +108,7 @@ setReplaceMethod("path", "H5SparseMatrixSeed",
setMethod("dim", "H5SparseMatrixSeed", function(x) x@dim)
setMethod("dimnames", "H5SparseMatrixSeed",
- function(x) DelayedArray:::simplify_NULL_dimnames(x@dimnames)
+ function(x) S4Arrays:::simplify_NULL_dimnames(x@dimnames)
)
@@ -485,7 +485,7 @@ setMethod(".load_sparse_data", "CSR_H5SparseMatrixSeed",
.extract_array_from_H5SparseMatrixSeed <- function(x, index)
{
- ans_dim <- DelayedArray:::get_Nindex_lengths(index, dim(x))
+ ans_dim <- S4Arrays:::get_Nindex_lengths(index, dim(x))
if (any(ans_dim == 0L)) {
## Return an empty matrix.
data0 <- .read_h5sparse_data(x@filepath, x@group, x@subdata,
@@ -631,8 +631,8 @@ setGeneric("extractNonzeroDataByCol", signature="x",
setMethod("extractNonzeroDataByCol", "CSC_H5SparseMatrixSeed",
function(x, j)
{
- j <- DelayedArray:::normalizeSingleBracketSubscript2(j, ncol(x),
- colnames(x))
+ j <- S4Arrays:::normalizeSingleBracketSubscript2(j, ncol(x),
+ colnames(x))
.extract_nonzero_csc_sparse_data_by_col(x, j)
}
)
@@ -646,8 +646,8 @@ setGeneric("extractNonzeroDataByRow", signature="x",
setMethod("extractNonzeroDataByRow", "CSR_H5SparseMatrixSeed",
function(x, i)
{
- i <- DelayedArray:::normalizeSingleBracketSubscript2(i, nrow(x),
- rownames(x))
+ i <- S4Arrays:::normalizeSingleBracketSubscript2(i, nrow(x),
+ rownames(x))
.extract_nonzero_csc_sparse_data_by_col(t(x), i)
}
)
@@ -697,7 +697,7 @@ setAs("CSR_H5SparseMatrixSeed", "sparseMatrix",
setMethod("show", "H5SparseMatrixSeed",
function(object)
{
- cat(DelayedArray:::array_as_one_line_summary(object), ":\n", sep="")
+ cat(S4Arrays:::array_as_one_line_summary(object), ":\n", sep="")
cat("# dirname: ", dirname(object), "\n", sep="")
cat("# basename: ", basename(object), "\n", sep="")
cat("# group: ", object@group, "\n", sep="")
diff --git a/R/HDF5ArraySeed-class.R b/R/HDF5ArraySeed-class.R
index dcfd9a9..8ed34ed 100644
--- a/R/HDF5ArraySeed-class.R
+++ b/R/HDF5ArraySeed-class.R
@@ -84,14 +84,14 @@ validate_HDF5ArraySeed_dataset_geometry <- function(x, what="object")
return("'as_sparse' slot must be TRUE or FALSE")
## 'dim' slot.
- msg <- DelayedArray:::validate_dim_slot(x, "dim")
+ msg <- S4Arrays:::validate_dim_slot(x, "dim")
if (!isTRUE(msg))
return(msg)
## 'chunkdim' slot.
x_chunkdim <- x@chunkdim
if (!is.null(x_chunkdim)) {
- msg <- DelayedArray:::validate_dim_slot(x, "chunkdim")
+ msg <- S4Arrays:::validate_dim_slot(x, "chunkdim")
if (!isTRUE(msg))
return(msg)
}
@@ -239,7 +239,7 @@ setMethod("dimnames", "HDF5ArraySeed",
as.integer=FALSE, as.sparse=FALSE)
{
if (!is.null(index))
- index <- DelayedArray:::expand_Nindex_RangeNSBS(index)
+ index <- S4Arrays:::expand_Nindex_RangeNSBS(index)
h5mread(filepath, name, starts=index,
as.integer=as.integer, as.sparse=as.sparse)
}
diff --git a/R/ReshapedHDF5ArraySeed-class.R b/R/ReshapedHDF5ArraySeed-class.R
index 07e44b6..3f8e37f 100644
--- a/R/ReshapedHDF5ArraySeed-class.R
+++ b/R/ReshapedHDF5ArraySeed-class.R
@@ -33,7 +33,7 @@ setMethod("dim", "ReshapedHDF5ArraySeed", function(x) x@reshaped_dim)
.extract_array_from_ReshapedHDF5ArraySeed <- function(x, index)
{
- ans_dim <- DelayedArray:::get_Nindex_lengths(index, dim(x))
+ ans_dim <- S4Arrays:::get_Nindex_lengths(index, dim(x))
h5mread_from_reshaped(path(x), x@name, x@reshaped_dim, starts=index)
}
@@ -60,7 +60,7 @@ setMethod("chunkdim", "ReshapedHDF5ArraySeed", function(x) x@reshaped_chunkdim)
ReshapedHDF5ArraySeed <- function(filepath, name, dim, type=NA)
{
seed <- HDF5ArraySeed(filepath, name, type=type)
- reshaped_dim <- DelayedArray:::normarg_dim(dim)
+ reshaped_dim <- S4Arrays:::normarg_dim(dim)
collapse_along <- find_dims_to_collapse(reshaped_dim, seed@dim)
if (is.null(seed@chunkdim)) {
reshaped_chunkdim <- NULL
diff --git a/R/h5mread_from_reshaped.R b/R/h5mread_from_reshaped.R
index 34cd49a..72d0217 100644
--- a/R/h5mread_from_reshaped.R
+++ b/R/h5mread_from_reshaped.R
@@ -83,7 +83,7 @@ collapse_dims <- function(dim0, collapse_along)
h5mread_from_reshaped <- function(filepath, name, dim, starts, noreduce=FALSE,
as.integer=FALSE, method=0L)
{
- dim <- DelayedArray:::normarg_dim(dim)
+ dim <- S4Arrays:::normarg_dim(dim)
dim0 <- h5dim(filepath, name)
collapse_along <- find_dims_to_collapse(dim, dim0)
ndim <- length(dim)
@@ -134,6 +134,6 @@ h5mread_from_reshaped <- function(filepath, name, dim, starts, noreduce=FALSE,
as.integer=as.integer,
method=method)
})
- do.call(DelayedArray:::simple_abind, c(tmp, list(along=along1)))
+ do.call(S4Arrays:::simple_abind, c(tmp, list(along=along1)))
}
diff --git a/R/h5writeDimnames.R b/R/h5writeDimnames.R
index 3a31afb..68df0d1 100644
--- a/R/h5writeDimnames.R
+++ b/R/h5writeDimnames.R
@@ -233,7 +233,7 @@ h5readDimnames <- function(filepath, name, as.character=FALSE)
## explicitly drop the "dim" attribute.
as.character(dn)
} else {
- DelayedArray:::set_dim(dn, NULL)
+ S4Arrays:::set_dim(dn, NULL)
}
})
}
diff --git a/debian/changelog b/debian/changelog
index 883e643..9004be2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+r-bioc-hdf5array (1.28.1-1) UNRELEASED; urgency=low
+
+ * New upstream release.
+
+ -- Debian Janitor <janitor@jelmer.uk> Tue, 23 May 2023 09:58:31 -0000
+
r-bioc-hdf5array (1.26.0-1) unstable; urgency=medium
* Team upload.
diff --git a/debian/patches/use_debian_packaged_libhdf5.patch b/debian/patches/use_debian_packaged_libhdf5.patch
index 4283512..48ecb65 100644
--- a/debian/patches/use_debian_packaged_libhdf5.patch
+++ b/debian/patches/use_debian_packaged_libhdf5.patch
@@ -3,9 +3,11 @@ Last-Update: Wed, 09 Sep 2020 15:28:06 +0200
Description: Use Debian packaged libhdf5
Forwarded: No
---- a/src/Makevars
-+++ b/src/Makevars
-@@ -17,10 +17,8 @@
+Index: r-bioc-hdf5array.git/src/Makevars
+===================================================================
+--- r-bioc-hdf5array.git.orig/src/Makevars
++++ r-bioc-hdf5array.git/src/Makevars
+@@ -17,10 +17,8 @@ OBJECTS = \
h5summarize.o \
R_init_HDF5Array.o
diff --git a/man/H5SparseMatrixSeed-class.Rd b/man/H5SparseMatrixSeed-class.Rd
index a473086..79072e5 100644
--- a/man/H5SparseMatrixSeed-class.Rd
+++ b/man/H5SparseMatrixSeed-class.Rd
@@ -106,11 +106,11 @@ H5SparseMatrixSeed(filepath, group, subdata=NULL)
An H5SparseMatrixSeed derivative.
}
\item{index}{
- See \code{?\link[DelayedArray]{extract_array}} in the \pkg{DelayedArray}
+ See \code{?\link[S4Arrays]{extract_array}} in the \pkg{S4Arrays}
package.
}
\item{viewport}{
- See \code{?\link[DelayedArray]{read_block}} in the \pkg{DelayedArray}
+ See \code{?\link[S4Arrays]{read_block}} in the \pkg{S4Arrays}
package.
}
\item{j}{
@@ -140,7 +140,7 @@ H5SparseMatrixSeed(filepath, group, subdata=NULL)
\item \code{chunkdim()}, \code{extract_array()},
\code{extract_sparse_array()}, \code{read_sparse_block()},
\code{is_sparse()}: These generics are defined and documented
- in the \pkg{DelayedArrray} package.
+ in the \pkg{DelayedArray} package.
\item \code{sparsity()}: Returns the number of zero-valued matrix elements
in the object divided by its total number of elements (a.k.a. its
length).
diff --git a/man/HDF5ArraySeed-class.Rd b/man/HDF5ArraySeed-class.Rd
index 30707b3..25f1779 100644
--- a/man/HDF5ArraySeed-class.Rd
+++ b/man/HDF5ArraySeed-class.Rd
@@ -74,7 +74,7 @@ HDF5ArraySeed(filepath, name, as.sparse=FALSE, type=NA)
For the \code{is_sparse()} setter: \code{TRUE} or \code{FALSE}.
}
\item{index}{
- See \code{?\link[DelayedArray]{extract_array}} in the \pkg{DelayedArray}
+ See \code{?\link[S4Arrays]{extract_array}} in the \pkg{S4Arrays}
package.
}
}
@@ -92,9 +92,13 @@ HDF5ArraySeed(filepath, name, as.sparse=FALSE, type=NA)
\item \code{path()}: Returns the path to the HDF5 file where the dataset
is located.
\item \code{dim()}, \code{dimnames()}.
- \item \code{type()}, \code{is_sparse()}, \code{chunkdim()},
- \code{extract_array()}, \code{extract_sparse_array()}: These generics
- are defined and documented in the \pkg{DelayedArrray} package.
+ \item \code{type()}, \code{extract_array()}, \code{is_sparse()},
+ \code{extract_sparse_array()}, \code{chunkdim()}:
+ These generics are defined and documented in other packages e.g.
+ in \pkg{S4Arrays} for \code{\link[S4Arrays]{extract_array}()}
+ and \code{\link[S4Arrays]{is_sparse}()}, and in \pkg{DelayedArray}
+ for \code{\link[DelayedArray]{extract_sparse_array}()} and
+ \code{\link[DelayedArray]{chunkdim}()}.
}
}
@@ -120,6 +124,14 @@ HDF5ArraySeed(filepath, name, as.sparse=FALSE, type=NA)
\itemize{
\item \link{HDF5Array} objects.
+ \item \code{\link[S4Arrays]{type}}, \code{\link[S4Arrays]{extract_array}},
+ and \code{\link[S4Arrays]{is_sparse}}, in the the \pkg{S4Arrays}
+ package.
+
+ \item \code{\link[DelayedArray]{extract_sparse_array}} and
+ \code{\link[DelayedArray]{chunkdim}} in the \pkg{DelayedArray}
+ package.
+
\item \code{\link{h5ls}} to list the content of an HDF5 file.
}
}
diff --git a/man/h5mread.Rd b/man/h5mread.Rd
index 7451228..656f7b5 100644
--- a/man/h5mread.Rd
+++ b/man/h5mread.Rd
@@ -63,7 +63,7 @@ get_h5mread_returned_type(filepath, name, as.integer=FALSE)
list element indicates a single position selection along the corresponding
dimension. Note that in this case the \code{starts} argument is
equivalent to the \code{index} argument of \code{\link[rhdf5]{h5read}}
- and \code{\link[DelayedArray]{extract_array}} (with the caveat that
+ and \code{\link[S4Arrays]{extract_array}} (with the caveat that
\code{\link[rhdf5]{h5read}} doesn't accept empty selections).
Finally note that when \code{counts} is not \code{NULL} then the
@@ -109,7 +109,7 @@ get_h5mread_returned_type(filepath, name, as.integer=FALSE)
\item \code{\link[rhdf5]{h5read}} in the \pkg{rhdf5} package.
- \item \code{\link[DelayedArray]{extract_array}} in the \pkg{DelayedArray}
+ \item \code{\link[S4Arrays]{extract_array}} in the \pkg{S4Arrays}
package.
\item The \code{\link[TENxBrainData]{TENxBrainData}} dataset (in the
diff --git a/src/H5DSetDescriptor.c b/src/H5DSetDescriptor.c
index 89d32e9..e7e1e4e 100644
--- a/src/H5DSetDescriptor.c
+++ b/src/H5DSetDescriptor.c
@@ -153,7 +153,8 @@ static const char *predef_native_type_as_string(hid_t native_type_id)
/* Should never happen if predef_native_type_as_string()
is kept in sync with map_native_type_to_predef_type(). */
- sprintf(s, "unknown native type (%lld)", (long long) native_type_id);
+ snprintf(s, sizeof(s), "unknown native type (%lld)",
+ (long long) native_type_id);
return s;
}
@@ -197,7 +198,7 @@ static const char *H5class2str(H5T_class_t h5class)
in switch. */
default: break;
}
- sprintf(s, "unknown class (%d)", h5class);
+ snprintf(s, sizeof(s), "unknown class (%d)", h5class);
return s;
}
@@ -214,7 +215,7 @@ static const char *H5layout2str(H5D_layout_t H5layout)
in switch. */
default: break;
}
- sprintf(s, "unknown layout (%d)", H5layout);
+ snprintf(s, sizeof(s), "unknown layout (%d)", H5layout);
return s;
}
diff --git a/src/H5File.c b/src/H5File.c
index 9eb712d..2a39cd6 100644
--- a/src/H5File.c
+++ b/src/H5File.c
@@ -27,7 +27,7 @@ static const char *hid_to_string(hid_t hid)
{
static char buf[21];
- sprintf(buf, "%lld", (long long) hid);
+ snprintf(buf, sizeof(buf), "%lld", (long long) hid);
return buf;
}