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gnu: r-h5mread: Patch for compatibility with R 4.6.0.

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* gnu/packages/patches/r-h5mread-0001-h5mread-1.3.2-Get-rid-of-non-API-calls-to-R.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Record it.
* gnu/packages/bioconductor.scm (r-h5mread)[source]: Register patch.

Change-Id: Iecbf0eb41b554169b36c00b74072b1fca7a31943
This commit is contained in:
Ricardo Wurmus
2026-04-27 14:45:40 +02:00
parent e2173901c2
commit 8d07dd9ef7
3 changed files with 147 additions and 1 deletions
Download Patch File Download Diff File Expand all files Collapse all files
gnu/local.mk
+1
View File
@@ -2350,6 +2350,7 @@ dist_patch_DATA = \
%D%/packages/patches/reposurgeon-add-missing-docbook-files.patch \
%D%/packages/patches/rdkit-unbundle-external-dependencies.patch \
%D%/packages/patches/r-biostrings-r4.6.0-compat.patch \
%D%/packages/patches/r-h5mread-0001-h5mread-1.3.2-Get-rid-of-non-API-calls-to-R.patch \
%D%/packages/patches/r-httpuv-1.6.6-unvendor-libuv.patch \
%D%/packages/patches/r-rsamtools-r-4.6.0-compat.patch \
%D%/packages/patches/r-snpstats-0001-fixed-non-API-except-for-IS_S4_OBJECT.patch \
gnu/packages/bioconductor.scm
+4 -1
View File
@@ -25556,7 +25556,10 @@ assays such as Hi-C.")
(method url-fetch)
(uri (bioconductor-uri "h5mread" version))
(sha256
(base32 "0xdjp5y0wkv2aazj17hi65qmsjaa9jaadim5hx525h5gb0c6p8nw"))))
(base32 "0xdjp5y0wkv2aazj17hi65qmsjaa9jaadim5hx525h5gb0c6p8nw"))
(patches
(search-patches
"r-h5mread-0001-h5mread-1.3.2-Get-rid-of-non-API-calls-to-R.patch"))))
(properties
'((upstream-name . "h5mread")
;; Avoid dependency cycle.
gnu/packages/patches/r-h5mread-0001-h5mread-1.3.2-Get-rid-of-non-API-calls-to-R.patch
+142
View File
@@ -0,0 +1,142 @@
From 7fe34542bff0183c3a6a35a62df9035a71698eb2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
Date: Fri, 6 Mar 2026 15:54:23 -0800
Subject: [PATCH] h5mread 1.3.2: Get rid of non-API calls to R
---
DESCRIPTION | 2 +-
R/H5File-class.R | 27 ++++++++++++++++-----------
src/h5mread_index.c | 5 +++--
src/h5mread_startscounts.c | 3 ++-
4 files changed, 22 insertions(+), 15 deletions(-)
diff --git a/R/H5File-class.R b/R/H5File-class.R
index 2735166..6aeb80f 100644
--- a/R/H5File-class.R
+++ b/R/H5File-class.R
@@ -73,19 +73,23 @@
}
}
-.h5openfile <- function(filepath, s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
+.h5openfile <- function(filepath, readonly=TRUE,
+ s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
{
if (!isSingleString(filepath))
stop(wmsg("'filepath' must be a single string specifying ",
"the path or URL to an HDF5 file"))
+ if (!isTRUEorFALSE(readonly))
+ stop(wmsg("'readonly' must be TRUE or FALSE"))
if (!isTRUEorFALSE(s3))
stop(wmsg("'s3' must be TRUE or FALSE"))
-
+ if (s3 && !readonly)
+ stop(wmsg("'readonly' must be set to TRUE when 's3' is TRUE"))
if (s3) {
ID <- .h5openS3file(filepath, s3credentials=s3credentials,
use.rhdf5=use.rhdf5)
} else {
- ID <- .h5openlocalfile(filepath, readonly=TRUE, use.rhdf5=use.rhdf5)
+ ID <- .h5openlocalfile(filepath, readonly=readonly, use.rhdf5=use.rhdf5)
}
ID
}
@@ -136,16 +140,16 @@
.ID_is_closed <- function(ID) { is.null(ID) || is.na(ID) }
-.open_H5FileID_xp <- function(xp, filepath, s3=FALSE, s3credentials=NULL,
- use.rhdf5=FALSE)
+.open_H5FileID_xp <- function(xp, filepath, readonly=TRUE,
+ s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
{
ID <- .get_H5FileID_xp_ID(xp)
if (!.ID_is_closed(ID)) {
## H5FileID object is already open.
return(FALSE)
}
- ID <- .h5openfile(filepath, s3=s3, s3credentials=s3credentials,
- use.rhdf5=use.rhdf5)
+ ID <- .h5openfile(filepath, readonly=readonly,
+ s3=s3, s3credentials=s3credentials, use.rhdf5=use.rhdf5)
.set_H5FileID_xp_ID(xp, ID)
TRUE
}
@@ -183,10 +187,11 @@ close.H5FileID <- function(con, ...)
.close_H5FileID_xp(con@xp, ..., use.rhdf5=con@from_rhdf5)
}
-H5FileID <- function(filepath, s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
+H5FileID <- function(filepath, readonly=TRUE,
+ s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
{
- ID <- .h5openfile(filepath, s3=s3, s3credentials=s3credentials,
- use.rhdf5=use.rhdf5)
+ ID <- .h5openfile(filepath, readonly=readonly,
+ s3=s3, s3credentials=s3credentials, use.rhdf5=use.rhdf5)
xp <- .new_H5FileID_xp(ID)
reg.finalizer(xp,
function(e) .close_H5FileID_xp(e, use.rhdf5=use.rhdf5),
@@ -272,7 +277,7 @@ H5File <- function(filepath, s3=FALSE, s3credentials=NULL, .no_rhdf5_h5id=FALSE)
rhdf5_h5id <- new("H5FileID")
} else {
rhdf5_h5id <- H5FileID(filepath, s3=s3, s3credentials=s3credentials,
- use.rhdf5=TRUE)
+ use.rhdf5=TRUE)
}
if (!s3)
filepath <- file_path_as_absolute(filepath)
diff --git a/src/h5mread_index.c b/src/h5mread_index.c
index 7284815..ec93c25 100644
--- a/src/h5mread_index.c
+++ b/src/h5mread_index.c
@@ -9,6 +9,7 @@
#include "h5mread_helpers.h"
#include "TouchedChunks.h"
+#include <R_ext/Altrep.h> /* only for DATAPTR_RW() */
#include <stdlib.h> /* for malloc, free */
#include <string.h> /* for memcmp */
//#include <time.h>
@@ -444,7 +445,7 @@ static int read_chunk_data_4_5(const H5DSetDescriptor *h5dset,
const size_t *Rarray_dim, SEXP Rarray,
int method, int use_H5Dread_chunk)
{
- void *out = DATAPTR(Rarray);
+ void *out = DATAPTR_RW(Rarray);
if (out == NULL)
return -1;
@@ -874,7 +875,7 @@ static int read_data_6(const AllTChunks *all_tchunks,
size_t *inner_nchip_buf = R_alloc0_size_t_array(ndim);
LLongAEAE *inner_breakpoint_bufs = new_LLongAEAE(ndim, ndim);
- void *out = DATAPTR(Rarray);
+ void *out = DATAPTR_RW(Rarray);
if (out == NULL) {
_destroy_TChunkIterator(&tchunk_iter);
return -1;
diff --git a/src/h5mread_startscounts.c b/src/h5mread_startscounts.c
index de57fd5..959014f 100644
--- a/src/h5mread_startscounts.c
+++ b/src/h5mread_startscounts.c
@@ -8,6 +8,7 @@
#include "uaselection.h"
#include "h5mread_helpers.h"
+#include <R_ext/Altrep.h> /* only for DATAPTR_RW() */
#include <stdlib.h> /* for malloc, free */
//#include <time.h>
@@ -402,7 +403,7 @@ SEXP _h5mread_startscounts(const H5DSetDescriptor *h5dset,
SEXP ans = PROTECT(allocVector(h5dset->h5type->Rtype, ans_len));
if (ans_len != 0) {
- void *mem = DATAPTR(ans);
+ void *mem = DATAPTR_RW(ans);
if (mem == NULL)
goto on_error;
--
2.52.0