path: root/gnu/packages/patches/r-sparsearray-r-4.6.0-compat.patch

From 633aa6e3f671e9b58b3508b3944ff0dd45f34f8a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
Date: Thu, 5 Mar 2026 14:58:23 -0800
Subject: [PATCH] SparseArray 1.11.11: Get rid of non-API calls to R

From 65383c02f986832b1416c6ad39da800d8ced05df Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
Date: Tue, 31 Mar 2026 11:38:20 -0700
Subject: [PATCH] SparseArray 1.11.13: Use R_getVar() instead of findVar() when
 R >= 4.6.0

---
 DESCRIPTION                     |  2 +-
 src/Makevars                    |  1 +
 src/Rvector_utils.c             | 15 ++++++++-------
 src/SparseArray_aperm.c         |  2 +-
 src/SparseArray_matrixStats.c   |  5 +++--
 src/SparseArray_subassignment.c |  6 +++---
 src/SparseVec.h                 |  3 ++-
 src/leaf_utils.c                |  5 +++--
 src/test.c                      |  3 +++
 9 files changed, 25 insertions(+), 17 deletions(-)

diff --git a/src/Makevars b/src/Makevars
index 0ee3615..1c5b86e 100644
--- a/src/Makevars
+++ b/src/Makevars
@@ -1,2 +1,3 @@
+## See https://cran.r-project.org/doc/manuals/r-release/R-exts.html#OpenMP-support
 PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
diff --git a/src/Rvector_utils.c b/src/Rvector_utils.c
index ad80168..7e61ac1 100644
--- a/src/Rvector_utils.c
+++ b/src/Rvector_utils.c
@@ -4,6 +4,7 @@
  ****************************************************************************/
 #include "Rvector_utils.h"
 
+#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
 #include <string.h>  /* for memset() and memcpy() */
 
 
@@ -242,7 +243,7 @@ void _fill_Rvector_block_with_val(SEXP Rvector,
 				     (const SEXP) val);
 		return;
 	}
-	_set_elts_to_val(TYPEOF(Rvector), DATAPTR(Rvector),
+	_set_elts_to_val(TYPEOF(Rvector), DATAPTR_RW(Rvector),
 			 block_offset, block_len, val);
 }
 
@@ -260,7 +261,7 @@ void _fill_Rvector_block_with_zeros(SEXP Rvector,
 				     R_NilValue);
 		return;
 	}
-	_set_elts_to_zero(Rtype, DATAPTR(Rvector), block_offset, block_len);
+	_set_elts_to_zero(Rtype, DATAPTR_RW(Rvector), block_offset, block_len);
 	return;
 }
 
@@ -268,7 +269,7 @@ void _fill_Rvector_block_with_zeros(SEXP Rvector,
 void _fill_Rvector_block_with_ones(SEXP Rvector,
 		R_xlen_t block_offset, R_xlen_t block_len)
 {
-	_set_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector),
+	_set_elts_to_one(TYPEOF(Rvector), DATAPTR_RW(Rvector),
 			 block_offset, block_len);
 	return;
 }
@@ -277,7 +278,7 @@ void _fill_Rvector_block_with_ones(SEXP Rvector,
 void _fill_Rvector_block_with_minus_one(SEXP Rvector,
 		R_xlen_t block_offset, R_xlen_t block_len)
 {
-	_set_elts_to_minus_one(TYPEOF(Rvector), DATAPTR(Rvector),
+	_set_elts_to_minus_one(TYPEOF(Rvector), DATAPTR_RW(Rvector),
 			 block_offset, block_len);
 	return;
 }
@@ -293,7 +294,7 @@ void _fill_Rvector_block_with_NA(SEXP Rvector,
 					  NA_STRING);
 		return;
 	}
-	_set_elts_to_NA(Rtype, DATAPTR(Rvector), block_offset, block_len);
+	_set_elts_to_NA(Rtype, DATAPTR_RW(Rvector), block_offset, block_len);
 	return;
 }
 
@@ -460,7 +461,7 @@ void _fill_Rvector_subset_with_zeros(SEXP Rvector,
 				R_NilValue);
 		return;
 	}
-	_set_selected_elts_to_zero(Rtype, DATAPTR(Rvector),
+	_set_selected_elts_to_zero(Rtype, DATAPTR_RW(Rvector),
 				selection, selection_len, selection_offset);
 	return;
 }
@@ -470,7 +471,7 @@ void _fill_Rvector_subset_with_ones(SEXP Rvector,
 		const int *selection, int selection_len,
 		R_xlen_t selection_offset)
 {
-	_set_selected_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector),
+	_set_selected_elts_to_one(TYPEOF(Rvector), DATAPTR_RW(Rvector),
 				  selection, selection_len, selection_offset);
 	return;
 }
diff --git a/src/SparseArray_aperm.c b/src/SparseArray_aperm.c
index 0bd092e..bbeaf2c 100644
--- a/src/SparseArray_aperm.c
+++ b/src/SparseArray_aperm.c
@@ -721,7 +721,7 @@ static SEXP REC_grow_output_tree(const int *dim, int ndim,
 	const type *nzvals_p = NULL;  /* -Wmaybe-uninitialized */	\
 	type v;								\
 	if (nzvals != R_NilValue) {  /* standard leaf */		\
-		nzvals_p = (const type *) DATAPTR(nzvals);		\
+		nzvals_p = DATAPTR_RO(nzvals);				\
 	} else {  /* lacunar leaf */					\
 		v = type ## 1;						\
 	}								\
diff --git a/src/SparseArray_matrixStats.c b/src/SparseArray_matrixStats.c
index b626553..debacf6 100644
--- a/src/SparseArray_matrixStats.c
+++ b/src/SparseArray_matrixStats.c
@@ -16,6 +16,7 @@
 #include "leaf_utils.h"
 #include "SparseArray_summarization.h"
 
+#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
 #include <string.h>  /* for memcpy() and memset() */
 
 
@@ -272,7 +273,7 @@ SEXP C_colStats_SVT(SEXP x_dim, SEXP x_dimnames, SEXP x_type,
 	int warn = 0;
 	REC_colStats_SVT(x_SVT, x_bg_is_na, INTEGER(x_dim), LENGTH(x_dim),
 			 &summarize_op,
-			 DATAPTR(ans), ans_Rtype,
+			 DATAPTR_RW(ans), ans_Rtype,
 			 out_incs, ans_ndim, pardim,
 			 &warn);
 	if (warn)
@@ -1175,7 +1176,7 @@ SEXP C_rowStats_SVT(SEXP x_dim, SEXP x_dimnames, SEXP x_type,
 		SVT_rowMinsMaxs(x_SVT, x_Rtype, x_bg_is_na,
 			INTEGER(x_dim), LENGTH(x_dim),
 			opcode, narm,
-			DATAPTR(ans), LENGTH(ans), ans_Rtype,
+			DATAPTR_RW(ans), LENGTH(ans), ans_Rtype,
 			out_incs, ans_ndim, nstrata);
 		break;
 	    case SUM_OPCODE:
diff --git a/src/SparseArray_subassignment.c b/src/SparseArray_subassignment.c
index 4cf1c3d..c3b2d5e 100644
--- a/src/SparseArray_subassignment.c
+++ b/src/SparseArray_subassignment.c
@@ -966,13 +966,13 @@ static inline int next_coords0(NindexIterator *Nindex_iter)
 		midx_p++;
 		coords0_p++;
 	}
-	printf("coords0: ");
+	//printf("coords0: ");
 	coords0_p = Nindex_iter->coords0_buf;
 	for (along = Nindex_iter->margin; along < Nindex_iter->ndim; along++) {
-		printf(" %3d", *coords0_p);
+		//printf(" %3d", *coords0_p);
 		coords0_p++;
 	}
-	printf("\n");
+	//printf("\n");
 	return 1;
 }
 
diff --git a/src/SparseVec.h b/src/SparseVec.h
index 894709b..73cd841 100644
--- a/src/SparseVec.h
+++ b/src/SparseVec.h
@@ -5,6 +5,7 @@
 
 #include "Rvector_utils.h"
 
+#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
 #include <limits.h>  /* for INT_MAX */
 
 
@@ -122,7 +123,7 @@ static inline SparseVec toSparseVec(SEXP nzvals, SEXP nzoffs,
 		if (IS_STRSXP_OR_VECSXP(Rtype)) {
 			sv.nzvals = nzvals;
 		} else {
-			sv.nzvals = DATAPTR(nzvals);
+			sv.nzvals = DATAPTR_RW(nzvals);
 		}
 	}
 	sv.nzoffs = INTEGER(nzoffs);
diff --git a/src/leaf_utils.c b/src/leaf_utils.c
index e8066c3..c5ff3aa 100644
--- a/src/leaf_utils.c
+++ b/src/leaf_utils.c
@@ -10,6 +10,7 @@
 #include "SparseVec_subsetting.h"
 #include "SparseVec_subassignment.h"
 
+#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
 #include <string.h>  /* for memcpy() */
 
 
@@ -129,7 +130,7 @@ SEXP _make_leaf_from_two_arrays(SEXPTYPE Rtype,
 			return ans;
 		}
 		ans_nzvals = PROTECT(allocVector(Rtype, nzcount));
-		memcpy(DATAPTR(ans_nzvals), nzvals_p, Rtype_size * nzcount);
+		memcpy(DATAPTR_RW(ans_nzvals), nzvals_p, Rtype_size * nzcount);
 	}
 	SEXP ans = zip_leaf(ans_nzvals, ans_nzoffs, 0);
 	UNPROTECT(2);
@@ -156,7 +157,7 @@ static SEXP make_leaf_from_Rvector_subset(SEXP Rvector,
 
 	if (avoid_copy_if_all_selected &&
 	    selection_offset == 0 && selection_len == XLENGTH(Rvector) &&
-	    ATTRIB(Rvector) == R_NilValue)
+	    !ANY_ATTRIB(Rvector))
 	{
 		/* The full 'Rvector' is selected so can be reused as-is
 		   with no need to copy the selected elements to a new SEXP. */
diff --git a/src/test.c b/src/test.c
index 493538f..2205fa2 100644
--- a/src/test.c
+++ b/src/test.c
@@ -111,6 +111,9 @@ SEXP C_simple_omp_parallel_for_loop(SEXP nloop)
 	for (int i = 0; i < INTEGER(nloop)[0]; i++) {
 #ifdef _OPENMP
 		int thread_num = omp_get_thread_num();
+		/* Can't use Rprintf() here because it's not thread-safe (it
+		   can trigger R's garbage collector which itself is not
+		   thread-safe). */
 		printf("thread_num = %d\n", thread_num);
 #endif
 	}
diff --git a/src/readSparseCSV.c b/src/readSparseCSV.c
index a3d8da0..de1cb95 100644
--- a/src/readSparseCSV.c
+++ b/src/readSparseCSV.c
@@ -11,6 +11,7 @@
 #include "ExtendableJaggedArray.h"
 
 #include <R_ext/Connections.h>
+#include <Rversion.h>
 
 #include <string.h>  /* for memcpy() */
 
@@ -111,7 +112,11 @@ static SEXP dump_env_as_list_or_R_NilValue(SEXP env, int ans_len)
 	is_empty = 1;
 	for (i = 0; i < ans_len; i++) {
 		key = PROTECT(idx0_to_key(i));
+#if R_VERSION < R_Version(4, 6, 0)
 		ans_elt = findVar(install(translateChar(key)), env);
+#else
+		ans_elt = R_getVar(install(translateChar(key)), env, FALSE);
+#endif
 		UNPROTECT(1);
 		if (ans_elt == R_UnboundValue)
 			continue;