tribes/guix
1
0
Fork 1
mirror of https://git.savannah.gnu.org/git/guix.git synced 2026-05-08 02:05:54 +02:00
Code Activity

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

Browse Source 
* gnu/packages/patches/r-shortread-0001-ShortRead-1.69.3-Get-rid-of-non-API-calls-to-R.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Record it.
* gnu/packages/bioconductor.scm (r-shortread)[source]: Register patch.

Change-Id: I9fd85076db6a86b25f4389d3226e0fde8a38a3b5
This commit is contained in:
Ricardo Wurmus
2026-04-27 15:00:18 +02:00
parent 8d07dd9ef7
commit de4a5e2b3d
3 changed files with 108 additions and 1 deletions
Download Patch File Download Diff File Expand all files Collapse all files
gnu/local.mk
+1
View File
@@ -2356,6 +2356,7 @@ dist_patch_DATA = \
%D%/packages/patches/r-snpstats-0001-fixed-non-API-except-for-IS_S4_OBJECT.patch \
%D%/packages/patches/r-snpstats-0002-fixed-IS_S4_OBJECT.patch \
%D%/packages/patches/r-sapa-lapack.patch \
%D%/packages/patches/r-shortread-0001-ShortRead-1.69.3-Get-rid-of-non-API-calls-to-R.patch \
%D%/packages/patches/r-sparsearray-r-4.6.0-compat.patch \
%D%/packages/patches/ripperx-missing-file.patch \
%D%/packages/patches/rpcbind-CVE-2017-8779.patch \
gnu/packages/bioconductor.scm
+4 -1
View File
@@ -14027,7 +14027,10 @@ methylation array data. Both the 450k and EPIC array are supported.")
(uri (bioconductor-uri "ShortRead" version))
(sha256
(base32
"16vjfqsj5mjzq8sh8px6qkcq6d9r95vnp77cgqxm80gqrqny9bj2"))))
"16vjfqsj5mjzq8sh8px6qkcq6d9r95vnp77cgqxm80gqrqny9bj2"))
(patches
(search-patches
"r-shortread-0001-ShortRead-1.69.3-Get-rid-of-non-API-calls-to-R.patch"))))
(properties
'((upstream-name . "ShortRead")
(updater-ignored-native-inputs . ("r-hilbertvis"))))
gnu/packages/patches/r-shortread-0001-ShortRead-1.69.3-Get-rid-of-non-API-calls-to-R.patch
+103
View File
@@ -0,0 +1,103 @@
From e39852a54312bbc6ba435848890cc2a7f612357c 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 17:04:19 -0800
Subject: [PATCH] ShortRead 1.69.3: Get rid of non-API calls to R
---
DESCRIPTION | 2 +-
src/call.h | 3 +--
src/io.c | 10 +++++-----
3 files changed, 7 insertions(+), 8 deletions(-)
diff --git a/src/call.h b/src/call.h
index e15bb5e..e72bbd6 100644
--- a/src/call.h
+++ b/src/call.h
@@ -6,8 +6,7 @@ extern "C" {
#endif
#define NEW_CALL(S, T, NAME, ENV, N) \
- PROTECT((S) = (T) = allocList((N))); \
- SET_TYPEOF((T), LANGSXP); \
+ PROTECT((S) = (T) = LCONS(R_NilValue, allocList((N)-1))); \
SETCAR((T), findFun(install((NAME)), (ENV))); \
(T) = CDR((T))
#define CSET_CDR(T, NAME, VALUE) \
diff --git a/src/io.c b/src/io.c
index 25a0111..9cf4bf8 100644
--- a/src/io.c
+++ b/src/io.c
@@ -46,9 +46,9 @@ SEXP write_fastq(SEXP id, SEXP sread, SEXP quality,
SEXP fname, SEXP fmode, SEXP full, SEXP compress,
SEXP max_width)
{
- if (!(IS_S4_OBJECT(id) && strcmp(get_classname(id), "BStringSet") == 0))
+ if (!(Rf_isS4(id) && strcmp(get_classname(id), "BStringSet") == 0))
Rf_error("'%s' must be '%s'", "id", "BStringSet");
- if (!(IS_S4_OBJECT(sread) &&
+ if (!(Rf_isS4(sread) &&
strcmp(get_classname(sread), "DNAStringSet") == 0))
Rf_error("'%s' must be '%s'", "sread", "DNAStringSet");
/* check in R -- C-level R_check_super... is not adequate */
@@ -693,14 +693,14 @@ int _solexa_export_make_id(SEXP result)
*x = INTEGER(VECTOR_ELT(result, SLX_X)),
*y = INTEGER(VECTOR_ELT(result, SLX_Y)), *pairedReadNumber = NULL;
const SEXP
- * run = STRING_PTR(VECTOR_ELT(result, SLX_RUN)),
+ * run = STRING_PTR_RO(VECTOR_ELT(result, SLX_RUN)),
*multiplexIndex = NULL,
- *machine = STRING_PTR(VECTOR_ELT(result, SLX_MACHINE));
+ *machine = STRING_PTR_RO(VECTOR_ELT(result, SLX_MACHINE));
const Rboolean
withMultiplexIndex = R_NilValue != VECTOR_ELT(result, SLX_MULTIPLEX),
withPairedReadNumber = R_NilValue != VECTOR_ELT(result, SLX_PAIRID);
if (withMultiplexIndex)
- multiplexIndex = STRING_PTR(VECTOR_ELT(result, SLX_MULTIPLEX));
+ multiplexIndex = STRING_PTR_RO(VECTOR_ELT(result, SLX_MULTIPLEX));
if (withPairedReadNumber)
pairedReadNumber = INTEGER(VECTOR_ELT(result, SLX_PAIRID));
--
2.52.0
From 2e3368a35e3955a0a92b7f3e2c8dface6709d135 Mon Sep 17 00:00:00 2001
From: vjcitn <stvjc@channing.harvard.edu>
Date: Thu, 16 Apr 2026 16:54:15 +0000
Subject: [PATCH] fixapi
---
src/util.c | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
diff --git a/src/util.c b/src/util.c
index 4a10a90..59c089b 100644
--- a/src/util.c
+++ b/src/util.c
@@ -6,6 +6,14 @@ unsigned char _bDecode(char);
unsigned char _dnaDecode(char);
unsigned char _rnaDecode(char);
+
+#include <Rversion.h>
+
+#if R_VERSION < R_Version(4, 6, 0)
+# define R_getVar(x,y,z) findVar(x,y)
+#endif
+
+
/*
* Encode / decode XString wrappers
*/
@@ -80,7 +88,7 @@ SEXP _get_namespace(const char *pkg)
SEXP _get_strand_levels()
{
SEXP nmspc = PROTECT(_get_namespace("ShortRead"));
- SEXP ans = eval(findVar(install(".STRAND_LEVELS"), nmspc), nmspc);
+ SEXP ans = eval(R_getVar(install(".STRAND_LEVELS"), nmspc, TRUE), nmspc);
UNPROTECT(1);
return ans;
}
--
2.52.0