Bug#1103227: [PATCH] Backport for fixing FTBFS error
can you propose a patch based on the upstream commit? Do you have write access to our Salsa repositories? Hi, Charles: I had been test on local chroot, then found that needs another commit on upstream. I start a PR on Salsa repositories, please check it. PR:backport for fixing FTBFS error (!1) · 合并请求 · Debian R Packages Maintainers / r-bioc-grohmm · GitLab <https://salsa.debian.org/r-pkg-team/r-bioc-grohmm/-/merge_requests/1> By the way, this is two commits on upstream bellow: 1.Bioconductor Code: groHMM <https://code.bioconductor.org/browse/groHMM/commit/261791bdd2802badced2ba6dc1f0b07a85df> 2.Bioconductor Code: groHMM <https://code.bioconductor.org/browse/groHMM/commit/5752698373578e1575918a8d4ac71508d296fbc2> Have a nice day, liwenjun
Bug#1103199: [PATCH] Fix for FTBFS with R 4.5.0
I tested an upgrade locally, but it gets convoluted with the Bioconductor transition that we can not do during the Freeze, so let's go the patch way. Hi Charles, Do you need me start a PR to Salsa repositories? I would like to help you about this. Have a nice day, Li Wenjun
Bug#1103201: [PATCH] Fix for FTBFS with R 4.5.0
Package: src:r-cran-genabel Version: 1.8-0-7 Severity: serious Tags: ftbfs trixie sid Dear maintainer: Hi, I'm summitting a patch for fixing this FTBFS problem while building with R 4.5.0 on Debian sid,trixie. My patch Fix-FTBFS-error.patch replace Calloc() and Free() with R_Calloc() and R_Free(), accoding to the R-project's NEWS(R: R News <https://cran.r-project.org/doc/manuals/r-release/NEWS.html>) And by the way, Please help me for uploading this patch to upstream if you think it's necessary. Best regards, liwenjun Description: Fix FTBFS error on R 4.5.0 This patch replace Calloc() and Free() to R_Calloc() R_Free() for fixing FTBFS errors on DEBIAN sid, trixy. Accoding to the R-project's NEWS.(https://cran.r-project.org/doc/manuals/r-release/NEWS.html). R 4.5.0 has been changed those funtions. Author: liwenjun Origin: other, None Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1103201 Last-Update: 2025-04-16 --- r-cran-genabel-1.8-0.orig/src/fexact.c +++ r-cran-genabel-1.8-0/src/fexact.c @@ -178,7 +178,7 @@ fexact(int *nrow, int *ncol, int *table, //Maksim Struchalin, 14-June-2010: // In case of use R_alloc memory is freed only when routine .C finishes. We have got memorry leak in case when we call fexat in a loop "inside" ".C" . //equiv = (double *) R_alloc(iwkmax / 2, sizeof(double)); - equiv = (double *) Calloc(iwkmax / 2, double); // call Free(equiv) at the end. + equiv = (double *) R_Calloc(iwkmax / 2, double); // call R_Free(equiv) at the end. //_ @@ -302,7 +302,7 @@ fexact(int *nrow, int *ncol, int *table, dwrk + irwk); - Free(equiv); + R_Free(equiv); return; }
Bug#1103227: [reply ] r-bioc-grohmm: FTBFS: DecayAlgorithm.c:94:15: error: expected identifier or '(' before 'false'
Package: src:r-bioc-grohmm Version: 1.40.3-2 Severity: serious Tags: ftbfs trixie sid Dear maintainer: I founded a commit on the upstream for fixing this problem: Bioconductor Code: groHMM <https://code.bioconductor.org/browse/groHMM/commit/261791bdd2802badced2ba6dc1f0b07a85df> Or you might prefer to upgrade the major version to their lastest release 1.42.0. Bioconductor Code: groHMM <https://code.bioconductor.org/browse/groHMM/RELEASE_3_21/> Best Regards, liwenjun
Bug#1103199: [PATCH] Fix for FTBFS with R 4.5.0
Package: src:r-bioc-oligo
Version: 1.70.0+ds-2
Severity: serious
Tags: ftbfs trixie sid
Dear maintainer:
Hi, I'm summitting a patch for fixing this FTBFS problem while building with R
4.5.0 on Debian sid,trixie.
My patch Fix-FTBFS-error.patch replace Calloc(),Realloc(),Free() to
R_Calloc(),R_Realloc(),R_Free(), accoding to the R-project's NEWS(R: R News
<https://cran.r-project.org/doc/manuals/r-release/NEWS.html>)
And by the way, Please help me for uploading this patch to upstream if you
think it's necessary.
Best regards,
liwenjun
Description: Fix FTBFS error on R 4.5.0
This patch replace Calloc(),Realloc() and Free() to R_Calloc(), R_Realloc()
and R_Free()
for fixing FTBFS errors on DEBIAN sid, trixy.
Accoding to the R-project's
NEWS.(https://cran.r-project.org/doc/manuals/r-release/NEWS.html).
R 4.5.0 has been changed those funtions.
Author: liwenjun
Origin: other, None
Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1103199
Last-Update: 2025-04-16
--- r-bioc-oligo-1.70.0+ds.orig/src/ParserGzXYS.c
+++ r-bioc-oligo-1.70.0+ds/src/ParserGzXYS.c
@@ -59,7 +59,7 @@ static char *gzxys_header_field(const ch
error("Can't find \'%s\' field. %s corrupted?", field, currentFile);
result = strtok(result, "=");
result = strtok(NULL, "\t");
- final = Calloc(strlen(result)+1, char);
+ final = R_Calloc(strlen(result)+1, char);
strcpy(final, result);
return final;
}
@@ -144,15 +144,15 @@ SEXP R_read_gzxys_files(SEXP filenames,
for (i = 1; i < nfiles; i++){
d1 = gzxys_header_field(CHAR(STRING_ELT(filenames, i)), "designname=");
if(strcasecmp(d1, d0) != 0){
- Free(d0);
- Free(d1);
+ R_Free(d0);
+ R_Free(d1);
error("\'%s\' and \'%s\' use different designs.\n",
CHAR(STRING_ELT(filenames, 0)),
CHAR(STRING_ELT(filenames, i)));
}
- Free(d1); // Missed: 12/02/09
+ R_Free(d1); // Missed: 12/02/09
}
- Free(d0);
+ R_Free(d0);
if (verbose) Rprintf("Done.\n");
// Allocating memory in R
@@ -170,7 +170,7 @@ SEXP R_read_gzxys_files(SEXP filenames,
ptr2xy, i, nrows, verbose);
d0 = gzxys_header_field(CHAR(STRING_ELT(filenames, i)), "date=");
SET_STRING_ELT(dates, i, mkChar(d0));
-Free(d0);
+R_Free(d0);
}
PROTECT(output = allocVector(VECSXP, 3));
--- r-bioc-oligo-1.70.0+ds.orig/src/ParserXYS.c
+++ r-bioc-oligo-1.70.0+ds/src/ParserXYS.c
@@ -74,10 +74,10 @@ static void tokenizer(tokenset *header,
int i;
i = header->n;
header->n++;
- header->key = Realloc(header->key, header->n, char*);
- header->value = Realloc(header->value, header->n, char*);
- header->key[i] = Calloc(strlen(key)+1, char);
- header->value[i] = Calloc(strlen(value)+1, char);
+ header->key = R_Realloc(header->key, header->n, char*);
+ header->value = R_Realloc(header->value, header->n, char*);
+ header->key[i] = R_Calloc(strlen(key)+1, char);
+ header->value[i] = R_Calloc(strlen(value)+1, char);
strcpy(header->key[i], key);
strcpy(header->value[i], value);
}
@@ -90,12 +90,12 @@ static void tokenizer(tokenset *header,
static void untokenizer(tokenset *header){
int i;
for (i=0; i < header->n; i++){
-Free(header->key[i]);
-Free(header->value[i]);
+R_Free(header->key[i]);
+R_Free(header->value[i]);
}
- Free(header->key);
- Free(header->value);
- Free(header);
+ R_Free(header->key);
+ R_Free(header->value);
+ R_Free(header);
}
/***
@@ -105,7 +105,7 @@ static void untokenizer(tokenset *header
***/
static tokenset *buffer2tokenset(char *buffer){
- tokenset *header = Calloc(1, tokenset);
+ tokenset *header = R_Calloc(1, tokenset);
char *eq, *key, *value;
header->n = 0;
header->key = NULL;
@@ -157,7 +157,7 @@ static char *xys_header_field(const char
error("Can't find \'%s\' field. %s corrupted?", field, currentFile);
result = strtok(result, "=");
result = strtok(NULL, "\t");
- final = Calloc(strlen(result)+1, char);
+ final = R_Calloc(strlen(result)+1, char);
strcpy(final, result);
return final;
}
@@ -238,15 +238,15 @@ SEXP R_read_xys_files(SEXP filenames, SE
for (i = 1; i < nfiles; i++){
d1 = xys_header_field(CHAR(STRING_ELT(filenames, i)), "designname=");
if(strcasecmp(d1, d0) != 0){
- Free(d0);
- Free(d1);
+ R_Free(d0);
+ R_Free(d1);
error("\'%s\' and \'%s\' use different designs.\n",
CHAR(STRING_ELT(filenames, 0)),
CHAR(STRING_ELT(filenames, i)));
}
- Free(d1); /
Bug#1103217: [PATCH] Fix for FTBFS with r-base-dev=4.5.0-1
Package: src:r-bioc-affxparser
Version: 1.78.0-2
Severity: serious
Tags: ftbfs trixie sid
Dear maintainer:
Hi, I'm summitting a patch for fixing this FTBFS problem while building with
r-base-dev=4.5.0-1 on Debian sid,trixie.
My patch Fix-FTBFS.patch replace Calloc() and Free() with R_Calloc() and R_Free(),
accoding to the R-project's NEWS(R: R News
<https://cran.r-project.org/doc/manuals/r-release/NEWS.html>)
And by the way, Please help me for uploading this patch to upstream if you
think it's necessary.
Best regards,
liwenjun
Description: Fix FTBFS error on r-base-dev=4.5.0-1
This patch replace Calloc and Free to R_Calloc R_Free for fixing FTBFS errors
on DEBIAN sid, trixy.
Accoding to the R-project's
NEWS.(https://cran.r-project.org/doc/manuals/r-release/NEWS.html).
Latest version(4.5.0) has been changed those funtions to R_xxx.
Author: liwenjun
Origin: other, None
Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1103217
Last-Update: 2025-04-16
--- r-bioc-affxparser-1.78.0.orig/src/R_affx_bpmap_parser.cpp
+++ r-bioc-affxparser-1.78.0/src/R_affx_bpmap_parser.cpp
@@ -90,41 +90,41 @@ extern "C" {
SET_STRING_ELT(seqInfoNames, kk, mkChar("name"));
str =
seq.GetName();
str_length =
str.size();
- cstr =
Calloc(str_length+1, char);
+ cstr =
R_Calloc(str_length+1, char);
strncpy(cstr,
str.c_str(), str_length);
cstr[str_length] = '\0';
SET_VECTOR_ELT(seqInfo, kk++, ScalarString(mkChar(cstr)));
-Free(cstr);
+R_Free(cstr);
SET_STRING_ELT(seqInfoNames, kk, mkChar("groupname"));
str =
seq.GroupName();
str_length =
str.size();
- cstr =
Calloc(str_length+1, char);
+ cstr =
R_Calloc(str_length+1, char);
strncpy(cstr,
str.c_str(), str_length);
cstr[str_length] = '\0';
SET_VECTOR_ELT(seqInfo, kk++,
ScalarString(mkChar(cstr)));
-Free(cstr);
+R_Free(cstr);
SET_STRING_ELT(seqInfoNames, kk, mkChar("fullname"));
str =
seq.FullName();
str_length =
str.size();
- cstr =
Calloc(str_length+1, char);
+ cstr =
R_Calloc(str_length+1, char);
strncpy(cstr,
str.c_str(), str_length);
cstr[str_length] = '\0';
SET_VECTOR_ELT(seqInfo, kk++,
ScalarString(mkChar(cstr)));
-Free(cstr);
+R_Free(cstr);
SET_STRING_ELT(seqInfoNames, kk, mkChar("version"));
str =
seq.GetSeqVersion();
str_length =
str.size();
- cstr =
Calloc(str_length+1, char);
+ cstr =
R_Calloc(str_length+1, char);
strncpy(cstr,
str.c_str(), str_length);
cstr[str_length] = '\0';
SET_VECTOR_ELT(seqInfo, kk++,
ScalarString(mkChar(cstr)));
-Free(cstr);
+R_Free(cstr);
SET_STRING_ELT(seqInfoNames, kk, mkChar("mapping"));
if(seq.GetProbeMapping() == 0)
@@ -154,19 +154,19 @@ extern "C" {
{
str = seq.GetParameter(j).Tag;
str_length = str.size();
-
