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 <liwen...@kylinos.cn> 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); // 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 @@ -264,7 +264,7 @@ SEXP R_read_xys_files(SEXP filenames, SE ptr2xy, i, nrows, verbose); d0 = xys_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/chipbackground.c +++ r-bioc-oligo-1.70.0+ds/src/chipbackground.c @@ -64,8 +64,8 @@ void static get_centroids(int rows, int cols, int grid_dim_rows, int grid_dim_cols, double *centroidx, double *centroidy){ int i,j; - double *cuts_x = (double *)Calloc(grid_dim_rows,double); - double *cuts_y = (double *)Calloc(grid_dim_cols,double); + double *cuts_x = (double *)R_Calloc(grid_dim_rows,double); + double *cuts_y = (double *)R_Calloc(grid_dim_cols,double); for (i = 0; i < grid_dim_rows; i++) cuts_x[i] = ((double)(i+1)*(double)rows)/(double)grid_dim_rows - (double)rows/(2.0*(double)grid_dim_rows); @@ -78,8 +78,8 @@ void static get_centroids(int rows, int centroidy[j*grid_dim_rows + i] = cuts_y[(j*grid_dim_rows + i) % grid_dim_rows]+0.5; } } - Free(cuts_x); - Free(cuts_y); + R_Free(cuts_x); + R_Free(cuts_y); } @@ -178,14 +178,14 @@ void static find_distances(int x, int y, void static compute_weights_individual(int x, int y, int grid_dim, double *centroidx, double *centroidy, double *weights, double smooth){ int i=0; - double *distance = (double *)Calloc(grid_dim,double); + double *distance = (double *)R_Calloc(grid_dim,double); find_distances(x, y, grid_dim, centroidx, centroidy, distance); for (i = 0; i < grid_dim; i++){ weights[i] = 1.0/((double)distance[i] + smooth); } - Free(distance); + R_Free(distance); } /********************************************************************************************* @@ -348,9 +348,9 @@ void static compute_background_quadrant( int lower2pc; int i=0,j=0; - int *nprobes_in_sec = (int *)Calloc(grid_dim,int); - int *cur_n = (int *)Calloc(grid_dim,int); - double **data_by_sector =(double **)Calloc(grid_dim,double *); + int *nprobes_in_sec = (int *)R_Calloc(grid_dim,int); + int *cur_n = (int *)R_Calloc(grid_dim,int); + double **data_by_sector =(double **)R_Calloc(grid_dim,double *); double sumx,sumx2; for (j = 0; j < grid_dim; j++){ @@ -362,7 +362,7 @@ void static compute_background_quadrant( } for (j =0; j < grid_dim; j++){ - data_by_sector[j] = (double *)Calloc(nprobes_in_sec[j],double); + data_by_sector[j] = (double *)R_Calloc(nprobes_in_sec[j],double); } for (j =0; j < grid_dim; j++){ @@ -406,12 +406,12 @@ void static compute_background_quadrant( } for (j =0; j < grid_dim; j++){ - Free(data_by_sector[j]); + R_Free(data_by_sector[j]); } - Free(nprobes_in_sec); - Free(cur_n); - Free(data_by_sector); + R_Free(nprobes_in_sec); + R_Free(cur_n); + R_Free(data_by_sector); } @@ -475,14 +475,14 @@ double static max(double one, double two void static affy_background_adjust(double *probeintensity,int *x, int *y, int nprobes, int nchips, int rows, int cols, int grid_dim){ int i=0,j=0; - int *whichgrid = (int *)Calloc(nprobes,int); - double *bg_q = (double *)Calloc(grid_dim,double); - double *noise_q = (double *)Calloc(grid_dim,double); - double *weights = (double *)Calloc(grid_dim*nprobes,double); - double *centroidx = (double *)Calloc(grid_dim,double); - double *centroidy = (double *)Calloc(grid_dim,double); - int *gridpt_x = (int *)Calloc(((int)(sqrt(grid_dim) -1.0)),int); - int *gridpt_y = (int *)Calloc(((int)(sqrt(grid_dim) -1.0)),int); + int *whichgrid = (int *)R_Calloc(nprobes,int); + double *bg_q = (double *)R_Calloc(grid_dim,double); + double *noise_q = (double *)R_Calloc(grid_dim,double); + double *weights = (double *)R_Calloc(grid_dim*nprobes,double); + double *centroidx = (double *)R_Calloc(grid_dim,double); + double *centroidy = (double *)R_Calloc(grid_dim,double); + int *gridpt_x = (int *)R_Calloc(((int)(sqrt(grid_dim) -1.0)),int); + int *gridpt_y = (int *)R_Calloc(((int)(sqrt(grid_dim) -1.0)),int); get_centroids(rows, cols, (int)sqrt(grid_dim),(int)sqrt(grid_dim), centroidx, centroidy); get_gridpts(rows, cols, grid_dim, gridpt_x, gridpt_y); @@ -499,14 +499,14 @@ void static affy_background_adjust(doubl } } - Free(gridpt_x); - Free(gridpt_y); - Free(centroidx); - Free(centroidy); - Free(weights); - Free(whichgrid); - Free(noise_q); - Free(bg_q); + R_Free(gridpt_x); + R_Free(gridpt_y); + R_Free(centroidx); + R_Free(centroidy); + R_Free(weights); + R_Free(whichgrid); + R_Free(noise_q); + R_Free(bg_q); } --- r-bioc-oligo-1.70.0+ds.orig/src/rma_common.c +++ r-bioc-oligo-1.70.0+ds/src/rma_common.c @@ -59,7 +59,7 @@ int sort_double(const double *a1,const d double median(double *x, int length){ int half; double med; - double *buffer = Calloc(length,double); + double *buffer = R_Calloc(length,double); memcpy(buffer,x,length*sizeof(double)); @@ -81,7 +81,7 @@ double median(double *x, int length){ med = (med + buffer[half])/2.0; } - Free(buffer); + R_Free(buffer); return med; } @@ -101,7 +101,7 @@ double median(double *x, int length){ double median_nocopy(double *x, int length){ int half; double med; - double *buffer = x; //Calloc(length,double); + double *buffer = x; //R_Calloc(length,double); memcpy(buffer,x,length*sizeof(double)); --- r-bioc-oligo-1.70.0+ds.orig/src/trimmed.c +++ r-bioc-oligo-1.70.0+ds/src/trimmed.c @@ -20,7 +20,7 @@ static void trimmed_mean(double *datavec if (classvec[i] == class) n++; - double *buffer=Calloc(n, double); + double *buffer=R_Calloc(n, double); for (i = 0; i < cols; i++) if (classvec[i] == class){ buffer[j]=datavec[i]; @@ -41,13 +41,13 @@ static void trimmed_mean(double *datavec m1[i_ext + (class-1) * rows]=sum; m2[i_ext + (class-1) * rows]=sum2; m3[i_ext + (class-1) * rows]=j; - Free(buffer); + R_Free(buffer); } static void trimmed_stats(double *data, double *m1, double *m2, double *m3, int *class, int rows, int cols, double *trim){ int i, j, n1, n2, n3; - double *datvec=Calloc(cols,double); - int *classvec=Calloc(cols,int); + double *datvec=R_Calloc(cols,double); + int *classvec=R_Calloc(cols,int); for (i=0; i < rows; i++){ n1=0; @@ -76,8 +76,8 @@ static void trimmed_stats(double *data, trimmed_mean(datvec, classvec, 2, trim[0], cols, rows, m1, m2, m3, i); trimmed_mean(datvec, classvec, 3, trim[0], cols, rows, m1, m2, m3, i); } - Free(datvec); - Free(classvec); + R_Free(datvec); + R_Free(classvec); }
