diff -Nru orig/oligo/src/ParserGzXYS.c patched/oligo/src/ParserGzXYS.c
--- orig/oligo/src/ParserGzXYS.c	2024-10-24 01:25:08.000000000 +0200
+++ patched/oligo/src/ParserGzXYS.c	2025-03-04 12:54:16.353330400 +0100
@@ -59,7 +59,7 @@
     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 @@
     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 @@
 		 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));
diff -Nru orig/oligo/src/ParserXYS.c patched/oligo/src/ParserXYS.c
--- orig/oligo/src/ParserXYS.c	2024-10-24 01:25:08.000000000 +0200
+++ patched/oligo/src/ParserXYS.c	2025-03-04 12:54:16.353330400 +0100
@@ -5,7 +5,7 @@
 **  
 **  I) HISTORY
 **
-**  Dec   02, 2009 - Fixed memory leak (forgotten Free(d0))
+**  Dec   02, 2009 - Fixed memory leak (forgotten R_Free(d0))
 **  July  30, 2009 - Removed 'dimnamesout' from
 **                   the variable definition in
 **                   R_read_xys_files
@@ -74,10 +74,10 @@
   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 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 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 @@
     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 @@
     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 @@
 		 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));
diff -Nru orig/oligo/src/chipbackground.c patched/oligo/src/chipbackground.c
--- orig/oligo/src/chipbackground.c	2024-10-24 01:25:08.000000000 +0200
+++ patched/oligo/src/chipbackground.c	2025-03-04 12:54:16.369351400 +0100
@@ -32,7 +32,7 @@
  **
  ** Mar 10, 2003 - Check indexing, see that it roams on x =1..ncol  and y=1..nrow. Note
  **                that affy cdf files are on x=0.. ncol-1  and y=0..nrow-1
- ** Mar 6, 2004 - All mallocs/free are now Calloc/Free
+ ** Mar 6, 2004 - All mallocs/free are now R_Calloc/R_Free
  ** Jun 7, 2006 - change distance calculations to be computed using floating point
  **               rather than integer arithmetic.
  **
@@ -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 @@
       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 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 @@
 
   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 @@
   }
   
   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 @@
   }
  
   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 @@
 
 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 @@
     }
   }
 
-  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);
 }
 
 
diff -Nru orig/oligo/src/rma2.c patched/oligo/src/rma2.c
--- orig/oligo/src/rma2.c	2024-10-24 01:25:08.000000000 +0200
+++ patched/oligo/src/rma2.c	2025-03-04 12:54:16.384555600 +0100
@@ -82,8 +82,8 @@
  **               verbage when running rma
  ** Feb 25, 2003 - try to reduce or eliminate compiler warnings (from gcc -Wall) 
  ** Apr 4, 2003 - fix up so that the number of probes in a probeset is allowed to be more dynamic
- ** Dec 9, 2003 - fix a bug in do_RMA (max_nrows in Calloc)
- ** Mar 6, 2004 - all mallocs/frees are now Calloc/Frees. Removed
+ ** Dec 9, 2003 - fix a bug in do_RMA (max_nrows in R_Calloc)
+ ** Mar 6, 2004 - all mallocs/frees are now R_Calloc/R_Frees. Removed
  **               the function R_median_polish
  ** Jul 27, 2004 - fix a small memory leak
  ** Aug 4, 2004 - move the "Background correcting" message. 
diff -Nru orig/oligo/src/rma_common.c patched/oligo/src/rma_common.c
--- orig/oligo/src/rma_common.c	2024-10-24 01:25:08.000000000 +0200
+++ patched/oligo/src/rma_common.c	2025-03-04 12:54:16.400783600 +0100
@@ -59,7 +59,7 @@
 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 @@
     med = (med + buffer[half])/2.0;
   }
   
-  Free(buffer);
+  R_Free(buffer);
   return med;
 }
 
@@ -101,7 +101,7 @@
 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));
 
diff -Nru orig/oligo/src/trimmed.c patched/oligo/src/trimmed.c
--- orig/oligo/src/trimmed.c	2024-10-24 01:25:08.000000000 +0200
+++ patched/oligo/src/trimmed.c	2025-03-04 12:54:16.400783600 +0100
@@ -20,7 +20,7 @@
     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 @@
   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 @@
     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);
 }