Changes to make package compatible with R 3.2

DESCRIPTION

@@ -1,29 +1,35 @@
 Package: ChIPKernels
 Type: Package
 Title: String kernels for ChIP-Seq
-Version: 1.0
-Date: 2013-06-21
+Version: 1.1
+Date: 2015-05-25
 Author: Manu Setty
 Maintainer: Manu Setty <[email protected]>
 Depends:
+    IRanges,
+    XVector,
     Biostrings,
     BSgenome,
     gtools,
     GenomicRanges,
     sfsmisc,
     parallel,
     kernlab,
-    Matrix
+    Matrix,
+    S4Vectors
 Imports:
+    IRanges,
+    XVector,
     graphics,
     methods,
     stats,
     utils,
     BiocGenerics,
     IRanges,
     Biostrings, 
-    XVector
-LinkingTo: IRanges, Biostrings, XVector
+    XVector,
+    S4Vectors
+LinkingTo: IRanges, Biostrings, XVector, S4Vectors
 Description: Collection of methods for building different string kernels used
     for ChIP-Seq
 License: GPL (>= 2)

src/hamming_distance.c

@@ -1,38 +1,39 @@
-
+#include <Rdefines.h>
 #include "Biostrings_interface.h"
 
+
 /************************************************************************
  Adding code for y (Hamming distance)
 
 *******************************************************/
-static int nmismatch_at_Pshift_fixedPfixedS(const cachedCharSeq *P,
-				     const cachedCharSeq *S, int Pshift, int max_nmis)
+static int nmismatch_at_Pshift_fixedPfixedS(const Chars_holder *P,
+             const Chars_holder *S, int Pshift, int max_nmis)
 {
-	int nmis, i, j;
-	const char *p, *s;
-
-	nmis = 0;
-	for (i = 0, j = Pshift, p = P->seq, s = S->seq + Pshift;
-	     i < P->length;
-	     i++, j++, p++, s++)
-	{
-		if (j >= 0 && j < S->length && *p == *s)
-			continue;
-		if (nmis++ >= max_nmis)
-			break;
-	}
-	return nmis;
+  int nmis, i, j;
+  const char *p, *s;
+
+  nmis = 0;
+  for (i = 0, j = Pshift, p = P->ptr, s = S->ptr + Pshift;
+       i < P->length;
+       i++, j++, p++, s++)
+  {
+    if (j >= 0 && j < S->length && *p == *s)
+      continue;
+    if (nmis++ >= max_nmis)
+      break;
+  }
+  return nmis;
 }
 
 
-static int nmismatch_at_Pshift_fixedPnonfixedS(const cachedCharSeq *P,
-    const cachedCharSeq *S, int Pshift, int max_nmis)
+static int nmismatch_at_Pshift_fixedPnonfixedS(const Chars_holder *P,
+    const Chars_holder *S, int Pshift, int max_nmis)
 {
   int nmis, i, j;
   const char *p, *s;
 
   nmis = 0;
-  for (i = 0, j = Pshift, p = P->seq, s = S->seq + Pshift;
+  for (i = 0, j = Pshift, p = P->ptr, s = S->ptr + Pshift;
        i < P->length;
        i++, j++, p++, s++)
   {
@@ -51,8 +52,8 @@ SEXP XStringSet_dist_hamming_xy (SEXP x, SEXP y, SEXP max_nmis, SEXP fixed)
 
   static int block_size = 250000;
 
-  cachedCharSeq x_j, y_i;
-  cachedXStringSet X, Y;
+  Chars_holder x_j, y_i;
+  XStringSet_holder X, Y;
   int X_length, Y_length, i, j, val, index, prev_index=-1;
   SEXP ans;
   int *ans_elt;
@@ -66,45 +67,45 @@ SEXP XStringSet_dist_hamming_xy (SEXP x, SEXP y, SEXP max_nmis, SEXP fixed)
   int *accumulator = (int *)Calloc (block_size, int);
   int acc_count = 0;
 
-  X = cache_XStringSet(x);
-  Y = cache_XStringSet(y);
+  X = hold_XStringSet(x);
+  Y = hold_XStringSet(y);
 
-  X_length = get_cachedXStringSet_length(&X);
-  Y_length = get_cachedXStringSet_length(&Y);
-  x_j = get_cachedXStringSet_elt(&X, 0);
+  X_length = get_length_from_XStringSet_holder(&X);
+  Y_length = get_length_from_XStringSet_holder(&Y);
+  x_j = get_elt_from_XStringSet_holder(&X, 0);
 
   for (i = 0; i < Y_length; i++) {
 
-    y_i = get_cachedXStringSet_elt(&Y, i);
+    y_i = get_elt_from_XStringSet_holder(&Y, i);
     for (j = 0; j < X_length; j++) {
 
       // Reallocate memory if necessary
       if (acc_count % block_size >= block_size - 3) {
-	index = (int)ceil (acc_count/block_size);
-	if (index != prev_index) {
-	  accumulator = (int *)Realloc(accumulator, (index + 2) * block_size, int);
-	  prev_index = index;
-	}
+  index = (int)ceil (acc_count/block_size);
+  if (index != prev_index) {
+    accumulator = (int *)Realloc(accumulator, (index + 2) * block_size, int);
+    prev_index = index;
+  }
 
       }
 
       if (y_i.length != x_j.length) {
-	Free (accumulator);
-	error("Hamming distance requires equal length strings");
+  Free (accumulator);
+  error("Hamming distance requires equal length strings");
       }
 
       // Determine score
-      x_j = get_cachedXStringSet_elt(&X, j);
+      x_j = get_elt_from_XStringSet_holder(&X, j);
       if (fix)
         val = nmismatch_at_Pshift_fixedPfixedS (&y_i, &x_j, 0, max_nmis0);
       else
         val = nmismatch_at_Pshift_fixedPnonfixedS (&x_j, &y_i, 0, max_nmis0);
 
       // Accumulate only if distance > 0
       if (val <= max_nmis0 ) {
-	accumulator[acc_count++] = j + 1;
-	accumulator[acc_count++] = i + 1;
-	accumulator[acc_count++] = val;
+  accumulator[acc_count++] = j + 1;
+  accumulator[acc_count++] = i + 1;
+  accumulator[acc_count++] = val;
       }
     }