From 2c93f5e18055126bfb229edb6b9272167eeaa133 Mon Sep 17 00:00:00 2001
From: Peter Kharchenko <peter.kharchenko@gmail.com>
Date: Thu, 2 Jun 2016 04:34:35 -0400
Subject: [PATCH] fixes for R 3.3.0

---
 DESCRIPTION        |  4 ++--
 src/bed2vector.cpp |  4 ++--
 src/maqread.cpp    |  4 ++--
 src/peaks.cpp      | 20 +++++++++++---------
 src/wdl.cpp        |  6 ++++--
 5 files changed, 21 insertions(+), 17 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a3e1deb..46e9a94 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: spp
 Type: Package
 Title: some description
-Version: 1.13
-Date: 2015-08-21
+Version: 1.14
+Date: 2016-06-02
 Author: Peter K
 Depends: caTools
 Imports: Rsamtools
diff --git a/src/bed2vector.cpp b/src/bed2vector.cpp
index 8b242b3..63e9499 100644
--- a/src/bed2vector.cpp
+++ b/src/bed2vector.cpp
@@ -17,8 +17,8 @@
 #endif 
 
 extern "C" {
-#include "R.h"
-#include "Rmath.h"
+//#include "R.h"
+//#include "Rmath.h"
 #include "Rinternals.h"
 #include "Rdefines.h"
   // for getline
diff --git a/src/maqread.cpp b/src/maqread.cpp
index 2c1334a..896068f 100644
--- a/src/maqread.cpp
+++ b/src/maqread.cpp
@@ -12,8 +12,8 @@
 #include <zlib.h>
 
 extern "C" {
-#include "R.h"
-#include "Rmath.h"
+//#include "R.h"
+//#include "Rmath.h"
 #include "Rinternals.h"
 #include "Rdefines.h"
 #include "maqmap.h"
diff --git a/src/peaks.cpp b/src/peaks.cpp
index ace6855..37770d5 100644
--- a/src/peaks.cpp
+++ b/src/peaks.cpp
@@ -3,10 +3,12 @@
 #include <iostream>
 #include <string>
 #include <set>
+#include <cmath>
+#include <cstdlib>
 
 extern "C" {
-#include "R.h"
-#include "Rmath.h"
+//#include "R.h"
+//#include "Rmath.h"
 #include "Rinternals.h"
 #include "Rdefines.h"
 }
@@ -108,14 +110,14 @@ extern "C" {
     
     for(int i=0;i<nd;i++) {
       // increment k until pos[k]+size>=d[i]
-      while((abs(pos[k])+size) < d[i]) { k++; if(k==npos) { break; };
+      while((std::abs(pos[k])+size) < d[i]) { k++; if(k==npos) { break; };
 #ifdef DEBUG  
 	Rprintf("advancing k to %d\n",k);
 #endif
       }
       if(k==npos) { break; };
       // increment i until d[i]>=pos[k]-size
-      while((abs(pos[k])-size) > d[i]) { i++; if(i==nd) { break; }
+      while((std::abs(pos[k])-size) > d[i]) { i++; if(i==nd) { break; }
 #ifdef DEBUG  
 	Rprintf("advancing i to %d\n",i);
 #endif
@@ -124,14 +126,14 @@ extern "C" {
 
 
       int l=k;
-      while((l<npos) && ((abs(pos[l])-size) <= d[i])) { l++; 
+      while((l<npos) && ((std::abs(pos[l])-size) <= d[i])) { l++; 
 #ifdef DEBUG  
 	Rprintf("advancing l to %d\n",l);
 #endif
       }
       for(int j=k;j<l;j++) {
-	int pd=d[i]-abs(pos[j]);
-	if(abs(pd)<=size) {
+	int pd=d[i]-std::abs(pos[j]);
+	if(std::abs(pd)<=size) {
 	  // record
 	  if(pos[j]>0) {
 	    x.push_back(pd);
@@ -698,9 +700,9 @@ extern "C" {
       // update flags
       int f=flags[i];
       if(f>0) {
-	s[abs(f)-1]++;
+	s[std::abs(f)-1]++;
       } else {
-	s[abs(f)-1]--;
+	s[std::abs(f)-1]--;
       }
       
       if(max_val!=0 && val[i]*max_val > mval*max_val) { mval=val[i]; }
diff --git a/src/wdl.cpp b/src/wdl.cpp
index 02a2f31..18a2258 100644
--- a/src/wdl.cpp
+++ b/src/wdl.cpp
@@ -3,10 +3,12 @@
 #include <iostream>
 #include <string>
 #include <set>
+#include <cmath>
+#include <cstdlib>
 
 extern "C" {
-#include "R.h"
-#include "Rmath.h"
+//#include "R.h"
+//#include "Rmath.h"
 #include "Rinternals.h"
 #include "Rdefines.h"
 }