gentoo-overlay/sci-biology/vaal/files/vaal-1.6-gcc47.patch

Fix building with gcc-4.7

https://bugs.gentoo.org/show_bug.cgi?id=423497

Patch written by Kacper Kowalik <xarthisius@gentoo.org>
--- a/src/feudal/MasterVec.h
+++ b/src/feudal/MasterVec.h
@@ -62,20 +62,20 @@
     /// This function is deprecated: Use reserve() instead.
     /// The pool size argument is ignored, anyway.
     MasterVec& Reserve( unsigned long raw_mem_size_ignored, size_type capacity )
-    { reserve(capacity); return *this; }
+    { this->reserve(capacity); return *this; }
 
     /// This function is deprecated:  Use clear().shrink_to_fit().
     MasterVec& destroy() { BaseT::clear(); BaseT::shrink_to_fit(); return *this; }
 
     /// This function is deprecated:  Use push_back().
     MasterVec& push_back_external( T const& val )
-    { push_back(val); return *this; }
+    { this->push_back(val); return *this; }
 
     /// This function is deprecated:  Use push_back().
     MasterVec& push_back_reserve( T const& val,
                                   size_type growthIncr = 0,
                                   float growthFact = 1.3f )
-    { push_back(val,growthFact,growthIncr); return *this; }
+    { this->push_back(val,growthFact,growthIncr); return *this; }
 
     /// This function is deprecated:  Use append().
     MasterVec& Append( MasterVec const& that )
@@ -83,7 +83,7 @@
 
     /// This function is deprecated:  Use append().
     MasterVec& Append( MasterVec const& that, size_type from, size_type to )
-    { append(that.begin(from),that.begin(to)); return *this; }
+    { this->append(that.begin(from),that.begin(to)); return *this; }
 
     MasterVec const& WriteAll( String const& fileName ) const
     { return WriteRange(fileName,0UL,BaseT::size()); return *this; }
@@ -108,7 +108,7 @@
     { if ( !append ) BaseT::clear();
       FeudalFileReader rdr(fileName.c_str());
       size_type siz = rdr.getNElements();
-      reserve(BaseT::size()+siz);
+      this->reserve(BaseT::size()+siz);
       preAlloc(rdr,0,siz);
       for ( size_type iii = 0; iii < siz; ++iii )
         appendFromReader(rdr,iii);
--- a/src/feudal/FeudalControlBlock.cc
+++ b/src/feudal/FeudalControlBlock.cc
@@ -24,6 +24,7 @@
 #include <string.h>
 #include <errno.h>
 #include <iostream>
+#include <unistd.h>
 
 using std::cout;
 using std::endl;
--- a/src/feudal/SerfVec.h
+++ b/src/feudal/SerfVec.h
@@ -83,9 +83,9 @@
     { AssertLe(pos,that.size());
       AssertLe(len,that.size()-pos);
       if ( this != &that )
-      { assign(that.begin(pos),that.begin(pos+len)); }
+      { this->assign(that.begin(pos),that.begin(pos+len)); }
       else
-      { erase(BaseT::begin(),BaseT::begin(pos));
+      { this->erase(BaseT::begin(),BaseT::begin(pos));
         BaseT::resize(len); }
       return *this; }
 
--- a/src/system/ProcBuf.cc
+++ b/src/system/ProcBuf.cc
@@ -195,12 +195,12 @@
 	    Assert(M_internal_put_buffer == NULL);
 	    M_internal_put_buffer = new char_type [DEFAULT_PUT_BUFFER_SIZE];
 	    M_internal_put_buffer_end = M_internal_put_buffer+DEFAULT_PUT_BUFFER_SIZE;
-	    setp(M_internal_put_buffer,
+	    this->setp(M_internal_put_buffer,
 		 M_internal_put_buffer_end);
 	} else if (!flush())
 	    return traits_type::eof();
 	if (!traits_type::eq_int_type(c, traits_type::eof()))
-	    return sputc(c);
+	    return this->sputc(c);
 	else
 	    return traits_type::not_eof(c);
     }
@@ -240,7 +240,7 @@
 	// (which is start of buffer)
 	std::copy_backward(this->eback(), this->egptr(), this->egptr()+1);
 	*(this->gptr()) = traits_type::to_char_type(c);
-	setg(this->eback(), this->gptr(), this->egptr()+1);
+	this->setg(this->eback(), this->gptr(), this->egptr()+1);
         return traits_type::not_eof(c);
     } else
 	return traits_type::eof();
@@ -269,7 +269,7 @@
 	// doing wchars and we write an odd # of bytes?
 	return false;
     } else {
-	setp(this->pbase(), this->epptr());
+	this->setp(this->pbase(), this->epptr());
 	return true;
     }
 }
@@ -283,7 +283,7 @@
 	Assert(M_internal_get_buffer == NULL);
 	M_internal_get_buffer = new char_type[DEFAULT_GET_BUFFER_SIZE];
 	M_internal_get_buffer_end = M_internal_get_buffer + DEFAULT_GET_BUFFER_SIZE;
-	setg(M_internal_get_buffer, M_internal_get_buffer_end, M_internal_get_buffer_end);
+	this->setg(M_internal_get_buffer, M_internal_get_buffer_end, M_internal_get_buffer_end);
     }
     // The "get" pointer should be at the end of the buffer - that's
     // why we need to fill it.
@@ -318,7 +318,7 @@
     //
     // reset the get pointers
     //
-    setg(M_internal_get_buffer, 
+    this->setg(M_internal_get_buffer, 
 	 M_internal_get_buffer, 
 	 M_internal_get_buffer+numusable/sizeof(char_type));
     return true;
--- a/src/system/SysConf.cc
+++ b/src/system/SysConf.cc
@@ -19,6 +19,7 @@
 #include "system/SysConf.h"
 #include "system/Exit.h"
 #include <iostream>
+#include <unistd.h>
 
 namespace
 {
--- a/src/Vec.h
+++ b/src/Vec.h
@@ -261,11 +261,11 @@
 
   template <class U>
   void append( const vec<U>& y ) 
-  {    insert( this->end( ), y.begin( ), y.end( ) );    }
+  {    this->insert( this->end( ), y.begin( ), y.end( ) );    }
   
   void append( const vec<T>& y, size_type i, size_type j ) {
-    if ( j == y.size( ) ) insert( this->end( ), y.begin( ) + i, y.end( ) );
-    else insert( this->end( ), y.begin( ) + i, y.begin( ) + j );   
+    if ( j == y.size( ) ) this->insert( this->end( ), y.begin( ) + i, y.end( ) );
+    else this->insert( this->end( ), y.begin( ) + i, y.begin( ) + j );   
   }
 
   // appends values in y, but only those whose indices are in entries