Fix building with gcc-4.7 wrt #423497 by Diego Elio Pettenò <flameeyes@gentoo.org>, drop -O3 -ggdb from CXXFLAGS

(Portage version: 2.2.0_alpha110/cvs/Linux x86_64)

4 files changed, 166 insertions, 6 deletions

diff --git a/sci-biology/vaal/ChangeLog b/sci-biology/vaal/ChangeLog
index 9cc70847a133..0decdfec329d 100644
--- a/sci-biology/vaal/ChangeLog
+++ b/sci-biology/vaal/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/vaal
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/ChangeLog,v 1.7 2011/02/11 19:50:04 hwoarang Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/ChangeLog,v 1.8 2012/06/25 18:42:57 xarthisius Exp $
+
+  25 Jun 2012; Kacper Kowalik <xarthisius@gentoo.org>
+  +files/vaal-1.6-gcc47.patch, files/vaal-1.6-respect-flags.patch,
+  vaal-1.6.ebuild:
+  Fix building with gcc-4.7 wrt #423497 by Diego Elio Pettenò
+  <flameeyes@gentoo.org>, drop -O3 -ggdb from CXXFLAGS
 
   11 Feb 2011; Markos Chandras <hwoarang@gentoo.org> vaal-1.6.ebuild:
   Stable on amd64 wrt bug #353572
diff --git a/sci-biology/vaal/files/vaal-1.6-gcc47.patch b/sci-biology/vaal/files/vaal-1.6-gcc47.patch
new file mode 100644
index 000000000000..0d80f08d3c21
--- /dev/null
+++ b/sci-biology/vaal/files/vaal-1.6-gcc47.patch
@@ -0,0 +1,153 @@
+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
diff --git a/sci-biology/vaal/files/vaal-1.6-respect-flags.patch b/sci-biology/vaal/files/vaal-1.6-respect-flags.patch
index c17910c2ce6a..2004cc7e23ff 100644
--- a/sci-biology/vaal/files/vaal-1.6-respect-flags.patch
+++ b/sci-biology/vaal/files/vaal-1.6-respect-flags.patch
@@ -6,7 +6,7 @@ diff -dur vaal-33805.orig/configure.ac vaal-33805/configure.ac
  AC_OPENMP_CEHCK
  
 -CXXFLAGS=" -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3  -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote ."
-+CXXFLAGS=" ${CXXFLAGS} -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3  -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote ."
++CXXFLAGS=" ${CXXFLAGS} -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote ."
  
  OS_RELEASE="`uname -r`"
  AC_SUBST(CXXFLAGS)
diff --git a/sci-biology/vaal/vaal-1.6.ebuild b/sci-biology/vaal/vaal-1.6.ebuild
index 7e5d66619bb8..f836a0393ec9 100644
--- a/sci-biology/vaal/vaal-1.6.ebuild
+++ b/sci-biology/vaal/vaal-1.6.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/vaal-1.6.ebuild,v 1.3 2011/02/11 19:50:04 hwoarang Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/vaal-1.6.ebuild,v 1.4 2012/06/25 18:42:57 xarthisius Exp $
 
 EAPI="2"
 
@@ -21,9 +21,10 @@ RDEPEND="${DEPEND}"
 
 PATCHES=(
 	"${FILESDIR}"/${P}-respect-flags.patch
+	"${FILESDIR}"/${P}-gcc47.patch
 )
 
-S="${WORKDIR}/vaal-33805"
+S=${WORKDIR}/vaal-33805
 
 src_prepare() {
 	base_src_prepare