GCC 3.4 fix

Package-Manager: portage-2.0.51-r14

4 files changed, 200 insertions, 4 deletions

diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog
index 3850740444be..233cc1793ebe 100644
--- a/sci-biology/staden/ChangeLog
+++ b/sci-biology/staden/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/staden
 # Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/staden/ChangeLog,v 1.8 2005/01/18 00:18:29 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/staden/ChangeLog,v 1.9 2005/01/25 04:19:24 ribosome Exp $
+
+  24 Jan 2005; Olivier Fisette <ribosome@gentoo.org>
+  +files/staden-1.5.3-mutlib-gcc-3.4.patch, staden-1.5.3.ebuild:
+  Fixed GCC 3.4 oddity.
 
   17 Jan 2005; Olivier Fisette <ribosome@gentoo.org>
   +files/staden-1.5.3-mutscan.patch, +files/staden-1.5.3-prefinish.patch,
diff --git a/sci-biology/staden/Manifest b/sci-biology/staden/Manifest
index 92a85cc24430..74ea884017d4 100644
--- a/sci-biology/staden/Manifest
+++ b/sci-biology/staden/Manifest
@@ -1,6 +1,6 @@
-MD5 269f8f498bc1c0fb2ec9d33bd2ee7623 staden-1.5.3.ebuild 10023
+MD5 35eac01b4e2df807dff698c633982530 staden-1.5.3.ebuild 10069
 MD5 fe19fbd7368ca77e37fab8ee461dddda staden-1.4.1-r7.ebuild 9894
-MD5 104405704662a5eaaef1121e34bfd1c1 ChangeLog 3786
+MD5 7abc1ac30ae08fd3ed6f23aaddf2adae ChangeLog 3929
 MD5 f189a3c4ff5ae55bcee4f8ed0ace5d20 metadata.xml 254
 MD5 6ce4d77a48d0377a1ada09f1990fb2af files/staden-1.5.3-text_utils.patch 478
 MD5 e908bf4692dd3494ec22f07db2e7a9f5 files/staden-1.4.1-env 225
@@ -12,6 +12,7 @@ MD5 2d495d394e31807f84859f854024b3fc files/staden-1.5.3-mutscan.patch 330
 MD5 8650f58c55b83838846447c89543255d files/staden-1.4.1-getopt.patch 375
 MD5 690ec96f38a668c6cda216d7a3960ecf files/staden-1.5.3-tracediff.patch 334
 MD5 0857e0bf79953bfa46b1224f6218701a files/staden-1.5.3-top.patch 230
+MD5 82a31125cf882d95d15578040add39c3 files/staden-1.5.3-mutlib-gcc-3.4.patch 5460
 MD5 7717f77ecd800d0b3049974db3fcd0a9 files/staden-1.4.1-prefinish.patch 362
 MD5 daf40c222b80ffc48d9a2ac2544ab631 files/staden-1.5.3-getopt.patch 367
 MD5 9f05ecafdd38d17d8dd40ff581dda1a2 files/staden-1.5.3-prefinish.patch 362
diff --git a/sci-biology/staden/files/staden-1.5.3-mutlib-gcc-3.4.patch b/sci-biology/staden/files/staden-1.5.3-mutlib-gcc-3.4.patch
new file mode 100644
index 000000000000..1d33096e3d0f
--- /dev/null
+++ b/sci-biology/staden/files/staden-1.5.3-mutlib-gcc-3.4.patch
@@ -0,0 +1,190 @@
+--- src/mutlib/array.hpp.old	2004-11-09 04:53:27.000000000 -0500
++++ src/mutlib/array.hpp	2005-01-24 21:59:12.639686328 -0500
+@@ -316,12 +316,12 @@
+ template <typename T>
+ double NumericArray<T>::Mean() const
+ {
+-   assert(m_pArray != NULL);
++   assert(this->m_pArray != NULL);
+    double acc = 0.0;
+-   for( int n=m_nLowerLimit; n<=m_nUpperLimit; n++ )
+-      acc += m_pArray[n];
+-   return (m_nUpperLimit-m_nLowerLimit+1)
+-     ? acc / (m_nUpperLimit-m_nLowerLimit+1)
++   for( int n=this->m_nLowerLimit; n<=this->m_nUpperLimit; n++ )
++      acc += this->m_pArray[n];
++   return (this->m_nUpperLimit - this->m_nLowerLimit+1)
++     ? acc / (this->m_nUpperLimit - this->m_nLowerLimit+1)
+      : 0;
+ }
+ 
+@@ -334,18 +334,18 @@
+ template <typename T>
+ double NumericArray<T>::Variance( double* nMean ) const
+ {
+-   assert(m_pArray != NULL);
++   assert(this->m_pArray != NULL);
+    double tmp;
+    double acc  = 0.0;
+    double mean = nMean ? *nMean : Mean();
+-   for( int n=m_nLowerLimit; n<=m_nUpperLimit; n++ )
++   for( int n=this->m_nLowerLimit; n<=this->m_nUpperLimit; n++ )
+    {
+-      tmp  = double(m_pArray[n]) - mean;
++      tmp  = double(this->m_pArray[n]) - mean;
+       tmp *= tmp;
+       acc += tmp;
+    }
+-   assert(m_nUpperLimit-m_nLowerLimit!=0);
+-   return acc / static_cast<double>(m_nUpperLimit-m_nLowerLimit);
++   assert(this->m_nUpperLimit - this->m_nLowerLimit!=0);
++   return acc / static_cast<double>(this->m_nUpperLimit - this->m_nLowerLimit);
+ }
+ 
+ 
+@@ -358,10 +358,10 @@
+ T NumericArray<T>::Min() const
+ {
+    T minval = std::numeric_limits<T>::max();
+-   for( int n=m_nLowerLimit; n<=m_nUpperLimit; n++ )
++   for( int n=this->m_nLowerLimit; n<=this->m_nUpperLimit; n++ )
+    {
+-      if( m_pArray[n] < minval )
+-         minval = m_pArray[n];
++      if( this->m_pArray[n] < minval )
++         minval = this->m_pArray[n];
+    }
+    return minval;
+ }
+@@ -376,10 +376,10 @@
+ T NumericArray<T>::Max() const
+ {
+    T maxval = std::numeric_limits<T>::min();
+-   for( int n=m_nLowerLimit; n<=m_nUpperLimit; n++ )
++   for( int n=this->m_nLowerLimit; n<=this->m_nUpperLimit; n++ )
+    {
+-      if( m_pArray[n] > maxval )
+-         maxval = m_pArray[n];
++      if( this->m_pArray[n] > maxval )
++         maxval = this->m_pArray[n];
+    }
+    return maxval;
+ }
+@@ -392,14 +392,14 @@
+    // Linear interpolation between two points using equation y = mx + c
+    assert(x1<x2);
+    assert(x1>=0);
+-   assert(x2<m_nLength);
++   assert(x2<this->m_nLength);
+    if( x2 > x1 )
+    {
+       int    points = x2 - x1;
+-      T      c      = m_pArray[x1];
+-      double m      = static_cast<double>(m_pArray[x2] - m_pArray[x1]) / static_cast<double>(points);
++      T      c      = this->m_pArray[x1];
++      double m      = static_cast<double>(this->m_pArray[x2] - this->m_pArray[x1]) / static_cast<double>(points);
+       for( int x=0; x<points; x++, x1++ )
+-         m_pArray[x1] = static_cast<T>( m*x + c );
++	  this->m_pArray[x1] = static_cast<T>( m*x + c );
+   }
+ }
+ 
+@@ -436,8 +436,8 @@
+ bool DNAArray<CharT>::IsACGT( int nBasePos ) const
+ {
+     assert(nBasePos>=0);
+-    assert(nBasePos<m_nLength);
+-    switch( m_pArray[nBasePos] )
++    assert(nBasePos<this->m_nLength);
++    switch( this->m_pArray[nBasePos] )
+     {
+         case 'A':
+         case 'C':
+@@ -467,11 +467,11 @@
+    Base numbers are assumed to be zero-based.
+ */
+    assert(nBasePos>=0);
+-   assert(nBasePos<m_nLength);
++   assert(nBasePos<this->m_nLength);
+    int bp = 0;
+-   for( int n=0; n<m_nLength; n++ )
++   for( int n=0; n<this->m_nLength; n++ )
+    {
+-      if( m_pArray[n] == cPad )
++      if( this->m_pArray[n] == cPad )
+          continue;
+       if( bp == nBasePos )
+          return n;
+@@ -493,9 +493,9 @@
+     Counts the number of pad characters contained in the current range.
+ */
+     int nPads = 0;
+-    for( int n=m_nLowerLimit; n<=m_nUpperLimit; n++ )
++    for( int n=this->m_nLowerLimit; n<=this->m_nUpperLimit; n++ )
+     {
+-        if( m_pArray[n] == cPad )
++        if( this->m_pArray[n] == cPad )
+             nPads++;
+     }
+     return nPads;
+@@ -519,9 +519,9 @@
+     {
+         // Scan from left
+         i = 0;
+-        while( (i<m_nLength) && (n>0) )
++        while( (i<this->m_nLength) && (n>0) )
+         {
+-            if( m_pArray[i] != cPad )
++            if( this->m_pArray[i] != cPad )
+                 n--;
+             i++;
+         }
+@@ -529,10 +529,10 @@
+     else
+     {
+         // Scan from right
+-        i = m_nLength - 1;
++        i = this->m_nLength - 1;
+         while( (i>=0) && (n>0) )
+         {
+-            if( m_pArray[i] != cPad )
++            if( this->m_pArray[i] != cPad )
+                 n--;
+             i--;
+         }
+@@ -546,12 +546,12 @@
+ int DNAArray<CharT>::GetOriginalPosition( int i, bool bLeft, char cPad ) const
+ {
+     assert(i>=0);
+-    assert(i<m_nLength);
++    assert(i<this->m_nLength);
+ 
+ 
+     // Check input
+     int n = -1;
+-    if( i >= m_nLength )
++    if( i >= this->m_nLength )
+         return n;
+ 
+ 
+@@ -561,7 +561,7 @@
+         // Scan to left
+         while( i >= 0 )
+         {
+-            if( m_pArray[i] != cPad )
++            if( this->m_pArray[i] != cPad )
+                 n++;
+             i--;
+         }
+@@ -569,9 +569,9 @@
+     else
+     {
+         // Scan to right
+-        while( i < m_nLength )
++        while( i < this->m_nLength )
+         {
+-            if( m_pArray[i] != cPad )
++            if( this->m_pArray[i] != cPad )
+                 n++;
+             i++;
+         }
diff --git a/sci-biology/staden/staden-1.5.3.ebuild b/sci-biology/staden/staden-1.5.3.ebuild
index f92e65b1c732..0d0a5891b7fc 100644
--- a/sci-biology/staden/staden-1.5.3.ebuild
+++ b/sci-biology/staden/staden-1.5.3.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2005 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/staden/staden-1.5.3.ebuild,v 1.2 2005/01/18 00:18:29 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/staden/staden-1.5.3.ebuild,v 1.3 2005/01/25 04:19:24 ribosome Exp $
 
 inherit eutils toolchain-funcs
 
@@ -73,6 +73,7 @@ src_unpack() {
 	epatch ${FILESDIR}/${P}-prefinish.patch
 	epatch ${FILESDIR}/${P}-tracediff.patch
 	epatch ${FILESDIR}/${P}-mutscan.patch
+	epatch ${FILESDIR}/${P}-mutlib-gcc-3.4.patch
 	cd ${S}/src/mk
 	# Remove the "-fpic" flag. This will be replaced by "-fPIC".
 	sed -i -e 's/SHLIB_CFLAGS		= -fpic/SHLIB_CFLAGS		= /' linux.mk