sci-biology/plink: Moved to EAPI=4, add fix for building with gcc-4.7, #424709

(Portage version: 2.2.0_alpha115/cvs/Linux x86_64)

3 files changed, 79 insertions, 10 deletions

diff --git a/sci-biology/plink/ChangeLog b/sci-biology/plink/ChangeLog
index ea9fc7da651e..7de52d937314 100644
--- a/sci-biology/plink/ChangeLog
+++ b/sci-biology/plink/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/plink
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/plink/ChangeLog,v 1.11 2011/12/13 23:38:07 ago Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/plink/ChangeLog,v 1.12 2012/07/04 09:31:26 jlec Exp $
+
+  04 Jul 2012; Justin Lecher <jlec@gentoo.org> plink-1.07-r1.ebuild,
+  +files/plink-1.07-gcc47.patch:
+  Moved to EAPI=4, add fix for building with gcc-4.7, #424709
 
   13 Dec 2011; Agostino Sarubbo <ago@gentoo.org> plink-1.07-r1.ebuild:
   Stable for AMD64, wrt bug #392783
diff --git a/sci-biology/plink/files/plink-1.07-gcc47.patch b/sci-biology/plink/files/plink-1.07-gcc47.patch
new file mode 100644
index 000000000000..6c289edae153
--- /dev/null
+++ b/sci-biology/plink/files/plink-1.07-gcc47.patch
@@ -0,0 +1,64 @@
+ elf.cpp    |    6 +++---
+ idhelp.cpp |    8 ++++----
+ sets.cpp   |    8 ++++----
+ 3 files changed, 11 insertions(+), 11 deletions(-)
+
+diff --git a/elf.cpp b/elf.cpp
+index ec2ed3d..a57665f 100644
+--- a/elf.cpp
++++ b/elf.cpp
+@@ -1175,10 +1175,10 @@ void Plink::elfBaseline()
+ 	  << setw(8) << gcnt << " "
+ 	  << setw(8) << (double)cnt / (double)gcnt << "\n";
+ 
+-      map<int,int>::iterator i = chr_cnt.begin();
+-      while ( i != chr_cnt.end() )
++      map<int,int>::iterator j = chr_cnt.begin();
++      while ( j != chr_cnt.end() )
+ 	{
+-	  int c = i->first;
++	  int c = j->first;
+ 	  int x = chr_cnt.find( c )->second;
+ 	  int y = chr_gcnt.find( c )->second;
+ 	  
+diff --git a/idhelp.cpp b/idhelp.cpp
+index a9244fa..8882097 100644
+--- a/idhelp.cpp
++++ b/idhelp.cpp
+@@ -772,12 +772,12 @@ void IDHelper::idHelp()
+       for (int j = 0 ; j < jointField.size(); j++ )
+ 	{
+ 	  set<IDField*> & jf = jointField[j];
+-	  set<IDField*>::iterator j = jf.begin();
++	  set<IDField*>::iterator k = jf.begin();
+ 	  PP->printLOG(" { ");
+-	  while ( j != jf.end() )
++	  while ( k != jf.end() )
+ 	    {
+-	      PP->printLOG( (*j)->name + " " );
+-	      ++j;
++	      PP->printLOG( (*k)->name + " " );
++	      ++k;
+ 	    }
+ 	  PP->printLOG(" }");
+ 	}
+diff --git a/sets.cpp b/sets.cpp
+index 3a8f92f..66787e8 100644
+--- a/sets.cpp
++++ b/sets.cpp
+@@ -768,11 +768,11 @@ vector_t Set::profileTestScore()
+       //////////////////////////////////////////////
+       // Reset original missing status
+ 
+-      vector<Individual*>::iterator i = PP->sample.begin();
+-      while ( i != PP->sample.end() )
++      vector<Individual*>::iterator j = PP->sample.begin();
++      while ( j != PP->sample.end() )
+ 	{
+-	  (*i)->missing = (*i)->flag;
+-	  ++i;
++	  (*j)->missing = (*j)->flag;
++	  ++j;
+ 	}
+ 
+       ////////////////////////////////////////////////
diff --git a/sci-biology/plink/plink-1.07-r1.ebuild b/sci-biology/plink/plink-1.07-r1.ebuild
index 96e64d95b785..6f0e5a4233d8 100644
--- a/sci-biology/plink/plink-1.07-r1.ebuild
+++ b/sci-biology/plink/plink-1.07-r1.ebuild
@@ -1,8 +1,8 @@
-# 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/plink/plink-1.07-r1.ebuild,v 1.4 2011/12/13 23:38:07 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/plink/plink-1.07-r1.ebuild,v 1.5 2012/07/04 09:31:26 jlec Exp $
 
-EAPI="2"
+EAPI=4
 
 inherit eutils toolchain-funcs
 
@@ -26,7 +26,9 @@ S="${WORKDIR}/${P}-src"
 # Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream.
 
 src_prepare() {
-	epatch "${FILESDIR}"/${PV}-flags.patch
+	epatch \
+		"${FILESDIR}"/${PV}-flags.patch \
+		"${FILESDIR}"/${P}-gcc47.patch
 	use webcheck || sed -i '/WITH_WEBCHECK =/ s/^/#/' "${S}/Makefile" || die
 	use R || sed -i '/WITH_R_PLUGINS =/ s/^/#/' "${S}/Makefile" || die
 	use lapack || sed -i '/WITH_LAPACK =/ s/^/#/' "${S}/Makefile" || die
@@ -34,11 +36,10 @@ src_prepare() {
 
 src_compile() {
 	emake \
-		CXX_UNIX=$(tc-getCXX) \
-		|| die
+		CXX_UNIX=$(tc-getCXX)
 }
 
 src_install() {
-	newbin plink p-link || die
-	dodoc README.txt || die
+	newbin plink p-link
+	dodoc README.txt
 }