Version bump and gcc-4.3 compatibility patch (fixes bug #217921).

(Portage version: 2.1.5_rc3)

4 files changed, 102 insertions, 2 deletions

diff --git a/sci-biology/amap/ChangeLog b/sci-biology/amap/ChangeLog
index bbc900934f0f..fcbb619bae1b 100644
--- a/sci-biology/amap/ChangeLog
+++ b/sci-biology/amap/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-biology/amap
-# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/amap/ChangeLog,v 1.3 2008/02/03 04:37:36 je_fro Exp $
+# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/amap/ChangeLog,v 1.4 2008/04/17 18:20:13 markusle Exp $
+
+*amap-2.2 (17 Apr 2008)
+
+  17 Apr 2008; Markus Dittrich <markusle@gentoo.org>
+  +files/amap-2.2-cxxflags.patch, +files/amap-2.2-gcc4.3.patch,
+  +amap-2.2.ebuild:
+  Version bump and gcc-4.3 compatibility patch (fixes bug #217921). Thanks
+  much to Peter Alfredsen <peter.alfredsen@gmail.com> for his patches.
 
   15 Oct 2007; Jeff Gardner <je_fro@gentoo.org> amap-2.1.ebuild:
   Adding ~amd64
diff --git a/sci-biology/amap/amap-2.2.ebuild b/sci-biology/amap/amap-2.2.ebuild
new file mode 100644
index 000000000000..d87f645770f2
--- /dev/null
+++ b/sci-biology/amap/amap-2.2.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/amap/amap-2.2.ebuild,v 1.1 2008/04/17 18:20:13 markusle Exp $
+
+inherit eutils toolchain-funcs
+
+MY_P="${PN}.${PV}"
+DESCRIPTION="Protein multiple-alignment-based sequence annealing"
+HOMEPAGE="http://bio.math.berkeley.edu/amap/"
+SRC_URI="http://baboon.math.berkeley.edu/amap/download/${MY_P}.tar.gz"
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE=""
+RDEPEND=""
+DEPEND="${RDEPEND}"
+S="${WORKDIR}/${PN}-align"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}"/${P}-cxxflags.patch
+	epatch "${FILESDIR}"/${P}-gcc4.3.patch
+}
+
+src_compile() {
+	cd "${S}"/align
+	emake \
+		CXX="$(tc-getCXX)" \
+		OPT_CXXFLAGS="${CXXFLAGS}" \
+		|| die "make failed"
+}
+
+src_install() {
+	dobin align/${PN}
+	dodoc align/README align/PROBCONS.README
+	insinto /usr/share/${PN}/examples
+	doins examples/* || die "Failed to install examples"
+}
diff --git a/sci-biology/amap/files/amap-2.2-cxxflags.patch b/sci-biology/amap/files/amap-2.2-cxxflags.patch
new file mode 100644
index 000000000000..314763a49ef2
--- /dev/null
+++ b/sci-biology/amap/files/amap-2.2-cxxflags.patch
@@ -0,0 +1,22 @@
+diff -Naur amap-align.old/align/Makefile amap-align/align/Makefile
+--- amap-align.old/align/Makefile	2008-02-13 19:36:31.000000000 -0500
++++ amap-align/align/Makefile	2008-04-17 13:22:17.000000000 -0400
+@@ -15,6 +15,8 @@
+ #    c) RELEASE mode
+ ################################################################################
+ 
++OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops
++
+ OTHERFLAGS = -DNumInsertStates=1 -DVERSION='"AMAP.2.2"'
+ 
+ # debug mode    
+@@ -26,8 +28,7 @@
+ 
+ # release mode
+ #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer 
+-CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
+-
++CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS)
+ ################################################################################
+ # 3) Dependencies
+ ################################################################################
diff --git a/sci-biology/amap/files/amap-2.2-gcc4.3.patch b/sci-biology/amap/files/amap-2.2-gcc4.3.patch
new file mode 100644
index 000000000000..2725ab485598
--- /dev/null
+++ b/sci-biology/amap/files/amap-2.2-gcc4.3.patch
@@ -0,0 +1,31 @@
+diff -Naur amap-align/align/Amap.cc amap-align.new/align/Amap.cc
+--- amap-align/align/Amap.cc	2007-07-24 18:59:22.000000000 -0400
++++ amap-align.new/align/Amap.cc	2008-04-17 13:43:12.000000000 -0400
+@@ -12,6 +12,8 @@
+ #include "ProbabilisticModel.h"
+ #include "EvolutionaryTree.h"
+ #include "SparseMatrix.h"
++#include <limits>
++#include <climits>
+ #include <string>
+ #include <sstream>
+ #include <iomanip>
+@@ -23,6 +25,7 @@
+ #include <cstdlib>
+ #include <cerrno>
+ #include <iomanip>
++#include <cstring>
+ 
+ string parametersInputFilename = "";
+ string parametersOutputFilename = "no training";
+diff -Naur amap-align/align/MultiSequenceDag.h amap-align.new/align/MultiSequenceDag.h
+--- amap-align/align/MultiSequenceDag.h	2007-07-24 18:59:22.000000000 -0400
++++ amap-align.new/align/MultiSequenceDag.h	2008-04-17 13:43:12.000000000 -0400
+@@ -13,6 +13,7 @@
+ #include <map>
+ #include <queue>
+ #include <iostream>
++#include <limits>
+ #include "MultiSequence.h"
+ #include "SparseMatrix.h"
+