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

Package-Manager: portage-2.1.5_rc3

5 files changed, 107 insertions, 3 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/Manifest b/sci-biology/amap/Manifest
index 0da10e47627c..786b0a2f7e48 100644
--- a/sci-biology/amap/Manifest
+++ b/sci-biology/amap/Manifest
@@ -1,8 +1,12 @@
 AUX 2.0-fix-cxxflags.patch 835 RMD160 d31c598e91e58ada05320f8c536a2b61c4d50f5d SHA1 42911d9882e4c359f68e318fe65efb9f877fb680 SHA256 fe3e568f785d1d4ee28deeb62cba28aa700066bab7d41828c84d9fcc612fff4e
 AUX 2.1-fix-cxxflags.patch 882 RMD160 003609b0c9ad3c74c28fa4f7be83ee24512b5722 SHA1 193671beb78a2ac6e7db037d782d7228dec1e23b SHA256 f2e9edef582eae51762703be4d34dcf6b760fecbcd338883efc926b120506a01
+AUX amap-2.2-cxxflags.patch 964 RMD160 e39ec71fbf1a65500037dd0d88aa7679f142d755 SHA1 63afb43ecb5f567a4ca81c7d7f17cf1c3ac2f3a4 SHA256 63f78e4384d7f00486097aea1c37ee1721c1bd3d3ddfc5f413849e959d6678bd
+AUX amap-2.2-gcc4.3.patch 985 RMD160 f7673879698f34ee5c9ba4ab1fe9a05e99de6781 SHA1 67fc3f54443bbc2f2a6e8e7b465f876573c18236 SHA256 cd10644c92e8ea8c3e71a1723c2eb1d4d9d63291b67357d3476746c2bdf7d923
 DIST amap.2.0.tar.gz 42389 RMD160 1577da7c930dc72aadda095b24107f933bde4006 SHA1 9a6c083e868ae85ae177445d284dd4c54422e4ef SHA256 3930c4b5d149f01277bc6de2339c5f058d7d2ca36f69f328f1dac2f1a4b5ba92
 DIST amap.2.1.tar.gz 103301 RMD160 b8ade9699c0fa81100ebce8cbb3d0f812ba80824 SHA1 4addca6e9f19392d33b35e080e8004dba44f9854 SHA256 3040968f318b7856624361e53017fe84ae706aa6f2702cea1d29646fd378df38
+DIST amap.2.2.tar.gz 102861 RMD160 6b47b66ab5095e35bcb14a599a25687fef8e799c SHA1 618e498581302e140270a0e029ab87d378c450ef SHA256 81f8c7328c59775a5430d2210f1e4cbed7072bfd8a37f62c8d387db15b7757f4
 EBUILD amap-2.0.ebuild 802 RMD160 f18976169ccd0f9e9b3cf451bfb9050bd8cd1ad4 SHA1 307ff9955bcda4c041c147c43376d5b9d4d3523e SHA256 d579540cf8279214386ef0f0982d9a159d217ebe2a1ba0c14a3f27cead90a7e0
 EBUILD amap-2.1.ebuild 929 RMD160 2f3ccd91756e6c0257d1a3494dbab6568a5ddc6a SHA1 af196511bb2c04488f1010129c58c7acd75ab98c SHA256 844dba80f3ea12062dcfbbc4392e1991a4df752b82b773efc0f3645d4dae1c65
-MISC ChangeLog 752 RMD160 68373e37fb34de7ce392a9a5ccf0279808b2ad05 SHA1 c82675eb5d02d78d24b09bd1ede93f359685ba98 SHA256 df2a3900944b0602d73ec6e3c6d5e45dbb3bbfe1de2746335878f81259acbd2a
+EBUILD amap-2.2.ebuild 980 RMD160 ca076f2a81306b313c2861dbe5781a29c179f8f8 SHA1 bea1a904b24caab224c01159801fc572bb6b5ba5 SHA256 7172952f43000517cdb71065c594b38cd4fd6345b1c900f9c3ce1d16decb6b5e
+MISC ChangeLog 1063 RMD160 9ef1bbb7ac62ffe5f46d40a0a9ed02ff18e98dd3 SHA1 25fd10093515dc4509b6e930b090abfba9a57377 SHA256 9599d7a3172b5dc6ae9dcfa8435eacebc5f7f2dde5b6ef1cbc04fd88738af75b
 MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f
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"
+