Clean java bits thanks to sera. General cleanup, fix linking order, fix building with gcc 4.6 wrt #360517. Drop old.

Package-Manager: portage-2.2.0_alpha27/cvs/Linux x86_64

6 files changed, 106 insertions, 83 deletions

diff --git a/sci-biology/amap/ChangeLog b/sci-biology/amap/ChangeLog
index f75092c591f3..943c3a54f0d0 100644
--- a/sci-biology/amap/ChangeLog
+++ b/sci-biology/amap/ChangeLog
@@ -1,6 +1,15 @@
 # ChangeLog for sci-biology/amap
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/amap/ChangeLog,v 1.6 2010/08/10 15:26:30 xarthisius Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/amap/ChangeLog,v 1.7 2011/03/26 10:56:00 xarthisius Exp $
+
+*amap-2.2-r2 (26 Mar 2011)
+
+  26 Mar 2011; Kacper Kowalik <xarthisius@gentoo.org> -amap-2.2-r1.ebuild,
+  +amap-2.2-r2.ebuild, -files/amap-2.2-cxxflags.patch,
+  -files/amap-2.2-gcc4.3.patch, +files/amap-2.2-includes.patch,
+  +files/amap-2.2-makefile.patch:
+  Clean java bits thanks to sera. General cleanup, fix linking order, fix
+  building with gcc 4.6 wrt #360517. Drop old.
 
   10 Aug 2010; Kacper Kowalik <xarthisius@gentoo.org>
   -files/2.0-fix-cxxflags.patch, -amap-2.0.ebuild, -amap-2.2.ebuild,
diff --git a/sci-biology/amap/Manifest b/sci-biology/amap/Manifest
index 8975445bbec6..4ba479255c4f 100644
--- a/sci-biology/amap/Manifest
+++ b/sci-biology/amap/Manifest
@@ -1,18 +1,18 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA1
 
-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
+AUX amap-2.2-includes.patch 1088 RMD160 3ae210368fdec45d50eb9f6241532565fdd53e3f SHA1 2490543359fe46476f3a4df6aec273d2873b45db SHA256 3b22dd095d3dcf674528eb4641f325f7f3e30dc2f8d1173eefa8e1474d1fc5e2
+AUX amap-2.2-makefile.patch 1201 RMD160 29838ba7cdc4a8fc45ed025c246fc28bfa9626ee SHA1 64ff2882785fc414fbf0ce2df21d8cfb7699d7a7 SHA256 e5ab2e395a610632080c8736bd7e5e91ca36e87ee2165c8b2780772fb85f0cdc
 DIST amap.2.2.tar.gz 102861 RMD160 6b47b66ab5095e35bcb14a599a25687fef8e799c SHA1 618e498581302e140270a0e029ab87d378c450ef SHA256 81f8c7328c59775a5430d2210f1e4cbed7072bfd8a37f62c8d387db15b7757f4
-EBUILD amap-2.2-r1.ebuild 1524 RMD160 0e37d8cb34d7b0b25f0d7a18b3d5cc44dd251c12 SHA1 bada2e8c85d4fcf8553280743c96840a34a9130f SHA256 bbbe07c7b0421e853489b6ee49d0d5321b7ff42b3c7294fa06045028a77320bf
-MISC ChangeLog 1531 RMD160 f339b2f14fce1ff24636fe06acdfc5b0dbe811f6 SHA1 2c7eb0ebaed694f6f381450b59a009aa12967619 SHA256 02d9880189a24614e9e0a56830b3920d3b4cc4573c82b0b28f29178c43d8ad8e
+EBUILD amap-2.2-r2.ebuild 1236 RMD160 be409fd19b8930367ea3ec3d89a2d1af69f0237e SHA1 70d6a211f0f06b07eb5b77b2e8a9c395d340ac56 SHA256 3af0730a336676519c13c1cff04785469952df377ee710c0f830f93d4177218e
+MISC ChangeLog 1909 RMD160 b0b070a3c4e34f90d793929e1959776bd86a9551 SHA1 640c6c39fa8d1f0ac4a151e6a0148c90f83fc31f SHA256 483d897d4db46baf9efcd1e7208f33d86c8fc33c4adbf438751f082034b380a4
 MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.15 (GNU/Linux)
+Version: GnuPG v2.0.17 (GNU/Linux)
 
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-=cmq0
+iJwEAQECAAYFAk2NxkkACgkQIiMqcbOVdxT78QQAg5WbhBmMCrPamL7L3ETUf7r6
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+LrW2beh1uYHo+GZcOAF7zphg/+tSodkf1RyvELJ5wh/Npv6MrM/T3sf0aXBO8Ubu
+MMgXeOXBRgJUEFY/Wi0=
+=kpTV
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/amap/amap-2.2-r1.ebuild b/sci-biology/amap/amap-2.2-r1.ebuild
deleted file mode 100644
index cdb8db6bf72b..000000000000
--- a/sci-biology/amap/amap-2.2-r1.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/amap/amap-2.2-r1.ebuild,v 1.2 2010/08/10 15:26:30 xarthisius Exp $
-
-# Java is optional, don't force an ant dependency
-JAVA_ANT_DISABLE_ANT_CORE_DEP="yes"
-
-inherit eutils toolchain-funcs java-pkg-opt-2 java-ant-2
-
-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/${MY_P}.tar.gz"
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-RDEPEND="
-	java? (
-		>=virtual/jre-1.5
-	)"
-DEPEND="${RDEPEND}
-	java? (
-		>=dev-java/ant-core-1.7.0
-		>=dev-java/javatoolkit-0.3.0-r2
-		>=virtual/jdk-1.5
-	)"
-S="${WORKDIR}/${PN}-align"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}"/${P}-cxxflags.patch
-	epatch "${FILESDIR}"/${P}-gcc4.3.patch
-	sed -i -e "s/\$(CXX)/& \$(LDFLAGS)/" "${S}"/align/Makefile || die #332009
-}
-
-src_compile() {
-	pushd "${S}"/align
-	emake \
-		CXX="$(tc-getCXX)" \
-		OPT_CXXFLAGS="${CXXFLAGS}" \
-		|| die "make failed"
-	popd
-
-	if use java; then
-		pushd "${S}"/display
-		eant all || die
-		popd
-	fi
-}
-
-src_install() {
-	dobin align/${PN}
-	dodoc align/README align/PROBCONS.README
-	insinto /usr/share/${PN}/examples
-	doins examples/* || die "Failed to install examples"
-	if use java; then
-		java-pkg_newjar "${S}"/display/AmapDisplay.jar amapdisplay.jar
-		java-pkg_dolauncher amapdisplay --jar amapdisplay.jar
-	fi
-}
diff --git a/sci-biology/amap/amap-2.2-r2.ebuild b/sci-biology/amap/amap-2.2-r2.ebuild
new file mode 100644
index 000000000000..5e47337e2554
--- /dev/null
+++ b/sci-biology/amap/amap-2.2-r2.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/amap/amap-2.2-r2.ebuild,v 1.1 2011/03/26 10:56:00 xarthisius Exp $
+
+EAPI="2"
+
+inherit eutils toolchain-funcs java-pkg-opt-2 java-ant-2
+
+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/${PN}/download/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="java"
+
+RDEPEND="java? ( >=virtual/jre-1.5 )"
+DEPEND="java? ( >=virtual/jdk-1.5 )"
+
+S=${WORKDIR}/${PN}-align
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-makefile.patch \
+		"${FILESDIR}"/${P}-includes.patch
+}
+
+src_compile() {
+	emake -C align CXX="$(tc-getCXX)" \
+		OPT_CXXFLAGS="${CXXFLAGS}" || die "make failed"
+
+	if use java; then
+		pushd "${S}"/display
+		eant -Ddisplay all || die
+		popd
+	fi
+}
+
+src_install() {
+	dobin align/${PN} || die
+	dodoc align/{README,PROBCONS.README} || die
+	insinto /usr/share/${PN}/examples
+	doins examples/* || die
+	if use java; then
+		java-pkg_newjar "${S}"/display/AmapDisplay.jar amapdisplay.jar
+		java-pkg_dolauncher amapdisplay --jar amapdisplay.jar
+	fi
+}
diff --git a/sci-biology/amap/files/amap-2.2-gcc4.3.patch b/sci-biology/amap/files/amap-2.2-includes.patch
index 2725ab485598..77c4261db5cf 100644
--- a/sci-biology/amap/files/amap-2.2-gcc4.3.patch
+++ b/sci-biology/amap/files/amap-2.2-includes.patch
@@ -1,6 +1,10 @@
-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
+Fixes build with gcc 4.3 and 4.6
+
+http://bugs.gentoo.org/217921
+http://bugs.gentoo.org/360517
+
+--- amap-align/align/Amap.cc
++++ amap-align/align/Amap.cc
 @@ -12,6 +12,8 @@
  #include "ProbabilisticModel.h"
  #include "EvolutionaryTree.h"
@@ -18,9 +22,8 @@ diff -Naur amap-align/align/Amap.cc amap-align.new/align/Amap.cc
  
  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
+--- amap-align/align/MultiSequenceDag.h
++++ amap-align/align/MultiSequenceDag.h
 @@ -13,6 +13,7 @@
  #include <map>
  #include <queue>
@@ -29,3 +32,13 @@ diff -Naur amap-align/align/MultiSequenceDag.h amap-align.new/align/MultiSequenc
  #include "MultiSequence.h"
  #include "SparseMatrix.h"
  
+--- amap-align/align/SafeVector.h.org	2011-03-26 11:50:11.935069583 +0100
++++ amap-align/align/SafeVector.h	2011-03-26 11:50:21.112553151 +0100
+@@ -9,6 +9,7 @@
+ #define SAFEVECTOR_H
+ 
+ #include <cassert>
++#include <cstddef>
+ #include <vector>
+ 
+ /////////////////////////////////////////////////////////////////
diff --git a/sci-biology/amap/files/amap-2.2-cxxflags.patch b/sci-biology/amap/files/amap-2.2-makefile.patch
index 314763a49ef2..5a9841c98255 100644
--- a/sci-biology/amap/files/amap-2.2-cxxflags.patch
+++ b/sci-biology/amap/files/amap-2.2-makefile.patch
@@ -1,6 +1,9 @@
-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
+Respect {CXX,LD}FLAGS
+
+http://bugs.gentoo.org/332009
+
+--- amap-align/align/Makefile
++++ amap-align/align/Makefile
 @@ -15,6 +15,8 @@
  #    c) RELEASE mode
  ################################################################################
@@ -20,3 +23,13 @@ diff -Naur amap-align.old/align/Makefile amap-align/align/Makefile
  ################################################################################
  # 3) Dependencies
  ################################################################################
+ 
+@@ -38,7 +37,7 @@
+ all : $(TARGETS)
+ 
+ amap : MultiSequenceDag.h MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Amap.cc
+-	$(CXX) $(CXXFLAGS) -lm -o amap Amap.cc 
++	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o amap Amap.cc -lm
+ 
+ .PHONY : clean
+ clean: