Respect LDFLAGS wrt bug 332009. Thanks to Diego for report. Remove old.

(Portage version: 2.1.8.3/cvs/Linux x86_64)

7 files changed, 10 insertions, 156 deletions

diff --git a/sci-biology/amap/ChangeLog b/sci-biology/amap/ChangeLog
index 4f44c918c66a..f75092c591f3 100644
--- a/sci-biology/amap/ChangeLog
+++ b/sci-biology/amap/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/amap
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/amap/ChangeLog,v 1.5 2009/07/27 05:52:01 dberkholz Exp $
+# 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 $
+
+  10 Aug 2010; Kacper Kowalik <xarthisius@gentoo.org>
+  -files/2.0-fix-cxxflags.patch, -amap-2.0.ebuild, -amap-2.2.ebuild,
+  -files/2.1-fix-cxxflags.patch, -amap-2.1.ebuild, amap-2.2-r1.ebuild:
+  Respect LDFLAGS wrt bug 332009. Thanks to Diego for report. Remove old.
 
 *amap-2.2-r1 (27 Jul 2009)
 
diff --git a/sci-biology/amap/amap-2.0.ebuild b/sci-biology/amap/amap-2.0.ebuild
deleted file mode 100644
index 2b77bb206199..000000000000
--- a/sci-biology/amap/amap-2.0.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2007 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/amap/amap-2.0.ebuild,v 1.2 2007/10/13 13:13:58 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://bio.math.berkeley.edu/amap/download/${MY_P}.tar.gz"
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="~x86"
-IUSE=""
-RDEPEND=""
-DEPEND="${RDEPEND}"
-S="${WORKDIR}/${PN}"
-
-src_unpack() {
-	unpack ${A}
-	epatch "${FILESDIR}"/${PV}-fix-cxxflags.patch
-}
-
-src_compile() {
-	emake \
-		CXX="$(tc-getCXX)" \
-		OPT_CXXFLAGS="${CXXFLAGS}" \
-		|| die "make failed"
-}
-
-src_install() {
-	dobin ${PN}
-	dodoc README PROBCONS.README
-}
diff --git a/sci-biology/amap/amap-2.1.ebuild b/sci-biology/amap/amap-2.1.ebuild
deleted file mode 100644
index bae8b1a66a21..000000000000
--- a/sci-biology/amap/amap-2.1.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# 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-2.1.ebuild,v 1.2 2008/02/03 04:37:36 je_fro 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://bio.math.berkeley.edu/amap/download/${MY_P}.tar.gz"
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-RDEPEND=""
-DEPEND="${RDEPEND}"
-S="${WORKDIR}/${PN}-align"
-
-src_unpack() {
-	unpack ${A}
-	epatch "${FILESDIR}"/${PV}-fix-cxxflags.patch
-}
-
-src_compile() {
-	cd "${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/amap-2.2-r1.ebuild b/sci-biology/amap/amap-2.2-r1.ebuild
index bef78dab765f..cdb8db6bf72b 100644
--- a/sci-biology/amap/amap-2.2-r1.ebuild
+++ b/sci-biology/amap/amap-2.2-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2009 Gentoo Foundation
+# 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 1.1 2009/07/27 05:52:01 dberkholz Exp $
+# $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"
@@ -32,6 +32,7 @@ src_unpack() {
 	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() {
diff --git a/sci-biology/amap/amap-2.2.ebuild b/sci-biology/amap/amap-2.2.ebuild
deleted file mode 100644
index d87f645770f2..000000000000
--- a/sci-biology/amap/amap-2.2.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# 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/2.0-fix-cxxflags.patch b/sci-biology/amap/files/2.0-fix-cxxflags.patch
deleted file mode 100644
index 37155513790d..000000000000
--- a/sci-biology/amap/files/2.0-fix-cxxflags.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff -urN amap.orig/Makefile amap/Makefile
---- amap.orig/Makefile	2006-12-10 22:31:54.000000000 -0800
-+++ amap/Makefile	2006-12-10 22:32:35.000000000 -0800
-@@ -15,6 +15,8 @@
- #    c) RELEASE mode
- ################################################################################
- 
-+OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops
-+
- OTHERFLAGS = -DNumInsertStates=1 -DVERSION='"AMAP.2.0"'
- 
- # debug mode    
-@@ -26,7 +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/2.1-fix-cxxflags.patch b/sci-biology/amap/files/2.1-fix-cxxflags.patch
deleted file mode 100644
index 925bebea84b5..000000000000
--- a/sci-biology/amap/files/2.1-fix-cxxflags.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff -Naur amap-align/align/Makefile amap-align.new/align/Makefile
---- amap-align/align/Makefile	2007-07-21 19:45:16.000000000 -0400
-+++ amap-align.new/align/Makefile	2007-10-13 08:54:22.000000000 -0400
-@@ -15,6 +15,8 @@
- #    c) RELEASE mode
- ################################################################################
- 
-+OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops
-+
- OTHERFLAGS = -DNumInsertStates=1 -DVERSION='"AMAP.2.1"'
- 
- # debug mode    
-@@ -26,7 +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