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

Package-Manager: portage-2.1.8.3/cvs/Linux x86_64

8 files changed, 18 insertions, 169 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/Manifest b/sci-biology/amap/Manifest
index 7401e09e5527..8975445bbec6 100644
--- a/sci-biology/amap/Manifest
+++ b/sci-biology/amap/Manifest
@@ -1,23 +1,18 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA1
 
-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
-EBUILD amap-2.2-r1.ebuild 1448 RMD160 efd711f93c8861d0938fbd96bd8b57b74aef869b SHA1 91392d7b837739573108b684ec1aea92bc4066e5 SHA256 fef2949a0b2b76cfac001029ed754db012a75783bdf830be9b1303cd28b73173
-EBUILD amap-2.2.ebuild 980 RMD160 ca076f2a81306b313c2861dbe5781a29c179f8f8 SHA1 bea1a904b24caab224c01159801fc572bb6b5ba5 SHA256 7172952f43000517cdb71065c594b38cd4fd6345b1c900f9c3ce1d16decb6b5e
-MISC ChangeLog 1261 RMD160 5514b8cf43edb3ed672ac86851750d1cf4c405d2 SHA1 a1caaa32a55e23ca44568feca24c532a908754be SHA256 25e04a32bcda6add908d3bc71a054864945126542fa421de068342d8fa1b9f72
+EBUILD amap-2.2-r1.ebuild 1524 RMD160 0e37d8cb34d7b0b25f0d7a18b3d5cc44dd251c12 SHA1 bada2e8c85d4fcf8553280743c96840a34a9130f SHA256 bbbe07c7b0421e853489b6ee49d0d5321b7ff42b3c7294fa06045028a77320bf
+MISC ChangeLog 1531 RMD160 f339b2f14fce1ff24636fe06acdfc5b0dbe811f6 SHA1 2c7eb0ebaed694f6f381450b59a009aa12967619 SHA256 02d9880189a24614e9e0a56830b3920d3b4cc4573c82b0b28f29178c43d8ad8e
 MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.11 (GNU/Linux)
+Version: GnuPG v2.0.15 (GNU/Linux)
 
-iEYEARECAAYFAkptQIkACgkQXVaO67S1rttUAwCfe+hHm3OoFuKkAJkoI+u2JPyT
-ez0AoN2F7cOrwJ7blDVXGO9qQeyVQDkQ
-=Rwnc
+iJwEAQECAAYFAkxhb68ACgkQIiMqcbOVdxTCoAP+JJGp3HDXoW3k1VHG+2xKWWov
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+=cmq0
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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