Version bump (fixes bug #191861).

Package-Manager: portage-2.1.3.12

6 files changed, 93 insertions, 13 deletions

diff --git a/sci-biology/amap/ChangeLog b/sci-biology/amap/ChangeLog
index d4819372f458..9df88c2d257d 100644
--- a/sci-biology/amap/ChangeLog
+++ b/sci-biology/amap/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/amap
-# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/amap/ChangeLog,v 1.1 2006/12/11 06:59:29 dberkholz Exp $
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/amap/ChangeLog,v 1.2 2007/10/13 13:13:58 markusle Exp $
+
+*amap-2.1 (13 Oct 2007)
+
+  13 Oct 2007; Markus Dittrich <markusle@gentoo.org>
+  +files/2.1-fix-cxxflags.patch, +amap-2.1.ebuild:
+  Version bump (fixes bug #191861).
 
 *amap-2.0 (11 Dec 2006)
 
diff --git a/sci-biology/amap/Manifest b/sci-biology/amap/Manifest
index 4613eadbc095..13aa017223ad 100644
--- a/sci-biology/amap/Manifest
+++ b/sci-biology/amap/Manifest
@@ -2,15 +2,24 @@ AUX 2.0-fix-cxxflags.patch 835 RMD160 d31c598e91e58ada05320f8c536a2b61c4d50f5d S
 MD5 76ed725e190bde137cbee78a6d4771ce files/2.0-fix-cxxflags.patch 835
 RMD160 d31c598e91e58ada05320f8c536a2b61c4d50f5d files/2.0-fix-cxxflags.patch 835
 SHA256 fe3e568f785d1d4ee28deeb62cba28aa700066bab7d41828c84d9fcc612fff4e files/2.0-fix-cxxflags.patch 835
+AUX 2.1-fix-cxxflags.patch 882 RMD160 003609b0c9ad3c74c28fa4f7be83ee24512b5722 SHA1 193671beb78a2ac6e7db037d782d7228dec1e23b SHA256 f2e9edef582eae51762703be4d34dcf6b760fecbcd338883efc926b120506a01
+MD5 ac9e3c05c3bd30dcbc86c550fb4ea986 files/2.1-fix-cxxflags.patch 882
+RMD160 003609b0c9ad3c74c28fa4f7be83ee24512b5722 files/2.1-fix-cxxflags.patch 882
+SHA256 f2e9edef582eae51762703be4d34dcf6b760fecbcd338883efc926b120506a01 files/2.1-fix-cxxflags.patch 882
 DIST amap.2.0.tar.gz 42389 RMD160 1577da7c930dc72aadda095b24107f933bde4006 SHA1 9a6c083e868ae85ae177445d284dd4c54422e4ef SHA256 3930c4b5d149f01277bc6de2339c5f058d7d2ca36f69f328f1dac2f1a4b5ba92
-EBUILD amap-2.0.ebuild 801 RMD160 21aab7ea289680bd65caa731962ed599716177b9 SHA1 7612a7d574fd59fe18c0dcb54f0ba1322ec561f7 SHA256 b15121d2b7daa8ef42d8bbee88b1c78a085c122a2978deb9ba1408aed35d3036
-MD5 3657e7ca2e283eba851217b4140a8e39 amap-2.0.ebuild 801
-RMD160 21aab7ea289680bd65caa731962ed599716177b9 amap-2.0.ebuild 801
-SHA256 b15121d2b7daa8ef42d8bbee88b1c78a085c122a2978deb9ba1408aed35d3036 amap-2.0.ebuild 801
-MISC ChangeLog 507 RMD160 6e825c7e091cb0a6bb46d8faae6b5a6e326c5f2a SHA1 c314a34e3b92104f34446898495cb21323ecceef SHA256 b112da675d039557f89d77038d2551b5545a7a064c9d2da701f59732ecf01331
-MD5 3fa86e42a4d24ac84a64302e077cede4 ChangeLog 507
-RMD160 6e825c7e091cb0a6bb46d8faae6b5a6e326c5f2a ChangeLog 507
-SHA256 b112da675d039557f89d77038d2551b5545a7a064c9d2da701f59732ecf01331 ChangeLog 507
+DIST amap.2.1.tar.gz 103301 RMD160 b8ade9699c0fa81100ebce8cbb3d0f812ba80824 SHA1 4addca6e9f19392d33b35e080e8004dba44f9854 SHA256 3040968f318b7856624361e53017fe84ae706aa6f2702cea1d29646fd378df38
+EBUILD amap-2.0.ebuild 802 RMD160 f18976169ccd0f9e9b3cf451bfb9050bd8cd1ad4 SHA1 307ff9955bcda4c041c147c43376d5b9d4d3523e SHA256 d579540cf8279214386ef0f0982d9a159d217ebe2a1ba0c14a3f27cead90a7e0
+MD5 c3f5e836c66de88223f0fee5ae8b13e1 amap-2.0.ebuild 802
+RMD160 f18976169ccd0f9e9b3cf451bfb9050bd8cd1ad4 amap-2.0.ebuild 802
+SHA256 d579540cf8279214386ef0f0982d9a159d217ebe2a1ba0c14a3f27cead90a7e0 amap-2.0.ebuild 802
+EBUILD amap-2.1.ebuild 935 RMD160 d194391d9afafeb37c7c1944417be7950d0416de SHA1 c529d3a27834172ce45fc2bb2b1200afe50bf25d SHA256 c1462f7fbd47b3f189e6b76f7b308adc6787e64413d15a1ebc370710e7902ce9
+MD5 3c052936e7106356c2f5f1ca46a7d0bc amap-2.1.ebuild 935
+RMD160 d194391d9afafeb37c7c1944417be7950d0416de amap-2.1.ebuild 935
+SHA256 c1462f7fbd47b3f189e6b76f7b308adc6787e64413d15a1ebc370710e7902ce9 amap-2.1.ebuild 935
+MISC ChangeLog 672 RMD160 98d0c9302518dbba84ab6e78847dded5fece88e3 SHA1 5fd078b77a8475dd5ad297ed99b9320e4396b2d1 SHA256 2e938044da472c0e53fb7be3ad0057e8a49f134d7958c63335549304541ba17f
+MD5 2cfcbf02594a2769f71ca3af85ba8661 ChangeLog 672
+RMD160 98d0c9302518dbba84ab6e78847dded5fece88e3 ChangeLog 672
+SHA256 2e938044da472c0e53fb7be3ad0057e8a49f134d7958c63335549304541ba17f ChangeLog 672
 MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f
 MD5 86813ca8050bc98ba326cb74e88150a5 metadata.xml 164
 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c metadata.xml 164
@@ -18,3 +27,6 @@ SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f metadata
 MD5 5510a75e0abff7dfa6adbe1826614057 files/digest-amap-2.0 223
 RMD160 1b902d1cc9581642a5f47f234de94e2fd5831ab2 files/digest-amap-2.0 223
 SHA256 8c039a4dfb9875f4ca84bb6c15037c6d94a8ac00e20e545f60f1a4eef14cbc93 files/digest-amap-2.0 223
+MD5 c24abce0eba9aae893495d303d2d6a3b files/digest-amap-2.1 226
+RMD160 4fde2224914436a43add959ee980306f831d1170 files/digest-amap-2.1 226
+SHA256 d0e824f3f90bdc8d6b2ab5842099c07d6739857295d0911ad9e98a7731bfb20f files/digest-amap-2.1 226
diff --git a/sci-biology/amap/amap-2.0.ebuild b/sci-biology/amap/amap-2.0.ebuild
index 5c681cd0df34..2b77bb206199 100644
--- a/sci-biology/amap/amap-2.0.ebuild
+++ b/sci-biology/amap/amap-2.0.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2006 Gentoo Foundation
+# 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 1.1 2006/12/11 06:59:29 dberkholz Exp $
+# $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
 
@@ -18,7 +18,7 @@ S="${WORKDIR}/${PN}"
 
 src_unpack() {
 	unpack ${A}
-	epatch ${FILESDIR}/${PV}-fix-cxxflags.patch
+	epatch "${FILESDIR}"/${PV}-fix-cxxflags.patch
 }
 
 src_compile() {
diff --git a/sci-biology/amap/amap-2.1.ebuild b/sci-biology/amap/amap-2.1.ebuild
new file mode 100644
index 000000000000..75077a393dfb
--- /dev/null
+++ b/sci-biology/amap/amap-2.1.ebuild
@@ -0,0 +1,38 @@
+# 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-2.1.ebuild,v 1.1 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/${MY_P}.tar.gz"
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+RDEPEND=""
+DEPEND="${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() {
+	cd "${S}"
+	dobin align/${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/2.1-fix-cxxflags.patch b/sci-biology/amap/files/2.1-fix-cxxflags.patch
new file mode 100644
index 000000000000..925bebea84b5
--- /dev/null
+++ b/sci-biology/amap/files/2.1-fix-cxxflags.patch
@@ -0,0 +1,21 @@
+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
diff --git a/sci-biology/amap/files/digest-amap-2.1 b/sci-biology/amap/files/digest-amap-2.1
new file mode 100644
index 000000000000..040f002c0e85
--- /dev/null
+++ b/sci-biology/amap/files/digest-amap-2.1
@@ -0,0 +1,3 @@
+MD5 a37ef3431c45c71ec48200e70c837ad0 amap.2.1.tar.gz 103301
+RMD160 b8ade9699c0fa81100ebce8cbb3d0f812ba80824 amap.2.1.tar.gz 103301
+SHA256 3040968f318b7856624361e53017fe84ae706aa6f2702cea1d29646fd378df38 amap.2.1.tar.gz 103301