Version Bump

Package-Manager: portage-2.2.0_alpha28/cvs/Linux x86_64

5 files changed, 115 insertions, 19 deletions

diff --git a/sci-biology/vienna-rna/ChangeLog b/sci-biology/vienna-rna/ChangeLog
index 03349a499abf..cc3ae6c7df59 100644
--- a/sci-biology/vienna-rna/ChangeLog
+++ b/sci-biology/vienna-rna/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/vienna-rna
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.34 2010/10/15 07:15:15 xarthisius Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.35 2011/03/20 12:15:50 jlec Exp $
+
+*vienna-rna-1.8.5 (20 Mar 2011)
+
+  20 Mar 2011; Justin Lecher <jlec@gentoo.org> vienna-rna-1.8.4-r1.ebuild,
+  vienna-rna-1.8.4-r2.ebuild, +vienna-rna-1.8.5.ebuild:
+  Version Bump
 
 *vienna-rna-1.8.4-r2 (15 Oct 2010)
 
diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest
index efa90b66bec9..5ac721275950 100644
--- a/sci-biology/vienna-rna/Manifest
+++ b/sci-biology/vienna-rna/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX vienna-rna-1.6.5-c-fixes.patch 728 RMD160 5f427bb976200f58599b1878ca7273844b21aac0 SHA1 7089237c787d780d53b92c4c38ba73ec60b81218 SHA256 49955a6244eb3be73f8d2472f3a4f9b8d1f8f92ba11327961b901a2c1f1e24d8
 AUX vienna-rna-1.7.2-LDFLAGS.patch 978 RMD160 ab19413ba9c5468e7d755c0eb979462d00112cb0 SHA1 5f29863572d3c16fa7616ee7aa0d2e140d94c497 SHA256 0c7db17c7a1a8a075e26f6b98b19c84a3f98f9ecdaa06755e4e426fcb1b8ce8c
 AUX vienna-rna-1.8.3-disable-gd.patch 655 RMD160 e918a233e1f1c8f3bee8c721ca793dcde60b2bcb SHA1 97a6f785187ffb9005696a8fa10207b66065b5b0 SHA256 f84d41142fd7368d809895b2feec057ed69d0022c6bfb2b521c7491295e56990
@@ -7,7 +10,16 @@ AUX vienna-rna-1.8.4-implicits.patch 1163 RMD160 489b9a557c7cae23da0491ba7f5f872
 AUX vienna-rna-1.8.4-jobserver-fix.patch 681 RMD160 c72649a57ece3d511cc18f2cac47c7ab103c258d SHA1 0c5e67318c826f12553cf8cb807c3061c1e70574 SHA256 bec5248214ba303d85afda03e663f84061258cd06f2f50773011251299a42b84
 AUX vienna-rna-1.8.4-overflows.patch 740 RMD160 ec5f8a0f22eb7ddc845d515cd7896e90d31ecdbd SHA1 084eea746bf2ae44775063397baa2f9314a05bde SHA256 cd977c5acfca05890768893ab5e18fca5fee167dac341e0edd16bc4fd7cd2a08
 DIST ViennaRNA-1.8.4.tar.gz 1397733 RMD160 29939511e560d898164c21d2452316b0a3a6771e SHA1 6e3a0751849f1b43d4751ce64670a21a3718f040 SHA256 90a5408d05f7dd35031a527d1823607daa8fc8f394b438fb072be78afc7174b7
-EBUILD vienna-rna-1.8.4-r1.ebuild 2442 RMD160 1cf550fbdd5ccad33d78c80dd28daee9d7ca26a7 SHA1 f4f38670188a33cb1573bf9212fcad74e780eb87 SHA256 c50070023678a5ac1d8564a7c3ea1c42e27490ecf10478854ec1bab8697ca1b6
-EBUILD vienna-rna-1.8.4-r2.ebuild 2286 RMD160 47f68939f61cdd3075d1ee568c26b16893924e31 SHA1 8cfccd0b55f7607d78276f5e6b5d150757cb205c SHA256 a7ccbaa4dcbf73dc0c687e270a3dc0f7c6134c94adbd05cebf76f7d638a6529f
-MISC ChangeLog 5496 RMD160 28716bb03cf7b94d00722f5413a90e3a42f926e3 SHA1 684c288fe75cdc1f326e9794505a21f0c279af50 SHA256 ec04f3254f744ab1b3dd8f57d10c4448e6a69b9260447afa78189feac57c7a7f
+DIST ViennaRNA-1.8.5.tar.gz 1306792 RMD160 5c67030f4e9ff2f5d8c4595178c030781f3a2e56 SHA1 c20dd5ffa6d46ea48de5dd1f3d5e6eff8ae2d385 SHA256 f4e2d94beaf77165e8321758e4ab0ad1c5d49879cefa12e48b07d09ed2d0ecf9
+EBUILD vienna-rna-1.8.4-r1.ebuild 2388 RMD160 54055b0e3c32047f18a0d5a495062d7ac60b1ee4 SHA1 ab7741045246a0c6d8ef7850f18f2214144c3096 SHA256 d5c4dffbd110ea0554d04602fcb0520f77f3fc087bf33272432454bcfc3e3a4a
+EBUILD vienna-rna-1.8.4-r2.ebuild 2258 RMD160 5ccabec4d753a975e02635e4613af453a3d101ce SHA1 c1b57e876319787f8e90f0c064e0c1a1a640681c SHA256 81102e45751d57f68bb83821bacc5acd3e7f22a10a05b84f616f9a4ede802570
+EBUILD vienna-rna-1.8.5.ebuild 2215 RMD160 dc81764bb321aa4e66cda6fe89559d9fe7e937e1 SHA1 13d9f7f6b6e498212c940225d8fc046ce29baced SHA256 42be75f81cc0d5a08bd5aa99168ce0405615dbc2737a0e447d1d8939a90f8aeb
+MISC ChangeLog 5670 RMD160 0e559647aafb2fa8c5577318e323494b0f26fc92 SHA1 1f5c7f83f8eb4565df0fc8ef15899fe370e01ae2 SHA256 cbbac12aab6b6d0f436b86b00c306c16052602c5418b7b4a3fffffbf448bc160
 MISC metadata.xml 1210 RMD160 41d50f7af8428b196c4ef855b68dcb657588bb34 SHA1 08f8e1aa88086fd9a3f5fa03fa46c31e12a3f776 SHA256 9c8b3f60f6098accff7c67f26ea07cb5b57e9ed8eae5d3d03949f1718ab6517e
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.17 (GNU/Linux)
+
+iEYEARECAAYFAk2F7/0ACgkQgAnW8HDreRbS6QCgkxl2Kxumk6mnUqWcT504jzRM
+OHIAoMJF0B3xXepnSxW1IyGwvYbzUQXb
+=IvWr
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/vienna-rna/vienna-rna-1.8.4-r1.ebuild b/sci-biology/vienna-rna/vienna-rna-1.8.4-r1.ebuild
index 85685972ae08..03f87f752f23 100644
--- a/sci-biology/vienna-rna/vienna-rna-1.8.4-r1.ebuild
+++ b/sci-biology/vienna-rna/vienna-rna-1.8.4-r1.ebuild
@@ -1,21 +1,22 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.8.4-r1.ebuild,v 1.3 2010/07/15 09:11:27 fauli Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.8.4-r1.ebuild,v 1.4 2011/03/20 12:15:50 jlec Exp $
 
 EAPI="2"
 
 inherit toolchain-funcs multilib autotools perl-module
 
-DESCRIPTION="The Vienna RNA Package - RNA secondary structure prediction and comparison"
-LICENSE="vienna-rna"
-HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA"
+DESCRIPTION="RNA secondary structure prediction and comparison"
+HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/"
 SRC_URI="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-${PV}.tar.gz"
 
+LICENSE="vienna-rna"
 SLOT="0"
 IUSE=""
 KEYWORDS="amd64 ~ppc x86"
 
-DEPEND="dev-lang/perl
+DEPEND="
+	dev-lang/perl
 	media-libs/gd"
 RDEPEND="${DEPEND}"
 
@@ -40,7 +41,7 @@ src_prepare() {
 }
 
 src_configure() {
-	econf --with-cluster || die "Configuration failed."
+	econf --with-cluster
 	sed -e "s:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/$(get_libdir):" \
 		-e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \
 		-i RNAforester/g2-0.70/Makefile \
diff --git a/sci-biology/vienna-rna/vienna-rna-1.8.4-r2.ebuild b/sci-biology/vienna-rna/vienna-rna-1.8.4-r2.ebuild
index 0fffa5e85e05..7821e390c2d6 100644
--- a/sci-biology/vienna-rna/vienna-rna-1.8.4-r2.ebuild
+++ b/sci-biology/vienna-rna/vienna-rna-1.8.4-r2.ebuild
@@ -1,21 +1,22 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.8.4-r2.ebuild,v 1.1 2010/10/15 07:15:15 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.8.4-r2.ebuild,v 1.2 2011/03/20 12:15:50 jlec Exp $
 
 EAPI="2"
 
 inherit toolchain-funcs multilib autotools perl-module
 
-DESCRIPTION="The Vienna RNA Package - RNA secondary structure prediction and comparison"
-LICENSE="vienna-rna"
-HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA"
+DESCRIPTION="RNA secondary structure prediction and comparison"
+HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/"
 SRC_URI="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-${PV}.tar.gz"
 
+LICENSE="vienna-rna"
 SLOT="0"
 IUSE=""
 KEYWORDS="~amd64 ~ppc ~x86"
 
-DEPEND="dev-lang/perl
+DEPEND="
+	dev-lang/perl
 	media-libs/gd"
 RDEPEND="${DEPEND}"
 
@@ -38,7 +39,7 @@ src_prepare() {
 	sed -i '1 i #include <cstdio>' RNAforester/src/rnafuncs.cpp || die
 
 	eautoreconf
-	(cd RNAforester; eautoreconf)
+	cd RNAforester && eautoreconf
 }
 
 src_configure() {
diff --git a/sci-biology/vienna-rna/vienna-rna-1.8.5.ebuild b/sci-biology/vienna-rna/vienna-rna-1.8.5.ebuild
new file mode 100644
index 000000000000..c31ba770d710
--- /dev/null
+++ b/sci-biology/vienna-rna/vienna-rna-1.8.5.ebuild
@@ -0,0 +1,76 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.8.5.ebuild,v 1.1 2011/03/20 12:15:50 jlec Exp $
+
+EAPI="2"
+
+inherit toolchain-funcs multilib autotools perl-module
+
+DESCRIPTION="RNA secondary structure prediction and comparison"
+HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA/"
+SRC_URI="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-${PV}.tar.gz"
+
+LICENSE="vienna-rna"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~ppc ~x86"
+
+DEPEND="
+	dev-lang/perl
+	media-libs/gd"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/ViennaRNA-${PV}"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.6.5-c-fixes.patch
+	"${FILESDIR}"/${PN}-1.7.2-LDFLAGS.patch
+	"${FILESDIR}"/${PN}-1.8.3-gcc4.3.patch
+	"${FILESDIR}"/${PN}-1.8.3-disable-gd.patch
+	"${FILESDIR}"/${PN}-1.8.4-jobserver-fix.patch
+	"${FILESDIR}"/${PN}-1.8.4-bindir.patch
+	"${FILESDIR}"/${PN}-1.8.4-overflows.patch
+	"${FILESDIR}"/${PN}-1.8.4-implicits.patch
+)
+
+src_prepare() {
+	base_src_prepare
+	sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
+
+	eautoreconf
+	cd RNAforester && eautoreconf
+}
+
+src_configure() {
+	econf --with-cluster
+	sed -e "s:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/$(get_libdir):" \
+		-e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \
+		-i RNAforester/g2-0.70/Makefile \
+			|| die "Failed patching RNAForester build system."
+	sed -e "s:CC=cc:CC=$(tc-getCC):" -e "s:CFLAGS=:CFLAGS=${CFLAGS}:" \
+		-i Readseq/Makefile || die "Failed patching readseq Makefile."
+}
+
+src_compile() {
+	emake clean || die
+	emake || die
+	emake -C Readseq || die "Failed to compile readseq."
+	# TODO: Add (optional?) support for the NCBI toolkit.
+}
+
+src_test() {
+	cd "${S}"/Perl && emake check || die "Perl tests failed"
+	cd "${S}"/Readseq && emake test || die "Readseq tests failed"
+}
+
+src_install() {
+	emake DESTDIR="${D}" install || die
+	dodoc AUTHORS ChangeLog NEWS README THANKS || die
+	newbin Readseq/readseq readseq-vienna || die
+	dodoc Readseq/Readseq.help || die
+	newdoc Readseq/Readme README.readseq || die
+	newdoc Readseq/Formats Formats.readseq || die
+
+	# remove perlocal.pod to avoid file collisions (see #240358)
+	fixlocalpod || die "Failed to remove perlocal.pod"
+}