Removed alpha and beta versions. New version. Removed dependency on X11.

(Portage version: 2.0.54)

8 files changed, 63 insertions, 75 deletions

diff --git a/sci-biology/vienna-rna/ChangeLog b/sci-biology/vienna-rna/ChangeLog
index af7939b49a1d..7d246d19d838 100644
--- a/sci-biology/vienna-rna/ChangeLog
+++ b/sci-biology/vienna-rna/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/vienna-rna
-# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.7 2005/10/19 02:52:02 ribosome Exp $
+# Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.8 2006/02/03 04:50:55 ribosome Exp $
+
+*vienna-rna-1.6 (03 Feb 2006)
+
+  03 Feb 2006; Olivier Fisette <ribosome@gentoo.org>
+  -vienna-rna-1.5_beta.ebuild, -vienna-rna-1.6_alpha.ebuild,
+  +vienna-rna-1.6.ebuild:
+  Removed alpha and beta versions. New version. Removed dependency on X11.
 
 *vienna-rna-1.6_alpha (19 Oct 2005)
 
diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest
index f90280beb2dd..8b0b953e1091 100644
--- a/sci-biology/vienna-rna/Manifest
+++ b/sci-biology/vienna-rna/Manifest
@@ -1,8 +1,10 @@
-MD5 3bb50b8cfbc48270128a17049473d2d4 vienna-rna-1.4.ebuild 2407
-MD5 1bf4f8374ea8e5f35b1c88ba10ce7349 vienna-rna-1.5_beta.ebuild 833
 MD5 7651da38e8c4fa0f89a722278b9929e6 ChangeLog 1320
-MD5 07151097bf19cf3d886552b62d5f13c4 metadata.xml 1317
-MD5 903982bac76cfedcd174f94458145fe8 vienna-rna-1.6_alpha.ebuild 1079
 MD5 f1a1d167e6d5e17687cee4ffb95c6044 files/digest-vienna-rna-1.4 65
-MD5 570ea507ab248c0d5cf89fe326ac57ef files/digest-vienna-rna-1.6_alpha 71
 MD5 d44512d781a7870d4d116af561bb3e75 files/digest-vienna-rna-1.5_beta 69
+MD5 6f5659558516fa70fdc62ca69172db47 files/digest-vienna-rna-1.6 66
+MD5 570ea507ab248c0d5cf89fe326ac57ef files/digest-vienna-rna-1.6_alpha 71
+MD5 07151097bf19cf3d886552b62d5f13c4 metadata.xml 1317
+MD5 3bb50b8cfbc48270128a17049473d2d4 vienna-rna-1.4.ebuild 2407
+MD5 1bf4f8374ea8e5f35b1c88ba10ce7349 vienna-rna-1.5_beta.ebuild 833
+MD5 453fb67caea7e32cf83c5e5d14f17ee3 vienna-rna-1.6.ebuild 1586
+MD5 903982bac76cfedcd174f94458145fe8 vienna-rna-1.6_alpha.ebuild 1079
diff --git a/sci-biology/vienna-rna/files/digest-vienna-rna-1.5_beta b/sci-biology/vienna-rna/files/digest-vienna-rna-1.5_beta
deleted file mode 100644
index c6d97162531a..000000000000
--- a/sci-biology/vienna-rna/files/digest-vienna-rna-1.5_beta
+++ /dev/null
@@ -1 +0,0 @@
-MD5 f8737e07fc82ccd130cc30bfd09ccca5 ViennaRNA-1.5beta.tar.gz 640555
diff --git a/sci-biology/vienna-rna/files/digest-vienna-rna-1.6 b/sci-biology/vienna-rna/files/digest-vienna-rna-1.6
new file mode 100644
index 000000000000..5057a248d697
--- /dev/null
+++ b/sci-biology/vienna-rna/files/digest-vienna-rna-1.6
@@ -0,0 +1 @@
+MD5 d80af9db77fc68375980bea39158b32c ViennaRNA-1.6.tar.gz 1159849
diff --git a/sci-biology/vienna-rna/files/digest-vienna-rna-1.6_alpha b/sci-biology/vienna-rna/files/digest-vienna-rna-1.6_alpha
deleted file mode 100644
index b37c61d86f35..000000000000
--- a/sci-biology/vienna-rna/files/digest-vienna-rna-1.6_alpha
+++ /dev/null
@@ -1 +0,0 @@
-MD5 d4f55fdaddb9443b26f619b2ed86608f ViennaRNA-1.6alpha.tar.gz 1366101
diff --git a/sci-biology/vienna-rna/vienna-rna-1.5_beta.ebuild b/sci-biology/vienna-rna/vienna-rna-1.5_beta.ebuild
deleted file mode 100644
index 83961a8153a7..000000000000
--- a/sci-biology/vienna-rna/vienna-rna-1.5_beta.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.5_beta.ebuild,v 1.2 2005/08/30 00:16:56 ribosome Exp $
-
-inherit flag-o-matic
-
-DESCRIPTION="The Vienna RNA Package - RNA secondary structure prediction and comparison"
-LICENSE="vienna-rna"
-HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA"
-SRC_URI="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-1.5beta.tar.gz"
-
-KEYWORDS="x86 ~ppc"
-SLOT=0
-IUSE=""
-
-DEPEND="dev-lang/perl"
-
-S="${WORKDIR}/ViennaRNA-1.5"
-
-src_compile() {
-	append-flags "-fPIC"
-	econf || die
-	emake || die
-}
-
-src_install() {
-	make install DESTDIR=${D}
-	newbin Readseq/readseq readseq-vienna
-	dodoc AUTHORS ChangeLog NEWS README THANKS Readseq/Readseq.help
-	newdoc Readseq/Readme README.readseq
-}
diff --git a/sci-biology/vienna-rna/vienna-rna-1.6.ebuild b/sci-biology/vienna-rna/vienna-rna-1.6.ebuild
new file mode 100644
index 000000000000..c0fda506595a
--- /dev/null
+++ b/sci-biology/vienna-rna/vienna-rna-1.6.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.6.ebuild,v 1.1 2006/02/03 04:50:55 ribosome Exp $
+
+inherit toolchain-funcs
+
+DESCRIPTION="The Vienna RNA Package - RNA secondary structure prediction and comparison"
+LICENSE="vienna-rna"
+HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA"
+SRC_URI="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-${PV}.tar.gz"
+
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86 ~ppc"
+
+DEPEND="dev-lang/perl
+	media-libs/gd"
+
+S="${WORKDIR}/ViennaRNA-${PV}"
+
+src_compile() {
+	econf --with-cluster || die "Configuration failed."
+	cd "${S}"/RNAforester/g2-0.70
+	sed -e "s:LIBDIR = /usr/lib:LIBDIR = ${D}/usr/lib:" \
+		-e "s:INCDIR = /usr/include:INCDIR = ${D}/usr/include:" \
+		-i Makefile || die "Failed patching RNAForester build system."
+	cd "${S}"
+	emake || die "Compilation failed."
+	cd "${S}"/Readseq
+	sed -e "s:CC=cc:CC=$(tc-getCC):" -e "s:CFLAGS=:CFLAGS=${CFLAGS}:" \
+		-i Makefile || die "Failed patching readseq Makefile."
+	make || die "Failed to compile readseq."
+	# TODO: Add (optional?) support for the NCBI toolkit.
+}
+
+src_install() {
+	make install DESTDIR="${D}" || die "Installation failed."
+	dodoc AUTHORS ChangeLog NEWS README THANKS || \
+		die "Failed to install documentation."
+	newbin Readseq/readseq readseq-vienna || die \
+		"Installing readseq failed."
+	dodoc Readseq/Readseq.help || die \
+		"Readseq Documentation installation failed."
+	newdoc Readseq/Readme README.readseq || die \
+		"Installing readseq Readme failed."
+}
diff --git a/sci-biology/vienna-rna/vienna-rna-1.6_alpha.ebuild b/sci-biology/vienna-rna/vienna-rna-1.6_alpha.ebuild
deleted file mode 100644
index 85a0ba8ec4d5..000000000000
--- a/sci-biology/vienna-rna/vienna-rna-1.6_alpha.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.6_alpha.ebuild,v 1.1 2005/10/19 02:52:02 ribosome Exp $
-
-inherit flag-o-matic
-
-DESCRIPTION="The Vienna RNA Package - RNA secondary structure prediction and comparison"
-LICENSE="vienna-rna"
-HOMEPAGE="http://www.tbi.univie.ac.at/~ivo/RNA"
-SRC_URI="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-1.6alpha.tar.gz"
-
-SLOT="0"
-IUSE=""
-KEYWORDS="~x86 ~ppc"
-
-DEPEND="dev-lang/perl
-	virtual/x11
-	media-libs/gd"
-
-S="${WORKDIR}/ViennaRNA-1.6"
-
-src_compile() {
-	econf --with-cluster --without-forester || die "Configuration failed."
-	emake || die "Compilation failed."
-}
-
-src_install() {
-	make install DESTDIR="${D}" || die "Installation failed."
-	newbin Readseq/readseq readseq-vienna || die \
-		"Installing programs failed."
-	dodoc AUTHORS ChangeLog NEWS README THANKS Readseq/Readseq.help || die \
-		"Document installation failed."
-	newdoc Readseq/Readme README.readseq || die \
-		"Installing Readme failed."
-}