sci-biology/vienna-rna: Cleaned old

Package-Manager: portage-2.2.0_alpha116/cvs/Linux x86_64

5 files changed, 21 insertions, 167 deletions

diff --git a/sci-biology/vienna-rna/ChangeLog b/sci-biology/vienna-rna/ChangeLog
index 6280263d5a5f..70f828adeae7 100644
--- a/sci-biology/vienna-rna/ChangeLog
+++ b/sci-biology/vienna-rna/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/vienna-rna
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.44 2012/07/10 18:02:37 ranger Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.45 2012/07/10 18:58:02 jlec Exp $
+
+  10 Jul 2012; Justin Lecher <jlec@gentoo.org> -vienna-rna-1.8.4-r1.ebuild,
+  -vienna-rna-1.8.4-r2.ebuild, metadata.xml:
+  Cleaned old
 
   10 Jul 2012; Brent Baude <ranger@gentoo.org> vienna-rna-1.8.5.ebuild:
   Marking vienna-rna-1.8.5 ppc for bug 393867
diff --git a/sci-biology/vienna-rna/Manifest b/sci-biology/vienna-rna/Manifest
index de88dfd972b1..8d060e948224 100644
--- a/sci-biology/vienna-rna/Manifest
+++ b/sci-biology/vienna-rna/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA256
+
 AUX vienna-rna-1.6.5-c-fixes.patch 728 SHA256 49955a6244eb3be73f8d2472f3a4f9b8d1f8f92ba11327961b901a2c1f1e24d8 SHA512 5c3694d595e8382a3946366ddae9be2556d4b772fbf20fc2c8612b707b3b8d5f797d5b04d1ed48966f8ec6eb9a846830c12d574293b05e016ad4eacf8196c122 WHIRLPOOL a73d73eed88a62257db1e3033382c0e1acaf110a634034b13c58e78818ffd22e18c96ea049af824037ebc77184ecc431d4a965f0cc03f3e6f6ff949e5bce6269
 AUX vienna-rna-1.7.2-LDFLAGS.patch 978 SHA256 0c7db17c7a1a8a075e26f6b98b19c84a3f98f9ecdaa06755e4e426fcb1b8ce8c SHA512 a5fea1fc9c969d2bde9094b8303ee5d0b77f0570107d403279bcc3884d2925f81789d3d08627caadf92f435bbf369721dbc95e1122bde5741340104526a532b2 WHIRLPOOL 82d3e59c9a399cd352f72477fc9803012ef288e3198b0c69e86ce184cfe75c1c824b149b6ea55771da88180d9d402e1d8ed8444aac1f1bcd9211ded54f15d917
 AUX vienna-rna-1.8.3-disable-gd.patch 655 SHA256 f84d41142fd7368d809895b2feec057ed69d0022c6bfb2b521c7491295e56990 SHA512 65d185600f8329611fbe2ab280f77074d5a4a5785d98e81c3a19e648c6812d1040be9623eb632705e0e1f0f65e59686aaabdbe36dc09cfcd5368c4cd7bb539f3 WHIRLPOOL 10b30ff93fa16b2ae09601ce02238453fc13a3a7fe4f1bede2a30de028939697717dc7b75b52d32397773d04e87fd8f415cf49f024fd875f7e496b17c114f47b
@@ -7,10 +10,15 @@ AUX vienna-rna-1.8.4-implicits.patch 1163 SHA256 f49e60dc866e7844fea32e90b9e91ce
 AUX vienna-rna-1.8.4-jobserver-fix.patch 681 SHA256 bec5248214ba303d85afda03e663f84061258cd06f2f50773011251299a42b84 SHA512 33ddeb32bb5739081b7c9f9d863f9b4760cb72764bd3e5e2181a9859579e76261af31726021bd3c183862ada1bb5e81aa93b380fa44935b82c296a4b79a64b21 WHIRLPOOL 84af3a01b5b38f11e680ee896dcb93f21828da5aa0f021dce672182725d6a0cbe10df26bec8760b9800e972916a66fea02c78a2d1d3a3f24412b29ca326a07d6
 AUX vienna-rna-1.8.4-overflows.patch 740 SHA256 cd977c5acfca05890768893ab5e18fca5fee167dac341e0edd16bc4fd7cd2a08 SHA512 17bed70ff24f452f042dcf14f303941f21e309c96ffcb2ac38a82cc80a85806d9f8a0d9923ca4446ee021d7f156ab82ac402c51f0178aa180f5893720f57c48e WHIRLPOOL 1f6ba4c537658e383768551561002235bb2c2ed948651898cdb5b24857fa2feb6160586e622e40105f01e7962404a1b9473be6a0f509eb93f14135c98782395c
 AUX vienna-rna-1.8.5-setup.py 810 SHA256 91e4caa304aa97430552f2a3a46f57ced23239d55b1a52a658bbcf91e0835f62 SHA512 85587e631ed98c5f10ab4000a6fe4e2ff7f230e11449f3f8d99e578a56e70b15362bb929f2ddf715065197ac22877f6de253fa8e113ddea276a43ad673bca8aa WHIRLPOOL e1fdf83df88c366d8bf0cac5ba1a5b14b37720fc820a9640e91e890de77e0566763643a0a160699985143f1ed3ef37adf2bff29720b053e881557f2bbe3411a3
-DIST ViennaRNA-1.8.4.tar.gz 1397733 RMD160 29939511e560d898164c21d2452316b0a3a6771e SHA1 6e3a0751849f1b43d4751ce64670a21a3718f040 SHA256 90a5408d05f7dd35031a527d1823607daa8fc8f394b438fb072be78afc7174b7
-DIST ViennaRNA-1.8.5.tar.gz 1306792 RMD160 5c67030f4e9ff2f5d8c4595178c030781f3a2e56 SHA1 c20dd5ffa6d46ea48de5dd1f3d5e6eff8ae2d385 SHA256 f4e2d94beaf77165e8321758e4ab0ad1c5d49879cefa12e48b07d09ed2d0ecf9
-EBUILD vienna-rna-1.8.4-r1.ebuild 2470 SHA256 866cf64631b76be36341ed24a9e061b07c8eef6f1a0546d84a7543c2881135d7 SHA512 e13e5e1f4d2269c2b77cbce461da26f642e06619bd3081fde837bda5d28cfe16fe96c18ef9816d10405ae953dcff8a7b7675a59bcebc0f91d91951f65fa9aecf WHIRLPOOL c85eaba0f6d4dad3ccaf4b1fbc95c9651c58051e2a04d864cba18cc544b8508cfd663ec93cb94fcae7c001a2c6e9648572618a8b026c3a502bf6709de56c4217
-EBUILD vienna-rna-1.8.4-r2.ebuild 2338 SHA256 e762b0a04f2288f0c767f888d874c8ef0abcb722999f619398be2b2516fd1959 SHA512 7657f7ddcdbbb4c993ae0d99eece24c044849e59741de056271474eefe787677c981335d2a1a8b5a5887feaba680085b4d044637904a73061d034842ea6c3e1f WHIRLPOOL 9f3629ed154c9eeb6e265f5348e6f5da55c97411b640620a592878a26a9532a13ebb4b95c4bdbc7010186abdd8a15a654d9c8b58187396a1569dfb0ab1909fbc
+DIST ViennaRNA-1.8.5.tar.gz 1306792 SHA256 f4e2d94beaf77165e8321758e4ab0ad1c5d49879cefa12e48b07d09ed2d0ecf9
 EBUILD vienna-rna-1.8.5.ebuild 2779 SHA256 f7895bd94c952187f32627a59aff36aaaf70d03a45ee2bb0b4b55b520ef43e5d SHA512 f0438b1fa52e5210887b4aefd61687845c7163b0e54e57196505c305bfe10bb508ac219ac00984aec2ed54e206e3a35a22d6191484a37ff9954b8465046cb036 WHIRLPOOL ed777176b6936d3039df5c4e99b7f0bf907d51fe28d172c1864110d540a66b1a62514d80a5305f8cbef1412cdb72e42287e21a9226042acc5bfb55dc8bcaa7c7
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diff --git a/sci-biology/vienna-rna/metadata.xml b/sci-biology/vienna-rna/metadata.xml
index 925c942d9fed..a7da09cf6677 100644
--- a/sci-biology/vienna-rna/metadata.xml
+++ b/sci-biology/vienna-rna/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-biology</herd>
-<longdescription>
+	<herd>sci-biology</herd>
+	<longdescription>
 	The Vienna RNA Package consists of a C code library and several
 	stand-alone programs for the prediction and comparison of RNA secondary
 	structures. RNA secondary structure prediction through energy
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
deleted file mode 100644
index de0595b9a5fd..000000000000
--- a/sci-biology/vienna-rna/vienna-rna-1.8.4-r1.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2012 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 1.7 2012/02/26 01:44:58 patrick 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
-	"${FILESDIR}"/${P}-jobserver-fix.patch
-	"${FILESDIR}"/${P}-bindir.patch
-)
-
-src_prepare() {
-	base_src_prepare
-	sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
-	sed -i '1 i #include <cstdio>' RNAforester/src/rnafuncs.cpp || die
-	sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' Perl/Makefile.am || 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=${CFLAGS}:" \
-		-i Readseq/Makefile || die "Failed patching readseq Makefile."
-}
-
-src_compile() {
-	emake clean || die
-	emake || die "Compilation failed."
-	emake -C Readseq || die "Failed to compile readseq."
-	# TODO: Add (optional?) support for the NCBI toolkit.
-}
-
-src_test() {
-	cd "${S}"/Perl && emake check || die "Perl tests failed"
-	cd "${S}"/Readseq && emake test || die "Readseq tests failed"
-}
-
-src_install() {
-	make install DESTDIR="${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 && \
-		newdoc Readseq/Formats Formats.readseq \
-		|| die "Installing readseq Readme failed."
-
-	# remove perlocal.pod to avoid file collisions (see #240358)
-	fixlocalpod || die "Failed to remove perlocal.pod"
-}
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
deleted file mode 100644
index 84f8fb36ab68..000000000000
--- a/sci-biology/vienna-rna/vienna-rna-1.8.4-r2.ebuild
+++ /dev/null
@@ -1,78 +0,0 @@
-# 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 1.3 2011/03/20 20:32:09 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
-	"${FILESDIR}"/${P}-jobserver-fix.patch
-	"${FILESDIR}"/${P}-bindir.patch
-	"${FILESDIR}"/${P}-overflows.patch
-	"${FILESDIR}"/${P}-implicits.patch
-)
-
-src_prepare() {
-	base_src_prepare
-	sed -i 's/ getline/ v_getline/' Readseq/ureadseq.c || die
-	sed -i '1 i #include <cstdio>' RNAforester/src/rnafuncs.cpp || die
-	sed -i 's/@PerlCmd@ Makefile.PL/& INSTALLDIRS=vendor/' Perl/Makefile.am || 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"
-}