From ec51fb15a29a8049f3d27dc8ae64bdd759c79d17 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Sun, 20 Mar 2011 12:15:50 +0000 Subject: Version Bump Package-Manager: portage-2.2.0_alpha28/cvs/Linux x86_64 --- sci-biology/vienna-rna/ChangeLog | 10 ++- sci-biology/vienna-rna/Manifest | 18 +++++- sci-biology/vienna-rna/vienna-rna-1.8.4-r1.ebuild | 15 ++--- sci-biology/vienna-rna/vienna-rna-1.8.4-r2.ebuild | 15 ++--- sci-biology/vienna-rna/vienna-rna-1.8.5.ebuild | 76 +++++++++++++++++++++++ 5 files changed, 115 insertions(+), 19 deletions(-) create mode 100644 sci-biology/vienna-rna/vienna-rna-1.8.5.ebuild (limited to 'sci-biology/vienna-rna') 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 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 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(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 ' 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" +} -- cgit v1.2.3-65-gdbad