[gentoo-commits] gentoo-x86 commit in sci-biology/vienna-rna: metadata.xml ChangeLog vienna-rna-1.8.3.ebuild vienna-rna-1.4.ebuild vienna-rna-1.7.0.ebuild

[Andrey Kislyuk (weaver)]

weaver      09/09/10 18:43:01

  Modified:             metadata.xml ChangeLog
  Added:                vienna-rna-1.8.3.ebuild
  Removed:              vienna-rna-1.4.ebuild vienna-rna-1.7.0.ebuild
  Log:
  Version bump and cleanup
  (Portage version: 2.2_rc30/cvs/Linux x86_64)

Revision  Changes    Path
1.5                  sci-biology/vienna-rna/metadata.xml

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/metadata.xml?rev=1.5&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/metadata.xml?rev=1.5&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/metadata.xml?r1=1.4&r2=1.5

Index: metadata.xml
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/metadata.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- metadata.xml	6 Aug 2008 15:06:58 -0000	1.4
+++ metadata.xml	10 Sep 2009 18:43:01 -0000	1.5
@@ -19,10 +19,4 @@
 	(Shapiro and Zhang 1990). Finally, we provide an algorithm to design
 	sequences with a predefined structure (inverse folding).
 </longdescription>
-<use>
-  <flag name='no-readseq'>Do not include the modified version of Don Gilbert's
-    readseq program</flag>
-  <flag name='no-utils'>Do not include sequence format conversion and
-    representation utilities</flag>
-</use>
 </pkgmetadata>



1.21                 sci-biology/vienna-rna/ChangeLog

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/ChangeLog?rev=1.21&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/ChangeLog?rev=1.21&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/ChangeLog?r1=1.20&r2=1.21

Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -r1.20 -r1.21
--- ChangeLog	30 Jul 2009 08:31:01 -0000	1.20
+++ ChangeLog	10 Sep 2009 18:43:01 -0000	1.21
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/vienna-rna
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.20 2009/07/30 08:31:01 ssuominen Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.21 2009/09/10 18:43:01 weaver Exp $
+
+*vienna-rna-1.8.3 (10 Sep 2009)
+
+  10 Sep 2009; Andrey Kislyuk <weaver@g.o>
+  +files/vienna-rna-1.8.3-gcc4.3.patch, +vienna-rna-1.8.3.ebuild:
+  Version bump and cleanup
 
   30 Jul 2009; Samuli Suominen <ssuominen@g.o>
   vienna-rna-1.7.2.ebuild, +files/vienna-rna-1.7.2-gcc4.4.patch:



1.1                  sci-biology/vienna-rna/vienna-rna-1.8.3.ebuild

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.8.3.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.8.3.ebuild?rev=1.1&content-type=text/plain

Index: vienna-rna-1.8.3.ebuild
===================================================================
# Copyright 1999-2009 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.8.3.ebuild,v 1.1 2009/09/10 18:43:01 weaver 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"
SRC_URI="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-${PV}.tar.gz"

SLOT="0"
IUSE=""
KEYWORDS="~amd64 ~x86 ~ppc"

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
	"${FILESDIR}"/${P}-gcc4.3.patch
	"${FILESDIR}"/${P}-disable-gd.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 || die "Configuration failed."
	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 || 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"
}