sci-biology/vaal: Drop old, #309127; Handle openmp, don't install license

(Portage version: 2.2.0_alpha112/cvs/Linux x86_64)

4 files changed, 30 insertions, 54 deletions

diff --git a/sci-biology/vaal/ChangeLog b/sci-biology/vaal/ChangeLog
index 0decdfec329d..aaf5089dc5ca 100644
--- a/sci-biology/vaal/ChangeLog
+++ b/sci-biology/vaal/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/vaal
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/ChangeLog,v 1.8 2012/06/25 18:42:57 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/ChangeLog,v 1.9 2012/06/25 18:50:32 jlec Exp $
+
+  25 Jun 2012; Justin Lecher <jlec@gentoo.org> -vaal-1.2-r1.ebuild,
+  vaal-1.6.ebuild, files/vaal-1.6-respect-flags.patch:
+  Drop old, #309127; Handle openmp, don't install license
 
   25 Jun 2012; Kacper Kowalik <xarthisius@gentoo.org>
   +files/vaal-1.6-gcc47.patch, files/vaal-1.6-respect-flags.patch,
diff --git a/sci-biology/vaal/files/vaal-1.6-respect-flags.patch b/sci-biology/vaal/files/vaal-1.6-respect-flags.patch
index 2004cc7e23ff..152fb423e924 100644
--- a/sci-biology/vaal/files/vaal-1.6-respect-flags.patch
+++ b/sci-biology/vaal/files/vaal-1.6-respect-flags.patch
@@ -6,7 +6,7 @@ diff -dur vaal-33805.orig/configure.ac vaal-33805/configure.ac
  AC_OPENMP_CEHCK
  
 -CXXFLAGS=" -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -O3 -ggdb3  -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote ."
-+CXXFLAGS=" ${CXXFLAGS} -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote ."
++CXXFLAGS+=" -imacros config.h -Wextra -Wall -Wno-unused -ansi -pedantic -Wno-long-long -Wsign-promo -Woverloaded-virtual -Wendif-labels  -ftemplate-depth-50 -Wno-deprecated -Wno-parentheses -fno-strict-aliasing -mieee-fp -iquote ."
  
  OS_RELEASE="`uname -r`"
  AC_SUBST(CXXFLAGS)
diff --git a/sci-biology/vaal/vaal-1.2-r1.ebuild b/sci-biology/vaal/vaal-1.2-r1.ebuild
deleted file mode 100644
index ead9c7a77f65..000000000000
--- a/sci-biology/vaal/vaal-1.2-r1.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/vaal-1.2-r1.ebuild,v 1.1 2010/02/14 19:50:10 weaver Exp $
-
-EAPI="2"
-
-inherit base
-
-DESCRIPTION="A variant ascertainment algorithm that can be used to detect SNPs, indels, and other polymorphisms"
-HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
-SRC_URI="ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL.${PV}.tgz
-	ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc"
-
-LICENSE="Whitehead-MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=">=dev-libs/boost-1.37.0"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-gcc-x86-no-autocast.patch
-	"${FILESDIR}"/${P}-as-needed.patch
-	"${FILESDIR}"/${P}-respect-flags.patch
-)
-
-S="${WORKDIR}/VAAL"
-
-src_install() {
-	exeinto /usr/libexec/${PN}
-	doexe bin/* || die
-	echo "PATH=\"/usr/libexec/${PN}\"" > "${S}/99${PN}"
-	doenvd "${S}/99${PN}" || die
-	dosym /usr/libexec/${PN}/VAALrun /usr/bin/VAALrun || die
-	insinto /usr/share/doc/${PF}
-	doins "${DISTDIR}/VAAL_manual.doc"
-}
diff --git a/sci-biology/vaal/vaal-1.6.ebuild b/sci-biology/vaal/vaal-1.6.ebuild
index f836a0393ec9..719765aec7ba 100644
--- a/sci-biology/vaal/vaal-1.6.ebuild
+++ b/sci-biology/vaal/vaal-1.6.ebuild
@@ -1,20 +1,23 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/vaal-1.6.ebuild,v 1.4 2012/06/25 18:42:57 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vaal/vaal-1.6.ebuild,v 1.5 2012/06/25 18:50:32 jlec Exp $
 
-EAPI="2"
+EAPI=4
 
-inherit base autotools
+AUTOTOOLS_AUTORECONF=yes
+
+inherit autotools-utils
 
 DESCRIPTION="A variant ascertainment algorithm that can be used to detect SNPs, indels, and other polymorphisms"
-HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
-SRC_URI="ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL.${PV}.tgz
+HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd/"
+SRC_URI="
+	ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL.${PV}.tgz
 	ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc"
 
 LICENSE="Whitehead-MIT"
 SLOT="0"
-IUSE=""
-KEYWORDS="amd64"
+KEYWORDS="amd64 ~x86"
+IUSE="openmp"
 
 DEPEND=">=dev-libs/boost-1.41.0-r3"
 RDEPEND="${DEPEND}"
@@ -24,15 +27,22 @@ PATCHES=(
 	"${FILESDIR}"/${P}-gcc47.patch
 )
 
-S=${WORKDIR}/vaal-33805
+DOCS=( "${DISTDIR}/VAAL_manual.doc" )
+
+S="${WORKDIR}/vaal-33805"
 
 src_prepare() {
-	base_src_prepare
-	eautoreconf
+	sed \
+		-e '/COPYING/d' \
+		-i src/Makefile.am || die
+
+	sed \
+		-e '/AC_OPENMP_CEHCK/d' \
+		-i configure.ac || die
+	autotools-utils_src_prepare
 }
 
-src_install() {
-	einstall || die
-	insinto /usr/share/doc/${PF}
-	doins "${DISTDIR}/VAAL_manual.doc"
+src_configure(){
+	local myeconfargs=( $(use_enable openmp) )
+	autotools-utils_src_configure
 }