[gentoo-commits] repo/gentoo:master commit in: sci-biology/vaal/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/vaal/

[David Seifert]

commit:     6decdcc1f979feaaf223a2b2e237946d3f0c704c
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 24 16:46:33 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Tue Jan 24 16:46:33 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6decdcc1

sci-biology/vaal: Remove old

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/vaal/vaal-46233.ebuild | 42 --------------------------------------
 1 file changed, 42 deletions(-)

diff --git a/sci-biology/vaal/vaal-46233.ebuild b/sci-biology/vaal/vaal-46233.ebuild
deleted file mode 100644
index 6aee878..00000000
--- a/sci-biology/vaal/vaal-46233.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-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/latest_source_code/${P}.tar.gz
-	ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc"
-
-LICENSE="Whitehead-MIT"
-SLOT="0"
-KEYWORDS="amd64"
-IUSE="openmp"
-
-DEPEND=">=dev-libs/boost-1.41.0-r3"
-RDEPEND="${DEPEND}"
-
-DOCS=( "${DISTDIR}/VAAL_manual.doc" )
-
-src_prepare() {
-	sed \
-		-e '/COPYING/d' \
-		-i src/Makefile.am || die
-
-	sed \
-		-e 's:-ggdb::g' \
-		-e '/AC_OPENMP_CEHCK/d' \
-		-i configure.ac || die
-	autotools-utils_src_prepare
-}
-
-src_configure(){
-	local myeconfargs=( $(use_enable openmp) )
-	autotools-utils_src_configure
-}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/vaal/

[Agostino Sarubbo]

commit:     eed30494742186559b07ab88794e1fdd91272c71
Author:     Agostino Sarubbo <ago <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 24 09:05:50 2017 +0000
Commit:     Agostino Sarubbo <ago <AT> gentoo <DOT> org>
CommitDate: Tue Jan 24 09:05:50 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=eed30494

sci-biology/vaal: amd64 stable wrt bug #606960

Package-Manager: portage-2.3.0
RepoMan-Options: --include-arches="amd64"
Signed-off-by: Agostino Sarubbo <ago <AT> gentoo.org>

 sci-biology/vaal/vaal-46233-r2.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/vaal/vaal-46233-r2.ebuild b/sci-biology/vaal/vaal-46233-r2.ebuild
index cb10e8e..2d66fae 100644
--- a/sci-biology/vaal/vaal-46233-r2.ebuild
+++ b/sci-biology/vaal/vaal-46233-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -14,7 +14,7 @@ SRC_URI="
 
 LICENSE="Whitehead-MIT"
 SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS="amd64"
 IUSE="openmp"
 
 RDEPEND="

[gentoo-commits] repo/gentoo:master commit in: sci-biology/vaal/

[David Seifert]

commit:     6fcc8510a6610468329a8eafe307273e523f8719
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 17 10:51:29 2016 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jan 17 10:52:26 2016 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6fcc8510

sci-biology/vaal: Place blockers on sci-biology/allpaths{,lg}

Gentoo-Bug: 572128

Package-Manager: portage-2.2.26

 .../vaal/{vaal-46233-r1.ebuild => vaal-46233-r2.ebuild}    | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/sci-biology/vaal/vaal-46233-r1.ebuild b/sci-biology/vaal/vaal-46233-r2.ebuild
similarity index 78%
rename from sci-biology/vaal/vaal-46233-r1.ebuild
rename to sci-biology/vaal/vaal-46233-r2.ebuild
index 20b3bf0..cb10e8e 100644
--- a/sci-biology/vaal/vaal-46233-r1.ebuild
+++ b/sci-biology/vaal/vaal-46233-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -17,11 +17,17 @@ SLOT="0"
 KEYWORDS="~amd64"
 IUSE="openmp"
 
-DEPEND=">=dev-libs/boost-1.41.0-r3"
-RDEPEND="${DEPEND}"
+RDEPEND="
+	!sci-biology/allpaths
+	!sci-biology/allpathslg"
+DEPEND="
+	${RDEPEND}
+	dev-libs/boost"
 
 DOCS=( "${DISTDIR}/VAAL_manual.doc" )
-PATCHES=( "${FILESDIR}/${P}_remove-namespace-std.patch" )
+PATCHES=(
+	"${FILESDIR}/${P}_remove-namespace-std.patch"
+)
 
 src_prepare() {
 	sed \