From 8ee85fd0668f17101b4dd8ad1b35ee0194521184 Mon Sep 17 00:00:00 2001
From: David Seifert <soap@gentoo.org>
Date: Sat, 24 Sep 2016 17:03:46 +0200
Subject: sci-libs/libmems: Allow for compiling with GCC 6

Gentoo-bug: 594814
* Patch taken from Debian
* Add sub-slot operator for dev-libs/boost
* Delete .la files

Package-Manager: portage-2.3.1
---
 .../libmems/files/libmems-1.6_p1-fix-c++14.patch   | 18 ++++++++
 sci-libs/libmems/libmems-1.6_p1-r1.ebuild          | 37 ----------------
 sci-libs/libmems/libmems-1.6_p1-r2.ebuild          | 50 ++++++++++++++++++++++
 3 files changed, 68 insertions(+), 37 deletions(-)
 create mode 100644 sci-libs/libmems/files/libmems-1.6_p1-fix-c++14.patch
 delete mode 100644 sci-libs/libmems/libmems-1.6_p1-r1.ebuild
 create mode 100644 sci-libs/libmems/libmems-1.6_p1-r2.ebuild

(limited to 'sci-libs')

diff --git a/sci-libs/libmems/files/libmems-1.6_p1-fix-c++14.patch b/sci-libs/libmems/files/libmems-1.6_p1-fix-c++14.patch
new file mode 100644
index 000000000000..bde8efeb4c9c
--- /dev/null
+++ b/sci-libs/libmems/files/libmems-1.6_p1-fix-c++14.patch
@@ -0,0 +1,18 @@
+Description: Correct compilation with g++-6
+Author: Gert Wollny <gw.fossdev@gmail.com>
+Bug-Debian: https://bugs.debian.org/811870
+Forwarded: yes
+Bug: https://sourceforge.net/p/mauve/bugs/46/
+Last-Update: 2016-06-30
+
+--- a/libMems/ProgressiveAligner.cpp
++++ b/libMems/ProgressiveAligner.cpp
+@@ -1599,7 +1599,7 @@
+ 		c.SetLeftEnd(child_1, ancestral_matches[mI]->LeftEnd(1));
+ 		c.SetOrientation(child_1, ancestral_matches[mI]->Orientation(1));
+ 		c.SetLength(ancestral_matches[mI]->Length(1), child_1);
+-		cga_list.push_back(make_tuple(c.Copy(), &bs[mI], ancestral_matches[mI]));
++		cga_list.push_back(boost::tuples::make_tuple(c.Copy(), &bs[mI], ancestral_matches[mI]));
+ 	}
+ 
+ 	stack<node_id_t> node_stack;
diff --git a/sci-libs/libmems/libmems-1.6_p1-r1.ebuild b/sci-libs/libmems/libmems-1.6_p1-r1.ebuild
deleted file mode 100644
index ac61e5455337..000000000000
--- a/sci-libs/libmems/libmems-1.6_p1-r1.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=6
-
-inherit autotools
-
-DESCRIPTION="Library for sci-biology/mauve"
-HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/"
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
-
-SLOT="0"
-LICENSE="GPL-2"
-IUSE="doc"
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="
-	dev-libs/boost
-	sci-libs/libgenome
-	sci-libs/libmuscle"
-DEPEND="${CDEPEND}
-	doc? ( app-doc/doxygen )"
-RDEPEND="${CDEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-build.patch
-	"${FILESDIR}"/${P}-boost.patch
-	"${FILESDIR}"/${P}-gcc-4.7.patch
-	"${FILESDIR}"/${P}-broken-constness.patch
-	"${FILESDIR}"/${P}-format-security.patch
-	)
-
-src_prepare() {
-	default
-	eautoreconf
-}
diff --git a/sci-libs/libmems/libmems-1.6_p1-r2.ebuild b/sci-libs/libmems/libmems-1.6_p1-r2.ebuild
new file mode 100644
index 000000000000..c00e615cd49b
--- /dev/null
+++ b/sci-libs/libmems/libmems-1.6_p1-r2.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit autotools
+
+DESCRIPTION="Library for sci-biology/mauve"
+HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/"
+SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
+
+SLOT="0"
+LICENSE="GPL-2"
+IUSE="doc static-libs"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-libs/boost:=
+	sci-libs/libgenome
+	sci-libs/libmuscle"
+DEPEND="${RDEPEND}
+	doc? ( app-doc/doxygen )"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-build.patch
+	"${FILESDIR}"/${P}-boost.patch
+	"${FILESDIR}"/${P}-gcc-4.7.patch
+	"${FILESDIR}"/${P}-broken-constness.patch
+	"${FILESDIR}"/${P}-format-security.patch
+	"${FILESDIR}"/${P}-fix-c++14.patch
+)
+
+src_prepare() {
+	default
+	eautoreconf
+}
+
+src_configure() {
+	econf \
+		--enable-shared \
+		$(use_enable static-libs static)
+}
+
+src_install() {
+	default
+
+	# package provides .pc files
+	find "${D}" -name '*.la' -delete || die
+}
-- 
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