From: David Seifert <soap@gentoo.org>
Date: Wed, 21 Sep 2016 21:18:29 +0000 (+0200)
Subject: sci-biology/tophat: Allow for compiling with GCC 6
X-Git-Url: http://git.tremily.us/gitweb.cgi?a=commitdiff_plain;h=32ec7cd438905d9c6f49d8ad16cfcc88d852e731;p=gentoo.git

sci-biology/tophat: Allow for compiling with GCC 6

Gentoo-bug: 594544

Package-Manager: portage-2.3.1
---

diff --git a/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch b/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch
new file mode 100644
index 000000000000..e8168bb91438
--- /dev/null
+++ b/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch
@@ -0,0 +1,14 @@
+Fix building with C++14, which errors out due to broken perfect forwarding signature.
+See also: https://bugs.gentoo.org/show_bug.cgi?id=594544
+
+--- a/src/tophat_reports.cpp
++++ b/src/tophat_reports.cpp
+@@ -2705,7 +2705,7 @@
+ 				junction_stat.gtf_match = true;
+ 				junction_stat.accepted = true;
+ 
+-				gtf_junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), junction_stat));
++				gtf_junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), junction_stat));
+ 			}
+ 		}
+ 		fprintf(stderr, "Loaded %d GFF junctions from %s.\n", (int)(gtf_junctions.size()), gtf_juncs.c_str());
diff --git a/sci-biology/tophat/tophat-2.1.1-r1.ebuild b/sci-biology/tophat/tophat-2.1.1-r1.ebuild
index a8501758f5d9..6c6690a7a86e 100644
--- a/sci-biology/tophat/tophat-2.1.1-r1.ebuild
+++ b/sci-biology/tophat/tophat-2.1.1-r1.ebuild
@@ -28,6 +28,7 @@ DEPEND="${RDEPEND}
 
 PATCHES=(
 	"${FILESDIR}/${P}-unbundle-seqan-samtools.patch"
+	"${FILESDIR}/${P}-fix-c++14.patch"
 )
 
 src_prepare() {