[gentoo-commits] repo/gentoo:master commit in: sci-biology/tophat/, sci-biology/tophat/files/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/tophat/, sci-biology/tophat/files/

[David Seifert]

commit:     32ec7cd438905d9c6f49d8ad16cfcc88d852e731
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 21 21:18:29 2016 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Sep 22 07:29:27 2016 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=32ec7cd4

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

Gentoo-bug: 594544

Package-Manager: portage-2.3.1

 sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch | 14 ++++++++++++++
 sci-biology/tophat/tophat-2.1.1-r1.ebuild             |  1 +
 2 files changed, 15 insertions(+)

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 00000000..e8168bb
--- /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 a850175..6c6690a 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() {