From a4da0209640e967dbbc8cd85820ff8858e34f872 Mon Sep 17 00:00:00 2001
From: David Seifert <soap@gentoo.org>
Date: Mon, 19 Sep 2016 00:39:18 +0200
Subject: sci-biology/bowtie: Allow for compiling with GCC 6

Gentoo-bug: 593966

Package-Manager: portage-2.3.0
---
 sci-biology/bowtie/bowtie-2.2.9.ebuild             |  3 ++-
 .../bowtie/files/bowtie-2.2.9-fix-c++14.patch      | 29 ++++++++++++++++++++++
 2 files changed, 31 insertions(+), 1 deletion(-)
 create mode 100644 sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch

(limited to 'sci-biology/bowtie')

diff --git a/sci-biology/bowtie/bowtie-2.2.9.ebuild b/sci-biology/bowtie/bowtie-2.2.9.ebuild
index 6e664202dfdf..8544512a3f0d 100644
--- a/sci-biology/bowtie/bowtie-2.2.9.ebuild
+++ b/sci-biology/bowtie/bowtie-2.2.9.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=6
 
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
 HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"
@@ -25,6 +25,7 @@ S="${WORKDIR}/${PN}2-${PV}"
 
 DOCS=( AUTHORS NEWS TUTORIAL )
 HTML_DOCS=( doc/{manual.html,style.css} )
+PATCHES=( "${FILESDIR}/${PN}-2.2.9-fix-c++14.patch" )
 
 pkg_pretend() {
 	if ! use cpu_flags_x86_sse2 ; then
diff --git a/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch b/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch
new file mode 100644
index 000000000000..cd2a67b6a52b
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch
@@ -0,0 +1,29 @@
+Fix building with C++14, which errors out due to differing semantics between C++98
+and C++14 with regards to allowing destructors to throw exceptions.
+See also: https://bugs.gentoo.org/show_bug.cgi?id=593966
+
+--- a/blockwise_sa.h
++++ b/blockwise_sa.h
+@@ -87,7 +87,11 @@
+ 	_logger(__logger)
+ 	{ }
+ 
+-	virtual ~BlockwiseSA() { }
++	virtual ~BlockwiseSA()
++#if __cplusplus >= 201103L
++	noexcept(false)
++#endif
++	{ }
+ 
+ 	/**
+ 	 * Get the next suffix; compute the next bucket if necessary.
+@@ -216,6 +220,9 @@
+     { _randomSrc.init(__seed); reset(); }
+     
+     ~KarkkainenBlockwiseSA()
++#if __cplusplus >= 201103L
++    noexcept(false)
++#endif
+     {
+ #ifdef WITH_TBB
+ 		    tbb_grp.wait();
-- 
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