commit: a4da0209640e967dbbc8cd85820ff8858e34f872 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Sep 18 22:39:18 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Sep 18 22:39:56 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a4da0209
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(-) diff --git a/sci-biology/bowtie/bowtie-2.2.9.ebuild b/sci-biology/bowtie/bowtie-2.2.9.ebuild index 6e66420..8544512 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 00000000..cd2a67b --- /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();
