sci-biology/bowtie: drop 2.2.9

Closes: https://bugs.gentoo.org/722870
Signed-off-by: David Seifert <soap@gentoo.org>

3 files changed, 0 insertions, 91 deletions

diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index 96d35e2bfd23..e62703395825 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,2 +1 @@
-DIST bowtie2-2.2.9-source.zip 5734235 BLAKE2B ec48e09fe05403d1085bb4e0c6ef1325b8912da0a8c942061c34f3381c6dd7ccdcc64c4bcdbb18c1da84ac57e1e34cc866fe79809c33c2769a8d75ecde7d0846 SHA512 ead8f7641f3231638d986f9e500bc4ec7afe1e542048465bfcc2e93e2b2d2e499f0dd8aa5c1e3e21df285c9d195b187682eb7e12be4a408f6c50fb97c0e0a205
 DIST bowtie2-2.4.4-source.zip 10515984 BLAKE2B be4ceb9d3155d2a9a1f580e5032251b04b89ce0c8c9c89fc3551b34fe3bd71a683362488be7aad6daef24734c6f95c19223f20e67f198f745c4432381243039c SHA512 1b5dadd7e41b90bb9b05f50bfa171fe219cfd03aa8bb6f800de4baaffeb975eef6efc4fb8b49cb0d18833f74a1741cbe1556b87388f59188e04a55dcee6a02da
diff --git a/sci-biology/bowtie/bowtie-2.2.9.ebuild b/sci-biology/bowtie/bowtie-2.2.9.ebuild
deleted file mode 100644
index 0bacb8ca25d7..000000000000
--- a/sci-biology/bowtie/bowtie-2.2.9.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"
-SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
-
-LICENSE="GPL-3"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="examples cpu_flags_x86_sse2 +tbb"
-
-RDEPEND="dev-lang/perl
-	tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
-	app-arch/unzip"
-
-S="${WORKDIR}/${PN}2-${PV}"
-
-DOCS=( AUTHORS NEWS TUTORIAL )
-HTML_DOCS=( doc/{manual.html,style.css} )
-PATCHES=( "${FILESDIR}/${PN}-2.2.9-fix-c++14.patch" )
-
-pkg_pretend() {
-	if ! use cpu_flags_x86_sse2 ; then
-		eerror "This package requires a CPU supporting the SSE2 instruction set."
-		die "SSE2 support missing"
-	fi
-}
-
-src_compile() {
-	emake \
-		CC="$(tc-getCC)" \
-		CPP="$(tc-getCXX)" \
-		CXX="$(tc-getCXX)" \
-		CFLAGS="" \
-		CXXFLAGS="" \
-		EXTRA_FLAGS="${LDFLAGS}" \
-		RELEASE_FLAGS="${CXXFLAGS} -msse2" \
-		WITH_TBB="$(usex tbb 1 0)"
-}
-
-src_install() {
-	dobin ${PN}2 ${PN}2-*
-
-	exeinto /usr/libexec/${PN}2
-	doexe scripts/*
-
-	newman MANUAL ${PN}2.1
-	einstalldocs
-
-	if use examples; then
-		insinto /usr/share/${PN}2
-		doins -r example
-	fi
-}
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
deleted file mode 100644
index cd2a67b6a52b..000000000000
--- a/sci-biology/bowtie/files/bowtie-2.2.9-fix-c++14.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-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();