commit: b3c6b97c03059d44b801c71c3ccf7a6165593149 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Aug 1 16:40:42 2021 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Aug 1 16:40:42 2021 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b3c6b97c
sci-biology/bowtie: drop 2.2.9 Closes: https://bugs.gentoo.org/722870 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/bowtie/Manifest | 1 - sci-biology/bowtie/bowtie-2.2.9.ebuild | 61 ---------------------- .../bowtie/files/bowtie-2.2.9-fix-c++14.patch | 29 ---------- 3 files changed, 91 deletions(-) diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest index 96d35e2bfd2..e6270339582 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 0bacb8ca25d..00000000000 --- 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 cd2a67b6a52..00000000000 --- 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();
