diff options
| author |   Justin Lecher <jlec@gentoo.org> | 2015-12-26 19:02:47 +0100 |
|---|---|---|
| committer | Justin Lecher <jlec@gentoo.org> | 2015-12-26 19:02:47 +0100 |
| commit | 369678cffc9f7ecae414f3800f01a2c2251e8669 (patch) | |
| tree | bd63aa0a85e4636964e1fe5477cb1a1ee42fa064 /sci-biology/bowtie | |
| parent | dev-python/pysvn: Drop vulnerable version for CVE-2015-0853 (diff) | |
| download | gentoo-369678cffc9f7ecae414f3800f01a2c2251e8669.tar.gz gentoo-369678cffc9f7ecae414f3800f01a2c2251e8669.tar.bz2 gentoo-369678cffc9f7ecae414f3800f01a2c2251e8669.zip | |
sci-biology/bowtie: Drop old
obsoletes:
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=564320
Package-Manager: portage-2.2.26
Signed-off-by: Justin Lecher <jlec@gentoo.org>
Diffstat (limited to 'sci-biology/bowtie')
| -rw-r--r-- | sci-biology/bowtie/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/bowtie/bowtie-0.12.8.ebuild | 44 | ||||
| -rw-r--r-- | sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch | 45 |
3 files changed, 0 insertions, 90 deletions
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest index c692c89b3bb4..1291400cabae 100644 --- a/sci-biology/bowtie/Manifest +++ b/sci-biology/bowtie/Manifest @@ -1,3 +1,2 @@ -DIST bowtie-0.12.8-src.zip 15569919 SHA256 f074a0f25e156976c4951fd69651d60caab925af9829054d107ec8b19af3082d SHA512 824eddd7db24177f7e15b90fb93a0426c2b8cee4dbcac2707f4cc7e7e42bafcad3775382b79d9b4d679e0c4b5c17a1b79ad134e91a968037336b34c6262e9c48 WHIRLPOOL 7056444822e7a0de619dcab933a7870ebe7db52008f3dbb2dd72aa189325d7ca4c353133d77150ec67c414e005a834458538f57746b13fd20f06bc7289869800 DIST bowtie-1.1.2-src.zip 7713258 SHA256 b1e9ccc825207efd1893d9e33244c681bcb89b9b2b811eb95a9f5a92eab637ae SHA512 3d3d69bc3a865bb577b5a91440215d0d5b606c7a8751d565e606e36adbfbdef695b1718ae81cd3e2682a39ca7784c4d00976441e7618264ad99b04c7f53c36e8 WHIRLPOOL 08cb824bf7a1ddfbe6692de67191aacf44776d7d4e0ab66bd2a13ecfffd087bc28cdde4c7285c781fa4759de0a239e68f87b702bcc2e24c9b81fda5804360ce7 DIST bowtie2-2.2.6-source.zip 5728779 SHA256 1000e90cdd90c3ca43c69d0d0ad951e190d36a6981a546f430a90ce86d64bfc8 SHA512 3ab5a5475cf214affd91e0d1782fd2d6dedccd979e3c809b5dfb272726d99ff1c7b59d92e387b187a7c2e43557786a1085186ccb96588de91212caf2eb94ce4f WHIRLPOOL 4fb02b3a0d76bbee0fe9abf91a71405922568bc38e593d5740df6279bad6f8b668df0debb0a81f3d3c23623558f34d842dd662a6838cf2d7f0fc8945fd00a298 diff --git a/sci-biology/bowtie/bowtie-0.12.8.ebuild b/sci-biology/bowtie/bowtie-0.12.8.ebuild deleted file mode 100644 index c26c986ed194..000000000000 --- a/sci-biology/bowtie/bowtie-0.12.8.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -inherit eutils toolchain-funcs - -DESCRIPTION="An ultrafast memory-efficient short read aligner" -HOMEPAGE="http://bowtie-bio.sourceforge.net/" -SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" - -LICENSE="Artistic" -SLOT="0" -IUSE="" -KEYWORDS="amd64 x86 ~x64-macos" - -DEPEND="app-arch/unzip" -RDEPEND="" - -# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de) -# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS - -src_prepare() { - epatch "${FILESDIR}"/${P}-gcc-47.patch -} - -src_compile() { - unset CFLAGS - emake \ - CC="$(tc-getCC)" \ - CPP="$(tc-getCXX)" \ - CXX="$(tc-getCXX)" \ - EXTRA_FLAGS="${LDFLAGS}" \ - RELEASE_FLAGS="" -} - -src_install() { - dobin bowtie bowtie-* - exeinto /usr/share/${PN}/scripts - doexe scripts/* - newman MANUAL bowtie.1 - dodoc AUTHORS NEWS TUTORIAL -} diff --git a/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch b/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch deleted file mode 100644 index 3c8a1e1d9ca4..000000000000 --- a/sci-biology/bowtie/files/bowtie-0.12.8-gcc-47.patch +++ /dev/null @@ -1,45 +0,0 @@ - alphabet.h | 24 ++++++++++++------------ - 1 files changed, 12 insertions(+), 12 deletions(-) - -diff --git a/alphabet.h b/alphabet.h -index b464ddf..08d0281 100644 ---- a/alphabet.h -+++ b/alphabet.h -@@ -38,6 +38,18 @@ static inline TStr reverseComplement(const TStr& s, bool color) { - return s_rc; - } - -+/// Reverse a string in-place -+template <typename TStr> -+static inline void reverseInPlace(TStr& s) { -+ typedef typename Value<TStr>::Type TVal; -+ size_t len = length(s); -+ for(size_t i = 0; i < (len>>1); i++) { -+ TVal tmp = s[i]; -+ s[i] = s[len-i-1]; -+ s[len-i-1] = tmp; -+ } -+} -+ - /** - * Reverse-complement s in-place. Ns go to Ns. - */ -@@ -69,18 +81,6 @@ static inline void reverseComplementInPlace(TStr& s, bool color) { - } - } - --/// Reverse a string in-place --template <typename TStr> --static inline void reverseInPlace(TStr& s) { -- typedef typename Value<TStr>::Type TVal; -- size_t len = length(s); -- for(size_t i = 0; i < (len>>1); i++) { -- TVal tmp = s[i]; -- s[i] = s[len-i-1]; -- s[len-i-1] = tmp; -- } --} -- - /** - * Return the reverse-complement of s. - */ |