commit: 6ca3886327f05d8ae741e1f3271e0cf1ba18982b Author: Michael Palimaka <kensington <AT> gentoo <DOT> org> AuthorDate: Sat Sep 30 04:31:52 2017 +0000 Commit: Michael Palimaka <kensington <AT> gentoo <DOT> org> CommitDate: Sat Sep 30 04:32:10 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6ca38863
sci-biology/clustal-omega: remove 1.2.1/1.2.3 Package-Manager: Portage-2.3.8, Repoman-2.3.3 sci-biology/clustal-omega/Manifest | 2 -- .../clustal-omega/clustal-omega-1.2.1.ebuild | 37 -------------------- .../clustal-omega/clustal-omega-1.2.3.ebuild | 39 ---------------------- .../files/clustal-omega-1.2.2-fix-c++14.patch | 25 -------------- 4 files changed, 103 deletions(-) diff --git a/sci-biology/clustal-omega/Manifest b/sci-biology/clustal-omega/Manifest index 7892ccb2c5d..4a66a070040 100644 --- a/sci-biology/clustal-omega/Manifest +++ b/sci-biology/clustal-omega/Manifest @@ -1,3 +1 @@ -DIST clustal-omega-1.2.1.tar.gz 1164492 SHA256 0ef32727aa25c6ecf732083e668a0f45bc17085c28a5c7b4459f4750419f2b0a SHA512 1aa69e319f999f7cd746e2d2ffcafeafc0eb15ed4777abb5b32df63a39a23fa2091977efccfcf9428468103b8e48c4ab0a3ce3967b9c55daaadf3a6a3b57e8de WHIRLPOOL b079dcd659839a85e7772b717ef5dce25b816f2c96eb0f6eea5a4a53f2abd25fb4435291f2a7b739d72d94c06fdbd9c85300ff4cbb03b2861d31d1ad3d196577 -DIST clustal-omega-1.2.3.tar.gz 1170684 SHA256 88f5ead3f09250872d77427d083182e5e44743ba79ab69294fb61fb50cd4e0cb SHA512 ade516475b243ab21ac3359bc13bc0593294de8f52bbff237bb558859d458b89b2d8773f28c1afc5bfba6c02284e9dbb30cf6e769c66b0bda61789e1602c9c23 WHIRLPOOL 5f4d69a8f4605fd74dfa906d1b530d235e5ba4aaa946b4ce0a645352325b2c4732f43fff930649044a5045ad9bef5c7952e995a0742a5470ccaff17bf6de80d3 DIST clustal-omega-1.2.4.tar.gz 1170516 SHA256 8683d2286d663a46412c12a0c789e755e7fd77088fb3bc0342bb71667f05a3ee SHA512 b31514c30b412d731ee22c9020156b65a6a6cbc6fd51edc195d17b560935184bc070feeb58964c54df9eecdefb00e5a21ce859cb0ea69d92917f6bd8e93b819e WHIRLPOOL 86fa6e6f4db128b122abeee470a7c1b0150e64f38d58c6ba620b4b9afd65d91f55d6971fef99b0dfd10ccdc550da1d195eec9a91cdde271947e7a703ca2384d3 diff --git a/sci-biology/clustal-omega/clustal-omega-1.2.1.ebuild b/sci-biology/clustal-omega/clustal-omega-1.2.1.ebuild deleted file mode 100644 index 54eb46e9e30..00000000000 --- a/sci-biology/clustal-omega/clustal-omega-1.2.1.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -AUTOTOOLS_AUTORECONF=true - -inherit autotools-utils - -DESCRIPTION="Scalable multiple alignment of protein sequences" -HOMEPAGE="http://www.clustal.org/omega/"; -SRC_URI="http://www.clustal.org/omega/${P}.tar.gz"; - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="static-libs" - -DEPEND="dev-libs/argtable" -RDEPEND="${DEPEND}" - -AUTOTOOLS_IN_SOURCE_BUILD=1 - -src_prepare() { - sed \ - -e "s:-O3::g" \ - -i configure.ac || die - autotools-utils_src_prepare -} - -src_install() { - autotools-utils_src_install - if ! use static-libs; then - rm -f "${ED}"/usr/$(get_libdir)/*.a || die - rm -fr "${ED}"/usr/$(get_libdir)/pkgconfig || die - fi -} diff --git a/sci-biology/clustal-omega/clustal-omega-1.2.3.ebuild b/sci-biology/clustal-omega/clustal-omega-1.2.3.ebuild deleted file mode 100644 index ee0b983480f..00000000000 --- a/sci-biology/clustal-omega/clustal-omega-1.2.3.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit autotools - -DESCRIPTION="Scalable multiple alignment of protein sequences" -HOMEPAGE="http://www.clustal.org/omega/"; -SRC_URI="http://www.clustal.org/omega/${P}.tar.gz"; - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="static-libs" - -DEPEND="dev-libs/argtable" -RDEPEND="${DEPEND}" - -PATCHES=( "${FILESDIR}/${PN}-1.2.2-fix-c++14.patch" ) - -src_prepare() { - sed \ - -e "s:-O3::g" \ - -i configure.ac || die - default - eautoreconf -} - -src_configure() { - econf \ - --enable-shared \ - $(use_enable static-libs static) -} - -src_install() { - default - find "${D}" -name '*.la' -delete || die -} diff --git a/sci-biology/clustal-omega/files/clustal-omega-1.2.2-fix-c++14.patch b/sci-biology/clustal-omega/files/clustal-omega-1.2.2-fix-c++14.patch deleted file mode 100644 index 1ebdbda3d32..00000000000 --- a/sci-biology/clustal-omega/files/clustal-omega-1.2.2-fix-c++14.patch +++ /dev/null @@ -1,25 +0,0 @@ -Fix building with C++14, which errors out due to collisions with the -internal log2 and log10 functions, which are now part of C++11. -See also: https://bugs.gentoo.org/show_bug.cgi?id=594692 - ---- a/src/hhalign/util-C.h -+++ b/src/hhalign/util-C.h -@@ -27,6 +27,7 @@ - #include <cstdio> // printf - #include <stdlib.h> // exit - #include <time.h> // clock -+#include <math.h> - #endif - #include <sys/time.h> - //#include "new_new.h" /* memory tracking */ -@@ -50,10 +51,6 @@ - //// Generalized mean: d=0: sqrt(x*y) d=1: (x+y)/2 d->-inf: min(x,y) d->+inf: max(x,y) - inline double fmean(double x, double y, double d) { return pow( (pow(x,d)+pow(y,d))/2 ,1./d);} - --// log base 2 --inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} --inline float log10(float x) {return (x<=0? (float)(-100000):0.434294481*log(x));} -- - - ///////////////////////////////////////////////////////////////////////////////////// - // fast log base 2
