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