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authorMichael Palimaka <kensington@gentoo.org>2017-09-30 14:31:52 +1000
committerMichael Palimaka <kensington@gentoo.org>2017-09-30 14:32:10 +1000
commit6ca3886327f05d8ae741e1f3271e0cf1ba18982b (patch)
treec6775094bcfbbf62f46a0898de05cb95a45fbc14
parentsci-biology/clustal-omega: stabilise 1.2.4 for amd64/x86 (diff)
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sci-biology/clustal-omega: remove 1.2.1/1.2.3
Package-Manager: Portage-2.3.8, Repoman-2.3.3
-rw-r--r--sci-biology/clustal-omega/Manifest2
-rw-r--r--sci-biology/clustal-omega/clustal-omega-1.2.1.ebuild37
-rw-r--r--sci-biology/clustal-omega/clustal-omega-1.2.3.ebuild39
-rw-r--r--sci-biology/clustal-omega/files/clustal-omega-1.2.2-fix-c++14.patch25
4 files changed, 0 insertions, 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