[gentoo-commits] repo/gentoo:master commit in: sci-biology/clustal-omega/, sci-biology/clustal-omega/files/
commit: 6ca3886327f05d8ae741e1f3271e0cf1ba18982b
Author: Michael Palimaka gentoo org>
AuthorDate: Sat Sep 30 04:31:52 2017 +
Commit: Michael Palimaka gentoo org>
CommitDate: Sat Sep 30 04:32:10 2017 +
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..000
--- 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..000
--- 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..000
--- 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 // printf
- #include// exit
- #include //
[gentoo-commits] repo/gentoo:master commit in: sci-biology/clustal-omega/, sci-biology/clustal-omega/files/
commit: 43b079fe3d77f86b19579969e78577d3825fcd44
Author: David Seifert gentoo org>
AuthorDate: Thu Sep 22 07:24:27 2016 +
Commit: David Seifert gentoo org>
CommitDate: Thu Sep 22 07:29:32 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=43b079fe
sci-biology/clustal-omega: Version bump, allow for compiling with GCC 6
Gentoo-bug: 594692
Package-Manager: portage-2.3.1
sci-biology/clustal-omega/Manifest | 2 +-
...-1.2.2-r1.ebuild => clustal-omega-1.2.3.ebuild} | 12 +--
.../files/clustal-omega-1.2.2-fix-c++14.patch | 25 ++
3 files changed, 36 insertions(+), 3 deletions(-)
diff --git a/sci-biology/clustal-omega/Manifest
b/sci-biology/clustal-omega/Manifest
index 7b133ae..72af644 100644
--- a/sci-biology/clustal-omega/Manifest
+++ b/sci-biology/clustal-omega/Manifest
@@ -1,2 +1,2 @@
DIST clustal-omega-1.2.1.tar.gz 1164492 SHA256
0ef32727aa25c6ecf732083e668a0f45bc17085c28a5c7b4459f4750419f2b0a SHA512
1aa69e319f999f7cd746e2d2ffcafeafc0eb15ed4777abb5b32df63a39a23fa2091977efccfcf9428468103b8e48c4ab0a3ce3967b9c55daaadf3a6a3b57e8de
WHIRLPOOL
b079dcd659839a85e7772b717ef5dce25b816f2c96eb0f6eea5a4a53f2abd25fb4435291f2a7b739d72d94c06fdbd9c85300ff4cbb03b2861d31d1ad3d196577
-DIST clustal-omega-1.2.2.tar.gz 1169632 SHA256
e48c533300f9ba75870861cf40516a36f3b184b1a39a5b2b926c73bd8639ea41 SHA512
82a97b1e0ca51b9ad61fa2ba3426e55d220003386dee124aaa6103665a2c566182fb4f5cf014d4af3892b2858453e95d4ff36ce90e49d1ae81d95da9ef2ffca0
WHIRLPOOL
a256cf2902df9969afefc0301806b18ee16376e510a47fc1f6f4efc755eb11a157caff375b46579750a577ee0cdceff64fdf6e8360cd29a8d3bb6fb8665a198a
+DIST clustal-omega-1.2.3.tar.gz 1170684 SHA256
88f5ead3f09250872d77427d083182e5e44743ba79ab69294fb61fb50cd4e0cb SHA512
ade516475b243ab21ac3359bc13bc0593294de8f52bbff237bb558859d458b89b2d8773f28c1afc5bfba6c02284e9dbb30cf6e769c66b0bda61789e1602c9c23
WHIRLPOOL
5f4d69a8f4605fd74dfa906d1b530d235e5ba4aaa946b4ce0a645352325b2c4732f43fff930649044a5045ad9bef5c7952e995a0742a5470ccaff17bf6de80d3
diff --git a/sci-biology/clustal-omega/clustal-omega-1.2.2-r1.ebuild
b/sci-biology/clustal-omega/clustal-omega-1.2.3.ebuild
similarity index 72%
rename from sci-biology/clustal-omega/clustal-omega-1.2.2-r1.ebuild
rename to sci-biology/clustal-omega/clustal-omega-1.2.3.ebuild
index 741fc68..12f64b0 100644
--- a/sci-biology/clustal-omega/clustal-omega-1.2.2-r1.ebuild
+++ b/sci-biology/clustal-omega/clustal-omega-1.2.3.ebuild
@@ -4,7 +4,7 @@
EAPI=6
-inherit autotools eutils
+inherit autotools
DESCRIPTION="Scalable multiple alignment of protein sequences"
HOMEPAGE="http://www.clustal.org/omega/;
@@ -18,6 +18,8 @@ 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" \
@@ -26,7 +28,13 @@ src_prepare() {
eautoreconf
}
+src_configure() {
+ econf \
+ --enable-shared \
+ $(use_enable static-libs static)
+}
+
src_install() {
default
- prune_libtool_files --all
+ find "${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
new file mode 100644
index ..1ebdbda
--- /dev/null
+++ b/sci-biology/clustal-omega/files/clustal-omega-1.2.2-fix-c++14.patch
@@ -0,0 +1,25 @@
+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 // printf
+ #include// exit
+ #include // clock
++#include
+ #endif
+ #include
+ //#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)(-10):1.442695041*log(x));}
+-inline float log10(float x) {return (x<=0?
(float)(-10):0.434294481*log(x));}
+-
+
+
/
+ // fast log base 2
