[gentoo-commits] repo/gentoo:master commit in: sci-biology/clustal-omega/, sci-biology/clustal-omega/files/

["David Seifert" <soap@gentoo.org>]

commit:     43b079fe3d77f86b19579969e78577d3825fcd44
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Sep 22 07:24:27 2016 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Sep 22 07:29:32 2016 +0000
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 00000000..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 <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