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
