| 1 |
commit: 43b079fe3d77f86b19579969e78577d3825fcd44 |
| 2 |
Author: David Seifert <soap <AT> gentoo <DOT> org> |
| 3 |
AuthorDate: Thu Sep 22 07:24:27 2016 +0000 |
| 4 |
Commit: David Seifert <soap <AT> gentoo <DOT> org> |
| 5 |
CommitDate: Thu Sep 22 07:29:32 2016 +0000 |
| 6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=43b079fe |
| 7 |
|
| 8 |
sci-biology/clustal-omega: Version bump, allow for compiling with GCC 6 |
| 9 |
|
| 10 |
Gentoo-bug: 594692 |
| 11 |
|
| 12 |
Package-Manager: portage-2.3.1 |
| 13 |
|
| 14 |
sci-biology/clustal-omega/Manifest | 2 +- |
| 15 |
...-1.2.2-r1.ebuild => clustal-omega-1.2.3.ebuild} | 12 +++++++++-- |
| 16 |
.../files/clustal-omega-1.2.2-fix-c++14.patch | 25 ++++++++++++++++++++++ |
| 17 |
3 files changed, 36 insertions(+), 3 deletions(-) |
| 18 |
|
| 19 |
diff --git a/sci-biology/clustal-omega/Manifest b/sci-biology/clustal-omega/Manifest |
| 20 |
index 7b133ae..72af644 100644 |
| 21 |
--- a/sci-biology/clustal-omega/Manifest |
| 22 |
+++ b/sci-biology/clustal-omega/Manifest |
| 23 |
@@ -1,2 +1,2 @@ |
| 24 |
DIST clustal-omega-1.2.1.tar.gz 1164492 SHA256 0ef32727aa25c6ecf732083e668a0f45bc17085c28a5c7b4459f4750419f2b0a SHA512 1aa69e319f999f7cd746e2d2ffcafeafc0eb15ed4777abb5b32df63a39a23fa2091977efccfcf9428468103b8e48c4ab0a3ce3967b9c55daaadf3a6a3b57e8de WHIRLPOOL b079dcd659839a85e7772b717ef5dce25b816f2c96eb0f6eea5a4a53f2abd25fb4435291f2a7b739d72d94c06fdbd9c85300ff4cbb03b2861d31d1ad3d196577 |
| 25 |
-DIST clustal-omega-1.2.2.tar.gz 1169632 SHA256 e48c533300f9ba75870861cf40516a36f3b184b1a39a5b2b926c73bd8639ea41 SHA512 82a97b1e0ca51b9ad61fa2ba3426e55d220003386dee124aaa6103665a2c566182fb4f5cf014d4af3892b2858453e95d4ff36ce90e49d1ae81d95da9ef2ffca0 WHIRLPOOL a256cf2902df9969afefc0301806b18ee16376e510a47fc1f6f4efc755eb11a157caff375b46579750a577ee0cdceff64fdf6e8360cd29a8d3bb6fb8665a198a |
| 26 |
+DIST clustal-omega-1.2.3.tar.gz 1170684 SHA256 88f5ead3f09250872d77427d083182e5e44743ba79ab69294fb61fb50cd4e0cb SHA512 ade516475b243ab21ac3359bc13bc0593294de8f52bbff237bb558859d458b89b2d8773f28c1afc5bfba6c02284e9dbb30cf6e769c66b0bda61789e1602c9c23 WHIRLPOOL 5f4d69a8f4605fd74dfa906d1b530d235e5ba4aaa946b4ce0a645352325b2c4732f43fff930649044a5045ad9bef5c7952e995a0742a5470ccaff17bf6de80d3 |
| 27 |
|
| 28 |
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 |
| 29 |
similarity index 72% |
| 30 |
rename from sci-biology/clustal-omega/clustal-omega-1.2.2-r1.ebuild |
| 31 |
rename to sci-biology/clustal-omega/clustal-omega-1.2.3.ebuild |
| 32 |
index 741fc68..12f64b0 100644 |
| 33 |
--- a/sci-biology/clustal-omega/clustal-omega-1.2.2-r1.ebuild |
| 34 |
+++ b/sci-biology/clustal-omega/clustal-omega-1.2.3.ebuild |
| 35 |
@@ -4,7 +4,7 @@ |
| 36 |
|
| 37 |
EAPI=6 |
| 38 |
|
| 39 |
-inherit autotools eutils |
| 40 |
+inherit autotools |
| 41 |
|
| 42 |
DESCRIPTION="Scalable multiple alignment of protein sequences" |
| 43 |
HOMEPAGE="http://www.clustal.org/omega/" |
| 44 |
@@ -18,6 +18,8 @@ IUSE="static-libs" |
| 45 |
DEPEND="dev-libs/argtable" |
| 46 |
RDEPEND="${DEPEND}" |
| 47 |
|
| 48 |
+PATCHES=( "${FILESDIR}/${PN}-1.2.2-fix-c++14.patch" ) |
| 49 |
+ |
| 50 |
src_prepare() { |
| 51 |
sed \ |
| 52 |
-e "s:-O3::g" \ |
| 53 |
@@ -26,7 +28,13 @@ src_prepare() { |
| 54 |
eautoreconf |
| 55 |
} |
| 56 |
|
| 57 |
+src_configure() { |
| 58 |
+ econf \ |
| 59 |
+ --enable-shared \ |
| 60 |
+ $(use_enable static-libs static) |
| 61 |
+} |
| 62 |
+ |
| 63 |
src_install() { |
| 64 |
default |
| 65 |
- prune_libtool_files --all |
| 66 |
+ find "${D}" -name '*.la' -delete || die |
| 67 |
} |
| 68 |
|
| 69 |
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 |
| 70 |
new file mode 100644 |
| 71 |
index 00000000..1ebdbda |
| 72 |
--- /dev/null |
| 73 |
+++ b/sci-biology/clustal-omega/files/clustal-omega-1.2.2-fix-c++14.patch |
| 74 |
@@ -0,0 +1,25 @@ |
| 75 |
+Fix building with C++14, which errors out due to collisions with the |
| 76 |
+internal log2 and log10 functions, which are now part of C++11. |
| 77 |
+See also: https://bugs.gentoo.org/show_bug.cgi?id=594692 |
| 78 |
+ |
| 79 |
+--- a/src/hhalign/util-C.h |
| 80 |
++++ b/src/hhalign/util-C.h |
| 81 |
+@@ -27,6 +27,7 @@ |
| 82 |
+ #include <cstdio> // printf |
| 83 |
+ #include <stdlib.h> // exit |
| 84 |
+ #include <time.h> // clock |
| 85 |
++#include <math.h> |
| 86 |
+ #endif |
| 87 |
+ #include <sys/time.h> |
| 88 |
+ //#include "new_new.h" /* memory tracking */ |
| 89 |
+@@ -50,10 +51,6 @@ |
| 90 |
+ //// Generalized mean: d=0: sqrt(x*y) d=1: (x+y)/2 d->-inf: min(x,y) d->+inf: max(x,y) |
| 91 |
+ inline double fmean(double x, double y, double d) { return pow( (pow(x,d)+pow(y,d))/2 ,1./d);} |
| 92 |
+ |
| 93 |
+-// log base 2 |
| 94 |
+-inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} |
| 95 |
+-inline float log10(float x) {return (x<=0? (float)(-100000):0.434294481*log(x));} |
| 96 |
+- |
| 97 |
+ |
| 98 |
+ ///////////////////////////////////////////////////////////////////////////////////// |
| 99 |
+ // fast log base 2 |
Archives