svn commit: r547370 - in head/biology/hyphy: . files
Joseph Mingrone
jrm at FreeBSD.org
Wed Sep 2 17:47:17 UTC 2020
Author: jrm
Date: Wed Sep 2 17:47:10 2020
New Revision: 547370
URL: https://svnweb.freebsd.org/changeset/ports/547370
Log:
biology/hyphy: Update to version 2.5.18 and add AVX option
The AVX option is off by default, because hyphy will crash on systems
without advanced vector extensions support.
Added:
head/biology/hyphy/files/
head/biology/hyphy/files/patch-src_core_matrix.cpp (contents, props changed)
Modified:
head/biology/hyphy/Makefile (contents, props changed)
head/biology/hyphy/distinfo (contents, props changed)
Modified: head/biology/hyphy/Makefile
==============================================================================
--- head/biology/hyphy/Makefile Wed Sep 2 17:01:38 2020 (r547369)
+++ head/biology/hyphy/Makefile Wed Sep 2 17:47:10 2020 (r547370)
@@ -1,7 +1,7 @@
# $FreeBSD$
PORTNAME= hyphy
-DISTVERSION= 2.5.17
+DISTVERSION= 2.5.18
CATEGORIES= biology
MAINTAINER= jrm at FreeBSD.org
@@ -14,10 +14,13 @@ ONLY_FOR_ARCHS= amd64 i386
LIB_DEPENDS= libcurl.so:ftp/curl
-USES= compiler:openmp cmake localbase:ldflags ssl
+USES= cmake compiler:openmp localbase:ldflags ssl
USE_GITHUB= yes
GH_ACCOUNT= veg
-CMAKE_ON= NOAVX
+OPTIONS_DEFINE= AVX
+AVX_DESC= Advanced vector extensions support
+
+AVX_CMAKE_OFF= -DNOAVX:BOOL=ON
.include <bsd.port.mk>
Modified: head/biology/hyphy/distinfo
==============================================================================
--- head/biology/hyphy/distinfo Wed Sep 2 17:01:38 2020 (r547369)
+++ head/biology/hyphy/distinfo Wed Sep 2 17:47:10 2020 (r547370)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1597935241
-SHA256 (veg-hyphy-2.5.17_GH0.tar.gz) = 8511a7beff1dfb5d274d1335c3fa20071f2f8262ada88ad30fae562d8b0f3e12
-SIZE (veg-hyphy-2.5.17_GH0.tar.gz) = 5244231
+TIMESTAMP = 1599060037
+SHA256 (veg-hyphy-2.5.18_GH0.tar.gz) = 8eb978eb55d659fccb7e6a29b5ff8a87425f3317d5237c3b706ea918d4d5cf82
+SIZE (veg-hyphy-2.5.18_GH0.tar.gz) = 5250528
Added: head/biology/hyphy/files/patch-src_core_matrix.cpp
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/hyphy/files/patch-src_core_matrix.cpp Wed Sep 2 17:47:10 2020 (r547370)
@@ -0,0 +1,20 @@
+--- src/core/matrix.cpp.orig 2020-09-02 16:12:43 UTC
++++ src/core/matrix.cpp
+@@ -3128,8 +3128,6 @@ void _Matrix::AddMatrix (_Matrix& storage, _Matrix
+ CELL_OP (idx+8);
+ CELL_OP (idx+12);
+ }
+- }
+-
+ #else
+ for (long idx = 0; idx < upto; idx+=4) {
+ stData[idx]+=argData[idx];
+@@ -3138,7 +3136,7 @@ void _Matrix::AddMatrix (_Matrix& storage, _Matrix
+ stData[idx+3]+=argData[idx+3];
+ }
+ #endif
+-
++ }
+ if (subtract)
+ for (long idx = upto; idx < secondArg.lDim; idx++) {
+ stData[idx]-=argData[idx];
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