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biology/hyphy: Update to upstream tag 2.5.46hf1 

Sponsored by:	The FreeBSD Foundation
Differential Revision:	https://reviews.freebsd.org/D37975
This commit is contained in:
Joseph Mingrone 2023-01-07 12:17:51 -04:00
parent 6130254524
commit c6a8b4ea40
No known key found for this signature in database
GPG Key ID: 36A40C83B0D6EF9E
3 changed files with 6 additions and 55 deletions
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5
biology/hyphy/Makefile
View File

@ -1,5 +1,5 @@
PORTNAME= hyphy
DISTVERSION= 2.5.43
DISTVERSION= 2.5.46hf1
CATEGORIES= biology
MAINTAINER= jrm@FreeBSD.org
@ -12,6 +12,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE
ONLY_FOR_ARCHS= aarch64 amd64 armv7 i386 powerpc powerpc64 powerpc64le
LIB_DEPENDS= libcurl.so:ftp/curl
TEST_DEPENDS= bash:shells/bash
USES= cmake:insource,testing localbase:ldflags # tests fail in outsource build, see https://github.com/veg/hyphy/issues/1528
@ -23,6 +24,6 @@ AVX_DESC= Advanced vector extensions support
AVX_CMAKE_OFF= -DNOAVX:BOOL=ON
# 2 tests fail, see https://github.com/veg/hyphy/issues/1529
# All tests pass as of DISTVERSION=2.5.46hf1
.include <bsd.port.mk>

6
biology/hyphy/distinfo
View File

@ -1,3 +1,3 @@
TIMESTAMP = 1672008666
SHA256 (veg-hyphy-2.5.43_GH0.tar.gz) = 9328916267811a95dbbff94b51066dfc481f8d49ae0cf4d58e8384c58afbea50
SIZE (veg-hyphy-2.5.43_GH0.tar.gz) = 5634198
TIMESTAMP = 1673313088
SHA256 (veg-hyphy-2.5.46hf1_GH0.tar.gz) = ec2f9e737741ce6811b7607b613b3c4be71e4ac57d0b516f0cb5174d8727be27
SIZE (veg-hyphy-2.5.46hf1_GH0.tar.gz) = 5645952

50
biology/hyphy/files/patch-src_core_matrix.cpp
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@ -1,50 +0,0 @@
--- src/core/matrix.cpp.orig 2022-04-24 18:04:11 UTC
+++ src/core/matrix.cpp
@@ -3405,7 +3405,6 @@ void _Matrix::AddMatrix (_Matrix& storage, _Matrix
#pragma GCC unroll 4
#pragma clang loop vectorize(enable)
#pragma clang loop interleave(enable)
- #pragma clang loop unroll(enable)
#pragma GCC ivdep
#pragma ivdep
for (long idx = 0; idx < upto; idx+=16) {
@@ -3909,7 +3908,6 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix
#pragma GCC unroll 4
#pragma clang loop vectorize(enable)
#pragma clang loop interleave(enable)
- #pragma clang loop unroll(enable)
for (long k = 0; k < vDim; k+=4) {
__m256d D4, B4;
DO_GROUP_OP (D4, B4, k);
@@ -3960,7 +3958,6 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix
#pragma GCC unroll 4
#pragma clang loop vectorize(enable)
#pragma clang loop interleave(enable)
- #pragma clang loop unroll(enable)
for (long k = 0; k < vDim; k+=2) {
__m128d D4, B4;
DO_GROUP_OP1 (D4, B4, k);
@@ -4177,7 +4174,6 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix
#pragma GCC unroll 4
#pragma clang loop vectorize(enable)
#pragma clang loop interleave(enable)
- #pragma clang loop unroll(enable)
for (long k = 0; k < dimm4; k+=4) {
__m256d D4, B4;
DO_GROUP_OP (D4, B4, k);
@@ -4285,7 +4281,6 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix
#pragma GCC unroll 4
#pragma clang loop vectorize(enable)
#pragma clang loop interleave(enable)
- #pragma clang loop unroll(enable)
for (long k = 0; k < dimm4; k+=2) {
__m128d D4, B4;
DO_GROUP_OP1 (D4, B4, k);
@@ -4455,7 +4450,6 @@ void _Matrix::Multiply (_Matrix& storage, _Matrix
#pragma GCC unroll 8
#pragma clang loop vectorize(enable)
#pragma clang loop interleave(enable)
- #pragma clang loop unroll(enable)
for (long k = 0, column = j*hDim; k < vDim; k++, column ++) {
resCell += row[k] * secondArg.theData [column];
}