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Tue, 10 Jan 2023 02:06:35 GMT (envelope-from git) Date: Tue, 10 Jan 2023 02:06:35 GMT Message-Id: <202301100206.30A26Zqw083082@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Joseph Mingrone Subject: git: c6a8b4ea40e0 - main - biology/hyphy: Update to upstream tag 2.5.46hf1 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jrm X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: c6a8b4ea40e092f95f6386c79972b4aa95ef7387 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jrm: URL: https://cgit.FreeBSD.org/ports/commit/?id=c6a8b4ea40e092f95f6386c79972b4aa95ef7387 commit c6a8b4ea40e092f95f6386c79972b4aa95ef7387 Author: Joseph Mingrone AuthorDate: 2023-01-07 16:17:51 +0000 Commit: Joseph Mingrone CommitDate: 2023-01-10 02:05:57 +0000 biology/hyphy: Update to upstream tag 2.5.46hf1 Sponsored by: The FreeBSD Foundation Differential Revision: https://reviews.freebsd.org/D37975 --- biology/hyphy/Makefile | 5 +-- biology/hyphy/distinfo | 6 ++-- biology/hyphy/files/patch-src_core_matrix.cpp | 50 --------------------------- 3 files changed, 6 insertions(+), 55 deletions(-) diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile index 1a44d2bb0695..486c296dcaa9 100644 --- a/biology/hyphy/Makefile +++ b/biology/hyphy/Makefile @@ -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 diff --git a/biology/hyphy/distinfo b/biology/hyphy/distinfo index 11533428b33d..7ae2966503aa 100644 --- a/biology/hyphy/distinfo +++ b/biology/hyphy/distinfo @@ -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 diff --git a/biology/hyphy/files/patch-src_core_matrix.cpp b/biology/hyphy/files/patch-src_core_matrix.cpp deleted file mode 100644 index a4a280d2d94c..000000000000 --- a/biology/hyphy/files/patch-src_core_matrix.cpp +++ /dev/null @@ -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]; - }