Date: Wed, 9 Aug 2023 17:39:46 GMT From: Joseph Mingrone <jrm@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 8d0b7976cd07 - main - biology/hyphy: Update to 2.5.52 Message-ID: <202308091739.379HdkcU043753@gitrepo.freebsd.org>
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The branch main has been updated by jrm: URL: https://cgit.FreeBSD.org/ports/commit/?id=8d0b7976cd078892b48202aa8acc0810135bf02a commit 8d0b7976cd078892b48202aa8acc0810135bf02a Author: Joseph Mingrone <jrm@FreeBSD.org> AuthorDate: 2023-08-09 15:23:50 +0000 Commit: Joseph Mingrone <jrm@FreeBSD.org> CommitDate: 2023-08-09 17:39:17 +0000 biology/hyphy: Update to 2.5.52 - FEL test is now passing, so remove comment about it failing. - Remove armv7 support since most tests are segfaulting. Changes: https://github.com/veg/hyphy/releases/tag/2.5.52 Sponsored by: The FreeBSD Foundation Differential Revision: https://reviews.freebsd.org/D41393 Tested by: fuz (armv7) --- biology/hyphy/Makefile | 6 ++---- biology/hyphy/distinfo | 6 +++--- biology/hyphy/files/patch-src_core_include_likefunc.h | 12 ------------ biology/hyphy/pkg-plist | 1 + 4 files changed, 6 insertions(+), 19 deletions(-) diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile index 68438851d8b7..2ac2c78ea0c5 100644 --- a/biology/hyphy/Makefile +++ b/biology/hyphy/Makefile @@ -1,5 +1,5 @@ PORTNAME= hyphy -DISTVERSION= 2.5.51hf +DISTVERSION= 2.5.52 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org @@ -9,7 +9,7 @@ WWW= https://www.hyphy.org/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE -ONLY_FOR_ARCHS= aarch64 amd64 armv7 i386 powerpc powerpc64 powerpc64le +ONLY_FOR_ARCHS= aarch64 amd64 i386 powerpc powerpc64 powerpc64le LIB_DEPENDS= libcurl.so:ftp/curl TEST_DEPENDS= bash:shells/bash @@ -24,6 +24,4 @@ AVX_DESC= Advanced vector extensions support AVX_CMAKE_OFF= -DNOAVX:BOOL=ON -# FEL test is failing. See https://github.com/veg/hyphy/issues/1585 - .include <bsd.port.mk> diff --git a/biology/hyphy/distinfo b/biology/hyphy/distinfo index 8a097550734b..d0aac6efd8a0 100644 --- a/biology/hyphy/distinfo +++ b/biology/hyphy/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1685303680 -SHA256 (veg-hyphy-2.5.51hf_GH0.tar.gz) = 403a5d07a4e7e67d3d8136fa83649713ad28223a2519e5fba3aa82697a03375f -SIZE (veg-hyphy-2.5.51hf_GH0.tar.gz) = 5620954 +TIMESTAMP = 1691588992 +SHA256 (veg-hyphy-2.5.52_GH0.tar.gz) = 9e57d7af4a2bb765c48e4eccd025f22a64b692e8951f258e7b9134f7bd8bffed +SIZE (veg-hyphy-2.5.52_GH0.tar.gz) = 5633837 diff --git a/biology/hyphy/files/patch-src_core_include_likefunc.h b/biology/hyphy/files/patch-src_core_include_likefunc.h deleted file mode 100644 index bd2ab76cc7cb..000000000000 --- a/biology/hyphy/files/patch-src_core_include_likefunc.h +++ /dev/null @@ -1,12 +0,0 @@ ---- src/core/include/likefunc.h.orig 2023-06-27 12:50:39 UTC -+++ src/core/include/likefunc.h -@@ -282,9 +282,6 @@ class _LikelihoodFunction: public BaseObj { (public) - long GetThreadCount (void) { - return 1L; - } -- void SetThreadCount (long) { -- -- } - #endif - #endif - diff --git a/biology/hyphy/pkg-plist b/biology/hyphy/pkg-plist index 6636b69c97e8..9f46ee3e53d6 100644 --- a/biology/hyphy/pkg-plist +++ b/biology/hyphy/pkg-plist @@ -190,6 +190,7 @@ bin/hyphy %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/SingleOmega.bf %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf +%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/contrast-meme.bf %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf
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