From nobody Wed Aug 09 17:39:46 2023 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4RLckp2cc7z4m4Dl; Wed, 9 Aug 2023 17:39:46 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4RLckp27nKz3RBq; Wed, 9 Aug 2023 17:39:46 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1691602786; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=OlPbQZpwLRqI5/R99I65rY7wgI2IjEq+Sl0pQWuzodw=; b=leAyxwsZ7xwpmLVakDEOj6a1ALQc9MAbDnh85luWmWppdELdarlnxDn0q13D6+N97TRHvj 1hjw9U+BQBQOt9ElmSCvmE3XvMfnMWeh3NB48ck0ji6fKbEm00WdqdrzOZyUSHHwDqhdn/ Q2gC1Igyy+UHw0yAjrpn/MFjs9VfTkP/PlQiUVBnViCtaQ//GuXLROV8rhSgyaMG86eKqd TbhUZQIsM42s2T7nny36Bx6f6yra2l0FBL+iKJeRXwcMeiLqP5dCpd81n8cbxqGdQvWkI7 zAa6ff5AoMrHAgoH7z9+Dc/w8sD+gY9DaQ4P3xnGwrbaLI+qKJTcSv7wTbK1bw== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1691602786; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=OlPbQZpwLRqI5/R99I65rY7wgI2IjEq+Sl0pQWuzodw=; b=MLsRHHcmEk0OB2iCvo7/27cH0tXBvWPPP3EO8qBjqHxdrl/58eg6pv6Lz0q7bskatSpuOU wZIQ1j+LqQUM6AVX01jSjILDRFAvJF3eERr+1LfOG6g5RBbDyXIn3Tj6ooKwECTX+0JfpC 3vOAOKSIHoCxuOWGuj1spRa9bEfs9rconlXlhZC9S9N8heDUmPd/Zm/V0W6kov2LnGMCwW Gl42VCbdArb1rvWuDjM2XS9ccCJvWvBBgeZJBqem9rxe+JUa6BnmXWCmIzBn/XW8TNSa+f EezdDew60V67G+IjlmsxXSdidxLTFDy2OX4qP15Xk77E8tp3m4QJ9H/fRCcDjA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1691602786; a=rsa-sha256; cv=none; b=PVAB6VFziyVAL/ubZqR4yAlXV1stsXeUOhL/6A0N54VXp859mkj5LkoW7ZK5wRqqI/YLw6 himYlZViqYIDrO5ijCrT0hbAJtG2sJk0L2wwh/7RTE0Nk370FIezYdnSIPOpLhOESM+ujQ i4g1+k5upLW/yBmeAhLDvufNfvihegsokKmEIX6yUm3Uc/jRlmEdqn2Z7wtrwcgqIS0o5d s8ydgV3t/FktA4PLOHiLKFjeDNqr+hPe9QSdOvID9GWz6RZyDgOnk9zo2sUlu7Vy+Yml6g A+WlE05WZFByr4WfFJ8fvq9kAGH4N2DWB94CDdjJXGeY9mRAznhBtbjogrfQsw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4RLckp1BM6z93s; Wed, 9 Aug 2023 17:39:46 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 379HdkRX043756; Wed, 9 Aug 2023 17:39:46 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 379HdkcU043753; Wed, 9 Aug 2023 17:39:46 GMT (envelope-from git) Date: Wed, 9 Aug 2023 17:39:46 GMT Message-Id: <202308091739.379HdkcU043753@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: 8d0b7976cd07 - main - biology/hyphy: Update to 2.5.52 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@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: 8d0b7976cd078892b48202aa8acc0810135bf02a Auto-Submitted: auto-generated The branch main has been updated by jrm: URL: https://cgit.FreeBSD.org/ports/commit/?id=8d0b7976cd078892b48202aa8acc0810135bf02a commit 8d0b7976cd078892b48202aa8acc0810135bf02a Author: Joseph Mingrone AuthorDate: 2023-08-09 15:23:50 +0000 Commit: Joseph Mingrone 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 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