From nobody Thu Nov 24 14:11:36 2022 X-Original-To: dev-commits-ports-all@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 4NJ0Kj1J3Fz4jGTj; Thu, 24 Nov 2022 14:11:37 +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 4NJ0Kj0rhnz4Glt; Thu, 24 Nov 2022 14:11:37 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1669299097; 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=2D6VLbvvxm+mDy16K4rmkgrG92cr4nND0T1MWg9Feh4=; b=Tc/wrtel1IoESfAlR7Ocfr1zMpg5jfxOH1uX2Jmb6lG51CUs2302xFFbX4BdGRJm0cp8H5 P+Rq/1BCNH+lU8XR5q7vJh9OImf90a+fFO0FV2bE6XTxJ6KKvoVYdCAYoLg9R90BD1AbW0 E5dylAU/9Fvii+ysgIsu8Cux2rmOqLA8003RvgfAohmbNMecQNGJUcLg9auBp0qYoIqj2L mHdgxF8fiXJwc2GQBolSFRoQ3Iu1Q6AqpFvnbiGcPt7SEL2WkRfkpGx9nzzjcDoBSB02Tx W+JL7IS1EjeOIdicsCze5BBZT8mkRfANxk4VC9dd4KMCJPnppZfFvzU8XzijOA== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1669299097; 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=2D6VLbvvxm+mDy16K4rmkgrG92cr4nND0T1MWg9Feh4=; b=OiLklnTfvE/vtDcTM5+CVQYmzuyMhNSD/iqi+fwM/zpRJbQonZNCrZ4OL3VUC5rAoOcz/q Hy+kY27vz5D3WmOR8RKwZWT6T1W/psya7JOFrXFv3AfT5+gvwNQRqEhNDUAYD99YfcxVSQ YCbz4buhpXkbMZ2AaBbprzWGhPJhpokvXtR3GiN9a5vjsQpWWU6SuBn49gnkc5AWSHQ9QW Pn6efzDaLYyh2ciVGCYA0C5X+afd2Fx10ETPuX08zb64xthaP03hDP7MnAoujZa770smyQ HTdyo04Qn6ohLMIIZlIcuDWvcZGJDJIrQ9+hfvsSQiORz1oaulFPAcJYPjuMRg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1669299097; a=rsa-sha256; cv=none; b=rU0BCO/igFZEBotaZSJH9857oU2aqW2LQZEcAbX+JOTKEqR+xf6Y5Mf5p9DrXw2rc484BK ojc4a9yYbbzVtezIn87vLkAn35SfWN9NlZEDmvhxmh0JZ7qKYxSSJVcuyAy3OjDwU2TtVi BS1GxTcrSb1Na3OJF9+IS1E6IuqE4AjPCxOMxOoGCr8PXBSRDYvkV8inWeL5eKT8CosS65 el2XeVqUTdJaz/Pklof3V8tEcrEYl31gM0qnluBdn8bW8mi/C0tBsLJPI6O9+BtxTBTS+E c5T2dO39pljb1g/BVqXVEMl+In11rWZdNhHDt5z+4R1iEdYqYtZejNmfZwG7fQ== 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 4NJ0Kh72YSz142r; Thu, 24 Nov 2022 14:11:36 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 2AOEBaro037953; Thu, 24 Nov 2022 14:11:36 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 2AOEBaBe037952; Thu, 24 Nov 2022 14:11:36 GMT (envelope-from git) Date: Thu, 24 Nov 2022 14:11:36 GMT Message-Id: <202211241411.2AOEBaBe037952@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: 4b987075629f - main - biology/megahit: Add cmake patch to respect ports build flags 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: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 4b987075629fc9516f81c5f2b94afe6c5f04f9d3 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=4b987075629fc9516f81c5f2b94afe6c5f04f9d3 commit 4b987075629fc9516f81c5f2b94afe6c5f04f9d3 Author: Jason W. Bacon AuthorDate: 2022-11-24 14:10:13 +0000 Commit: Jason W. Bacon CommitDate: 2022-11-24 14:10:13 +0000 biology/megahit: Add cmake patch to respect ports build flags Removes agressive optimizations hard-coded upstream --- biology/megahit/Makefile | 1 + biology/megahit/files/patch-CMakeLists.txt | 17 +++++++++++++++++ 2 files changed, 18 insertions(+) diff --git a/biology/megahit/Makefile b/biology/megahit/Makefile index 30080e9d2564..379440059baa 100644 --- a/biology/megahit/Makefile +++ b/biology/megahit/Makefile @@ -1,6 +1,7 @@ PORTNAME= megahit DISTVERSIONPREFIX= v DISTVERSION= 1.2.9 +PORTREVISION= 1 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/megahit/files/patch-CMakeLists.txt b/biology/megahit/files/patch-CMakeLists.txt new file mode 100644 index 000000000000..d879052c7f02 --- /dev/null +++ b/biology/megahit/files/patch-CMakeLists.txt @@ -0,0 +1,17 @@ +--- CMakeLists.txt.orig 2019-10-15 02:51:03 UTC ++++ CMakeLists.txt +@@ -42,13 +42,12 @@ find_package(OpenMP REQUIRED) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DXXH_INLINE_ALL -ftemplate-depth=3000") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-unused-function") +-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprefetch-loop-arrays -funroll-loops") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D__XROOT__='\"${CMAKE_SOURCE_DIR}/src\"'") + #set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D__XFILE__='\"$(subst ${CMAKE_SOURCE_DIR}/,,$(abspath $<))\"'") + + set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${ZLIB_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}") + +-set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG") ++set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG") + set(CMAKE_CXX_FLAGS_DEBUG "-g -ggdb -O1 -D_LIBCPP_DEBUG -D_GLIBCXX_DEBUG") + + if (COVERAGE)