From owner-svn-ports-all@freebsd.org Mon Jan 11 17:27:30 2021 Return-Path: Delivered-To: svn-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id F0DDA4E0986; Mon, 11 Jan 2021 17:27:30 +0000 (UTC) (envelope-from jwb@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 "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4DF0yV6V8Zz4Yt6; Mon, 11 Jan 2021 17:27:30 +0000 (UTC) (envelope-from jwb@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id D1A451E44E; Mon, 11 Jan 2021 17:27:30 +0000 (UTC) (envelope-from jwb@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id 10BHRUng050856; Mon, 11 Jan 2021 17:27:30 GMT (envelope-from jwb@FreeBSD.org) Received: (from jwb@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 10BHRUi0050855; Mon, 11 Jan 2021 17:27:30 GMT (envelope-from jwb@FreeBSD.org) Message-Id: <202101111727.10BHRUi0050855@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: jwb set sender to jwb@FreeBSD.org using -f From: "Jason W. Bacon" Date: Mon, 11 Jan 2021 17:27:30 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r561234 - head/biology/stacks X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: head/biology/stacks X-SVN-Commit-Revision: 561234 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 11 Jan 2021 17:27:31 -0000 Author: jwb Date: Mon Jan 11 17:27:30 2021 New Revision: 561234 URL: https://svnweb.freebsd.org/changeset/ports/561234 Log: biology/stacks: Drop dependency on gcc Replace compiler:openmp with compiler:c++11-lang and localbase Set USE_GCC for i386 to work around limitations in clang atomic (PR 230888) PR: port/247753, ports/252379 Modified: head/biology/stacks/Makefile Modified: head/biology/stacks/Makefile ============================================================================== --- head/biology/stacks/Makefile Mon Jan 11 17:17:35 2021 (r561233) +++ head/biology/stacks/Makefile Mon Jan 11 17:27:30 2021 (r561234) @@ -2,7 +2,7 @@ PORTNAME= stacks DISTVERSION= 2.4 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology perl5 python MASTER_SITES= http://catchenlab.life.illinois.edu/stacks/source/ @@ -12,7 +12,7 @@ COMMENT= Software pipeline for building loci from shor LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE -USES= compiler:openmp gmake python shebangfix +USES= compiler:c++11-lang gmake python shebangfix SHEBANG_FILES= scripts/*.pl scripts/*.py \ scripts/stacks-integrate-alignments scripts/stacks-gdb @@ -22,8 +22,8 @@ LDFLAGS+= -lpthread .include -# Force newer GCC on platforms using GCC 4.2 as base -.if ${CHOSEN_COMPILER_TYPE} == gcc +# Temp workaround, see PR 230888 +.if ${ARCH} == i386 USE_GCC= yes .endif