From owner-dev-commits-ports-all@freebsd.org Tue Jun 29 14:09:55 2021 Return-Path: Delivered-To: dev-commits-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 72CBD64C3CD; Tue, 29 Jun 2021 14:09:55 +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 4GDmZW2jTNz4vn3; Tue, 29 Jun 2021 14:09:55 +0000 (UTC) (envelope-from git@FreeBSD.org) 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 4166D1A5B7; Tue, 29 Jun 2021 14:09:55 +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 15TE9tut000551; Tue, 29 Jun 2021 14:09:55 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 15TE9tfe000550; Tue, 29 Jun 2021 14:09:55 GMT (envelope-from git) Date: Tue, 29 Jun 2021 14:09:55 GMT Message-Id: <202106291409.15TE9tfe000550@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: a881e9d0c3cc - main - biology/mmseqs2: Fix runtime error when built with clang 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: a881e9d0c3ccd79a71282e2e239cfbf2c22107f7 Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commit messages for all branches of the ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 29 Jun 2021 14:09:55 -0000 The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=a881e9d0c3ccd79a71282e2e239cfbf2c22107f7 commit a881e9d0c3ccd79a71282e2e239cfbf2c22107f7 Author: Jason W. Bacon AuthorDate: 2021-06-29 14:04:48 +0000 Commit: Jason W. Bacon CommitDate: 2021-06-29 14:04:48 +0000 biology/mmseqs2: Fix runtime error when built with clang Disable IPS4O to avoid deadlocks (upstream developer fix) Removing USE_GCC should fix pkg build errors caused by --- biology/mmseqs2/Makefile | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/biology/mmseqs2/Makefile b/biology/mmseqs2/Makefile index 755ed6f7aaa0..2ca647d74995 100644 --- a/biology/mmseqs2/Makefile +++ b/biology/mmseqs2/Makefile @@ -1,6 +1,6 @@ PORTNAME= MMseqs2 DISTVERSION= 13-45111 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -20,18 +20,14 @@ USE_PERL5= build SHEBANG_GLOB= *.sh GH_ACCOUNT= soedinglab -CMAKE_ARGS+= -DUSE_SYSTEM_ZSTD:BOOL=ON +CMAKE_ARGS+= -DUSE_SYSTEM_ZSTD:BOOL=ON -DDISABLE_IPS4O:BOOL=ON LDFLAGS+= -lpthread PLIST_FILES= bin/mmseqs ${DATADIR}/bash-completion.sh .include -# Hangs when built with clang and SSE or x86-64 only. Works fine with -# -march=native. Upstream is investigating. To build fully optimized, -# non-portable binary with clang: env CFLAGS='-O2 -march=native' make .if ${ARCH} == "amd64" && empty(CFLAGS:M*march=native*) -USE_GCC= yes # Need at least SSE2 for decent performance. x86-64 groups SSE2 with other # common features in low-end AMD64 CPUs. CFLAGS+= -march=x86-64