Date: Tue, 29 Jun 2021 14:09:55 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: a881e9d0c3cc - main - biology/mmseqs2: Fix runtime error when built with clang Message-ID: <202106291409.15TE9tfe000550@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=a881e9d0c3ccd79a71282e2e239cfbf2c22107f7 commit a881e9d0c3ccd79a71282e2e239cfbf2c22107f7 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-06-29 14:04:48 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> 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 <bsd.port.pre.mk> -# 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
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