Date: Thu, 20 Jul 2023 11:22:19 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: 290833541264 - main - biology/canu: Fix build under clang 16 Message-ID: <202307201122.36KBMJbN006025@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=290833541264e265124451053d402f61e2313504 commit 290833541264e265124451053d402f61e2313504 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2023-07-20 11:20:39 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2023-07-20 11:20:39 +0000 biology/canu: Fix build under clang 16 Also add cpu_any.c to theoretically support any 64-bit CPU Drop unused simde patches Reported by: pkg-fallout --- biology/canu/Makefile | 5 ++- biology/canu/files/cpuid_any.c | 52 ++++++++++++++++++++++ .../patch-utility_src_parasail_internal__sse.h | 12 ----- .../files/patch-utility_src_utility_align-ssw.H | 12 ----- 4 files changed, 56 insertions(+), 25 deletions(-) diff --git a/biology/canu/Makefile b/biology/canu/Makefile index 868d364ced15..d9b670ebf467 100644 --- a/biology/canu/Makefile +++ b/biology/canu/Makefile @@ -1,6 +1,6 @@ PORTNAME= canu DISTVERSION= 2.2 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology java perl5 # Github auto-generated tarballs lack submodules MASTER_SITES= https://github.com/marbl/canu/releases/download/v${DISTVERSION}/ @@ -28,6 +28,7 @@ WRKSRC_SUBDIR= src # Upstream Makefile compiles directly into ${DESTDIR}${PREFIX} rather than # using a separate install target. MAKE_ENV= DESTDIR=${WRKSRC} CANU_BUILD_ENV=ports +CXXFLAGS+= -std=c++14 .include <bsd.port.pre.mk> @@ -38,6 +39,8 @@ post-extract: ${CP} ${FILESDIR}/cpuid_arm.c ${WRKSRC}/utility/src/parasail/cpuid.c .elif ${ARCH} == "powerpc64" || ${ARCH} == "powerpc64le" ${CP} ${FILESDIR}/cpuid_ppc.c ${WRKSRC}/utility/src/parasail/cpuid.c +.elif ${ARCH} != "amd64" + ${CP} ${FILESDIR}/cpuid_any.c ${WRKSRC}/utility/src/parasail/cpuid.c .endif pre-configure: diff --git a/biology/canu/files/cpuid_any.c b/biology/canu/files/cpuid_any.c new file mode 100644 index 000000000000..be03bd4a479b --- /dev/null +++ b/biology/canu/files/cpuid_any.c @@ -0,0 +1,52 @@ +/** + * @file + * + * @author jeffrey.daily@gmail.com + * + * Copyright (c) 2015 Battelle Memorial Institute. + * + * For non-intel platforms, stub out the intel feature tests. + */ +#include "config.h" + +#include "parasail/cpuid.h" + +int parasail_can_use_avx512vbmi() +{ + return 0; +} + +int parasail_can_use_avx512bw() +{ + return 0; +} + +int parasail_can_use_avx512f() +{ + return 0; +} + +int parasail_can_use_avx2() +{ + return 0; +} + +int parasail_can_use_sse41() +{ + return 0; +} + +int parasail_can_use_sse2() +{ + return 0; +} + +int parasail_can_use_altivec() +{ + return 0; +} + +int parasail_can_use_neon() +{ + return 0; +} diff --git a/biology/canu/files/patch-utility_src_parasail_internal__sse.h b/biology/canu/files/patch-utility_src_parasail_internal__sse.h deleted file mode 100644 index ea03b5ab917c..000000000000 --- a/biology/canu/files/patch-utility_src_parasail_internal__sse.h +++ /dev/null @@ -1,12 +0,0 @@ ---- utility/src/parasail/internal_sse.h.orig 2021-12-17 22:10:09 UTC -+++ utility/src/parasail/internal_sse.h -@@ -10,7 +10,8 @@ - - #include <stdint.h> - --#include <emmintrin.h> -+#define SIMDE_ENABLE_NATIVE_ALIASES -+#include <simde.h> - - #include "parasail.h" - diff --git a/biology/canu/files/patch-utility_src_utility_align-ssw.H b/biology/canu/files/patch-utility_src_utility_align-ssw.H deleted file mode 100644 index 8da82c2d106a..000000000000 --- a/biology/canu/files/patch-utility_src_utility_align-ssw.H +++ /dev/null @@ -1,12 +0,0 @@ ---- utility/src/utility/align-ssw.H.orig 2021-12-17 22:12:23 UTC -+++ utility/src/utility/align-ssw.H -@@ -33,7 +33,8 @@ - #include <stdio.h> - #include <stdint.h> - #include <string.h> --#include <emmintrin.h> -+#define SIMDE_ENABLE_NATIVE_ALIASES -+#include <simde.h.h> - - - #define MAPSTR "MIDNSHP=X"
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