From nobody Thu Jul 20 11:22:19 2023 X-Original-To: dev-commits-ports-main@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 4R69JX0SQ4z4pCwN; Thu, 20 Jul 2023 11:22:20 +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 4R69JW71Prz3jjY; Thu, 20 Jul 2023 11:22:19 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1689852140; 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=Q+2HChqUsOOg6XB2cum55FOjE9JFM5sUE8yYvcVyQ/I=; b=QvLDIQa0P+3ATpF8iE6LhW+Wsgfc2lj1P3RKMdgDAyRI1Hm14e9vwFCdzjAOvjbsdEgWJ1 9kuesUEUq8MF9spoZCxCBT779tRzW2wseUUO48cPjvWnnHk/sQBPsBNuqC77m9MV91AZ7E lHnImMpPmlV7R07Za1/w9x0wqI5LiyoWt1BACWaCM+vv0AiZi582/Va3sEHnUtseKsi5YS kDmUlvDw9vD8qGniRP4EyMrPFaA4OQG7DvcPJPqslMetBN8O+XBwWgouH7q0P/4jpoITe7 iA/GcZvVK5av73o0P98yVUdMKmoY4nHUoXRv+494v2b9J/vgimw5LY5F4OF52A== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1689852140; 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=Q+2HChqUsOOg6XB2cum55FOjE9JFM5sUE8yYvcVyQ/I=; b=h/zReZx46/qJ2mSvp5kaqNOUfXDDxThA/VO0oKQyPbTJTImwhnmSucwQ/xOqdIDl8IDOxr gS8CNWdQ/yyGdY/2nlLkEwdSSwOfsDmjilTXNovQfZKSLIwt+EOk+2QPPo3YKOcJQkwVkx zvbSFvnBBZB3RIRJkwtOh2h9CIsJ6msUVMjoNXqVNKz7+2ra62CLHhICg7g5B42olk7NrS I8bRy/0VYLpUMTyRmrdFpnXCQe6rp1ffxxS5ggPB4lWJPAqe501PC/V68HSeyRXTKoQh7q 7JpaeFnaLT1q9Oa3cTtmz2xx3nnKnEkm3B+yNWcif4XrcVEN3kuQiAcoP3wjdw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1689852140; a=rsa-sha256; cv=none; b=NHNpkWWY9KpPjIz9/phlAgj8apOFrRmi7wXta2rVG0L2pJm2JD3lAU7qLyRrjYWXuC0USQ 5lTt44bzgpPfTMK/48VArKzCQtUfNepc0PY4NvIfkpzYcIA3vk5XBPTDXA41jgJGNvYoHX PvmqPYWAiXn8Bu7vimXQaYvcQV3T1RBlwWoiVg8yW39zvQOZhtl6OCh3nymZwutM8hgWwA uswAuLRA6nN2YnCmk6nXgFsUwN0Kvj1vd9hLj6SK8JuegT66fkdmJlsYCLAzpiRN2O77iJ vAKneghyMUFsr6JYttkWMtit0GLBGloAD5TJYB7yK8CQOSzBp1zmhQMDiEXKSw== 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 4R69JW66nzzTPQ; Thu, 20 Jul 2023 11:22:19 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 36KBMJ8R006026; Thu, 20 Jul 2023 11:22:19 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 36KBMJbN006025; Thu, 20 Jul 2023 11:22:19 GMT (envelope-from git) Date: Thu, 20 Jul 2023 11:22:19 GMT Message-Id: <202307201122.36KBMJbN006025@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: 290833541264 - main - biology/canu: Fix build under clang 16 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@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: 290833541264e265124451053d402f61e2313504 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=290833541264e265124451053d402f61e2313504 commit 290833541264e265124451053d402f61e2313504 Author: Jason W. Bacon AuthorDate: 2023-07-20 11:20:39 +0000 Commit: Jason W. Bacon 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 @@ -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 - --#include -+#define SIMDE_ENABLE_NATIVE_ALIASES -+#include - - #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 - #include - #include --#include -+#define SIMDE_ENABLE_NATIVE_ALIASES -+#include - - - #define MAPSTR "MIDNSHP=X"