From nobody Sun Dec 19 21:06:57 2021 X-Original-To: dev-commits-ports-all@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 6A7F018F93AA; Sun, 19 Dec 2021 21:06:58 +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 4JHFds68myz4rdr; Sun, 19 Dec 2021 21:06:57 +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 90FA61851; Sun, 19 Dec 2021 21:06:57 +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 1BJL6vcB079541; Sun, 19 Dec 2021 21:06:57 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 1BJL6v7J079540; Sun, 19 Dec 2021 21:06:57 GMT (envelope-from git) Date: Sun, 19 Dec 2021 21:06:57 GMT Message-Id: <202112192106.1BJL6v7J079540@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: b9105b7ef1e9 - main - biology/canu: Update to 2.2 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@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: b9105b7ef1e91bce177273f3031a98781ca6faf7 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1639948018; 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=sGViJvxw0SyoXMdyhqHlT91RS8jt7IzGLJoj8rkZyVQ=; b=YCCQWaLeBTL7LRLl4mTviRRq/pPxtYeU75cOkbNfhQC+iD1suqmVa9Cw/aCgORGtZ09zqZ BRc96aMfkOpbSxTzkArVAmNNS2iJTu/IxDVQQX2fZVfH2KZWIAIik6n3SpSKBVCtMyHT1D 8FometyKxdP1s7RluH4apNa/5R9GM7SLmzaeA3cZqcoNGYblXrjeZak2G9iwiUwd8po5Zn AxkQ9KNDvtNQHT3hjXvPl3LlRyCpzDJ3tjtouPN2jNKzloPdz1qMxo8EWJ/W2Djh7GxlR5 HQxn2XAPH5WZLuRAtZjcR6Uufda40nqyzFEIb7HrDOBTgpsSj9+dWuj8pk0qTw== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1639948018; a=rsa-sha256; cv=none; b=kuHKr8gi7qUJuzj7UOU3wyRPqvThNjh3vhBxKshY3aZ9aunrRnhomh3YstCTha1pgNbii3 iPkQWzAa2K+ALm1hvX5pS8qX9j2aFdDHA51h8PRlCGzW1MnQsb9HSsOwo88JOl6ftwZimN vvvPTYU/0TRVnNK9acWNoekcJga3b7Xdk5h49ocO9P3x2iGXGNeViB7N0QuSb5cs0pN6aZ 15vmbuDyLkJ3E37MLUokWf0C2yPfQ7fCKbLjHd4+VLKVb2NLHKzNHzu5jeSwJ794mykGT1 xXWtP33nd6VrSszdhYNP2nOpUwPIYmGjiMPBIACipgJlnoonTBpFmO5vWfSVWw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=b9105b7ef1e91bce177273f3031a98781ca6faf7 commit b9105b7ef1e91bce177273f3031a98781ca6faf7 Author: Jason W. Bacon AuthorDate: 2021-12-19 21:03:36 +0000 Commit: Jason W. Bacon CommitDate: 2021-12-19 21:06:56 +0000 biology/canu: Update to 2.2 FreeBSD port: Add support for aarch64 and powerpc64 using simde Not yet supported upstream Several upstream bug fixes and minor enhancements since 2.1 Changes: https://github.com/marbl/canu/tags --- biology/canu/Makefile | 27 ++++++---- biology/canu/distinfo | 6 +-- biology/canu/files/cpuid_arm.c | 57 ++++++++++++++++++++++ biology/canu/files/cpuid_ppc.c | 57 ++++++++++++++++++++++ ...boost_boost_smart__ptr_detail_shared__count.hpp | 10 ++++ .../patch-utility_src_parasail_internal__sse.h | 12 +++++ .../files/patch-utility_src_utility_align-ssw.H | 12 +++++ .../canu/files/patch-utility_src_utility_files.H | 11 +++++ .../canu/files/patch-utility_src_utility_system.H | 11 +++++ .../canu/files/patch-utility_src_utility_types.H | 11 +++++ biology/canu/pkg-plist | 3 +- 11 files changed, 204 insertions(+), 13 deletions(-) diff --git a/biology/canu/Makefile b/biology/canu/Makefile index 56ebc0779e5e..72a628226299 100644 --- a/biology/canu/Makefile +++ b/biology/canu/Makefile @@ -1,9 +1,8 @@ PORTNAME= canu -DISTVERSION= 2.1 -PORTREVISION= 1 -CATEGORIES= biology java perl5 +DISTVERSION= 2.2 +CATEGORIES= wip biology java perl5 # Github auto-generated tarballs lack submodules -MASTER_SITES= https://github.com/marbl/canu/releases/download/v2.1/ +MASTER_SITES= https://github.com/marbl/canu/releases/download/v${DISTVERSION}/ MAINTAINER= jwb@FreeBSD.org COMMENT= Single molecule sequence assembler @@ -11,14 +10,13 @@ COMMENT= Single molecule sequence assembler LICENSE= GPLv2 LICENSE_FILE= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/README.license.GPL -BROKEN_powerpc64= fails to build: utgcns/libboost/boost/smart_ptr/detail/sp_counted_impl.hpp:81:5: error: 'get_deleter' declared as a 'virtual' field -NOT_FOR_ARCHS= armv6 armv7 i386 powerpc -NOT_FOR_ARCHS_REASON= __int128 is not supported on this target +NOT_FOR_ARCHS= armv6 armv7 i386 mips powerpc powerpcspe +NOT_FOR_ARCHS_REASON= Requires 64-bit processor LIB_DEPENDS= libboost_regex.so:devel/boost-libs RUN_DEPENDS= gnuplot:math/gnuplot -USES= compiler:c++11-lang gmake localbase perl5 +USES= compiler:c++11-lang gmake localbase perl5 tar:xz USE_JAVA= yes JAVA_RUN= yes @@ -29,6 +27,17 @@ WRKSRC_SUBDIR= src # using a separate install target. MAKE_ENV= DESTDIR=${WRKSRC} CANU_BUILD_ENV=ports +.include + +# Parasail should be unbundled, but that would be a project because it's +# currently woven into the canu code +post-extract: +.if ${ARCH} == "aarch64" + ${CP} ${FILESDIR}/cpuid_arm.c ${WRKSRC}/utility/src/parasail/cpuid.c +.elif ${ARCH} == "powerpc64" || ${ARCH} == "powerpc64le" + ${CP} ${FILESDIR}/cpuid_ppc.c ${WRKSRC}/utility/src/parasail/cpuid.c +.endif + pre-configure: @${REINPLACE_CMD} \ -e 's|-O4||g' \ @@ -54,4 +63,4 @@ do-install: (cd ${WRKSRC}/build && \ ${COPYTREE_SHARE} "lib share" ${STAGEDIR}${PREFIX}) -.include +.include diff --git a/biology/canu/distinfo b/biology/canu/distinfo index 0ddec4d01a04..eace34089e15 100644 --- a/biology/canu/distinfo +++ b/biology/canu/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1599584712 -SHA256 (canu-2.1.tar.gz) = 73c70d2d6326bdaf471549f2d1eb7a1bf1e0fbf45cdc4a830bd6ce9fe3f3c231 -SIZE (canu-2.1.tar.gz) = 3313120 +TIMESTAMP = 1639774550 +SHA256 (canu-2.2.tar.xz) = e4d0c7b82149114f442ccd39e18f7fe2061c63b28d53700ad896e022b73b7404 +SIZE (canu-2.2.tar.xz) = 2400192 diff --git a/biology/canu/files/cpuid_arm.c b/biology/canu/files/cpuid_arm.c new file mode 100644 index 000000000000..3b35be06c087 --- /dev/null +++ b/biology/canu/files/cpuid_arm.c @@ -0,0 +1,57 @@ +/** + * @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() +{ +#if HAVE_NEON + return 1; +#else + return 0; +#endif +} + diff --git a/biology/canu/files/cpuid_ppc.c b/biology/canu/files/cpuid_ppc.c new file mode 100644 index 000000000000..4a832a90a32c --- /dev/null +++ b/biology/canu/files/cpuid_ppc.c @@ -0,0 +1,57 @@ +/** + * @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() +{ +#if HAVE_ALTIVEC + return 1; +#else + return 0; +#endif +} + +int parasail_can_use_neon() +{ + return 0; +} + diff --git a/biology/canu/files/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp b/biology/canu/files/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp new file mode 100644 index 000000000000..554c97a04af9 --- /dev/null +++ b/biology/canu/files/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp @@ -0,0 +1,10 @@ +--- utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp.orig 2021-12-18 13:01:24 UTC ++++ utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp +@@ -25,6 +25,7 @@ + #include + #include + #include ++#include + #include + #include + #include diff --git a/biology/canu/files/patch-utility_src_parasail_internal__sse.h b/biology/canu/files/patch-utility_src_parasail_internal__sse.h new file mode 100644 index 000000000000..ea03b5ab917c --- /dev/null +++ b/biology/canu/files/patch-utility_src_parasail_internal__sse.h @@ -0,0 +1,12 @@ +--- 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 new file mode 100644 index 000000000000..8da82c2d106a --- /dev/null +++ b/biology/canu/files/patch-utility_src_utility_align-ssw.H @@ -0,0 +1,12 @@ +--- 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" diff --git a/biology/canu/files/patch-utility_src_utility_files.H b/biology/canu/files/patch-utility_src_utility_files.H new file mode 100644 index 000000000000..3e72cbe4942b --- /dev/null +++ b/biology/canu/files/patch-utility_src_utility_files.H @@ -0,0 +1,11 @@ +--- utility/src/utility/files.H.orig 2021-12-17 20:57:15 UTC ++++ utility/src/utility/files.H +@@ -22,7 +22,7 @@ + + #include "types.H" + #include +- ++#include + + // Provides a safe and reliable mechanism for reading / writing + // binary data. diff --git a/biology/canu/files/patch-utility_src_utility_system.H b/biology/canu/files/patch-utility_src_utility_system.H new file mode 100644 index 000000000000..339c577b992d --- /dev/null +++ b/biology/canu/files/patch-utility_src_utility_system.H @@ -0,0 +1,11 @@ +--- utility/src/utility/system.H.orig 2021-12-17 20:57:47 UTC ++++ utility/src/utility/system.H +@@ -23,7 +23,7 @@ + #include "types.H" + + #include +- ++#include + + + double getTime(void); diff --git a/biology/canu/files/patch-utility_src_utility_types.H b/biology/canu/files/patch-utility_src_utility_types.H new file mode 100644 index 000000000000..e53536e09c8f --- /dev/null +++ b/biology/canu/files/patch-utility_src_utility_types.H @@ -0,0 +1,11 @@ +--- utility/src/utility/types.H.orig 2021-12-17 20:58:13 UTC ++++ utility/src/utility/types.H +@@ -55,7 +55,7 @@ + #include + + #include +-#include ++#include + + #include + #include diff --git a/biology/canu/pkg-plist b/biology/canu/pkg-plist index e3d2f84d51de..d76d4279c35e 100644 --- a/biology/canu/pkg-plist +++ b/biology/canu/pkg-plist @@ -1,6 +1,5 @@ bin/alignGFA bin/bogart -bin/bogus bin/canu bin/canu-time bin/canu.defaults @@ -32,6 +31,7 @@ bin/ovStoreIndexer bin/ovStoreSorter bin/ovStoreStats bin/overlapAlign +bin/overlapCheck bin/overlapConvert bin/overlapImport bin/overlapInCore @@ -59,6 +59,7 @@ lib/libcanu.a %%SITE_PERL%%/canu/Grid_Cloud.pm %%SITE_PERL%%/canu/Grid_DNANexus.pm %%SITE_PERL%%/canu/Grid_LSF.pm +%%SITE_PERL%%/canu/Grid_Local.pm %%SITE_PERL%%/canu/Grid_PBSTorque.pm %%SITE_PERL%%/canu/Grid_SGE.pm %%SITE_PERL%%/canu/Grid_Slurm.pm