Date: Sun, 19 Dec 2021 21:06:57 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: b9105b7ef1e9 - main - biology/canu: Update to 2.2 Message-ID: <202112192106.1BJL6v7J079540@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=b9105b7ef1e91bce177273f3031a98781ca6faf7 commit b9105b7ef1e91bce177273f3031a98781ca6faf7 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-12-19 21:03:36 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> 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 <bsd.port.pre.mk> + +# 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 <bsd.port.mk> +.include <bsd.port.post.mk> 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 <boost/config.hpp> + #include <boost/checked_delete.hpp> + #include <boost/throw_exception.hpp> ++#include <boost/detail/sp_typeinfo.hpp> + #include <boost/smart_ptr/bad_weak_ptr.hpp> + #include <boost/smart_ptr/detail/sp_counted_base.hpp> + #include <boost/smart_ptr/detail/sp_counted_impl.hpp> 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 <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 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 <stdio.h> + #include <stdint.h> + #include <string.h> +-#include <emmintrin.h> ++#define SIMDE_ENABLE_NATIVE_ALIASES ++#include <simde.h.h> + + + #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 <vector> +- ++#include <cmath> + + // 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 <signal.h> +- ++#include <cmath> + + + 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 <ctype.h> + + #include <float.h> +-#include <math.h> ++#include <cmath> + + #include <assert.h> + #include <errno.h> 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
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