From nobody Sun Jan 22 17:14:40 2023 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 4P0Kbj1xj6z3NBVt; Sun, 22 Jan 2023 17:14:41 +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 4P0Kbj1Wh0z4PSW; Sun, 22 Jan 2023 17:14:41 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1674407681; 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=XqFQlv74ihQHuj5gt8HGA24vr922khuKk80q/zEx3G0=; b=Fxl83mufh7HRuEkkKTKvc/0N9yU0f1UagnpcAmmX6rDO2BT+06D30dDwSQMrRpjNNho0zo uRulp1LDU+qgzAsznA+ezea9S/X6qfz4JdexTfoVKdV/QRmOM35syi+buoYPcMEQGYXDWV 3qzFOjLmz463r7/ZbuYgi0dXsdpygDOSHPZpHOtxMmsCOX1GbPWgo8sMna4ghB+JUNxy6i kP4LqzSmMujS53U8aBAk80hIKfB2JqLc1nqXcUiBp/JIhZPaQhi+hoshfkN3qlXp5l1KVX M+MaETGAwTrfz0YHo3C8JCaDlLHsy6dWRa33UTIta6OeCwWmkMAq+82h17Iclw== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1674407681; 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=XqFQlv74ihQHuj5gt8HGA24vr922khuKk80q/zEx3G0=; b=FceHbzYBH9KKyhydCQShBKJF4Z+XFqV7dacjfSk/4wu18lZfLIQoc+46Aw4qe7JBQdFWK7 6VB/OgcksvZQvfm4UOww6FWqRDYEdBTcyV7XmsFqdFY+kjdz8HlpPBR3gj+rOhVFeFloUE XnNeuBDjbmq4dGPX6McmsVhHCGVAMD6lAI1O5cOhdi10u07kQuFM31rDx96R1PY0cyVhHr 66NPXh6biXnhOJvK9E56Umz+Ld3uSYrWQzLykVQ/mAcceTmqvPjkXmk060Q3KtJaPu33Lf jkTnIPx72KCsHZPxcOTgdcGWwKnfimNf3qVnaJVBG/cnCEfOBf5FZOnWlXUZAg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1674407681; a=rsa-sha256; cv=none; b=r+J2jpUGRPFhJrQrGUn1XHb+ujo5jFDh7yC/nmiDPDQzhiPztxN7nQAy0yLg6hCq61R+mM 2RiaXr3J9St2YgkkDdZsjNbK+7kPCjzSNb8cb8PDN71YaLr/VtDPn74/4OYDGJ09k2j3en KGE9VaNfWGK5VIUW3xRl/wgg95yP5aT7N9hPgkx5zqmTHBNU8jb0IBfYjFy65oXdzNPRkG ca80m60PUB359I3hPBqvIQklLl5zqwOCr9JiyxXeD2jSaFTcJjrDAJn5ZRvwYxGHqROToF i5+dxndSUKpvZ7fO31k4ene4+DlN3N322R/kiaoeUSHMZra2RHJJ4ndAzYd7nw== 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 4P0Kbh74rpzxbF; Sun, 22 Jan 2023 17:14:40 +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 30MHEevb025311; Sun, 22 Jan 2023 17:14:40 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 30MHEeKr025310; Sun, 22 Jan 2023 17:14:40 GMT (envelope-from git) Date: Sun, 22 Jan 2023 17:14:40 GMT Message-Id: <202301221714.30MHEeKr025310@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: 459cb897f042 - main - biology/vcflib: Update to 1.0.5 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: 459cb897f0423111cd4b55fac5caabeef7c81d77 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=459cb897f0423111cd4b55fac5caabeef7c81d77 commit 459cb897f0423111cd4b55fac5caabeef7c81d77 Author: Jason W. Bacon AuthorDate: 2023-01-22 17:13:14 +0000 Commit: Jason W. Bacon CommitDate: 2023-01-22 17:13:14 +0000 biology/vcflib: Update to 1.0.5 Numerous new features and enhancements Changes: https://github.com/vcflib/vcflib/tags Reported by: portscout --- biology/vcflib/Makefile | 32 ++++++++++++++++++------------- biology/vcflib/distinfo | 10 +++++++--- biology/vcflib/files/patch-CMakeLists.txt | 30 ++++++++++++++++++++--------- biology/vcflib/pkg-plist | 14 ++++++++++++++ 4 files changed, 61 insertions(+), 25 deletions(-) diff --git a/biology/vcflib/Makefile b/biology/vcflib/Makefile index a42fa6c8898e..7038f110c052 100644 --- a/biology/vcflib/Makefile +++ b/biology/vcflib/Makefile @@ -1,7 +1,6 @@ PORTNAME= vcflib DISTVERSIONPREFIX= v -DISTVERSION= 1.0.3 -PORTREVISION= 1 +DISTVERSION= 1.0.5 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -10,22 +9,26 @@ WWW= https://github.com/vcflib/vcflib LICENSE= MIT +BUILD_DEPENDS= zig>0:lang/zig \ + pybind11>=0:devel/pybind11 LIB_DEPENDS= libhts.so:biology/htslib \ - libtabix.so:biology/tabixpp + libcurl.so:ftp/curl -USES= cmake localbase:ldflags pkgconfig python shebangfix +USES= cmake:noninja gmake localbase:ldflags pkgconfig python shebangfix USE_GITHUB= yes GH_ACCOUNT= ekg -GH_TUPLE= ekg:fastahack:bb33265:fastahack/fastahack \ - ekg:filevercmp:1a9b779:filevercmp/filevercmp \ - ekg:fsom:a6ef318:fsom/fsom \ - google:googletest:d225acc:googletest/googletest \ - ekg:intervaltree:aa59377:intervaltree/intervaltree \ - edawson:libVCFH:44b6580:libVCFH/libVCFH \ - ekg:multichoose:68733cd:multichoose/multichoose \ - ekg:smithwaterman:2610e25:smithwaterman/smithwaterman \ - simd-everywhere:simde-no-tests:9af03cd:simd/src/simde +GH_TUPLE= ekg:fastahack:bb33265:fastahack/contrib/fastahack \ + ekg:filevercmp:1a9b779:filevercmp/contrib/filevercmp \ + ekg:fsom:a6ef318:fsom/contrib/fsom \ + google:googletest:d225acc:googletest/contrib/googletest \ + ekg:intervaltree:aa59377:intervaltree/contrib/intervaltree \ + edawson:libVCFH:44b6580:libVCFH/contrib/libVCFH \ + ekg:multichoose:68733cd:multichoose/contrib/multichoose \ + ekg:smithwaterman:2610e25:smithwaterman/contrib/smithwaterman \ + simd-everywhere:simde-no-tests:9af03cd:simd/src/simde \ + vcflib:tabixpp:v1.1.2:tabixpp/contrib/tabixpp \ + smarco:WFA2-lib:v2.3:wfa2/contrib/WFA2-lib SHEBANG_FILES= scripts/* # Clang and GCC disable sse2 by default on i386, but it's required for vcflib @@ -33,4 +36,7 @@ CFLAGS_i386= -msse2 CONFLICTS_INSTALL= filevercmp libdisorder # include/disorder.h include/filevercmp.h include/pdflib.hpp +post-stage: + ${MV} ${STAGEDIR}/usr/lib/libzig.a ${STAGEDIR}${PREFIX}/lib + .include diff --git a/biology/vcflib/distinfo b/biology/vcflib/distinfo index bdbfdb931717..b009e8c070e7 100644 --- a/biology/vcflib/distinfo +++ b/biology/vcflib/distinfo @@ -1,6 +1,6 @@ -TIMESTAMP = 1643316477 -SHA256 (ekg-vcflib-v1.0.3_GH0.tar.gz) = 5fd05f46dc251a56a322809da92c93c85318036aa9ac39a2eefc4fbd39b5df6c -SIZE (ekg-vcflib-v1.0.3_GH0.tar.gz) = 19213097 +TIMESTAMP = 1674400989 +SHA256 (ekg-vcflib-v1.0.5_GH0.tar.gz) = f24b8553fcb37dfe35e704a415ff4be8fd657a5d94f0101723552805946fb7a3 +SIZE (ekg-vcflib-v1.0.5_GH0.tar.gz) = 23545058 SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760 SHA256 (ekg-filevercmp-1a9b779_GH0.tar.gz) = 34c21d1b58295bca72b92c1cd832a4171b07ec97c19ffc0d4d8ec67e266c6070 @@ -19,3 +19,7 @@ SHA256 (ekg-smithwaterman-2610e25_GH0.tar.gz) = f907becb50945d0858d3bf7a64959905 SIZE (ekg-smithwaterman-2610e25_GH0.tar.gz) = 39160 SHA256 (simd-everywhere-simde-no-tests-9af03cd_GH0.tar.gz) = 99dcb7d6a2e1dc3f51401ff16eaa5dde93c793e13b514ea9cae4d9819144b8fe SIZE (simd-everywhere-simde-no-tests-9af03cd_GH0.tar.gz) = 572867 +SHA256 (vcflib-tabixpp-v1.1.2_GH0.tar.gz) = c850299c3c495221818a85c9205c60185c8ed9468d5ec2ed034470bb852229dc +SIZE (vcflib-tabixpp-v1.1.2_GH0.tar.gz) = 6962 +SHA256 (smarco-WFA2-lib-v2.3_GH0.tar.gz) = 64a113895c74dd746ec52d768a2d56465fb4a86c40c13fe985af549f1ca86343 +SIZE (smarco-WFA2-lib-v2.3_GH0.tar.gz) = 4149234 diff --git a/biology/vcflib/files/patch-CMakeLists.txt b/biology/vcflib/files/patch-CMakeLists.txt index 2520c928273e..6de651bd1d98 100644 --- a/biology/vcflib/files/patch-CMakeLists.txt +++ b/biology/vcflib/files/patch-CMakeLists.txt @@ -1,11 +1,23 @@ ---- CMakeLists.txt.orig 2021-11-03 15:07:33 UTC +--- CMakeLists.txt.orig 2023-01-16 08:55:05 UTC +++ CMakeLists.txt -@@ -230,7 +230,7 @@ if (NOT BUILD_ONLY_LIB) - foreach(BIN ${BINS}) - add_executable(${BIN} src/${BIN}.cpp) - target_include_directories(${BIN} PUBLIC ${TABIXPP_LIBRARIES} ${HTSLIB_INCLUDE_DIRS}) -- target_link_libraries(${BIN} vcflib tabixpp -DGIT_VERSION=0.9.0 ${TABIXPP_LIBRARIES} ${HTSLIB_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${ZLIB_LIBRARIES} ${LIBLZMA_LIBRARIES} ${BZIP2_LIBRARIES}) -+ target_link_libraries(${BIN} vcflib tabix -DGIT_VERSION=0.9.0 ${TABIXPP_LIBRARIES} ${HTSLIB_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${ZLIB_LIBRARIES} ${LIBLZMA_LIBRARIES} ${BZIP2_LIBRARIES}) - endforeach(BIN ${BINS}) - install(TARGETS ${BINS} RUNTIME DESTINATION bin) +@@ -1,7 +1,7 @@ + cmake_minimum_required(VERSION 3.16) + project(vcflib) + +-set(CMAKE_CXX_STANDARD 17) ++set(CMAKE_CXX_STANDARD 14) + + include(ExternalProject) + include(FeatureSummary) +@@ -358,9 +358,9 @@ endif(HTSLIB_LOCAL) + + # FIXME: hard-coded compile switches need to be fixed upstream + if (ASAN) +- set(wfa_MAKE_ARGS BUILD_WFA_PARALLEL=1 BUILD_TOOLS=0 BUILD_EXAMPLES=0 CC=gcc CC_FLAGS=-fPIC setup asan lib_wfa) ++ set(wfa_MAKE_ARGS BUILD_WFA_PARALLEL=1 BUILD_TOOLS=0 BUILD_EXAMPLES=0 CC_FLAGS=-fPIC setup asan lib_wfa) + else() +- set(wfa_MAKE_ARGS BUILD_WFA_PARALLEL=1 BUILD_TOOLS=0 BUILD_EXAMPLES=0 CC=gcc CC_FLAGS=-fPIC setup lib_wfa) ++ set(wfa_MAKE_ARGS BUILD_WFA_PARALLEL=1 BUILD_TOOLS=0 BUILD_EXAMPLES=0 CC_FLAGS=-fPIC setup lib_wfa) endif() + + # if ((${CMAKE_BUILD_TYPE} MATCHES Release) OR (${CMAKE_BUILD_TYPE} MATCHES RelWithDebInfo)) diff --git a/biology/vcflib/pkg-plist b/biology/vcflib/pkg-plist index 14fd56d8448f..b5b53667909c 100644 --- a/biology/vcflib/pkg-plist +++ b/biology/vcflib/pkg-plist @@ -82,6 +82,7 @@ bin/vcfnobiallelicsnps bin/vcfnoindels bin/vcfnosnps bin/vcfnulldotslashdot +bin/vcfnullgenofields bin/vcfnumalt bin/vcfoverlay bin/vcfparsealts @@ -116,6 +117,7 @@ bin/vcfstreamsort bin/vcfuniq bin/vcfuniqalleles bin/vcfvarstats +bin/vcfwave bin/wcFst include/BandedSmithWaterman.h include/BedReader.h @@ -124,13 +126,16 @@ include/IndelAllele.h include/IntervalTree.h include/LargeFileSupport.h include/LeftAlign.h +include/LeftAlign.hpp include/Mosaik.h include/Region.h include/Repeats.h include/SmithWatermanGotoh.h include/Variant.h +include/allele.hpp include/catch.hpp include/cdflib.hpp +include/cigar.hpp include/convert.h include/disorder.h include/filevercmp.h @@ -140,15 +145,20 @@ include/makeUnique.h include/mt19937ar.h include/multichoose.h include/multipermute.h +include/murmur3.hpp include/pdflib.hpp +include/rkmh.hpp include/rnglib.hpp include/split.h include/ssw.hpp include/ssw_cpp.hpp include/var.hpp +include/vcf-c-api.h include/vec128int.h include/veclib_types.h lib/libvcflib.a +lib/libzig.a +lib/pyvcflib%%PYTHON_EXT_SUFFIX%%.so man/man1/abba-baba.1.gz man/man1/bFst.1.gz man/man1/dumpContigsFromHeader.1.gz @@ -163,6 +173,7 @@ man/man1/permuteGPAT++.1.gz man/man1/permuteSmooth.1.gz man/man1/plotHaps.1.gz man/man1/popStats.1.gz +man/man1/pyvcflib.1.gz man/man1/segmentFst.1.gz man/man1/segmentIhs.1.gz man/man1/sequenceDiversity.1.gz @@ -212,8 +223,10 @@ man/man1/vcfkeepsamples.1.gz man/man1/vcfld.1.gz man/man1/vcfleftalign.1.gz man/man1/vcflength.1.gz +man/man1/vcflib-api.1.gz man/man1/vcflib.1.gz man/man1/vcfnulldotslashdot.1.gz +man/man1/vcfnullgenofields.1.gz man/man1/vcfnumalt.1.gz man/man1/vcfoverlay.1.gz man/man1/vcfparsealts.1.gz @@ -233,4 +246,5 @@ man/man1/vcfstats.1.gz man/man1/vcfstreamsort.1.gz man/man1/vcfuniq.1.gz man/man1/vcfuniqalleles.1.gz +man/man1/vcfwave.1.gz man/man1/wcFst.1.gz