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Bacon" Subject: git: 3f6b18bb3857 - main - biology/vcflib: Update to 1.0.12 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: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-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: 3f6b18bb3857ff38fac6669dd23669e03afab42e Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=3f6b18bb3857ff38fac6669dd23669e03afab42e commit 3f6b18bb3857ff38fac6669dd23669e03afab42e Author: Jason W. Bacon AuthorDate: 2024-11-25 14:46:10 +0000 Commit: Jason W. Bacon CommitDate: 2024-11-25 14:49:37 +0000 biology/vcflib: Update to 1.0.12 A few fixes and enhancements Changes: https://github.com/vcflib/vcflib/releases Reported by: portscout --- biology/vcflib/Makefile | 12 ++--- biology/vcflib/distinfo | 10 ++-- biology/vcflib/files/patch-CMakeLists.txt | 22 ++++----- biology/vcflib/pkg-plist | 81 +++++++++++++++---------------- 4 files changed, 58 insertions(+), 67 deletions(-) diff --git a/biology/vcflib/Makefile b/biology/vcflib/Makefile index c4efb379e8f6..f53800bfa2d7 100644 --- a/biology/vcflib/Makefile +++ b/biology/vcflib/Makefile @@ -1,6 +1,6 @@ PORTNAME= vcflib DISTVERSIONPREFIX= v -DISTVERSION= 1.0.10 +DISTVERSION= 1.0.12 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -12,7 +12,8 @@ LICENSE= MIT NOT_FOR_ARCHS= armv6 armv7 NOT_FOR_ARCHS_REASON= requires OpenMP which is not supported -BUILD_DEPENDS= pybind11>0:devel/pybind11 +BUILD_DEPENDS= pybind11>0:devel/pybind11 \ + ${PYTHON_PKGNAMEPREFIX}pypandoc>=1.4:textproc/py-pypandoc@${PY_FLAVOR} LIB_DEPENDS= libhts.so:biology/htslib \ libcurl.so:ftp/curl \ libwfa2.so:biology/wfa2-lib @@ -29,7 +30,7 @@ GH_TUPLE= ekg:fastahack:bb33265:fastahack/contrib/fastahack \ ekg:multichoose:e1f94ae: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 + vcflib:tabixpp:ae5cdf8:tabixpp/contrib/tabixpp SHEBANG_FILES= scripts/* # FIXME: Add Zig option + lang/zig dep @@ -39,10 +40,9 @@ OPTIONS_SUB= yes ZIG_DESC= Include Zig language support -# FIXME: https://github.com/vcflib/vcflib/issues/399 -ZIG_BUILD_DEPENDS= zig010>0:lang/zig010 +ZIG_BUILD_DEPENDS= zig>0:lang/zig -CMAKE_ARGS+= -DWFA_GITMODULE=OFF -DWFALIB=${LOCALBASE}/lib/libwfa2.so +CMAKE_ARGS+= -DWFA_GITMODULE=OFF -DWFALIB=${LOCALBASE}/lib/libwfa2.so.0 ZIG_CMAKE_OFF= -DZIG=OFF # Clang and GCC disable sse2 by default on i386, but it's required for vcflib diff --git a/biology/vcflib/distinfo b/biology/vcflib/distinfo index e4d3f2180621..066030757d4d 100644 --- a/biology/vcflib/distinfo +++ b/biology/vcflib/distinfo @@ -1,6 +1,6 @@ -TIMESTAMP = 1713703391 -SHA256 (ekg-vcflib-v1.0.10_GH0.tar.gz) = 6f7f366555e5b191a509bda6d7a2078825827458ba7e9922094c4c1ebb48e693 -SIZE (ekg-vcflib-v1.0.10_GH0.tar.gz) = 23539349 +TIMESTAMP = 1732541764 +SHA256 (ekg-vcflib-v1.0.12_GH0.tar.gz) = 7ab5b6a87a39105107029f5e0da52ece612c71095ab2aec69a00320f44bc5300 +SIZE (ekg-vcflib-v1.0.12_GH0.tar.gz) = 23543176 SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760 SHA256 (ekg-filevercmp-df20dcc_GH0.tar.gz) = d34bec614be638e05eb6fa419c936b9e7de58d50b1a096a5ca02aadb7db6b059 @@ -17,5 +17,5 @@ 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 (vcflib-tabixpp-ae5cdf8_GH0.tar.gz) = edb15012b57c6bfc900c1b8275fc3d55f2e7c21e83601f8cfedcbdf3107fbb04 +SIZE (vcflib-tabixpp-ae5cdf8_GH0.tar.gz) = 6965 diff --git a/biology/vcflib/files/patch-CMakeLists.txt b/biology/vcflib/files/patch-CMakeLists.txt index 4203916395af..347b5a48ab73 100644 --- a/biology/vcflib/files/patch-CMakeLists.txt +++ b/biology/vcflib/files/patch-CMakeLists.txt @@ -1,15 +1,6 @@ ---- CMakeLists.txt.orig 2023-02-07 17:22:46 UTC +--- CMakeLists.txt.orig 2024-11-21 07:59:50 UTC +++ CMakeLists.txt -@@ -9,7 +9,7 @@ project(vcflib) - cmake_minimum_required(VERSION 3.16) - project(vcflib) - --set(CMAKE_CXX_STANDARD 17) -+set(CMAKE_CXX_STANDARD 14) - - include(ExternalProject) - include(FeatureSummary) -@@ -69,7 +69,7 @@ if (${CMAKE_BUILD_TYPE} MATCHES Release) +@@ -70,7 +70,7 @@ if (${CMAKE_BUILD_TYPE} MATCHES Release) endif() if (${CMAKE_BUILD_TYPE} MATCHES Release) @@ -18,9 +9,14 @@ # set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG") # reset CXX_FLAGS to replace -O3 with -Ofast endif() -@@ -570,4 +570,4 @@ install(FILES ${INCLUDES} DESTINATION include) +@@ -595,8 +595,8 @@ install(TARGETS vcflib ARCHIVE DESTINATION ${CMAKE_INS + # ---- Install + + install(TARGETS vcflib ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR}) +-install(TARGETS ${WFALIB} ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR}) ++# install(TARGETS ${WFALIB} ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR}) - install(FILES ${INCLUDES} DESTINATION include) + install(FILES ${INCLUDES} DESTINATION include/vcflib) -install(DIRECTORY ${CMAKE_SOURCE_DIR}/man/ DESTINATION ${CMAKE_INSTALL_PREFIX}/man/man1) +install(DIRECTORY ${CMAKE_SOURCE_DIR}/man/ DESTINATION ${CMAKE_INSTALL_PREFIX}/share/man/man1) diff --git a/biology/vcflib/pkg-plist b/biology/vcflib/pkg-plist index 20c3eeca8d4e..85671a488441 100644 --- a/biology/vcflib/pkg-plist +++ b/biology/vcflib/pkg-plist @@ -26,7 +26,6 @@ bin/vcf2tsv bin/vcf_strip_extra_headers bin/vcfaddinfo bin/vcfafpath -bin/vcfallelicprimitives bin/vcfaltcount bin/vcfannotate bin/vcfannotategenotypes @@ -35,7 +34,6 @@ bin/vcfbreakmulti bin/vcfcat bin/vcfcheck bin/vcfclassify -bin/vcfcleancomplex bin/vcfclearid bin/vcfclearinfo bin/vcfcombine @@ -85,7 +83,6 @@ bin/vcfnulldotslashdot bin/vcfnullgenofields bin/vcfnumalt bin/vcfoverlay -bin/vcfparsealts bin/vcfplotaltdiscrepancy.r bin/vcfplotaltdiscrepancy.sh bin/vcfplotsitediscrepancy.r @@ -105,59 +102,57 @@ bin/vcfremap bin/vcfremoveaberrantgenotypes bin/vcfremovenonATGC bin/vcfremovesamples -bin/vcfroc bin/vcfsample2info bin/vcfsamplediff bin/vcfsamplenames bin/vcfsitesummarize bin/vcfsnps bin/vcfsort -bin/vcfstats bin/vcfstreamsort bin/vcfuniq bin/vcfuniqalleles bin/vcfvarstats -bin/vcfwave bin/wcFst -include/BandedSmithWaterman.h -include/BedReader.h -include/Fasta.h -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 -include/gpatInfo.hpp -include/join.h -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/vcf-wfa.h +include/vcflib/BandedSmithWaterman.h +include/vcflib/BedReader.h +include/vcflib/Fasta.h +include/vcflib/IndelAllele.h +include/vcflib/IntervalTree.h +include/vcflib/LargeFileSupport.h +include/vcflib/LeftAlign.h +include/vcflib/LeftAlign.hpp +include/vcflib/Mosaik.h +include/vcflib/Region.h +include/vcflib/Repeats.h +include/vcflib/SmithWatermanGotoh.h +include/vcflib/Variant.h +include/vcflib/allele.hpp +include/vcflib/canonicalize.h +include/vcflib/catch.hpp +include/vcflib/cdflib.hpp +include/vcflib/cigar.hpp +include/vcflib/convert.h +include/vcflib/disorder.h +include/vcflib/filevercmp.h +include/vcflib/gpatInfo.hpp +include/vcflib/join.h +include/vcflib/legacy.h +include/vcflib/makeUnique.h +include/vcflib/mt19937ar.h +include/vcflib/multichoose.h +include/vcflib/murmur3.hpp +include/vcflib/pdflib.hpp +include/vcflib/rkmh.hpp +include/vcflib/rnglib.hpp +include/vcflib/split.h +include/vcflib/ssw.hpp +include/vcflib/ssw_cpp.hpp +include/vcflib/var.hpp +include/vcflib/vcf-c-api.h +include/vcflib/vcf-wfa.h lib/libvcflib.a -%%ZIG%%lib/libzig.a lib/pyvcflib%%PYTHON_EXT_SUFFIX%%.so +%%ZIG%%lib/libzig.a share/man/man1/abba-baba.1.gz share/man/man1/bFst.1.gz share/man/man1/dumpContigsFromHeader.1.gz