Date: Tue, 29 Aug 2023 16:59:03 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: e06be01f1ef1 - main - biology/spoa: update 4.0.7 =?utf-8?Q?=E2=86=92?= 4.1.0 Message-ID: <202308291659.37TGx3R8006649@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=e06be01f1ef131f645cf2177b38758acf7a2e48a commit e06be01f1ef131f645cf2177b38758acf7a2e48a Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2023-08-29 15:49:03 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2023-08-29 16:59:01 +0000 biology/spoa: update 4.0.7 → 4.1.0 Reported by: portscout --- biology/spoa/Makefile | 18 +++-- biology/spoa/distinfo | 6 +- biology/spoa/files/patch-CMakeLists.txt | 118 -------------------------------- biology/spoa/pkg-plist | 7 +- 4 files changed, 21 insertions(+), 128 deletions(-) diff --git a/biology/spoa/Makefile b/biology/spoa/Makefile index bf258c57ffe4..378002e2f801 100644 --- a/biology/spoa/Makefile +++ b/biology/spoa/Makefile @@ -1,6 +1,5 @@ PORTNAME= spoa -DISTVERSION= 4.0.7 -PORTREVISION= 4 +DISTVERSION= 4.1.0 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org @@ -11,7 +10,7 @@ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= bioparser>0:biology/bioparser \ - ${LOCALBASE}/include/biosoup/nucleic_acid.hpp:biology/biosoup \ + biosoup>0:biology/biosoup \ cereal>0:devel/cereal \ simde>0:devel/simde LIB_DEPENDS= libcpu_features.so:devel/cpu_features @@ -24,8 +23,17 @@ USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= rvaser -CMAKE_ON= BUILD_SHARED_LIBS spoa_optimize_for_portability spoa_build_executable spoa_use_simde spoa_use_simde_nonvec spoa_use_simde_openmp -CMAKE_OFF= spoa_optimize_for_native +CMAKE_ON= BUILD_SHARED_LIBS \ + spoa_build_exe \ + spoa_optimize_for_portability \ + spoa_build_executable \ + spoa_use_simde \ + spoa_use_simde_nonvec \ + spoa_use_simde_openmp \ + spoa_use_cereal \ + spoa_use_simde_openmp +CMAKE_OFF= spoa_optimize_for_native \ + spoa_build_tests CXXFLAGS+= -I${LOCALBASE}/include/cpu_features LDFLAGS+= -lz -lcpu_features diff --git a/biology/spoa/distinfo b/biology/spoa/distinfo index b004cd66001d..09296c5fd3cf 100644 --- a/biology/spoa/distinfo +++ b/biology/spoa/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1611045674 -SHA256 (rvaser-spoa-4.0.7_GH0.tar.gz) = f8cb409adcca20ca6cc0025371743b915790879957cf001ca5e155ed16fd14e0 -SIZE (rvaser-spoa-4.0.7_GH0.tar.gz) = 43574 +TIMESTAMP = 1693289273 +SHA256 (rvaser-spoa-4.1.0_GH0.tar.gz) = 43238356f00bce2ad9698fc18b3e320024172a82182dcff24d57c5cf19e342c8 +SIZE (rvaser-spoa-4.1.0_GH0.tar.gz) = 47814 diff --git a/biology/spoa/files/patch-CMakeLists.txt b/biology/spoa/files/patch-CMakeLists.txt deleted file mode 100644 index a5e7af7845e8..000000000000 --- a/biology/spoa/files/patch-CMakeLists.txt +++ /dev/null @@ -1,118 +0,0 @@ ---- CMakeLists.txt.orig 2021-01-15 03:44:02 UTC -+++ CMakeLists.txt -@@ -44,9 +44,10 @@ if (spoa_use_simde OR - endif () - endif () - --if (NOT TARGET cereal) -- add_subdirectory(vendor/cereal EXCLUDE_FROM_ALL) --endif () -+#if (NOT TARGET cereal) -+# add_subdirectory(vendor/cereal EXCLUDE_FROM_ALL) -+#endif () -+find_package(cereal REQUIRED) - - add_library(${PROJECT_NAME} - src/alignment_engine.cpp -@@ -55,19 +56,19 @@ add_library(${PROJECT_NAME} - src/dispatcher.cpp) - target_include_directories(${PROJECT_NAME} PUBLIC - $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include> -- $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/simde> -- $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/cpu_features/include> -+ #$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/simde> -+ #$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/cpu_features/include> - $<INSTALL_INTERFACE:include>) - target_link_libraries(${PROJECT_NAME} -- cereal) -+ cereal::cereal) - if (BUILD_SHARED_LIBS) - set_property(TARGET ${PROJECT_NAME} PROPERTY SOVERSION "7.0.0") - endif () - - if (spoa_generate_dispatch) -- if (NOT TARGET cpu_features) -- add_subdirectory(vendor/cpu_features EXCLUDE_FROM_ALL) -- endif () -+ #if (NOT TARGET cpu_features) -+ # add_subdirectory(vendor/cpu_features EXCLUDE_FROM_ALL) -+ #endif () - - list(APPEND ARCHITECTURES avx2 sse4.1 sse2) - foreach(arch IN LISTS ARCHITECTURES) -@@ -78,7 +79,7 @@ if (spoa_generate_dispatch) - $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/simde> - $<INSTALL_INTERFACE:include>) - target_link_libraries(${PROJECT_NAME}_${arch} -- cereal) -+ cereal::cereal) - set_target_properties(${PROJECT_NAME}_${arch} PROPERTIES - COMPILE_FLAGS "-m${arch}") - if (BUILD_SHARED_LIBS) -@@ -92,8 +93,8 @@ if (spoa_generate_dispatch) - ${PROJECT_NAME}_sse4.1 - ${PROJECT_NAME}_sse2) - -- target_link_libraries(${PROJECT_NAME} -- cpu_features) -+ #target_link_libraries(${PROJECT_NAME} -+ # cpu_features) - endif () - - include(GNUInstallDirs) -@@ -110,18 +111,19 @@ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/spoa-1.pc - - option(spoa_build_executable "Build spoa standalone tool" OFF) - if (spoa_build_executable) -- if (NOT TARGET biosoup) -- add_subdirectory(vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL) -- endif () -- if (NOT TARGET bioparser) -- add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL) -- endif () -+ #if (NOT TARGET biosoup) -+ # add_subdirectory(vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL) -+ #endif () -+ #if (NOT TARGET bioparser) -+ # add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL) -+ #endif () - add_executable(${PROJECT_NAME}_exe - src/main.cpp) - target_link_libraries(${PROJECT_NAME}_exe - ${PROJECT_NAME} -- bioparser -- biosoup) -+ #bioparser -+ #biosoup -+ ) - target_compile_definitions(${PROJECT_NAME}_exe PRIVATE - SPOA_VERSION="v${PROJECT_VERSION}") - set_property(TARGET ${PROJECT_NAME}_exe PROPERTY -@@ -134,19 +136,19 @@ endif () - option(spoa_build_tests "Build spoa unit tests" OFF) - if (spoa_build_tests) - find_package(GTest REQUIRED) -- if (NOT TARGET biosoup) -- add_subdirectory(vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL) -- endif () -- if (NOT TARGET bioparser) -- add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL) -- endif () -+ #if (NOT TARGET biosoup) -+ # add_subdirectory(vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL) -+ #endif () -+ #if (NOT TARGET bioparser) -+ # add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL) -+ #endif () - include_directories(${PROJECT_SOURCE_DIR}/src) - add_executable(${PROJECT_NAME}_test - test/spoa_test.cpp) - target_link_libraries(${PROJECT_NAME}_test - ${PROJECT_NAME} -- bioparser -- biosoup -+ #bioparser -+ #biosoup - GTest::Main) - target_compile_definitions(${PROJECT_NAME}_test PRIVATE - SPOA_DATA_PATH="${PROJECT_SOURCE_DIR}/test/data/sample.fastq.gz") diff --git a/biology/spoa/pkg-plist b/biology/spoa/pkg-plist index 7883602bf5f0..397027fc2850 100644 --- a/biology/spoa/pkg-plist +++ b/biology/spoa/pkg-plist @@ -1,8 +1,11 @@ bin/spoa include/spoa/alignment_engine.hpp -include/spoa/architectures.hpp include/spoa/graph.hpp include/spoa/spoa.hpp +include/spoa/version.hpp +lib/cmake/spoa/spoaConfig.cmake +lib/cmake/spoa/spoaConfigVersion.cmake +lib/cmake/spoa/spoaTargets-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/spoa/spoaTargets.cmake lib/libspoa.so lib/libspoa.so.7.0.0 -libdata/pkgconfig/spoa-1.pc
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