From nobody Tue Aug 29 16:59:03 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 4RZttb4cs4z4s0bc; Tue, 29 Aug 2023 16:59:03 +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 4RZttb45tLz3f3r; Tue, 29 Aug 2023 16:59:03 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1693328343; 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=oKZCcFQRaFyHdzItvQtzntHjjv1AcZY/v4GQLW6++YU=; b=Lg/wnZiEnQoyYC7CKx0b/hrBnpscdJzkWzGyvsRAyq6RnpulIOhBpsCLF/KplysD9Bo6UI lC0W8MGFbnBr/yUydfp6lWtHNFFK3bRu7yhxircIOnrVr9iNQsBcWVv2G0EKwbbDrsKPPW lFpujrGX1VS+Y3HDtVtdX2lrewpoYQoRFxX6Gvx5TDP4yFgsjZiMG3dGHTdY3fm+zmsekf 4S6PjV9zk45oIdpBDKr9WE9Zw78b1/IACHNAl0VvNfWsplwuJtUu2dCNXOYcHRFPCRr1cx 59nFRD+gyRFJ0gaqSXxDWqjTb0Oqcp2IFHNkBakHo7aH5yr3VELmbX0vx2oGaA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1693328343; a=rsa-sha256; cv=none; b=qWaglpj5dmSYBP+iKd6yhDsIEfqc6aP+hDz5FoBnGJS7kBQtcqUg011zyDwKjP/5CM7UT2 vhEdxBHOK0hNqCgRJKubRPldH0dEbxF+Cx64PPM9F2By20LPSVXnEGv1Vj6aAAQtIjtRdn iuyFXcGYZQ2VVm66izsnhWIozS0OxwtEnsWhf/iAXVGeeKLxrNdbTMVytQZHNvWfBSuULw U77pA2cGkSgXZ3O/A6pnnXv5wo2rLfniDFBK4iFT7O2XcQ+40m1l26X1GYzd68MsXXzm12 32NxnDr6dllcFrGUFPM0x3k16ItQFbU0O/zM7UiuzrZTGc4mVqBlOHLxCGHnOg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1693328343; 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=oKZCcFQRaFyHdzItvQtzntHjjv1AcZY/v4GQLW6++YU=; b=cXRFMnnvKMqMqfXpTYMuLLQ82a7Nduv5MiRNp4kJ/DWsUYQ2PgR4yjZ5mtTy9mFYxNIdQw trBQM/cO5poXItjvIOjUINe0QrDQtRDV/6tl0ncpK+moTHKgAcU82ar1/wFtjwmQEkmhxn KD1t5iYSvGjHZjGLF73yi1WlqEC0Zy/aCC24427mutlWsplMGgAZYxHWJqAkNjHOZYFyk4 xfSDZXf2rJovb56LVNFjV6SOYPeSF2MMdsKWPS5BqHbF3uEeOE0mmjkGiKUDc+je7g2tSY wFaUzMNyjHD2friecl3hHV0yqtZr1/U9rIVonG5UE1wPUGjNCM4REQMA4hjddA== 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 4RZttb2v7Jz10DZ; Tue, 29 Aug 2023 16:59:03 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 37TGx3Ji006652; Tue, 29 Aug 2023 16:59:03 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 37TGx3R8006649; Tue, 29 Aug 2023 16:59:03 GMT (envelope-from git) Date: Tue, 29 Aug 2023 16:59:03 GMT Message-Id: <202308291659.37TGx3R8006649@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: e06be01f1ef1 - main - biology/spoa: update 4.0.7 =?utf-8?Q?=E2=86=92?= 4.1.0 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: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: e06be01f1ef131f645cf2177b38758acf7a2e48a Auto-Submitted: auto-generated The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=e06be01f1ef131f645cf2177b38758acf7a2e48a commit e06be01f1ef131f645cf2177b38758acf7a2e48a Author: Yuri Victorovich AuthorDate: 2023-08-29 15:49:03 +0000 Commit: Yuri Victorovich 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 - $ -- $ -- $ -+ #$ -+ #$ - $) - target_link_libraries(${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) - $ - $) - target_link_libraries(${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