commit: 949a896e4942213cd4cb80667746e31590b21e03 Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> AuthorDate: Sun Dec 18 12:29:55 2022 +0000 Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> CommitDate: Mon Dec 19 14:44:57 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=949a896e
sci-biology/seqan: drop 2.4.0-r1 Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org> sci-biology/seqan/Manifest | 1 - .../seqan-2.4.0-cmake-add_library-static.patch | 38 ---------- .../seqan/files/seqan-2.4.0-fix-pthread.patch | 12 ---- .../seqan/files/seqan-2.4.0-installpaths.patch | 24 ------- sci-biology/seqan/metadata.xml | 3 - sci-biology/seqan/seqan-2.4.0-r1.ebuild | 83 ---------------------- 6 files changed, 161 deletions(-) diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest index f9ddca8ef871..ed2aa485711a 100644 --- a/sci-biology/seqan/Manifest +++ b/sci-biology/seqan/Manifest @@ -1,2 +1 @@ -DIST seqan-v2.4.0.tar.gz 109626901 BLAKE2B a10b5ee9a95667f560a8c2aec3808131f5f838f3c07d56584f4b29e9622912bf3d00b958b02db7c9d62dd52d9d08a171abcccef7f50cddf0407538168cf2c592 SHA512 f92cfc97304581920850c5d49fe4336f7c3855e99c3bcb035b6172fa7307e08e6f06fb06d1cd8f5b447c3220fc7f669684fbfe25641b43e9f6953999cf9ddd4b DIST seqan3-3.1.0-Source.tar.xz 2656120 BLAKE2B 6a18844f62d935fdbd7008822f83ffeefd596e93b704a8c7b0f478dec87b2265ff532be107ebfd1adc248e2b1db65e4b86cdce2e989c7ac097054d43633a24bd SHA512 686d0ffbe32951e7f831e399a3eab35b7249f45408b7de27ee9cfd6a012215603f033afa6082c8a81783de1cc7c93d3ffbae42cabc122d3b77988c236a049ffd diff --git a/sci-biology/seqan/files/seqan-2.4.0-cmake-add_library-static.patch b/sci-biology/seqan/files/seqan-2.4.0-cmake-add_library-static.patch deleted file mode 100644 index 7617d9f9a665..000000000000 --- a/sci-biology/seqan/files/seqan-2.4.0-cmake-add_library-static.patch +++ /dev/null @@ -1,38 +0,0 @@ -From 1877d143ad9f42d80692073538e3f32b37e15967 Mon Sep 17 00:00:00 2001 -From: Andreas Sturmlechner <[email protected]> -Date: Sun, 7 Mar 2021 19:35:44 +0100 -Subject: [PATCH] Fix linking with BUILD_SHARED_LIBS=ON default in EAPI-7 - -Signed-off-by: Andreas Sturmlechner <[email protected]> ---- - apps/mason2/CMakeLists.txt | 2 +- - apps/pair_align/lib/CMakeLists.txt | 2 +- - 2 files changed, 2 insertions(+), 2 deletions(-) - -diff --git a/apps/mason2/CMakeLists.txt b/apps/mason2/CMakeLists.txt -index 2218187..c042ea7 100644 ---- a/apps/mason2/CMakeLists.txt -+++ b/apps/mason2/CMakeLists.txt -@@ -52,7 +52,7 @@ add_definitions (-DSEQAN_REVISION="${SEQAN_REVISION}") - add_definitions (-DSEQAN_DATE="${SEQAN_DATE}") - - # We define a library for the reusable parts of Mason. --add_library (mason_sim -+add_library (mason_sim STATIC - external_split_merge.h - external_split_merge.cpp - fragment_generation.h -diff --git a/apps/pair_align/lib/CMakeLists.txt b/apps/pair_align/lib/CMakeLists.txt -index 75faef7..3b9576e 100644 ---- a/apps/pair_align/lib/CMakeLists.txt -+++ b/apps/pair_align/lib/CMakeLists.txt -@@ -53,5 +53,5 @@ endforeach(GAPS_T) - - # This part can be used instead for cmake version greater or equal to 2.8.8. - # This requires to update the script above as well. --add_library(pair_align_lib pair_align_lib.cpp pair_align_lib.h ${LIB_TARGETS}) -+add_library(pair_align_lib STATIC pair_align_lib.cpp pair_align_lib.h ${LIB_TARGETS}) - target_link_libraries(pair_align_lib ${SEQAN_LIBRARIES}) --- -2.30.1 - diff --git a/sci-biology/seqan/files/seqan-2.4.0-fix-pthread.patch b/sci-biology/seqan/files/seqan-2.4.0-fix-pthread.patch deleted file mode 100644 index b5e4b3642d42..000000000000 --- a/sci-biology/seqan/files/seqan-2.4.0-fix-pthread.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- a/util/cmake/seqan-config.cmake -+++ b/util/cmake/seqan-config.cmake -@@ -307,7 +307,8 @@ - - # some OSes don't link pthread fully when building statically so we explicitly include whole archive - if (UNIX AND NOT APPLE) -- set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,--whole-archive -lpthread -Wl,--no-whole-archive") -+ find_package (Threads) -+ set (SEQAN_LIBRARIES ${SEQAN_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT}) - endif () - - if ((${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD") OR (${CMAKE_SYSTEM_NAME} STREQUAL "OpenBSD")) diff --git a/sci-biology/seqan/files/seqan-2.4.0-installpaths.patch b/sci-biology/seqan/files/seqan-2.4.0-installpaths.patch deleted file mode 100644 index 35f0718f9d8d..000000000000 --- a/sci-biology/seqan/files/seqan-2.4.0-installpaths.patch +++ /dev/null @@ -1,24 +0,0 @@ ---- a/util/cmake/SeqAnBuildSystem.cmake 2018-01-11 12:32:45.591134000 +0100 -+++ b/util/cmake/SeqAnBuildSystem.cmake 2018-01-11 12:51:55.193282581 +0100 -@@ -399,10 +399,10 @@ - # Install pkg-config file, except on Windows. - if (NOT CMAKE_SYSTEM_NAME MATCHES Windows) - configure_file("util/pkgconfig/seqan.pc.in" "${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc" @ONLY) -- install(FILES "${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc" DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/pkgconfig) -+ install(FILES "${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc" DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) - endif (NOT CMAKE_SYSTEM_NAME MATCHES Windows) - # Install FindSeqAn TODO(h-2) rename seqan-config.cmake to seqan-config${SEQAN_VERSION_MAJOR}.cmake after 2.x cycle -- install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/util/cmake/seqan-config.cmake" DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/cmake/seqan/) -+ install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/util/cmake/seqan-config.cmake" DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/seqan2/) - - # Install headers - file (GLOB HEADERS -@@ -473,7 +473,7 @@ - set (CMAKE_INSTALL_DOCDIR "${CMAKE_INSTALL_DATAROOTDIR}/doc" CACHE STRING "Documentation root (DATAROOTDIR/doc)" FORCE) - endif () - set (SEQAN_PREFIX_SHARE "${CMAKE_INSTALL_DATADIR}/${APP_NAME}") -- set (SEQAN_PREFIX_SHARE_DOC "${CMAKE_INSTALL_DOCDIR}/${APP_NAME}") -+ set (SEQAN_PREFIX_SHARE_DOC "${CMAKE_INSTALL_DOCDIR}/examples/") - endif () - endmacro (seqan_setup_install_vars) - diff --git a/sci-biology/seqan/metadata.xml b/sci-biology/seqan/metadata.xml index 7b3d5730b341..bdabd1d83788 100644 --- a/sci-biology/seqan/metadata.xml +++ b/sci-biology/seqan/metadata.xml @@ -5,7 +5,4 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> - <use> - <flag name="tools">Build and install SeqAn commandline tools, such as the Yara aligner</flag> - </use> </pkgmetadata> diff --git a/sci-biology/seqan/seqan-2.4.0-r1.ebuild b/sci-biology/seqan/seqan-2.4.0-r1.ebuild deleted file mode 100644 index 933b55e04eab..000000000000 --- a/sci-biology/seqan/seqan-2.4.0-r1.ebuild +++ /dev/null @@ -1,83 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake multibuild toolchain-funcs - -DESCRIPTION="C++ Sequence Analysis Library" -HOMEPAGE="https://www.seqan.de/"; - -if [[ ${PV} == *9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/seqan/seqan.git"; - EGIT_BRANCH="develop" -else - SRC_URI="https://github.com/seqan/seqan/archive/seqan-v${PV}.tar.gz"; - KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - S="${WORKDIR}"/seqan-seqan-v${PV} -fi - -LICENSE="BSD GPL-3" -SLOT="0" -IUSE="cpu_flags_x86_sse4_1 tools" -REQUIRED_USE="cpu_flags_x86_sse4_1" - -RDEPEND=" - app-arch/bzip2:= - sys-libs/zlib - !!sci-biology/seqan:2.0 - !!sci-biology/seqan:2.1 - !!sci-biology/seqan:2.2" -DEPEND="${RDEPEND}" - -PATCHES=( - "${FILESDIR}"/${P}-fix-pthread.patch - "${FILESDIR}"/${P}-installpaths.patch - "${FILESDIR}"/${P}-cmake-add_library-static.patch -) - -pkg_pretend() { - [[ ${MERGE_TYPE} != binary ]] && use tools && tc-check-openmp -} - -pkg_setup() { - if [[ ${MERGE_TYPE} != binary ]]; then - use tools && tc-check-openmp - - MULTIBUILD_VARIANTS=( $(usev tools) library ) - fi -} - -src_configure() { - my_configure() { - local mycmakeargs=( - -DSEQAN_NO_DOX=ON - ) - case "${MULTIBUILD_ID}" in - tools) - mycmakeargs+=( - -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS - ) - ;; - library) - mycmakeargs+=( - -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY - ) - ;; - *) - die "${MULTIBUILD_ID} is not recognized" - ;; - esac - cmake_src_configure - } - multibuild_foreach_variant my_configure -} - -src_compile() { - multibuild_foreach_variant cmake_src_compile -} - -src_install() { - multibuild_foreach_variant cmake_src_install -}
