gentoo auto-resync : 19:12:2022 - 19:49:08

7 files changed, 1 insertions, 166 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 744adfe22363..7a1132df2b16 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest
index e2f7fa97b28e..a133c99314e9 100644
--- a/sci-biology/seqan/Manifest
+++ b/sci-biology/seqan/Manifest
@@ -1,8 +1,3 @@
-AUX seqan-2.4.0-cmake-add_library-static.patch 1542 BLAKE2B 08f006302c4b284bbbfc2967a34d94a20ebb65faefce293adac326eb46adb18a2442206a0cd3e98820af2372f0201627c3de259fb2df8fa9575e9568f26337f7 SHA512 e17058da311266e75bbef3d331b7a516490c8f8b63144e1466072a08b165ec88130e93336d164c58269920ad9ef9d34ced58e928c14a7b3a5352af6e7c3b255c
-AUX seqan-2.4.0-fix-pthread.patch 541 BLAKE2B 16d42c72d6ea0654ba6727ce1007b89d3fc76141320f5a71cfd0fe102b8e511ccb36d48e021baf0928ac8857e97f6addde3f15f4f0577c531285027f23f5eea8 SHA512 f8a3df0892a81a65562dbd85f0945e5722df524e07b9949f860df4e0f07c285df3a48a112c8e1e5dca28a97c219dc9feed677e803ec5d3964216f7052b6f431b
-AUX seqan-2.4.0-installpaths.patch 1661 BLAKE2B 6548f5b7cd0e26d187ff61a8e8e3db008700b5131a57228f0cd567642fae12778ff2a77960fa318f6244a80f94e771ebeb218fee8eaf6ec1a4c827e972d1ac90 SHA512 9b2100cd2a4069fd9022723ca6972251d2307f4886b3dcdf68816e78d38359d8767e20e19b4170213abb905bc3b570ed257e025e063a475ff3406d8f1e8d3313
-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
-EBUILD seqan-2.4.0-r1.ebuild 1674 BLAKE2B 706295eac1c0a74f33823afc6968b5ac971f578a7f2bf99a690d4e351ee2a82a52fe125095b0bb3982f1c39d500ca83b5e367f6ad30a0e38373f2647a2c40022 SHA512 42ee3ad643cb535fa8e0831debff9e8c33a71c510f722f83140de0a9177e8d33b677af3b7569ee59242ec5e26189a73a84ec8eae83a8ae5d89d7071c8c3610e9
 EBUILD seqan-3.1.0.ebuild 636 BLAKE2B b8bc983979a79cded722d13d4b8206472a5542ef917896b8a08592ff5e1f1e481b9f526258a0ae30b1e090374599cba744160b2fdc3709579d5d22018b7bc544 SHA512 4446b71a6ca1d5d9d7212f9916c8750b01d98ffd426c2f441234635b41b6431c7497aa3601814366a42e93317b864baddd9e14990474ecea3194a74de887e907
-MISC metadata.xml 373 BLAKE2B 1fd7eb9978c4b1e8fee1edb30bef8e18de04fdbc6677f8442e0cb706512b7a49c0681737ade6b9c96f67e234907890694bafe8edfb6c35ef25cd570920ea07f7 SHA512 b273e12542b160e215945d85504a3e9ba9973b68e6870f9d27104024fb09b8e293d8f6f71f8a005ad35690a530cec608e5e01a5158b747e1003ce9c87add8486
+MISC metadata.xml 262 BLAKE2B adaacf2ac22ce09f8b1b68f538773c1e2101156181ff302eca2ce1280ee5d45db4eb302a8eee1bbead5e55942443dd16ef924cfbfdc95a1658dc6a9f460468a2 SHA512 ac924b6b530d96645f173d40f7a2bf0e3abbf49048ebf7fadcea3dd553cd25504f0e68a103395de1fb59a2e5e11497dcead601be01cc6f0295ccbc4155f67e3f
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 <asturm@gentoo.org>
-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 <asturm@gentoo.org>
----
- 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>sci-biology@gentoo.org</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
-}