gentoo resync : 12.03.2021

5 files changed, 82 insertions, 104 deletions

diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest
index 97b76d002547..8d7f1285b2e6 100644
--- a/sci-biology/seqan/Manifest
+++ b/sci-biology/seqan/Manifest
@@ -1,5 +1,6 @@
+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
-EBUILD seqan-2.4.0.ebuild 1624 BLAKE2B e2b8d8c2e7f87abc063255e0c6c826a57e4da29b063eb3fc82d143593e06d8cbbf5744cd6e39e9cc1b2623c010d181e4361665946a8489ad454f3e1fb9a33c88 SHA512 1d39216baa3877df91b19f36519103114a6858b4600d5bfe3ba01e5619bcfb2543d208e7d5af2806a5c964ebcb8399a8244ca65f4e7ecf169e02827e055545d3
-EBUILD seqan-9999.ebuild 1567 BLAKE2B b171570acf62243121541b771c26fd7ef86e4be86878c060050af2cd665973182e2498f9ba9c336e8a382768b71aa3547edde927682dcdd844c6fd0ed9e2cd99 SHA512 b91b532d3655de47c0cfb9f243e46c120d5259f9166be4e41d7b0dd02a6f681e714fd5941aadb54b6ee89a0f5a4aa10628157c9b25bfd8074178dc36b70e5944
+EBUILD seqan-2.4.0-r1.ebuild 1592 BLAKE2B 98ca9dce72bca2d2069eb94a9f998c5f7d25d303c053930264a51231dc3972243ef7433d9a750f9b0d4b26950a7adc7ccf7f863a8a87f3393821f72f285591bd SHA512 e63405b1c8ab04bf2e635601b27effa62b116e4d5c14f4244f2a5cbd1047e22c2b4c8793602535225ad426ccf8f69b0f68967d47db81b65ae3c0abeee6b5d057
 MISC metadata.xml 372 BLAKE2B d620401f1aab9be80ddb6dc7abe737fd3e6322c560136e2c3b33d9246beca2986b4d91225b506e8c3035550994c3f714a11c0d8b17efd30c29278002d4eb7a12 SHA512 ae6c49e7e45c0ce4dd4fe27d21c5376c6fb8d7bfd2f98b7775f4689811680fa92c0b71ac0db70f6969660c4aee344f710ef752a467d6d46dd83aa47386d2ec17
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
new file mode 100644
index 000000000000..7617d9f9a665
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-2.4.0-cmake-add_library-static.patch
@@ -0,0 +1,38 @@
+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 ${SEQAN_LIBRARIES})
+-- 
+2.30.1
+
diff --git a/sci-biology/seqan/files/seqan-2.4.0-installpaths.patch b/sci-biology/seqan/files/seqan-2.4.0-installpaths.patch
new file mode 100644
index 000000000000..35f0718f9d8d
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-2.4.0-installpaths.patch
@@ -0,0 +1,24 @@
+--- a/util/cmake/SeqAnBuildSystem.cmake	2018-01-11 12:32:45.591134000 +0100
++++ b/util/cmake/SeqAnBuildSystem.cmake	2018-01-11 12:51:55.193282581 +0100
+@@ -399,10 +399,10 @@
+         # Install pkg-config file, except on Windows.
+         if (NOT CMAKE_SYSTEM_NAME MATCHES Windows)
+             configure_file("util/pkgconfig/seqan.pc.in" "${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/seqan-9999.ebuild b/sci-biology/seqan/seqan-2.4.0-r1.ebuild
index b344b39cbc46..76a73d759bef 100644
--- a/sci-biology/seqan/seqan-9999.ebuild
+++ b/sci-biology/seqan/seqan-2.4.0-r1.ebuild
@@ -1,14 +1,12 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-: ${CMAKE_MAKEFILE_GENERATOR:=ninja}
-
-inherit cmake-utils multibuild toolchain-funcs
+inherit cmake multibuild toolchain-funcs
 
 DESCRIPTION="C++ Sequence Analysis Library"
-HOMEPAGE="http://www.seqan.de/"
+HOMEPAGE="https://www.seqan.de/"
 
 if [[ ${PV} == *9999 ]]; then
 	inherit git-r3
@@ -17,8 +15,7 @@ if [[ ${PV} == *9999 ]]; then
 else
 	SRC_URI="https://github.com/seqan/seqan/archive/seqan-v${PV}.tar.gz"
 	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-	S=${WORKDIR}/seqan-seqan-v${PV}
+	S="${WORKDIR}"/seqan-seqan-v${PV}
 fi
 
 LICENSE="BSD GPL-3"
@@ -28,28 +25,29 @@ REQUIRED_USE="cpu_flags_x86_sse4_1"
 
 RDEPEND="
 	app-arch/bzip2:=
-	sys-libs/zlib:=
+	sys-libs/zlib
 	!!sci-biology/seqan:2.0
 	!!sci-biology/seqan:2.1
 	!!sci-biology/seqan:2.2"
-DEPEND="
-	${RDEPEND}"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-fix-pthread.patch
+	"${FILESDIR}"/${P}-installpaths.patch
+	"${FILESDIR}"/${P}-cmake-add_library-static.patch
+)
 
 pkg_setup() {
 	if [[ ${MERGE_TYPE} != binary ]]; then
 		use tools && tc-check-openmp
 
-		MULTIBUILD_VARIANTS=(
-			$(usev tools)
-			library
-		)
+		MULTIBUILD_VARIANTS=( $(usev tools) library )
 	fi
 }
 
 src_configure() {
 	my_configure() {
 		local mycmakeargs=(
-			-DCMAKE_INSTALL_DOCDIR="share/doc/${PF}"
 			-DSEQAN_NO_DOX=ON
 		)
 		case "${MULTIBUILD_ID}" in
@@ -67,15 +65,15 @@ src_configure() {
 				die "${MULTIBUILD_ID} is not recognized"
 				;;
 		esac
-		cmake-utils_src_configure
+		cmake_src_configure
 	}
 	multibuild_foreach_variant my_configure
 }
 
 src_compile() {
-	multibuild_foreach_variant cmake-utils_src_compile
+	multibuild_foreach_variant cmake_src_compile
 }
 
 src_install() {
-	multibuild_foreach_variant cmake-utils_src_install
+	multibuild_foreach_variant cmake_src_install
 }
diff --git a/sci-biology/seqan/seqan-2.4.0.ebuild b/sci-biology/seqan/seqan-2.4.0.ebuild
deleted file mode 100644
index 5653a1ec94e4..000000000000
--- a/sci-biology/seqan/seqan-2.4.0.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-: ${CMAKE_MAKEFILE_GENERATOR:=ninja}
-
-inherit cmake-utils multibuild toolchain-funcs
-
-DESCRIPTION="C++ Sequence Analysis Library"
-HOMEPAGE="http://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}"/${PN}-2.4.0-fix-pthread.patch )
-
-pkg_setup() {
-	if [[ ${MERGE_TYPE} != binary ]]; then
-		use tools && tc-check-openmp
-
-		MULTIBUILD_VARIANTS=(
-			$(usev tools)
-			library
-		)
-	fi
-}
-
-src_configure() {
-	my_configure() {
-		local mycmakeargs=(
-			-DCMAKE_INSTALL_DOCDIR="share/doc/${PF}"
-			-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-utils_src_configure
-	}
-	multibuild_foreach_variant my_configure
-}
-
-src_compile() {
-	multibuild_foreach_variant cmake-utils_src_compile
-}
-
-src_install() {
-	multibuild_foreach_variant cmake-utils_src_install
-}