From: "Andreas Sturmlechner" <asturm@gentoo.org>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/seqan/files/, sci-biology/seqan/
Date: Mon, 19 Dec 2022 14:47:07 +0000 (UTC) [thread overview]
Message-ID: <1671461097.949a896e4942213cd4cb80667746e31590b21e03.asturm@gentoo> (raw)
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 <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
-}
next reply other threads:[~2022-12-19 14:47 UTC|newest]
Thread overview: 3+ messages / expand[flat|nested] mbox.gz Atom feed top
2022-12-19 14:47 Andreas Sturmlechner [this message]
-- strict thread matches above, loose matches on Subject: below --
2020-09-09 10:36 [gentoo-commits] repo/gentoo:master commit in: sci-biology/seqan/files/, sci-biology/seqan/ Michał Górny
2018-02-11 12:21 David Seifert
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