[gentoo-commits] repo/gentoo:master commit in: sci-biology/seqan/files/, sci-biology/seqan/

["Michał Górny" <mgorny@gentoo.org>]

commit:     3e408d3f2978b724a7e8b870a6f20100e9a3d7f2
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Wed Sep  9 10:24:35 2020 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Wed Sep  9 10:34:30 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3e408d3f

sci-biology/seqan: Remove old (drop to ~arch)

Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>

 sci-biology/seqan/Manifest                         |  2 -
 .../seqan/files/seqan-1.4.2-buildsystem.patch      | 30 -------
 sci-biology/seqan/files/seqan-1.4.2-include.patch  | 16 ----
 sci-biology/seqan/files/seqan-1.4.2-shared.patch   | 22 -----
 sci-biology/seqan/seqan-1.4.2-r1.ebuild            | 79 ------------------
 sci-biology/seqan/seqan-2.2.0-r1.ebuild            | 94 ----------------------
 6 files changed, 243 deletions(-)

diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest
index d26b1ac375f..b8572815a1e 100644
--- a/sci-biology/seqan/Manifest
+++ b/sci-biology/seqan/Manifest
@@ -1,3 +1 @@
-DIST seqan-src-1.4.2.tar.gz 120601994 BLAKE2B 62de2f961ba3c7c564090d746877d2b0b94ec7967c56f28786a286160770e66f0a8f08aacbe76d828cf429f92f0aa640ab29f5220297686979df9b7e9f9a0408 SHA512 dbb56167c507b70111619a414054d9e70f1db42507bbfdf9e40c5dcbbe9489ad4187d882e638a675e96551c860c08f8203c929c4c9a558b19ea7d6059f50492a
-DIST seqan-src-2.2.0.tar.gz 110936119 BLAKE2B be41f266e140ec5992f7e9e507659dc7902aad0e0dd17e6a8c6c9ef0b11f690454a771ba10a5998ccf70e2e50ef9b24904ebf537d982b2cbc68963c004097614 SHA512 1097372976ec9c86baa3787ac38aa4fde3a3e153d81c22435e6a12df87d8063165f27406de33851bffadd904b0ac4ea579a28625cff6257fe8c14d906f408421
 DIST seqan-v2.4.0.tar.gz 109626901 BLAKE2B a10b5ee9a95667f560a8c2aec3808131f5f838f3c07d56584f4b29e9622912bf3d00b958b02db7c9d62dd52d9d08a171abcccef7f50cddf0407538168cf2c592 SHA512 f92cfc97304581920850c5d49fe4336f7c3855e99c3bcb035b6172fa7307e08e6f06fb06d1cd8f5b447c3220fc7f669684fbfe25641b43e9f6953999cf9ddd4b

diff --git a/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch b/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch
deleted file mode 100644
index 4c7893e90c0..00000000000
--- a/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-Add default disabled flag to enable generation of documentation.
-For SeqAn 1.4.2 we generally do not want docs, as 1.4.2 is only a
-support library for legacy tools.
-
---- seqan-1.4.2/CMakeLists.txt
-+++ seqan-1.4.2/CMakeLists.txt
-@@ -123,10 +123,12 @@
- add_subdirectory (core)
- message (STATUS "Configuring extras")
- add_subdirectory (extras)
-+if (NOT SEQAN_NO_DOX)
- message (STATUS "Configuring docs")
- add_subdirectory (docs)
- message (STATUS "Configuring manual")
- add_subdirectory (manual)
-+endif ()
- message (STATUS "Configuring sandbox")
- add_subdirectory (sandbox)
- message (STATUS "Configuring util/py_lib")
---- seqan-1.4.2/docs/main.py
-+++ seqan-1.4.2/docs/main.py
-@@ -123,7 +123,7 @@
- 
-         # Done, print end message.
-         print 'Documentation created/updated.'
--        return dddoc_html.WARNING_COUNT > 0
-+        return 0
-     
-     
- def main(argv):

diff --git a/sci-biology/seqan/files/seqan-1.4.2-include.patch b/sci-biology/seqan/files/seqan-1.4.2-include.patch
deleted file mode 100644
index 5baee4d8ebc..00000000000
--- a/sci-biology/seqan/files/seqan-1.4.2-include.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- core/include/seqan/index/index_qgram_openaddressing.h | 2 ++
- 1 file changed, 2 insertions(+)
-
-diff --git a/core/include/seqan/index/index_qgram_openaddressing.h b/core/include/seqan/index/index_qgram_openaddressing.h
-index 4a6c2e6..8cc9a42 100644
---- a/core/include/seqan/index/index_qgram_openaddressing.h
-+++ b/core/include/seqan/index/index_qgram_openaddressing.h
-@@ -35,6 +35,8 @@
- #ifndef SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H
- #define SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H
- 
-+#include <smmintrin.h>
-+
- namespace SEQAN_NAMESPACE_MAIN
- {
- 

diff --git a/sci-biology/seqan/files/seqan-1.4.2-shared.patch b/sci-biology/seqan/files/seqan-1.4.2-shared.patch
deleted file mode 100644
index 0f438ff07bc..00000000000
--- a/sci-biology/seqan/files/seqan-1.4.2-shared.patch
+++ /dev/null
@@ -1,22 +0,0 @@
- util/cmake/SeqAnBuildSystem.cmake | 8 ++++----
- 1 file changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/util/cmake/SeqAnBuildSystem.cmake b/util/cmake/SeqAnBuildSystem.cmake
-index bcba2c0..d53cd01 100644
---- a/util/cmake/SeqAnBuildSystem.cmake
-+++ b/util/cmake/SeqAnBuildSystem.cmake
-@@ -144,10 +144,10 @@ macro (seqan_register_apps)
-     set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DSEQAN_ENABLE_DEBUG=1")
- 
-     # enable static linkage for seqan apps
--    if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
--      set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
--      set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
--    endif ()
-+#    if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW)
-+#      set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
-+#      set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
-+#    endif ()
- 
-     # Get all direct entries of the current source directory into ENTRIES.
-     file (GLOB ENTRIES

diff --git a/sci-biology/seqan/seqan-1.4.2-r1.ebuild b/sci-biology/seqan/seqan-1.4.2-r1.ebuild
deleted file mode 100644
index 3a7f55c710c..00000000000
--- a/sci-biology/seqan/seqan-1.4.2-r1.ebuild
+++ /dev/null
@@ -1,79 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils python-any-r1 versionator
-
-DESCRIPTION="C++ Sequence Analysis Library"
-HOMEPAGE="http://www.seqan.de/"
-SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz"
-
-SLOT="$(get_version_component_range 1-2)"
-LICENSE="BSD GPL-3"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE="cpu_flags_x86_sse4_1 test"
-RESTRICT="!test? ( test )"
-REQUIRED_USE="cpu_flags_x86_sse4_1"
-
-RDEPEND="
-	app-arch/bzip2
-	sys-libs/zlib"
-DEPEND="
-	${RDEPEND}
-	test? (
-		$(python_gen_any_dep 'dev-python/nose[${PYTHON_USEDEP}]')
-		${PYTHON_DEPS}
-	)"
-
-PATCHES=(
-	"${FILESDIR}/${P}-shared.patch"
-	"${FILESDIR}/${P}-include.patch"
-	"${FILESDIR}/${P}-buildsystem.patch"
-)
-
-pkg_setup() {
-	use test && python-any-r1_pkg_setup
-}
-
-src_prepare() {
-	# pkg-config file, taken from seqan 2.1
-	cp "${FILESDIR}"/${PN}.pc.in ${PN}-${SLOT}.pc || die
-	sed -e "s#@CMAKE_INSTALL_PREFIX@#${EPREFIX}/usr#" \
-		-e "s#includedir=\${prefix}/include#includedir=\${prefix}/include/${PN}-${SLOT}#" \
-		-e "s#@CMAKE_PROJECT_NAME@#${PN}#" \
-		-e "s#@SEQAN_VERSION_STRING@#${PV}#" \
-		-i ${PN}-${SLOT}.pc || die
-
-	rm -f util/cmake/FindZLIB.cmake || die
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DBoost_NO_BOOST_CMAKE=ON
-		-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
-		-DSEQAN_NO_DOX=ON
-	)
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	# SLOT header such that different seqan versions can be used in parallel
-	mkdir "${ED}"/usr/include/${PN}-${SLOT} || die
-	mv "${ED}"/usr/include/{${PN},${PN}-${SLOT}/} || die
-
-	# pkg-config file
-	insinto /usr/share/pkgconfig/
-	doins ${PN}-${SLOT}.pc
-}
-
-pkg_postinst() {
-	einfo "${CATEGORY}/${PF} is only intended as support library for older"
-	einfo "bioinformatics tools relying on the SeqAn 1.* API. Please develop"
-	einfo "any new software against the latest SeqAn release and not this one."
-}

diff --git a/sci-biology/seqan/seqan-2.2.0-r1.ebuild b/sci-biology/seqan/seqan-2.2.0-r1.ebuild
deleted file mode 100644
index 5e139cd7e60..00000000000
--- a/sci-biology/seqan/seqan-2.2.0-r1.ebuild
+++ /dev/null
@@ -1,94 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils python-any-r1 versionator
-
-DESCRIPTION="C++ Sequence Analysis Library"
-HOMEPAGE="http://www.seqan.de/"
-SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD GPL-3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cpu_flags_x86_sse4_1 doc test"
-RESTRICT="!test? ( test )"
-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}
-	doc? (
-		$(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]')
-		${PYTHON_DEPS}
-	)
-	test? (
-		$(python_gen_any_dep 'dev-python/nose[${PYTHON_USEDEP}]')
-		${PYTHON_DEPS}
-	)"
-
-S="${WORKDIR}"/${PN}-${PN}-v${PV}
-
-pkg_setup() {
-	if use test || use doc; then
-		python-any-r1_pkg_setup
-	fi
-}
-
-src_prepare() {
-	seqan_major_ver=$(get_version_component_range 1)
-	seqan_majorminor_ver=$(get_version_component_range 1-2)
-
-	# install docs in proper Gentoo structure
-	sed -e "s#share/doc/seqan#share/doc/${PF}#" \
-		-e "s#\"share/doc/\${APP_NAME}\"#\"share/doc/${PF}/\${APP_NAME}\"#" \
-		-i util/cmake/SeqAnBuildSystem.cmake dox/CMakeLists.txt || die
-
-	# cmake module
-	sed -e "s#find_path(_SEQAN_BASEDIR \"seqan\"#find_path(_SEQAN_BASEDIR \"seqan-${seqan_majorminor_ver}\"#" \
-		-e 's#NO_DEFAULT_PATH)#PATHS /usr)#' \
-		-e "s#set(SEQAN_INCLUDE_DIRS_MAIN \${SEQAN_INCLUDE_DIRS_MAIN} \${_SEQAN_BASEDIR})#set(SEQAN_INCLUDE_DIRS_MAIN \${SEQAN_INCLUDE_DIRS_MAIN} \${_SEQAN_BASEDIR}/seqan-${seqan_majorminor_ver})#" \
-		-i util/cmake/FindSeqAn.cmake || die
-
-	# pkg-config file
-	sed -e "s#includedir=\${prefix}/include#includedir=\${prefix}/include/${PN}-${seqan_majorminor_ver}#" \
-		-i util/pkgconfig/${PN}.pc.in || die
-
-	rm -f util/cmake/FindZLIB.cmake || die
-	cmake-utils_src_prepare
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
-		-DSEQAN_NO_DOX=$(usex !doc)
-	)
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-	use doc && cmake-utils_src_compile -C "${BUILD_DIR}" dox
-}
-
-src_install() {
-	cmake-utils_src_install
-
-	# multi-version header such that different seqan versions can be installed in parallel
-	mkdir "${ED%/}"/usr/include/${PN}-${seqan_majorminor_ver} || die
-	mv "${ED%/}"/usr/include/${PN}{,-${seqan_majorminor_ver}/} || die
-
-	# pkg-config file
-	mv "${ED%/}"/usr/share/pkgconfig/${PN}-{${seqan_major_ver},${seqan_majorminor_ver}}.pc || die
-
-	# create pkg-config symlink to restore default behaviour
-	dosym ${PN}-${seqan_majorminor_ver}.pc /usr/share/pkgconfig/${PN}-${seqan_major_ver}.pc
-}