From 3e408d3f2978b724a7e8b870a6f20100e9a3d7f2 Mon Sep 17 00:00:00 2001 From: Michał Górny Date: Wed, 9 Sep 2020 12:24:35 +0200 Subject: sci-biology/seqan: Remove old (drop to ~arch) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Michał Górny --- 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(-) delete mode 100644 sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch delete mode 100644 sci-biology/seqan/files/seqan-1.4.2-include.patch delete mode 100644 sci-biology/seqan/files/seqan-1.4.2-shared.patch delete mode 100644 sci-biology/seqan/seqan-1.4.2-r1.ebuild delete mode 100644 sci-biology/seqan/seqan-2.2.0-r1.ebuild (limited to 'sci-biology') diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest index d26b1ac375fb..b8572815a1e0 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 4c7893e90c05..000000000000 --- 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 5baee4d8ebc0..000000000000 --- 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 -+ - 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 0f438ff07bce..000000000000 --- 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 "${CMAKE_CXX_FLAGS_DEBUG} -DSEQAN_ENABLE_DEBUG=1") - - # enable static linkage for seqan apps -- if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW) -- set(CMAKE_FIND_LIBRARY_SUFFIXES ".a") -- set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++") -- endif () -+# if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW) -+# set(CMAKE_FIND_LIBRARY_SUFFIXES ".a") -+# set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++") -+# endif () - - # Get all direct entries of the current source directory into ENTRIES. - file (GLOB ENTRIES diff --git a/sci-biology/seqan/seqan-1.4.2-r1.ebuild b/sci-biology/seqan/seqan-1.4.2-r1.ebuild deleted file mode 100644 index 3a7f55c710c3..000000000000 --- a/sci-biology/seqan/seqan-1.4.2-r1.ebuild +++ /dev/null @@ -1,79 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils python-any-r1 versionator - -DESCRIPTION="C++ Sequence Analysis Library" -HOMEPAGE="http://www.seqan.de/" -SRC_URI="http://packages.${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 5e139cd7e601..000000000000 --- 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 -} -- cgit v1.2.3-65-gdbad