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commit: 3e408d3f2978b724a7e8b870a6f20100e9a3d7f2 |
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Author: Michał Górny <mgorny <AT> gentoo <DOT> org> |
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AuthorDate: Wed Sep 9 10:24:35 2020 +0000 |
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Commit: Michał Górny <mgorny <AT> gentoo <DOT> org> |
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CommitDate: Wed Sep 9 10:34:30 2020 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3e408d3f |
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|
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sci-biology/seqan: Remove old (drop to ~arch) |
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|
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Signed-off-by: Michał Górny <mgorny <AT> gentoo.org> |
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|
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sci-biology/seqan/Manifest | 2 - |
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.../seqan/files/seqan-1.4.2-buildsystem.patch | 30 ------- |
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sci-biology/seqan/files/seqan-1.4.2-include.patch | 16 ---- |
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sci-biology/seqan/files/seqan-1.4.2-shared.patch | 22 ----- |
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sci-biology/seqan/seqan-1.4.2-r1.ebuild | 79 ------------------ |
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sci-biology/seqan/seqan-2.2.0-r1.ebuild | 94 ---------------------- |
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6 files changed, 243 deletions(-) |
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|
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diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest |
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index d26b1ac375f..b8572815a1e 100644 |
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--- a/sci-biology/seqan/Manifest |
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+++ b/sci-biology/seqan/Manifest |
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@@ -1,3 +1 @@ |
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-DIST seqan-src-1.4.2.tar.gz 120601994 BLAKE2B 62de2f961ba3c7c564090d746877d2b0b94ec7967c56f28786a286160770e66f0a8f08aacbe76d828cf429f92f0aa640ab29f5220297686979df9b7e9f9a0408 SHA512 dbb56167c507b70111619a414054d9e70f1db42507bbfdf9e40c5dcbbe9489ad4187d882e638a675e96551c860c08f8203c929c4c9a558b19ea7d6059f50492a |
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-DIST seqan-src-2.2.0.tar.gz 110936119 BLAKE2B be41f266e140ec5992f7e9e507659dc7902aad0e0dd17e6a8c6c9ef0b11f690454a771ba10a5998ccf70e2e50ef9b24904ebf537d982b2cbc68963c004097614 SHA512 1097372976ec9c86baa3787ac38aa4fde3a3e153d81c22435e6a12df87d8063165f27406de33851bffadd904b0ac4ea579a28625cff6257fe8c14d906f408421 |
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DIST seqan-v2.4.0.tar.gz 109626901 BLAKE2B a10b5ee9a95667f560a8c2aec3808131f5f838f3c07d56584f4b29e9622912bf3d00b958b02db7c9d62dd52d9d08a171abcccef7f50cddf0407538168cf2c592 SHA512 f92cfc97304581920850c5d49fe4336f7c3855e99c3bcb035b6172fa7307e08e6f06fb06d1cd8f5b447c3220fc7f669684fbfe25641b43e9f6953999cf9ddd4b |
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|
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diff --git a/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch b/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch |
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deleted file mode 100644 |
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index 4c7893e90c0..00000000000 |
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--- a/sci-biology/seqan/files/seqan-1.4.2-buildsystem.patch |
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+++ /dev/null |
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@@ -1,30 +0,0 @@ |
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-Add default disabled flag to enable generation of documentation. |
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-For SeqAn 1.4.2 we generally do not want docs, as 1.4.2 is only a |
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-support library for legacy tools. |
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- |
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---- seqan-1.4.2/CMakeLists.txt |
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-+++ seqan-1.4.2/CMakeLists.txt |
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-@@ -123,10 +123,12 @@ |
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- add_subdirectory (core) |
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- message (STATUS "Configuring extras") |
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- add_subdirectory (extras) |
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-+if (NOT SEQAN_NO_DOX) |
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- message (STATUS "Configuring docs") |
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- add_subdirectory (docs) |
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- message (STATUS "Configuring manual") |
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- add_subdirectory (manual) |
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-+endif () |
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- message (STATUS "Configuring sandbox") |
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- add_subdirectory (sandbox) |
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- message (STATUS "Configuring util/py_lib") |
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---- seqan-1.4.2/docs/main.py |
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-+++ seqan-1.4.2/docs/main.py |
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-@@ -123,7 +123,7 @@ |
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- |
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- # Done, print end message. |
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- print 'Documentation created/updated.' |
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-- return dddoc_html.WARNING_COUNT > 0 |
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-+ return 0 |
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- |
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- |
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- def main(argv): |
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|
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diff --git a/sci-biology/seqan/files/seqan-1.4.2-include.patch b/sci-biology/seqan/files/seqan-1.4.2-include.patch |
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deleted file mode 100644 |
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index 5baee4d8ebc..00000000000 |
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--- a/sci-biology/seqan/files/seqan-1.4.2-include.patch |
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+++ /dev/null |
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@@ -1,16 +0,0 @@ |
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- core/include/seqan/index/index_qgram_openaddressing.h | 2 ++ |
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- 1 file changed, 2 insertions(+) |
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- |
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-diff --git a/core/include/seqan/index/index_qgram_openaddressing.h b/core/include/seqan/index/index_qgram_openaddressing.h |
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-index 4a6c2e6..8cc9a42 100644 |
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---- a/core/include/seqan/index/index_qgram_openaddressing.h |
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-+++ b/core/include/seqan/index/index_qgram_openaddressing.h |
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-@@ -35,6 +35,8 @@ |
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- #ifndef SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H |
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- #define SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H |
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- |
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-+#include <smmintrin.h> |
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-+ |
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- namespace SEQAN_NAMESPACE_MAIN |
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- { |
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- |
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|
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diff --git a/sci-biology/seqan/files/seqan-1.4.2-shared.patch b/sci-biology/seqan/files/seqan-1.4.2-shared.patch |
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deleted file mode 100644 |
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index 0f438ff07bc..00000000000 |
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--- a/sci-biology/seqan/files/seqan-1.4.2-shared.patch |
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+++ /dev/null |
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@@ -1,22 +0,0 @@ |
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- util/cmake/SeqAnBuildSystem.cmake | 8 ++++---- |
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- 1 file changed, 4 insertions(+), 4 deletions(-) |
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- |
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-diff --git a/util/cmake/SeqAnBuildSystem.cmake b/util/cmake/SeqAnBuildSystem.cmake |
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-index bcba2c0..d53cd01 100644 |
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---- a/util/cmake/SeqAnBuildSystem.cmake |
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-+++ b/util/cmake/SeqAnBuildSystem.cmake |
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-@@ -144,10 +144,10 @@ macro (seqan_register_apps) |
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- set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DSEQAN_ENABLE_DEBUG=1") |
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- |
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- # enable static linkage for seqan apps |
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-- if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW) |
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-- set(CMAKE_FIND_LIBRARY_SUFFIXES ".a") |
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-- set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++") |
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-- endif () |
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-+# if (CMAKE_COMPILER_IS_GNUCXX OR COMPILER_IS_CLANG AND NOT MINGW) |
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-+# set(CMAKE_FIND_LIBRARY_SUFFIXES ".a") |
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-+# set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++") |
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-+# endif () |
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- |
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- # Get all direct entries of the current source directory into ENTRIES. |
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- file (GLOB ENTRIES |
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|
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diff --git a/sci-biology/seqan/seqan-1.4.2-r1.ebuild b/sci-biology/seqan/seqan-1.4.2-r1.ebuild |
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deleted file mode 100644 |
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index 3a7f55c710c..00000000000 |
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--- a/sci-biology/seqan/seqan-1.4.2-r1.ebuild |
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+++ /dev/null |
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@@ -1,79 +0,0 @@ |
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-# Copyright 1999-2019 Gentoo Authors |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-EAPI=6 |
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- |
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-PYTHON_COMPAT=( python2_7 ) |
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- |
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-inherit cmake-utils python-any-r1 versionator |
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- |
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-DESCRIPTION="C++ Sequence Analysis Library" |
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-HOMEPAGE="http://www.seqan.de/" |
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-SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz" |
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- |
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-SLOT="$(get_version_component_range 1-2)" |
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-LICENSE="BSD GPL-3" |
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-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" |
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-IUSE="cpu_flags_x86_sse4_1 test" |
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-RESTRICT="!test? ( test )" |
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-REQUIRED_USE="cpu_flags_x86_sse4_1" |
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- |
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-RDEPEND=" |
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- app-arch/bzip2 |
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- sys-libs/zlib" |
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-DEPEND=" |
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- ${RDEPEND} |
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- test? ( |
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- $(python_gen_any_dep 'dev-python/nose[${PYTHON_USEDEP}]') |
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- ${PYTHON_DEPS} |
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- )" |
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- |
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-PATCHES=( |
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- "${FILESDIR}/${P}-shared.patch" |
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- "${FILESDIR}/${P}-include.patch" |
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- "${FILESDIR}/${P}-buildsystem.patch" |
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-) |
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- |
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-pkg_setup() { |
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- use test && python-any-r1_pkg_setup |
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-} |
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- |
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-src_prepare() { |
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- # pkg-config file, taken from seqan 2.1 |
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- cp "${FILESDIR}"/${PN}.pc.in ${PN}-${SLOT}.pc || die |
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- sed -e "s#@CMAKE_INSTALL_PREFIX@#${EPREFIX}/usr#" \ |
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- -e "s#includedir=\${prefix}/include#includedir=\${prefix}/include/${PN}-${SLOT}#" \ |
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- -e "s#@CMAKE_PROJECT_NAME@#${PN}#" \ |
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- -e "s#@SEQAN_VERSION_STRING@#${PV}#" \ |
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- -i ${PN}-${SLOT}.pc || die |
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- |
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- rm -f util/cmake/FindZLIB.cmake || die |
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- cmake-utils_src_prepare |
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-} |
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- |
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-src_configure() { |
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- local mycmakeargs=( |
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- -DBoost_NO_BOOST_CMAKE=ON |
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- -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY |
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- -DSEQAN_NO_DOX=ON |
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- ) |
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- cmake-utils_src_configure |
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-} |
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- |
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-src_install() { |
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- cmake-utils_src_install |
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- |
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- # SLOT header such that different seqan versions can be used in parallel |
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- mkdir "${ED}"/usr/include/${PN}-${SLOT} || die |
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- mv "${ED}"/usr/include/{${PN},${PN}-${SLOT}/} || die |
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- |
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- # pkg-config file |
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- insinto /usr/share/pkgconfig/ |
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- doins ${PN}-${SLOT}.pc |
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-} |
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- |
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-pkg_postinst() { |
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- einfo "${CATEGORY}/${PF} is only intended as support library for older" |
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- einfo "bioinformatics tools relying on the SeqAn 1.* API. Please develop" |
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- einfo "any new software against the latest SeqAn release and not this one." |
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-} |
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|
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diff --git a/sci-biology/seqan/seqan-2.2.0-r1.ebuild b/sci-biology/seqan/seqan-2.2.0-r1.ebuild |
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deleted file mode 100644 |
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index 5e139cd7e60..00000000000 |
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--- a/sci-biology/seqan/seqan-2.2.0-r1.ebuild |
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+++ /dev/null |
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@@ -1,94 +0,0 @@ |
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-# Copyright 1999-2019 Gentoo Authors |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-EAPI=6 |
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- |
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-PYTHON_COMPAT=( python2_7 ) |
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- |
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-inherit cmake-utils python-any-r1 versionator |
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- |
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-DESCRIPTION="C++ Sequence Analysis Library" |
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-HOMEPAGE="http://www.seqan.de/" |
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-SRC_URI="http://packages.${PN}.de/${PN}-src/${PN}-src-${PV}.tar.gz" |
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- |
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-SLOT="0" |
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-LICENSE="BSD GPL-3" |
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-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
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-IUSE="cpu_flags_x86_sse4_1 doc test" |
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-RESTRICT="!test? ( test )" |
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-REQUIRED_USE="cpu_flags_x86_sse4_1" |
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- |
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-RDEPEND=" |
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- app-arch/bzip2 |
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- sys-libs/zlib |
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- !!sci-biology/seqan:2.0 |
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- !!sci-biology/seqan:2.1 |
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- !!sci-biology/seqan:2.2" |
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-DEPEND=" |
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- ${RDEPEND} |
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- doc? ( |
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- $(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]') |
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- ${PYTHON_DEPS} |
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- ) |
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- test? ( |
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- $(python_gen_any_dep 'dev-python/nose[${PYTHON_USEDEP}]') |
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- ${PYTHON_DEPS} |
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- )" |
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- |
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-S="${WORKDIR}"/${PN}-${PN}-v${PV} |
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- |
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-pkg_setup() { |
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- if use test || use doc; then |
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- python-any-r1_pkg_setup |
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- fi |
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-} |
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- |
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-src_prepare() { |
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- seqan_major_ver=$(get_version_component_range 1) |
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- seqan_majorminor_ver=$(get_version_component_range 1-2) |
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- |
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- # install docs in proper Gentoo structure |
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- sed -e "s#share/doc/seqan#share/doc/${PF}#" \ |
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- -e "s#\"share/doc/\${APP_NAME}\"#\"share/doc/${PF}/\${APP_NAME}\"#" \ |
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- -i util/cmake/SeqAnBuildSystem.cmake dox/CMakeLists.txt || die |
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- |
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- # cmake module |
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- sed -e "s#find_path(_SEQAN_BASEDIR \"seqan\"#find_path(_SEQAN_BASEDIR \"seqan-${seqan_majorminor_ver}\"#" \ |
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- -e 's#NO_DEFAULT_PATH)#PATHS /usr)#' \ |
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- -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-${seqan_majorminor_ver})#" \ |
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- -i util/cmake/FindSeqAn.cmake || die |
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- |
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- # pkg-config file |
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- sed -e "s#includedir=\${prefix}/include#includedir=\${prefix}/include/${PN}-${seqan_majorminor_ver}#" \ |
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- -i util/pkgconfig/${PN}.pc.in || die |
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- |
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- rm -f util/cmake/FindZLIB.cmake || die |
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- cmake-utils_src_prepare |
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-} |
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- |
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-src_configure() { |
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- local mycmakeargs=( |
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- -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY |
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- -DSEQAN_NO_DOX=$(usex !doc) |
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- ) |
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- cmake-utils_src_configure |
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-} |
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- |
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-src_compile() { |
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- cmake-utils_src_compile |
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- use doc && cmake-utils_src_compile -C "${BUILD_DIR}" dox |
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-} |
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- |
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-src_install() { |
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- cmake-utils_src_install |
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- |
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- # multi-version header such that different seqan versions can be installed in parallel |
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- mkdir "${ED%/}"/usr/include/${PN}-${seqan_majorminor_ver} || die |
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- mv "${ED%/}"/usr/include/${PN}{,-${seqan_majorminor_ver}/} || die |
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- |
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- # pkg-config file |
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- mv "${ED%/}"/usr/share/pkgconfig/${PN}-{${seqan_major_ver},${seqan_majorminor_ver}}.pc || die |
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- |
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- # create pkg-config symlink to restore default behaviour |
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- dosym ${PN}-${seqan_majorminor_ver}.pc /usr/share/pkgconfig/${PN}-${seqan_major_ver}.pc |
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-} |
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