* [gentoo-commits] repo/gentoo:master commit in: sci-biology/seqan/files/, sci-biology/seqan/
@ 2018-02-11 12:21 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2018-02-11 12:21 UTC (permalink / raw
To: gentoo-commits
commit: 3155495650f555369e58b58f54fc6766e9691f20
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 11 12:20:48 2018 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Feb 11 12:20:48 2018 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=31554956
sci-biology/seqan: Version bump to 2.4.0
* Add USE=tools option to install command-line tools
Closes: https://bugs.gentoo.org/618278
Package-Manager: Portage-2.3.24, Repoman-2.3.6
sci-biology/seqan/Manifest | 1 +
.../seqan/files/seqan-2.4.0-fix-pthread.patch | 12 +++
sci-biology/seqan/metadata.xml | 11 ++-
sci-biology/seqan/seqan-2.4.0.ebuild | 92 ++++++++++++++++++++++
4 files changed, 112 insertions(+), 4 deletions(-)
diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest
index 634425a0843..d26b1ac375f 100644
--- a/sci-biology/seqan/Manifest
+++ b/sci-biology/seqan/Manifest
@@ -1,2 +1,3 @@
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-2.4.0-fix-pthread.patch b/sci-biology/seqan/files/seqan-2.4.0-fix-pthread.patch
new file mode 100644
index 00000000000..b5e4b3642d4
--- /dev/null
+++ b/sci-biology/seqan/files/seqan-2.4.0-fix-pthread.patch
@@ -0,0 +1,12 @@
+--- 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/metadata.xml b/sci-biology/seqan/metadata.xml
index 959160fe46b..077f6458a92 100644
--- a/sci-biology/seqan/metadata.xml
+++ b/sci-biology/seqan/metadata.xml
@@ -1,8 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
+ <maintainer type="project">
+ <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.ebuild b/sci-biology/seqan/seqan-2.4.0.ebuild
new file mode 100644
index 00000000000..8b337e77e6b
--- /dev/null
+++ b/sci-biology/seqan/seqan-2.4.0.ebuild
@@ -0,0 +1,92 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+: ${CMAKE_MAKEFILE_GENERATOR:=ninja}
+PYTHON_COMPAT=( python2_7 )
+
+inherit cmake-utils multibuild python-any-r1 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 doc 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}
+ doc? (
+ $(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]')
+ ${PYTHON_DEPS}
+ )"
+
+PATCHES=( "${FILESDIR}"/${PN}-2.4.0-fix-pthread.patch )
+
+python_check_deps() {
+ use doc && has_version "dev-python/sphinx[${PYTHON_USEDEP}]"
+}
+
+pkg_setup() {
+ if [[ ${MERGE_TYPE} != binary ]]; then
+ use doc && python-any-r1_pkg_setup
+ use tools && tc-check-openmp
+
+ MULTIBUILD_VARIANTS=(
+ $(usev tools)
+ library
+ )
+ fi
+}
+
+src_configure() {
+ my_configure() {
+ local mycmakeargs=( -DCMAKE_INSTALL_DOCDIR="share/doc/${PF}" )
+ case "${MULTIBUILD_ID}" in
+ tools)
+ mycmakeargs+=(
+ -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS
+ -DSEQAN_NO_DOX=ON
+ )
+ ;;
+ library)
+ mycmakeargs+=(
+ -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
+ -DSEQAN_NO_DOX=$(usex !doc)
+ )
+ ;;
+ *)
+ 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
+}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/seqan/files/, sci-biology/seqan/
@ 2020-09-09 10:36 Michał Górny
0 siblings, 0 replies; 3+ messages in thread
From: Michał Górny @ 2020-09-09 10:36 UTC (permalink / raw
To: gentoo-commits
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
-}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/seqan/files/, sci-biology/seqan/
@ 2022-12-19 14:47 Andreas Sturmlechner
0 siblings, 0 replies; 3+ messages in thread
From: Andreas Sturmlechner @ 2022-12-19 14:47 UTC (permalink / raw
To: gentoo-commits
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
-}
^ permalink raw reply related [flat|nested] 3+ messages in thread
end of thread, other threads:[~2022-12-19 14:47 UTC | newest]
Thread overview: 3+ messages (download: mbox.gz follow: Atom feed
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2018-02-11 12:21 [gentoo-commits] repo/gentoo:master commit in: sci-biology/seqan/files/, sci-biology/seqan/ David Seifert
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2020-09-09 10:36 Michał Górny
2022-12-19 14:47 Andreas Sturmlechner
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