commit: bc0e06623a12a5686bc1fd87f95ab8d3344eab78 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat Apr 9 18:56:34 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat Apr 9 18:57:11 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bc0e0662
sci-biology/seqan: Remove old and broken ebuilds Package-Manager: portage-2.2.28 sci-biology/seqan/Manifest | 2 - sci-biology/seqan/files/seqan-2.0.0-zlib.patch | 15 ------- sci-biology/seqan/seqan-1.3.1-r1.ebuild | 50 --------------------- sci-biology/seqan/seqan-1.4.2.ebuild | 60 -------------------------- sci-biology/seqan/seqan-2.0.0.ebuild | 51 ---------------------- 5 files changed, 178 deletions(-) diff --git a/sci-biology/seqan/Manifest b/sci-biology/seqan/Manifest index d7fdca8..ab534dc 100644 --- a/sci-biology/seqan/Manifest +++ b/sci-biology/seqan/Manifest @@ -1,4 +1,2 @@ -DIST seqan-1.3.1.zip 8787521 SHA256 87eebe73ace9ada2f4664a768ae212d4acc5fb3ce87702709c3d15bf2d153aeb SHA512 dafacccb4647fd0fc5a055d33390cb85f1c00ca74132e9b3839a739916acf9a2990db7db4f09e34f899b283cad8ccf6553a60cc7693164f250f08260c8ce8ae4 WHIRLPOOL 5a0a80d09e80285a4fc9fb9fb71adbea6b0b324a6a219cd7c9ef3d30e88133f5b25b3cf792b2b89e4ed07ff612f4aa347dc6f94e06974f947fe980c2e0a5d26b DIST seqan-src-1.4.2.tar.gz 120601994 SHA256 2b2c48572ea82fc2ac6a6e46bbd4204b6f8200fde717612797426af5ff6b82c3 SHA512 dbb56167c507b70111619a414054d9e70f1db42507bbfdf9e40c5dcbbe9489ad4187d882e638a675e96551c860c08f8203c929c4c9a558b19ea7d6059f50492a WHIRLPOOL 3c7f38e35d826adad94d53d359df8b5f1fb51746f3103457b12b41bd0bf161dc463d4a1932b0b23f2274d723c796116af0940260e1922ce806bb2466445788f0 -DIST seqan-src-2.0.0.tar.gz 115731415 SHA256 69cb39574e63de2f728715255ac7ffd26db6480d6ce33c8601eef05f282aed28 SHA512 9823b109c27fa770b86a72530ebb4f6ca4541f8f6cf979724730cd8c59809192c14178c01a9ec13ef0277c997c4c37f00c80bba1fef5ef57c367ae8285b0215a WHIRLPOOL afa5dd41106390f63523990ce876ef74952ce7787a2772c2116bafd564d466e588809e4c5812b5aa1137408a0291de739b70a9a1e116d212967f68f5246217f4 DIST seqan-src-2.1.1.tar.gz 110874831 SHA256 df083d5939d7e73fd00bbc6bb291ac7ea7b8d446cf89a9758fdffdc0eca9ec1c SHA512 b82eb93129921eb867785add46d63f667c07f40556cd431acc73489c1032c19ff65b49415697415bdc7b788ffb8a80ab8d9e987fa38fc39c2399ff265fdc333f WHIRLPOOL b684d14db0cf22c7d1428c589293ee69674225e5b91845532f3135950a5a6178d4434b783177b3622e8661247856a20b42a7fb9275df4324124d2b21d728790f diff --git a/sci-biology/seqan/files/seqan-2.0.0-zlib.patch b/sci-biology/seqan/files/seqan-2.0.0-zlib.patch deleted file mode 100644 index de14e9d..0000000 --- a/sci-biology/seqan/files/seqan-2.0.0-zlib.patch +++ /dev/null @@ -1,15 +0,0 @@ - include/seqan/stream/zipstream/zutil.h | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/include/seqan/stream/zipstream/zutil.h b/include/seqan/stream/zipstream/zutil.h -index 2806344..f8b41e6 100644 ---- a/include/seqan/stream/zipstream/zutil.h -+++ b/include/seqan/stream/zipstream/zutil.h -@@ -152,6 +152,7 @@ extern const char *z_errmsg[10]; /* indexed by 2-zlib_error */ - - /* functions */ - -+#define OF(x) x - #ifdef HAVE_STRERROR - extern char *strerror OF((int)); - # define zstrerror(errnum) strerror(errnum) diff --git a/sci-biology/seqan/seqan-1.3.1-r1.ebuild b/sci-biology/seqan/seqan-1.3.1-r1.ebuild deleted file mode 100644 index 2bcb7f6..0000000 --- a/sci-biology/seqan/seqan-1.3.1-r1.ebuild +++ /dev/null @@ -1,50 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils flag-o-matic python-single-r1 - -DESCRIPTION="C++ Sequence Analysis Library" -HOMEPAGE="http://www.seqan.de/"; -SRC_URI="http://ftp.seqan.de/releases/${P}.zip"; - -SLOT="0" -LICENSE="BSD GPL-3" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - ~sci-biology/samtools-0.1.19" -DEPEND="${RDEPEND}" - -S="${WORKDIR}"/${P}/cmake - -pkg_setup() { - if [[ ${MERGE_TYPE} != binary ]]; then - [[ $(gcc-major-version) -gt 4 ]] || \ - ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -gt 8 ]] ) \ - && die "Sorry, but gcc 4.9 or higher is unsupported" - fi -} - -src_prepare() { - append-cppflags -I"${EPREFIX}/usr/include/bam" - rm -rf "${S}"/../lib/samtools || die - - sed \ - -e "s:docs:docs/.:g" \ - -e "/DESTINATION/s:seqan:doc/${PF}/html:g" \ - -i CMakeLists.txt || die - - sed \ - -e "/DESTINATION/s:bin):share/${PN}):g" \ - -i apps/CMakeLists.txt || die - - cmake-utils_src_prepare -} diff --git a/sci-biology/seqan/seqan-1.4.2.ebuild b/sci-biology/seqan/seqan-1.4.2.ebuild deleted file mode 100644 index 4b9740c..0000000 --- a/sci-biology/seqan/seqan-1.4.2.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils flag-o-matic python-single-r1 - -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" - -REQUIRED_USE="${PYTHON_REQUIRED_USE} cpu_flags_x86_sse4_1" - -RDEPEND="${PYTHON_DEPS} - sci-biology/samtools" -DEPEND="${RDEPEND}" - -PATCHES=( - "${FILESDIR}"/${P}-shared.patch - "${FILESDIR}"/${P}-include.patch -) - -src_prepare() { - append-cppflags -msse4.1 - rm -f \ - util/cmake/FindZLIB.cmake \ - || die - touch extras/apps/seqan_flexbar/README || die - sed \ - -e "s:share/doc:share/doc/${PF}:g" \ - -i docs/CMakeLists.txt util/cmake/SeqAnBuildSystem.cmake || die - cmake-utils_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DBoost_NO_BOOST_CMAKE=ON - ) - cmake-utils_src_configure -} - -src_install() { - mkdir -p "${BUILD_DIR}"/docs/html || die - cmake-utils_src_install - chmod 755 "${ED}"/usr/bin/*sh || die - - mv "${ED}"/usr/bin/{,seqan-}join || die -} - -pkg_postinst() { - elog "Due to filecollision the 'join' binary has been renamed to seqan-join" -} diff --git a/sci-biology/seqan/seqan-2.0.0.ebuild b/sci-biology/seqan/seqan-2.0.0.ebuild deleted file mode 100644 index 5437e6d..0000000 --- a/sci-biology/seqan/seqan-2.0.0.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils flag-o-matic python-single-r1 - -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" - -REQUIRED_USE="${PYTHON_REQUIRED_USE} cpu_flags_x86_sse4_1" - -RDEPEND="${PYTHON_DEPS} - dev-libs/boost:= - sci-biology/samtools" -DEPEND="${RDEPEND}" - -S="${WORKDIR}"/${PN}-${PN}-v${PV} - -PATCHES=( - "${FILESDIR}"/${P}-zlib.patch -) - -src_prepare() { - rm -f \ - util/cmake/FindZLIB.cmake \ - || die - cmake-utils_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DBoost_NO_BOOST_CMAKE=ON - ) - cmake-utils_src_configure -} - -src_install() { - mkdir -p "${BUILD_DIR}"/docs/html || die - cmake-utils_src_install - chmod 755 "${ED}"/usr/bin/*sh || die -}
