commit: 7a7bbd341b0f104d19176967a7020aa38de06dc4 Author: Michał Górny <mgorny <AT> gentoo <DOT> org> AuthorDate: Fri Oct 9 07:32:54 2020 +0000 Commit: Michał Górny <mgorny <AT> gentoo <DOT> org> CommitDate: Fri Oct 9 07:34:58 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7a7bbd34
sci-biology/shrimp: Remove last-rited pkg Closes: https://bugs.gentoo.org/735440 Signed-off-by: Michał Górny <mgorny <AT> gentoo.org> profiles/package.mask | 1 - sci-biology/shrimp/Manifest | 1 - sci-biology/shrimp/metadata.xml | 8 ---- sci-biology/shrimp/shrimp-2.2.3.ebuild | 82 ---------------------------------- 4 files changed, 92 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 409c8f2ad0e..2845ca18263 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -517,7 +517,6 @@ net-wireless/python-wifi sci-biology/amos sci-biology/embassy-meme sci-biology/meme -sci-biology/shrimp # Arfrever Frehtes Taifersar Arahesis <[email protected]> (2020-09-01) # Mismatched version (bug #695022). Masked to force upgrade to 2.0.4_pre20200306162733. diff --git a/sci-biology/shrimp/Manifest b/sci-biology/shrimp/Manifest deleted file mode 100644 index 5be68cd79e2..00000000000 --- a/sci-biology/shrimp/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST SHRiMP_2_2_3.src.tar.gz 4596867 BLAKE2B 64e485b8e2524062c11c581bbcac426800c9f42f61da467378dbfd3add63f721a9da9c04df61bde3704e654a20395e799e89fc5e47129b1d3f5bc93f960470fa SHA512 029179aeeb317194b998c29aa91d1d2ce5ccbc6f9ad4a1043d1e5fc75d3344c2f39500ab07e8389c09fa179f0c9b59afee22691bc4eb5d396777f4e0fe25f2d5 diff --git a/sci-biology/shrimp/metadata.xml b/sci-biology/shrimp/metadata.xml deleted file mode 100644 index 959160fe46b..00000000000 --- a/sci-biology/shrimp/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/shrimp/shrimp-2.2.3.ebuild b/sci-biology/shrimp/shrimp-2.2.3.ebuild deleted file mode 100644 index 2b57b032a1b..00000000000 --- a/sci-biology/shrimp/shrimp-2.2.3.ebuild +++ /dev/null @@ -1,82 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit flag-o-matic python-single-r1 toolchain-funcs - -MY_PV=${PV//./_} - -DESCRIPTION="SHort Read Mapping Package" -HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/"; -SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz"; - -LICENSE="shrimp" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="custom-cflags +cpu_flags_x86_sse2" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -# file collision on /usr/bin/utils #453044 -DEPEND="!sci-mathematics/cado-nfs" -RDEPEND="${DEPEND} - ${PYTHON_DEPS}" - -S=${WORKDIR}/SHRiMP_${MY_PV} - -pkg_pretend() { - use cpu_flags_x86_sse2 || die "This package needs sse2 support in your CPU" -} - -pkg_setup() { - if [[ ${CC} == *gcc* ]] && ! tc-has-openmp; then - elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc" - die "C compiler lacks OPENMP support" - fi - python-single-r1_pkg_setup -} - -src_prepare() { - sed \ - -e '1 a #include <stdint.h>' \ - -i common/dag_glue.cpp || die - # respect LDFLAGS wrt 331823 - sed \ - -e "s/LDFLAGS/LIBS/" \ - -e "s/\$(LD)/& \$(LDFLAGS)/" \ - -e 's/-static//' \ - -i Makefile || die - - append-flags -fopenmp - if ! use custom-cflags; then - append-flags -O3 - replace-flags -O* -O3 - fi - tc-export CXX - - cd utils || die - sed -e '/^#!/d' -i *py || die - sed -e '1i#!/usr/bin/python' -i *py || die -} - -src_compile() { - emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" -} - -src_install() { - local i - newdoc bin/README README.bin && rm bin/README - dobin bin/* utils/split-contigs utils/temp-sink - dodoc HISTORY README TODO SPLITTING_AND_MERGING SCORES_AND_PROBABILITES - - pushd utils > /dev/null - - python_doscript *py - - rm *.py *.o *.c split-contigs temp-sink || die - insinto /usr/share/${PN} - doins -r * -}
