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