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commit: 61b63e5e683cf45cb9f52dca6b4f5462a472dc84 |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Sun Apr 3 18:00:32 2016 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Sun Apr 3 18:00:32 2016 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=61b63e5e |
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|
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sci-biology/abyss: Remove old |
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|
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Package-Manager: portage-2.2.28 |
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|
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sci-biology/abyss/Manifest | 1 - |
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sci-biology/abyss/abyss-1.3.4.ebuild | 46 ------------------ |
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sci-biology/abyss/abyss-1.3.6.ebuild | 58 ----------------------- |
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sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch | 15 ------ |
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4 files changed, 120 deletions(-) |
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|
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diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest |
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index 77dfde1..9284afa 100644 |
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--- a/sci-biology/abyss/Manifest |
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+++ b/sci-biology/abyss/Manifest |
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@@ -1,3 +1,2 @@ |
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DIST abyss-1.3.3.tar.gz 621480 SHA256 60396e2c8813952ceb1c66a3ad7c87eda984aa1e4952a14265217d9f639706a0 SHA512 4ec7fdd24bdb1e3d66e2bda50929122ff347107010701703e81ca1609fb1b4913c713991b3fe84a48ccfbc069e126f4f4120aafbab81e54e567a95a2f1099fb2 WHIRLPOOL 35f6fdfe60b70316e67bcbbb0a9c67e952302333e9ec71d893f2de7a94482dca1a604dc8cfef1ecee49e464244bb5df7469a8ad7bdc37bd54ff455b0f75b7914 |
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-DIST abyss-1.3.4.tar.gz 640545 SHA256 6b6ccb04baaa9d244dd67d95e1512a934d2e54fd28a539149b6845ed5c496baf SHA512 0fa4c14117699945e007412deaeeccca27124a210669accbc1444baf5a4de1a17e1f9b48e6ee43fefed63f0d56b933c847363e59a0fc2bad60ae6d603cd8c09e WHIRLPOOL 42b16f22bc47c8f29b07c256d504d6f58119c64fdcf0e198fd8b836ceb45139fd5cadc7feec72adf958800e55eb1065a449ce7dd288339887dcea4ab13623c01 |
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DIST abyss-1.3.6.tar.gz 678880 SHA256 4432a8b5046bdcb548b6f1b22069a6cade4dea26fc6f83ad5467548e4f3e7c95 SHA512 2c6d72e0227c4af2d5740a989168ad35a84b9236dc53b65a29a010c4e5f77e5c4bfaa38bfaa2f14fd530ae6df204294ff167bd40e79f61e8bad6a7489bf34ace WHIRLPOOL 0677b1fd4090ba155fb876c0047a1ccd2ec2e220950e1e9940e1f3df05ef0abd3ba2e3dbabd500d6fab39a8f7d94e02e0a07410934733682a70fa605d2a8bc07 |
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|
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diff --git a/sci-biology/abyss/abyss-1.3.4.ebuild b/sci-biology/abyss/abyss-1.3.4.ebuild |
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deleted file mode 100644 |
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index e230da8..0000000 |
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--- a/sci-biology/abyss/abyss-1.3.4.ebuild |
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+++ /dev/null |
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@@ -1,46 +0,0 @@ |
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-# Copyright 1999-2013 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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-# $Id$ |
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- |
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-EAPI=5 |
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- |
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-AUTOTOOLS_AUTORECONF=true |
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- |
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-inherit autotools-utils |
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- |
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-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" |
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-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" |
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-SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz" |
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- |
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-LICENSE="abyss" |
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-SLOT="0" |
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-IUSE="+mpi openmp" |
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-KEYWORDS="~amd64 ~x86" |
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- |
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-DEPEND=" |
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- dev-cpp/sparsehash |
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- mpi? ( virtual/mpi )" |
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-RDEPEND="${DEPEND}" |
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- |
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-# todo: --enable-maxk=N configure option |
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-# todo: fix automagic mpi toggling |
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- |
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-PATCHES=( |
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- "${FILESDIR}"/${P}-gcc-4.7.patch |
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- "${FILESDIR}"/${PN}-1.3.3-ac_prog_ar.patch |
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- ) |
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- |
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-src_prepare() { |
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- tc-export AR |
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- sed -i -e "s/-Werror//" configure.ac || die #365195 |
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- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die |
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- autotools-utils_src_prepare |
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-} |
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- |
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-src_configure() { |
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- local myeconfargs=( |
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- --docdir="${EPREFIX}/usr/share/doc/${PF}" |
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- $(use_enable openmp) |
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- ) |
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- autotools-utils_src_configure |
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-} |
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|
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diff --git a/sci-biology/abyss/abyss-1.3.6.ebuild b/sci-biology/abyss/abyss-1.3.6.ebuild |
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deleted file mode 100644 |
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index 904b3e1..0000000 |
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--- a/sci-biology/abyss/abyss-1.3.6.ebuild |
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+++ /dev/null |
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@@ -1,58 +0,0 @@ |
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-# Copyright 1999-2014 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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-# $Id$ |
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- |
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-EAPI=5 |
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- |
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-AUTOTOOLS_AUTORECONF=true |
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- |
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-inherit autotools-utils |
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- |
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-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" |
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-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" |
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-SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz" |
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- |
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-LICENSE="abyss" |
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-SLOT="0" |
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-IUSE="+mpi openmp misc-haskell" |
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-KEYWORDS="~amd64 ~x86" |
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- |
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-RDEPEND=" |
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- dev-cpp/sparsehash |
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- dev-libs/boost |
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- misc-haskell? ( dev-libs/gmp:0= |
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- virtual/libffi:0= |
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- ) |
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- mpi? ( virtual/mpi ) |
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-" |
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-DEPEND="${RDEPEND} |
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- misc-haskell? ( dev-lang/ghc |
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- dev-haskell/mmap ) |
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-" |
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- |
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-# todo: --enable-maxk=N configure option |
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-# todo: fix automagic mpi toggling |
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- |
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-PATCHES=( |
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- "${FILESDIR}"/${P}-gcc-4.7.patch |
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- "${FILESDIR}"/${P}-ac_prog_ar.patch |
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- ) |
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- |
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-src_prepare() { |
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- tc-export AR |
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- sed -i -e "s/-Werror//" configure.ac || die #365195 |
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- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die |
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- autotools-utils_src_prepare |
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-} |
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- |
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-src_configure() { |
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- # disable building haskell tool Misc/samtobreak |
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- # unless request by user: bug #534412 |
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- use misc-haskell || export ac_cv_prog_ac_ct_GHC= |
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- |
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- local myeconfargs=( |
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- --docdir="${EPREFIX}/usr/share/doc/${PF}" |
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- $(use_enable openmp) |
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- ) |
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- autotools-utils_src_configure |
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-} |
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|
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diff --git a/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch |
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deleted file mode 100644 |
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index c2cc35c..0000000 |
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--- a/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch |
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+++ /dev/null |
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@@ -1,15 +0,0 @@ |
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- ParseAligns/abyss-fixmate.cc | 1 + |
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- 1 files changed, 1 insertions(+), 0 deletions(-) |
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- |
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-diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc |
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-index 1a169cf..36cc05b 100644 |
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---- a/ParseAligns/abyss-fixmate.cc |
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-+++ b/ParseAligns/abyss-fixmate.cc |
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-@@ -16,6 +16,7 @@ |
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- #include <iterator> |
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- #include <sstream> |
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- #include <string> |
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-+#include <unistd.h> |
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- |
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- using namespace std; |
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- |