commit: 59414166be981c4e44e9c712fd4474b428eb482d Author: Mikle Kolyada <zlogene <AT> gentoo <DOT> org> AuthorDate: Mon Jul 22 10:05:08 2019 +0000 Commit: Mikle Kolyada <zlogene <AT> gentoo <DOT> org> CommitDate: Mon Jul 22 10:05:08 2019 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=59414166
sci-biology/allpathslg: remove last rited package Signed-off-by: Mikle Kolyada <zlogene <AT> gentoo.org> sci-biology/allpathslg/Manifest | 2 - sci-biology/allpathslg/allpathslg-52488-r2.ebuild | 46 ---------------------- .../allpathslg/files/allpathslg-52488-gcc7.patch | 13 ------ sci-biology/allpathslg/metadata.xml | 8 ---- 4 files changed, 69 deletions(-) diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest deleted file mode 100644 index 22364d00b07..00000000000 --- a/sci-biology/allpathslg/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST allpathslg-52488-patchset.tar.bz2 11405 BLAKE2B 7a4c36884ac95a4eb23291720e422ce1ec41d0bea3a0b10582aa1d8154234971eb8d06979a969e65c1ec1eab031d2500a1ec40809019c8b4aa1d1d2e81427dbe SHA512 a1d58c131afeef04a9d7a2520fcd28a853317323fdcab1a253cb2548546bbc559993c74a68a8032a5d0e865ac2c2d53ff6b4c149aade2d1f87a2ab4116ebe4cc -DIST allpathslg-52488.tar.gz 3121949 BLAKE2B b75904f9e8256a14c97abae45a0cb41718f95d27a4a072b6144bd125abb57682faa180de6a18399ab4fa43988344c436ca1eab8412433353fcc746c432c33031 SHA512 c44ef1a3ed5b343bf096663309cc399e79d65e83175232743cf330fd0d426633bd0d388922fd0c73ac0927d85ea9005549c8e4f7711c79fea7107068510ef30d diff --git a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild deleted file mode 100644 index cc9498b65f7..00000000000 --- a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild +++ /dev/null @@ -1,46 +0,0 @@ -# Copyright 1999-2018 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit autotools flag-o-matic toolchain-funcs - -DESCRIPTION="De novo assembly of whole-genome shotgun microreads" -# see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12 -HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"; -SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz - https://dev.gentoo.org/~mgorny/dist/${P}-patchset.tar.bz2"; - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=" - !sci-biology/allpaths - !sci-biology/vaal" -DEPEND=" - ${RDEPEND} - dev-libs/boost:=" - -PATCHES=( - "${WORKDIR}"/${P}-patchset/${P}_fix-buildsystem.patch - "${WORKDIR}"/${P}-patchset/${P}_remove-namespace-std.patch - "${FILESDIR}"/${P}-gcc7.patch -) - -pkg_pretend() { - [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp -} - -pkg_setup() { - [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp -} - -src_prepare() { - default - - # Fix building with glibc-2.27, bug #647340 - sed -i -e 's/-mieee-fp//' configure.ac || die - - eautoreconf -} diff --git a/sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch b/sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch deleted file mode 100644 index 7c5e1267e4e..00000000000 --- a/sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- a/src/paths/long/VariantCallTools.cc -+++ b/src/paths/long/VariantCallTools.cc -@@ -1870,8 +1870,8 @@ - bool i_is_indel = (change[i].first.size() != change[i].second.size()); - if (i_is_indel) inserted_base += change[i].second.size()-1; - size_t j = i + 1; -- while (j < edits.size() && abs(edits[j].second - edits[j-1].second -- - change[j-1].first.size()) < MinClumpSep) { -+ while (j < edits.size() && std::abs(edits[j].second - edits[j-1].second -+ - static_cast<int>(change[j-1].first.size())) < MinClumpSep) { - nmatch += edits[j].second - edits[j-1].second - change[j-1].first.size(); - bool j_is_indel = (change[j].first.size() != change[j].second.size()); - if (j_is_indel) diff --git a/sci-biology/allpathslg/metadata.xml b/sci-biology/allpathslg/metadata.xml deleted file mode 100644 index 959160fe46b..00000000000 --- a/sci-biology/allpathslg/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>
