sci-biology/allpathslg: remove last rited package

Signed-off-by: Mikle Kolyada <zlogene@gentoo.org>

diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest
deleted file mode 100644 (file)
index 22364d0..0000000
--- 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 (file)
index cc9498b..0000000
--- 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 (file)
index 7c5e126..0000000
--- 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 (file)
index 959160f..0000000
--- 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>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>