gentoo resync : 02.08.2019

9 files changed, 0 insertions, 147 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index f1df43a13097..096f21431427 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest
deleted file mode 100644
index e53ae3bcab60..000000000000
--- a/sci-biology/allpathslg/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-AUX allpathslg-52488-gcc7.patch 790 BLAKE2B d3993e840b7b53791b0830fc993553c45c00d5d81881750066327106ad45f13bd0f4dba48c8cc0bdf3655d20ff3cefa659b8d41f582a73376188109860e5f2eb SHA512 bde085541f74278aba8edd1c41dd3a2541a7ce7f3a6647b5f3ed19613545bbfff287463e90e785b4476c677d2456d4c87818730b95941b27744549fcdd62d935
-DIST allpathslg-52488-patchset.tar.bz2 11405 BLAKE2B 7a4c36884ac95a4eb23291720e422ce1ec41d0bea3a0b10582aa1d8154234971eb8d06979a969e65c1ec1eab031d2500a1ec40809019c8b4aa1d1d2e81427dbe SHA512 a1d58c131afeef04a9d7a2520fcd28a853317323fdcab1a253cb2548546bbc559993c74a68a8032a5d0e865ac2c2d53ff6b4c149aade2d1f87a2ab4116ebe4cc
-DIST allpathslg-52488.tar.gz 3121949 BLAKE2B b75904f9e8256a14c97abae45a0cb41718f95d27a4a072b6144bd125abb57682faa180de6a18399ab4fa43988344c436ca1eab8412433353fcc746c432c33031 SHA512 c44ef1a3ed5b343bf096663309cc399e79d65e83175232743cf330fd0d426633bd0d388922fd0c73ac0927d85ea9005549c8e4f7711c79fea7107068510ef30d
-EBUILD allpathslg-52488-r2.ebuild 1106 BLAKE2B 13dc0cde0d77d22c93883e9bda7d58a1ba7efcb957cbb18aafecf51e87f089b97538106e4fa35e296ecab6a51f43fc7219bcb84fee01c1b19761ff9398515c55 SHA512 1b809a21a660027113199b8e68a21ce578a65ec9edcea8b4bfc4af14e7ff02a3cfa2340415349bd4d8ee72c3e4bdcb18db396c8787632eb23a5ba20f703409bc
-MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
deleted file mode 100644
index cc9498b65f70..000000000000
--- 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 7c5e1267e4e9..000000000000
--- 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 959160fe46b1..000000000000
--- 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>
diff --git a/sci-biology/vaal/Manifest b/sci-biology/vaal/Manifest
deleted file mode 100644
index e5f6839cafeb..000000000000
--- a/sci-biology/vaal/Manifest
+++ /dev/null
@@ -1,6 +0,0 @@
-AUX vaal-46233-libieee.patch 734 BLAKE2B 2215239d4ea107b497b64ab7dd702d7941d80976fd7bbe9c08c791ff8c6b65c7c438c8deda0bf229c9334f092d6a410a9f4565c555c1c07c9aa7018271c8859f SHA512 367bdc0b4826041b30d3e8d5c63b3691536bb1921c0b224a36a756d545f7cfbe364c89149bedad055550df60e350ad423e2e963968fab7154e0d6c41620bf4a3
-DIST VAAL_manual.doc 48128 BLAKE2B cc31bcdfd4d6faa8c247a9d23a6254ac8a8f8f5de20f8d188c7ed57b9f8231920b4fc7e246394b1bb48ebf457a777d82e704b51b91feb6191e5da331e5765aa9 SHA512 4da21b6559659764e108c118773bd8ed365b67e3a22de52c7c13429979bb765e7f5d05955ce746a7a55e8d3a6baa752ad575289e71dfd7fb5b8b7207f5cff171
-DIST vaal-46233.tar.gz 1148052 BLAKE2B c3fa8ebd722e41bfa1e821d988316900a07d502b6a6b2be394b7227f269ae60a47645b45b6616a782189dcef8a1ea341265e40f257d2ee3f005e8d023273e0b6 SHA512 7a6927d06e1788411063d38e446b7e3c93192e4322a33ea652855f72e550f35debcdb970b895f1fb8504411a54d9096f3dcf506faebd33d50eb033937e15a321
-DIST vaal-46233_remove-namespace-std.patch.bz2 5879 BLAKE2B eb10f5cec8c65c12461346b151dc2c6d60a6f980cdfda78bd97bf0cc33451f808481763e5766b76a78d3d8ef6d5f2f8798bf7b8a7b605e0d32867fdaa9073e3a SHA512 4141094b68b4f9c643abf15d2c5e1486525a69b9d8762cd8034abd3e6f85726ed50d7f25edfcf88fc429ab90db288a583f14b2b5d8e6605cdbfab515f295979c
-EBUILD vaal-46233-r2.ebuild 1020 BLAKE2B a9f96bf1d1598af1fe89148d5199f3d37117e9845028f627902f75d3816ac1159fc185745a958ee63282080c22d22c20c15997a87b02c8f6e8cf3135bdfe0123 SHA512 83f0ab583b3dfac46eda4bcd487b73f78ef3d04321fc353094e45dd140a6232513d361fe67e1f00d1d7320303f0cb261f176b3a6d2b1bc8d3358c77f211c1f92
-MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/vaal/files/vaal-46233-libieee.patch b/sci-biology/vaal/files/vaal-46233-libieee.patch
deleted file mode 100644
index 9f5760c0cb14..000000000000
--- a/sci-biology/vaal/files/vaal-46233-libieee.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -ruN vaal-46233.orig/configure.ac vaal-46233/configure.ac
---- vaal-46233.orig/configure.ac	2018-09-29 21:58:06.059065798 +0200
-+++ vaal-46233/configure.ac	2018-09-29 22:22:35.947845554 +0200
-@@ -12,7 +12,7 @@
- AX_PTHREAD
- AC_OPENMP
- 
--CXXFLAGS="$CXXFLAGS -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote .  -DNDEBUG"
-+CXXFLAGS="$CXXFLAGS -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -fno-nonansi-builtins -fno-strict-aliasing -iquote .  -DNDEBUG"
- 
- OS_RELEASE="`uname -r`"
- AC_SUBST(CXXFLAGS)
diff --git a/sci-biology/vaal/metadata.xml b/sci-biology/vaal/metadata.xml
deleted file mode 100644
index 959160fe46b1..000000000000
--- a/sci-biology/vaal/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/vaal/vaal-46233-r2.ebuild b/sci-biology/vaal/vaal-46233-r2.ebuild
deleted file mode 100644
index 0ac15e6ff63b..000000000000
--- a/sci-biology/vaal/vaal-46233-r2.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools
-
-DESCRIPTION="Algorithm for detecting SNPs, indels, and other polymorphisms"
-HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd/"
-SRC_URI="
-	ftp://ftp.broad.mit.edu/pub/crd/VAAL/latest_source_code/${P}.tar.gz
-	ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc
-	https://dev.gentoo.org/~mgorny/dist/${P}_remove-namespace-std.patch.bz2"
-
-LICENSE="Whitehead-MIT"
-SLOT="0"
-KEYWORDS="amd64"
-IUSE="openmp"
-
-RDEPEND="
-	!sci-biology/allpaths
-	!sci-biology/allpathslg"
-DEPEND="
-	${RDEPEND}
-	dev-libs/boost"
-
-DOCS=( "${DISTDIR}/VAAL_manual.doc" )
-PATCHES=(
-	"${FILESDIR}/${P}-libieee.patch"
-	"${WORKDIR}/${P}_remove-namespace-std.patch"
-)
-
-src_prepare() {
-	sed \
-		-e '/COPYING/d' \
-		-i src/Makefile.am || die
-
-	sed \
-		-e 's:-ggdb::g' \
-		-e '/AC_OPENMP_CEHCK/d' \
-		-i configure.ac || die
-	default
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		$(use_enable openmp)
-}