sci-biology/plinkseq: remove pack, upstream gone

Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>

4 files changed, 0 insertions, 127 deletions

diff --git a/sci-biology/plinkseq/Manifest b/sci-biology/plinkseq/Manifest
deleted file mode 100644
index fdf7b1f9d..000000000
--- a/sci-biology/plinkseq/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST plinkseq-0.10.tgz 6090698 BLAKE2B 86ddc1952c742f024fefdd8e3dec7af73bbe1be3231dc9a795650f3470b9b641ce86f6fa8157f6090943bf6cb53eb262204e2d4872b5cad14fa078b3cf27c514 SHA512 b8fa0a0b42a5f67612b1549d1f2fbed67333abb57ef024d4be683cd326e53a8ef08c6c0acae8ed3195fad619c8aea9005e315f937d76cd990a7ffff1d808af41
diff --git a/sci-biology/plinkseq/metadata.xml b/sci-biology/plinkseq/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/plinkseq/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/plinkseq/plinkseq-0.10.ebuild b/sci-biology/plinkseq/plinkseq-0.10.ebuild
deleted file mode 100644
index b1e4937d7..000000000
--- a/sci-biology/plinkseq/plinkseq-0.10.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit toolchain-funcs autotools-utils
-
-DESCRIPTION="C/C++ library for working with human genetic variation data"
-HOMEPAGE="http://atgu.mgh.harvard.edu/plinkseq"
-SRC_URI="http://psychgen.u.hpc.mssm.edu/plinkseq_downloads/plinkseq-src-latest.tgz -> ${P}.tgz"
-# https://bitbucket.org/statgen/plinkseq.git
-# http://pngu.mgh.harvard.edu/~purcell/plink/download.shtml
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="sys-libs/zlib
-	dev-libs/protobuf
-	!sci-biology/fsl" # file collision on /usr/bin/mm
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	sed -e "s/gcc/$(tc-getCC)/g;s/g++/$(tc-getCXX)/g;s/-O3/${CFLAGS}/g" -i config_defs.Makefile || die
-	sed -e "s/= -static/=/g" -i config_defs.Makefile || die
-	rm -rf sources/ext/protobuf-* || die
-	rm sources/ext/protobuf sources/ext/sources/include/google || die
-	rm -rf sources/mongoose || die
-	sed -e 's@^all:.*@all: # skipping compilation of bundled dev-libs/protobuf@' -i sources/ext/Makefile || die
-	# TODO: fix also sources/ext/sources/include/DUMMY/include/google/protobuf/compiler/plugin.proto causing:
-	# plugin.proto: Import "google/protobuf/descriptor.proto" was not found or had errors.
-	# plugin.proto:74:12: "FileDescriptorProto" is not defined.
-	find . -name \*.proto | while read f; do \
-		d=`dirname $f`; \
-		pushd $d; \
-		protoc --cpp_out=. *.proto || exit 255; \
-		popd; \
-	done || die
-	autotools-utils_src_prepare
-}
-
-src_install(){
-	cd build/execs || die
-	# TODO: avoid file collision with sci-biology/fsl
-	# https://bitbucket.org/statgen/plinkseq/issue/9/rename-mm-filename-to-plinkseq_mm
-	# TODO: avoid file collision with www-servers/mongoose
-	dobin gcol browser pseq behead mm smp tab2vcf pdas
-}
diff --git a/sci-biology/plinkseq/plinkseq-9999.ebuild b/sci-biology/plinkseq/plinkseq-9999.ebuild
deleted file mode 100644
index cffdaff97..000000000
--- a/sci-biology/plinkseq/plinkseq-9999.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-
-inherit toolchain-funcs git-r3
-
-DESCRIPTION="C/C++ library for working with human genetic variation data"
-HOMEPAGE="http://atgu.mgh.harvard.edu/plinkseq"
-EGIT_REPO_URI="https://bitbucket.org/statgen/plinkseq.git"
-# https://bitbucket.org/statgen/plinkseq/commits/all
-# http://pngu.mgh.harvard.edu/~purcell/plink/download.shtml
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="sys-libs/zlib
-	dev-libs/protobuf
-	!sci-biology/fsl" # file collision on /usr/bin/mm
-RDEPEND="${DEPEND}"
-
-src_prepare(){
-	sed -e "s/gcc/$(tc-getCC)/g;s/g++/$(tc-getCXX)/g;s/-O3/${CFLAGS}/g" -i config_defs.Makefile || die
-	sed -e "s/= -static/=/g" -i config_defs.Makefile || die
-	rm -rf sources/ext/protobuf-* || die
-	rm sources/ext/protobuf sources/ext/sources/include/google || die
-	# we cannot zap calls to bundled mongoose because www-servers/mongoose does not build a library at all
-	# rm -rf sources/mongoose || die
-	# sed -e "s@$(MONGOOSE_LIB_DIR) @@;s@$(MONGOOSE_INC) @@;s@$(MONGOOSE_LIB_BASE_DIR) @@" - Makefile || die
-	sed -e 's@^all:.*@all: # skipping compilation of bundled dev-libs/protobuf@' -i sources/ext/Makefile || die
-	find . -name \*.proto | while read f; do \
-		d=`dirname $f`; \
-		pushd $d; \
-		protoc --cpp_out=. *.proto || exit 255; \
-		popd; \
-	done || die
-	#
-	# recopy the updated files
-	cp -p sources/plinkseq/sources/lib/matrix.pb.h sources/plinkseq/sources/include/plinkseq/matrix.pb.h || die
-	cp -p sources/plinkseq/sources/lib/variant.pb.h sources/plinkseq/sources/include/plinkseq/variant.pb.h || die
-	sed -e 's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g' -i sources/plinkseq/sources/lib/matrix.pb.cpp || die
-	sed -e 's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g' -i sources/plinkseq/sources/lib/variant.pb.cpp || die
-	local myinc=`pkg-config protobuf --variable=includedir`
-	sed -e 's@$(PROTOBUF_LIB_BASE_DIR)/$(INC_DIR)/@'"${myinc}@" -i Makefile || die
-	local mylib=`pkg-config protobuf --variable=libdir`
-	sed -e 's@$(PROTOBUF_LIB_BASE_DIR)/$(BLD_LIB_DIR)/@'"-L${mylib} @" -i Makefile || die # note the trailing space as it get prepended to PROTOBUF_LIBS
-	# anyway $(PROTOBUF_LIB_FULL_PATH) is a necessary build target, just drop it
-	sed -e 's@^PROTOBUF_LIB_FULL_PATH =.*/@PROTOBUF_LIB_FULL_PATH =@' -i Makefile || die
-	local mylibs=`pkg-config protobuf --libs`
-	sed -e "s@libprotobuf.a@ ${mylibs}@ " -i Makefile || die
-}
-
-src_install(){
-	cd build/execs || die
-	# TODO: avoid file collision with sci-biology/fsl
-	# https://bitbucket.org/statgen/plinkseq/issue/9/rename-mm-filename-to-plinkseq_mm
-	# TODO: avoid file collision with www-servers/mongoose
-	dobin gcol browser pseq behead mm smp tab2vcf pdas
-}