commit: 9103b70e66e9d368c3ef7105b432183c07f49da5 Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Wed Jan 20 09:06:29 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Wed Jan 20 09:06:29 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9103b70e
sci-biology/plinkseq: remove pack, upstream gone Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> sci-biology/plinkseq/metadata.xml | 12 ------ sci-biology/plinkseq/plinkseq-0.10.ebuild | 51 ------------------------- sci-biology/plinkseq/plinkseq-9999.ebuild | 63 ------------------------------- 3 files changed, 126 deletions(-) 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>mmokr...@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biol...@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 -}
