commit: ea003571ac74c209954bfe016cb6a91319058080 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Mon Jun 25 22:23:40 2018 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Mon Jun 25 22:23:40 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ea003571
sci-biology/gffread: new package Does not compile, will report upstream. Package-Manager: Portage-2.3.40, Repoman-2.3.9 sci-biology/gffread/files/Makefile.patch | 39 +++++++++++++++++++++++++++++++ sci-biology/gffread/gffread-0.9.12.ebuild | 18 ++++++++++++++ sci-biology/gffread/metadata.xml | 12 ++++++++++ 3 files changed, 69 insertions(+) diff --git a/sci-biology/gffread/files/Makefile.patch b/sci-biology/gffread/files/Makefile.patch new file mode 100644 index 000000000..45f8c3ebd --- /dev/null +++ b/sci-biology/gffread/files/Makefile.patch @@ -0,0 +1,39 @@ +--- gffread-0.9.12/Makefile 2018-06-26 00:05:05.298388489 +0200 ++++ gffread-0.9.12/Makefile 2018-06-26 00:07:07.461729681 +0200 +@@ -1,4 +1,4 @@ +-GCLDIR := ../gclib ++GCLDIR := $(EPREFIX)/usr/include/gclib + SEARCHDIRS := -I. -I${GCLDIR} + + SYSTYPE := $(shell uname) +@@ -10,7 +10,7 @@ + MARCH = + endif + +-CC := g++ ++CXX ?= g++ + + BASEFLAGS := -Wall -Wextra ${SEARCHDIRS} $(MARCH) -D_FILE_OFFSET_BITS=64 \ + -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti +@@ -26,15 +26,17 @@ + GCC45OPTMAIN := + + ifeq ($(findstring release,$(MAKECMDGOALS)),release) +- CFLAGS := -O2 -DNDEBUG $(BASEFLAGS) ++ CXXFLAGS ?= -O2 ++ CXXFLAGS += -DNDEBUG $(BASEFLAGS) + LDFLAGS := + else +- CFLAGS := -g -DDEBUG $(BASEFLAGS) +- LDFLAGS := -g ++ CXXFLAGS ?= -g ++ CXXFLAGS += -DDEBUG $(BASEFLAGS) ++ LDFLAGS ?= -g + endif + + %.o : %.cpp +- ${CC} ${CFLAGS} -c $< -o $@ ++ ${CXX} ${CXXFLAGS} -c $< -o $@ + + # C/C++ linker + diff --git a/sci-biology/gffread/gffread-0.9.12.ebuild b/sci-biology/gffread/gffread-0.9.12.ebuild new file mode 100644 index 000000000..968ebc256 --- /dev/null +++ b/sci-biology/gffread/gffread-0.9.12.ebuild @@ -0,0 +1,18 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="GFF/GTF utility providing format conversions, filter/extract regions from FASTA" +HOMEPAGE="https://github.com/gpertea/gffread" +SRC_URI="https://github.com/gpertea/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="sci-biology/gclib" +RDEPEND="${DEPEND}" + +PATCHES=( "${FILESDIR}"/Makefile.patch ) diff --git a/sci-biology/gffread/metadata.xml b/sci-biology/gffread/metadata.xml new file mode 100644 index 000000000..138cb7705 --- /dev/null +++ b/sci-biology/gffread/metadata.xml @@ -0,0 +1,12 @@ +<?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>