commit: 5f0a37c2bd04745d627549bdfc77bb75fd70f0d1 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Tue Jun 26 08:20:29 2018 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Tue Jun 26 08:20:29 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5f0a37c2
sci-biology/gclib: removed as useless https://github.com/gpertea/gclib/issues/2#issuecomment-400125651 There is a bit of confusion here, this "library" is not meant to be a typical object library (no binary static file is being built) and certainly not meant to be built and installed globally into some ${prefix}/lib/ with corresponding headers under ${prefix}/include or so... It's just a loose collection of reusable source code which I directly include/source into a few of my bioinformatics projects, at compile time, as needed. As such there should be no reason to install it separately, system wide! (and I would advise against it). Moreover, the Makefile included here was simply meant for some quick testing during development, not for distribution. I have some simple scripts included in the actual projects themselves (e.g. gffread) which are pulling the minimum necessary source code files from the gclib directory in the process of creating a custom release tarball for distribution, which can then be found on the official release web page for each project (e.g. for gffread is http://ccb.jhu.edu/software/stringtie/dl/gffread-0.9.12.tar.gz). That "official" source code release tarball already includes the gclib source files that are needed to build the project -- so I would advise various distributions to use those releases instead as they should build properly with the gclib code "frozen" at the time of that particular release. Since gclib code is in continuous development/tweaking, as the various projects using it are too, there is no guarantee that the various automatic github releases are going to be all build compatible all the time (though I do try to keep the "master" branches in sync and ready to build, but beyond those "official", manually tested releases, it's hard to keep multiple projects in sync all the time). sci-biology/gclib/files/Makefile.patch | 41 ---------------------------------- sci-biology/gclib/gclib-0.10.2.ebuild | 25 --------------------- sci-biology/gclib/metadata.xml | 12 ---------- 3 files changed, 78 deletions(-) diff --git a/sci-biology/gclib/files/Makefile.patch b/sci-biology/gclib/files/Makefile.patch deleted file mode 100644 index 8b32aeca0..000000000 --- a/sci-biology/gclib/files/Makefile.patch +++ /dev/null @@ -1,41 +0,0 @@ ---- gclib-0.10.2/Makefile 2018-06-25 23:54:30.901037579 +0200 -+++ gclib-0.10.2/Makefile 2018-06-25 23:58:26.757488304 +0200 -@@ -38,7 +38,7 @@ - EXE = - endif - --CC := g++ -+CXX ?= g++ - - BASEFLAGS := -Wall -Wextra ${SEARCHDIRS} $(MARCH) \ - -D_REENTRANT -fno-exceptions -fno-rtti -@@ -54,23 +54,24 @@ - GCC45OPTMAIN := - - ifeq ($(findstring nodebug,$(MAKECMDGOALS)),) -- CFLAGS := -g -DDEBUG $(BASEFLAGS) -+ CXXFLAGS += -DDEBUG $(BASEFLAGS) - LDFLAGS += -g - else -- CFLAGS := -O2 -DNDEBUG $(BASEFLAGS) -+ CXXFLAGS ?= -O2 -+ CXXFLAGS += -DNDEBUG $(BASEFLAGS) - ifeq ($(shell expr $(GCC_MAJOR).$(GCC_MINOR) '>=' 4.5),1) -- CFLAGS += -flto -+ CXXFLAGS += -flto - GCC45OPTS := -flto - GCC45OPTMAIN := -fwhole-program - endif - endif - - %.o : %.cpp -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - # C/C++ linker - --LINKER := g++ -+LINKER ?= g++ - LIBS := - OBJS := GBase.o GStr.o GArgs.o - diff --git a/sci-biology/gclib/gclib-0.10.2.ebuild b/sci-biology/gclib/gclib-0.10.2.ebuild deleted file mode 100644 index de269eef1..000000000 --- a/sci-biology/gclib/gclib-0.10.2.ebuild +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -DESCRIPTION="GCLib - Genomic C(++) library of reusable code for bioinformatics projects" -HOMEPAGE="https://github.com/gpertea/gclib"; -SRC_URI="https://github.com/gpertea/gclib/archive/v0.10.2.tar.gz -> ${P}.tar.gz" - -LICENSE="Artistic-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="${DEPEND}" - -PATCHES=( "${FILESDIR}"/Makefile.patch ) - -src_install(){ - dobin gtest threads - dodoc README.md - insinto /usr/include/"${PN}" - doins *.h *.hh -} diff --git a/sci-biology/gclib/metadata.xml b/sci-biology/gclib/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/gclib/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>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata>
