[gentoo-commits] proj/sci:master commit in: sci-biology/gclib/files/, sci-biology/gclib/

[gentoo-commits] proj/sci:master commit in: sci-biology/gclib/files/, sci-biology/gclib/

[Martin Mokrejs]

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>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>