[gentoo-commits] proj/sci:master commit in: sci-biology/cd-hit-auxtools/files/, sci-biology/cd-hit-auxtools/

[Martin Mokrejs]

commit:     69b578f57aed0097521cb637b03a22139789cf84
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jun  1 18:49:23 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jun  1 18:49:23 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=69b578f5

sci-biology/cd-hit-auxtools: new package, needs gcc<=4.6.4 or some CXXFLAG to loosen g++ strictness

Package-Manager: portage-2.2.7

---
 sci-biology/cd-hit-auxtools/ChangeLog              | 10 +++++
 .../cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild     | 42 +++++++++++++++++++
 sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch | 47 ++++++++++++++++++++++
 sci-biology/cd-hit-auxtools/metadata.xml           |  9 +++++
 4 files changed, 108 insertions(+)

diff --git a/sci-biology/cd-hit-auxtools/ChangeLog b/sci-biology/cd-hit-auxtools/ChangeLog
new file mode 100644
index 0000000..6bee545
--- /dev/null
+++ b/sci-biology/cd-hit-auxtools/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/cd-hit-auxtools
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*cd-hit-auxtools-0.5 (01 Jun 2014)
+
+  01 Jun 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
+  +cd-hit-auxtools-0.5.ebuild, +files/0.5-gentoo.patch, +metadata.xml:
+  sci-biology/cd-hit-auxtools: new package, needs gcc<=4.6.4 or some CXXFLAG to
+  loosen g++ strictness

diff --git a/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild b/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild
new file mode 100644
index 0000000..c40e98b
--- /dev/null
+++ b/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/cd-hit-4.6.ebuild,v 1.1 2012/06/20 18:39:24 jlec Exp $
+
+EAPI=4
+
+inherit eutils flag-o-matic toolchain-funcs
+
+RELDATE="2012-03-07"
+RELEASE="${PN}-v${PV}-${RELDATE}"
+
+DESCRIPTION="Additional cd-hit itools: read-linker, cd-hit-lap and cd-hit-dup"
+HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
+SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE="GPL-2"
+IUSE="doc openmp"
+
+S="${WORKDIR}"/${RELEASE}
+
+pkg_setup() {
+	 use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
+}
+
+src_prepare() {
+	tc-export CXX
+	use openmp || append-flags -DNO_OPENMP
+	epatch "${FILESDIR}"/${PV}-gentoo.patch
+}
+
+src_compile() {
+	local myconf=
+	use openmp && myconf="openmp=yes"
+	make ${myconf} || die "If compilation failed try gcc-4.6.4 or older, newer versions are too picky about quality of the source code"
+}
+
+src_install() {
+	dodir /usr/bin
+	dobin read-linker cd-hit-lap cd-hit-dup
+}

diff --git a/sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch b/sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch
new file mode 100644
index 0000000..3977cbe
--- /dev/null
+++ b/sci-biology/cd-hit-auxtools/files/0.5-gentoo.patch
@@ -0,0 +1,47 @@
+--- Makefile.ori	2014-06-01 20:25:53.000000000 +0200
++++ Makefile	2014-06-01 20:27:15.000000000 +0200
+@@ -1,8 +1,8 @@
+ 
+-CC = g++
++CXX = g++
+ 
+-CFLAGS = -Wall -Wno-unused -I. -Imintlib
+-LFLAGS = -fPIC
++CXXFLAGS = -I. -Imintlib
++LDFLAGS = -fPIC
+ 
+ 
+ UNAME = $(shell uname)
+@@ -16,9 +16,9 @@
+ endif
+ 
+ ifeq ($(debug),yes)
+-CFLAGS += -ggdb
++CiXXFLAGS +=
+ else
+-CFLAGS += -O2
++CXXFLAGS +=
+ endif
+ 
+ 
+@@ -32,16 +32,16 @@
+ .SUFFIXES: .c .obj .cpp .cc .cxx .C
+ 
+ .cxx.o:
+-	$(CC) -c $(CFLAGS) -o $@ $<
++	$(CXX) -c $(CXXFLAGS) -o $@ $<
+ 
+ cd-hit-dup: $(OBJECTS) cdhit-dup.o
+-	$(CC) $(LFLAGS) $(OBJECTS) cdhit-dup.o -o cd-hit-dup
++	$(CXX) $(LDFLAGS) $(OBJECTS) cdhit-dup.o -o cd-hit-dup
+ 
+ cd-hit-lap: $(OBJECTS) cdhit-lap.o
+-	$(CC) $(LFLAGS) $(OBJECTS) cdhit-lap.o -o cd-hit-lap
++	$(CXX) $(LDFLAGS) $(OBJECTS) cdhit-lap.o -o cd-hit-lap
+ 
+ read-linker: $(OBJECTS) read-linker.o
+-	$(CC) $(LFLAGS) $(OBJECTS) read-linker.o -o read-linker
++	$(CXX) $(LDFLAGS) $(OBJECTS) read-linker.o -o read-linker
+ 
+ clean:
+ 	rm $(OBJECTS) cdhit-dup.o cdhit-lap.o read-linker.o

diff --git a/sci-biology/cd-hit-auxtools/metadata.xml b/sci-biology/cd-hit-auxtools/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/cd-hit-auxtools/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@×××××××××××××××.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>