sci-biology/cd-hit: Version Bump, which fixes compilation problems with gcc 4.7, #422569; add missing eutils.eclass

(Portage version: 2.2.0_alpha110/cvs/Linux x86_64)

6 files changed, 180 insertions, 13 deletions

diff --git a/sci-biology/cd-hit/ChangeLog b/sci-biology/cd-hit/ChangeLog
index 683abd5b6493..90f4c75dc61f 100644
--- a/sci-biology/cd-hit/ChangeLog
+++ b/sci-biology/cd-hit/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/cd-hit
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/ChangeLog,v 1.2 2011/05/12 06:27:48 jlec Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/ChangeLog,v 1.3 2012/06/20 18:39:24 jlec Exp $
+
+*cd-hit-4.6 (20 Jun 2012)
+
+  20 Jun 2012; Justin Lecher <jlec@gentoo.org> +files/4.6-gentoo.patch,
+  cd-hit-4.5.1.ebuild, cd-hit-4.5.4.ebuild, +cd-hit-4.6.ebuild, metadata.xml:
+  Version Bump, which fixes compilation problems with gcc 4.7, #422569; add
+  missing eutils.eclass
 
 *cd-hit-4.5.4 (12 May 2011)
 
diff --git a/sci-biology/cd-hit/cd-hit-4.5.1.ebuild b/sci-biology/cd-hit/cd-hit-4.5.1.ebuild
index c9e839eeab3c..bdbe4b94ee93 100644
--- a/sci-biology/cd-hit/cd-hit-4.5.1.ebuild
+++ b/sci-biology/cd-hit/cd-hit-4.5.1.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/cd-hit-4.5.1.ebuild,v 1.2 2011/05/12 06:27:48 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/cd-hit-4.5.1.ebuild,v 1.3 2012/06/20 18:39:24 jlec Exp $
 
 EAPI=3
 
-inherit flag-o-matic toolchain-funcs
+inherit eutils flag-o-matic toolchain-funcs
 
 RELDATE="2011-01-31"
 RELEASE="${PN}-v${PV}-${RELDATE}"
diff --git a/sci-biology/cd-hit/cd-hit-4.5.4.ebuild b/sci-biology/cd-hit/cd-hit-4.5.4.ebuild
index c4760b447462..6d2d393ff361 100644
--- a/sci-biology/cd-hit/cd-hit-4.5.4.ebuild
+++ b/sci-biology/cd-hit/cd-hit-4.5.4.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/cd-hit-4.5.4.ebuild,v 1.1 2011/05/12 06:27:48 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/cd-hit-4.5.4.ebuild,v 1.2 2012/06/20 18:39:24 jlec Exp $
 
 EAPI=4
 
-inherit flag-o-matic toolchain-funcs
+inherit eutils flag-o-matic toolchain-funcs
 
 RELDATE="2011-03-07"
 RELEASE="${PN}-v${PV}-${RELDATE}"
diff --git a/sci-biology/cd-hit/cd-hit-4.6.ebuild b/sci-biology/cd-hit/cd-hit-4.6.ebuild
new file mode 100644
index 000000000000..25b63012845f
--- /dev/null
+++ b/sci-biology/cd-hit/cd-hit-4.6.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2012 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="2012-04-25"
+RELEASE="${PN}-v${PV}-${RELDATE}"
+
+DESCRIPTION="Clustering Database at High Identity with Tolerance"
+HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
+SRC_URI="http://cdhit.googlecode.com/files/${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"
+	emake ${myconf}
+}
+
+src_install() {
+	dodir /usr/bin
+	emake PREFIX="${ED}/usr/bin" install
+	dodoc ChangeLog
+	use doc && dodoc doc/*
+}
diff --git a/sci-biology/cd-hit/files/4.6-gentoo.patch b/sci-biology/cd-hit/files/4.6-gentoo.patch
new file mode 100644
index 000000000000..7a376eb8e73c
--- /dev/null
+++ b/sci-biology/cd-hit/files/4.6-gentoo.patch
@@ -0,0 +1,117 @@
+ Makefile |   47 ++++++++++++++++++++++-------------------------
+ 1 files changed, 22 insertions(+), 25 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index e9796a1..97dd72b 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,16 +1,13 @@
+-
+-CC = g++ -Wall -ggdb
+-CC = g++ -pg
+-CC = g++
++CXX ?= g++
+ 
+ # without OpenMP
+-CCFLAGS = -DNO_OPENMP
++#CXXFLAGS = -DNO_OPENMP
+ 
+ # with OpenMP
+ # in command line: 
+ # make openmp=yes
+ ifeq ($(openmp),yes)
+-CCFLAGS = -fopenmp
++CXXFLAGS += -fopenmp
+ endif
+ 
+ # support debugging
+@@ -18,22 +15,22 @@ endif
+ # make debug=yes
+ # make openmp=yes debug=yes
+ ifeq ($(debug),yes)
+-CCFLAGS += -ggdb
++CXXFLAGS += 
+ else
+-CCFLAGS += -O2
++CXXFLAGS += 
+ endif
+ 
+ ifdef MAX_SEQ
+-CCFLAGS += -DMAX_SEQ=$(MAX_SEQ)
++CXXFLAGS += -DMAX_SEQ=$(MAX_SEQ)
+ endif
+ 
+ #LDFLAGS = -static -o
+-LDFLAGS = -o
++#LDFLAGS += -o
+ 
+ PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454
+ 
+ .c++.o:
+-	$(CC) $(CCFLAGS) -c $<
++	$(CXX) $(CXXFLAGS) -c $<
+ 
+ all: $(PROGS)
+ 
+@@ -43,47 +40,47 @@ clean:
+ # programs
+ 
+ cd-hit: cdhit-common.o cdhit-utility.o cdhit.o
+-	$(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit.o cdhit-common.o cdhit-utility.o -o cd-hit
+ 
+ cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o
+-	$(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-2d
+ 
+ cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o
+-	$(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o -o cd-hit-est
+ 
+ cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o
+-	$(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-est-2d
+ 
+ cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o
+-	$(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o -o cd-hit-div
+ 
+ cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o
+-	$(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o -o cd-hit-454
+ 
+ # objects
+ cdhit-common.o: cdhit-common.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-common.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-common.c++ -c
+ 
+ cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-utility.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-utility.c++ -c
+ 
+ cdhit.o: cdhit.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit.c++ -c
+ 
+ cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-2d.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-2d.c++ -c
+ 
+ cdhit-est.o: cdhit-est.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-est.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-est.c++ -c
+ 
+ cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h
+-	$(CC) $(CCFLAGS) cdhit-est-2d.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c
+ 
+ cdhit-div.o: cdhit-div.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-div.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-div.c++ -c
+ 
+ cdhit-454.o: cdhit-454.c++ cdhit-common.h
+-	$(CC) $(CCFLAGS) cdhit-454.c++ -c
++	$(CXX) $(CXXFLAGS) cdhit-454.c++ -c
+ 
+ PREFIX ?= /usr/local/bin
+ 
diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml
index e4184a444391..bd5607ab16b5 100644
--- a/sci-biology/cd-hit/metadata.xml
+++ b/sci-biology/cd-hit/metadata.xml
@@ -2,10 +2,8 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<herd>sci-biology</herd>
-	<maintainer>
-		<email>jlec@gentoo.org</email>
-	</maintainer>
-	<longdescription>CD-HIT is a very widely used program for clustering and comparing large sets 
+	<longdescription>
+CD-HIT is a very widely used program for clustering and comparing large sets 
 of protein or nucleotide sequences. CD-HIT is very fast and can handle 
 extremely large databases. CD-HIT helps to significantly reduce the 
 computational and manual efforts in many sequence analysis tasks and aids in 
@@ -17,7 +15,8 @@ user-defined similarity threshold. CD-HIT-2D (CD-HIT-EST-2D) compares 2
 datasets and identifies the sequences in db2 that are similar to db1 above 
 a threshold. CD-HIT-454 is a program to identify natural and artificial 
 duplicates from pyrosequencing reads. The usage of other programs and 
-scripts can be found in CD-HIT user's guide.</longdescription>
+scripts can be found in CD-HIT user's guide.
+</longdescription>
 	<upstream>
 		<remote-id type="google-code">cdhit</remote-id>
 	</upstream>