Version Bump, thanks for the notification by Martin Mokrejs

Package-Manager: portage-2.2.0_alpha32/cvs/Linux x86_64

5 files changed, 163 insertions, 15 deletions

diff --git a/sci-biology/cd-hit/ChangeLog b/sci-biology/cd-hit/ChangeLog
index 4d17282cd697..683abd5b6493 100644
--- a/sci-biology/cd-hit/ChangeLog
+++ b/sci-biology/cd-hit/ChangeLog
@@ -1,6 +1,12 @@
 # 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 1.1 2011/02/01 09:06:35 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/ChangeLog,v 1.2 2011/05/12 06:27:48 jlec Exp $
+
+*cd-hit-4.5.4 (12 May 2011)
+
+  12 May 2011; Justin Lecher <jlec@gentoo.org> +files/4.5.4-gentoo.patch,
+  cd-hit-4.5.1.ebuild, +cd-hit-4.5.4.ebuild:
+  Version Bump, thanks for the notification by Martin Mokrejs
 
 *cd-hit-4.5.1 (01 Feb 2011)
 
diff --git a/sci-biology/cd-hit/Manifest b/sci-biology/cd-hit/Manifest
index c3b5c4ff2dae..d7deb853aff3 100644
--- a/sci-biology/cd-hit/Manifest
+++ b/sci-biology/cd-hit/Manifest
@@ -2,14 +2,17 @@
 Hash: SHA1
 
 AUX 4.5.1-gentoo.patch 2651 RMD160 71063f7be6ba64fd1884a9a4b60a2d625b86a70b SHA1 da89f23f35304095cb8f8db8ea3ddb65640738f5 SHA256 6582f6138bac7d29956a4284e60139ae04c30db7fc635df97ce792324b0d96fe
+AUX 4.5.4-gentoo.patch 3144 RMD160 24c583c1e6c374e490d11b9cd2dfc7d9c8c99d2a SHA1 102e443c53c57969ef339ef205dda6f0316c64a0 SHA256 10868d02dab38a05338b7c124dadbcaed237467aa5e04383dc9c3275931439c5
 DIST cd-hit-v4.5.1-2011-01-31.tgz 368740 RMD160 118a37f44795db666cb9c6b53a5d29f4e72b73cb SHA1 5cd6e51390a7cee860fe97a51480d28f49bdcf61 SHA256 c1c3a3a772fc683fec3ff1763fdeec62a0a2a3925124f7a723fe3b271da35281
-EBUILD cd-hit-4.5.1.ebuild 1056 RMD160 58fda4827f77dd272ba0f72b264c26c9f2cb71c4 SHA1 9013bbdaf2d1e285eed4f63ade62bd71280b61a8 SHA256 6e73d3a504e0fd85786e36c2159fbfc651602bad2e0d43597e853f664b8bfa5b
-MISC ChangeLog 380 RMD160 cec5a6af887f75aa6525a01b2b91cf4f7e6a0b3e SHA1 988acaa3de1a3d921afb4e3f7962632dea249dd8 SHA256 3b97199e55f0f4ba0b36706fc36afa3ee0a4e71f0d107961f11c2ec13c5de2a7
+DIST cd-hit-v4.5.4-2011-03-07.tgz 370264 RMD160 00fca8d2527a4a6b1eda861f8f750e10ee565ae7 SHA1 743c4b6ec79b9d5acd1e1171587e96c03e3e3003 SHA256 6de9074fada3c5f8109b670b8bdf96679dab45b841d36270d6c5e61a34284f6a
+EBUILD cd-hit-4.5.1.ebuild 1057 RMD160 0d90a61ad3d34e87ef087dc9a571d93d6f9ba7a5 SHA1 964cc777fdbb42f65db24d440730906f6d8e3f0a SHA256 395efbd3b10fc7291631522569f794a294b69ecd4f2dc302e7d2b359a3849175
+EBUILD cd-hit-4.5.4.ebuild 1025 RMD160 ac295a6df75f9c173af4c06c0ac22f827d95f261 SHA1 f8852eabe1b07bffd6483867c6fb360ec95e9414 SHA256 722de756820a6b643c8d1ef1a4e30f142bb728bc9f229f33b7c4ec8038649184
+MISC ChangeLog 591 RMD160 5f57b115fc6935a0533112309051e10985d5c07e SHA1 0790f37144eb5505f47431ee80a035d4d84b7b22 SHA256 f58fa93eb10809610c0dba805a580b46a09989ba66496b3e327d64e2dd74d7e1
 MISC metadata.xml 1182 RMD160 fc96205490f768c92e7f3f846587a7900cb280e5 SHA1 1a23c6f28d8c27bf566681dbbfddfb80e925f068 SHA256 11b0329e729a4b0de427a402c47ce7d85b596e87c7296799c4fbad23a70cf558
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.16 (GNU/Linux)
+Version: GnuPG v2.0.17 (GNU/Linux)
 
-iEYEARECAAYFAk1HzSAACgkQgAnW8HDreRboDACePn+O5UTNY+lo2lU/uYDS7+MP
-c58AnR3Bk8KwKpE1MbtgBcAT9R6wIe1t
-=9vbS
+iEYEARECAAYFAk3LfeoACgkQgAnW8HDreRaJzQCgwCgjnYQ72kyXAW9ELpStT/Y1
+wZ8AoLrFseJYCNBnjlvnXMkBxUk2fI4Y
+=GI7O
 -----END PGP SIGNATURE-----
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 16119f159316..c9e839eeab3c 100644
--- a/sci-biology/cd-hit/cd-hit-4.5.1.ebuild
+++ b/sci-biology/cd-hit/cd-hit-4.5.1.ebuild
@@ -1,8 +1,8 @@
 # Copyright 1999-2011 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 1.1 2011/02/01 09:06:35 jlec Exp $
+# $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 $
 
-EAPI="3"
+EAPI=3
 
 inherit flag-o-matic toolchain-funcs
 
@@ -10,7 +10,7 @@ RELDATE="2011-01-31"
 RELEASE="${PN}-v${PV}-${RELDATE}"
 
 DESCRIPTION="Clustering Database at High Identity with Tolerance"
-HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit"
+HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
 SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz"
 
 SLOT="0"
@@ -31,11 +31,9 @@ src_prepare() {
 }
 
 src_compile() {
-	if use openmp; then
-		emake openmp=yes || die
-	else
-		emake || die
-	fi
+	local myconf=
+	use openmp && myconf="openmp=yes"
+	emake ${myconf} || die
 }
 
 src_install() {
diff --git a/sci-biology/cd-hit/cd-hit-4.5.4.ebuild b/sci-biology/cd-hit/cd-hit-4.5.4.ebuild
new file mode 100644
index 000000000000..c4760b447462
--- /dev/null
+++ b/sci-biology/cd-hit/cd-hit-4.5.4.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2011 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 $
+
+EAPI=4
+
+inherit flag-o-matic toolchain-funcs
+
+RELDATE="2011-03-07"
+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="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 cdhit-user-guide.pdf
+}
diff --git a/sci-biology/cd-hit/files/4.5.4-gentoo.patch b/sci-biology/cd-hit/files/4.5.4-gentoo.patch
new file mode 100644
index 000000000000..5aa9b79e02ae
--- /dev/null
+++ b/sci-biology/cd-hit/files/4.5.4-gentoo.patch
@@ -0,0 +1,98 @@
+ Makefile |   36 ++++++++++++++++++------------------
+ 1 files changed, 18 insertions(+), 18 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index e8bac1d..bd31093 100644
+--- a/Makefile
++++ b/Makefile
+@@ -10,7 +10,7 @@ CCFLAGS = -O2 -DNO_OPENMP
+ # in command line: 
+ # make openmp=yes
+ ifeq ($(openmp),yes)
+-CCFLAGS = -O2 -fopenmp
++CXXFLAGS += -fopenmp
+ endif
+ 
+ # support debugging
+@@ -18,16 +18,16 @@ endif
+ # make debug=yes
+ # make openmp=yes debug=yes
+ ifeq ($(debug),yes)
+-CCFLAGS += -ggdb
++CXXFLAGS += -ggdb
+ 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)
+ 
+@@ -37,47 +37,47 @@ 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) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) 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
+