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

[David Seifert]

commit:     297c25831be85619015cb3f854b757570601bb5e
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 25 19:17:42 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Feb 25 19:18:39 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=297c2583

sci-biology/cd-hit: Remove old

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/cd-hit/Manifest                 |   3 -
 sci-biology/cd-hit/cd-hit-4.5.1.ebuild      |  42 ----------
 sci-biology/cd-hit/cd-hit-4.5.4.ebuild      |  43 ----------
 sci-biology/cd-hit/cd-hit-4.6.ebuild        |  44 -----------
 sci-biology/cd-hit/files/4.5.1-gentoo.patch |  85 --------------------
 sci-biology/cd-hit/files/4.5.4-gentoo.patch |  98 -----------------------
 sci-biology/cd-hit/files/4.6-gentoo.patch   | 117 ----------------------------
 7 files changed, 432 deletions(-)

diff --git a/sci-biology/cd-hit/Manifest b/sci-biology/cd-hit/Manifest
index b671c47b32..f2d3e0b6ed 100644
--- a/sci-biology/cd-hit/Manifest
+++ b/sci-biology/cd-hit/Manifest
@@ -1,4 +1 @@
 DIST cd-hit-4.6.6.tar.gz 1152570 SHA256 97946f8ae62c3efa20ad4c527b8ea22200cf1b75c9941fb14de2bdaf1d6910f1 SHA512 8241d6674fb041559792dbbb58c12b41302d2275d3bacb1362946094b48a0b8e1236e71b5dc77d13405220b60f8253e6f996753a8b051995a72c8353d4333c51 WHIRLPOOL 4ee404e34a9c22aef0b809568aa1a7cefcd8d08e4a8c97d1c65b7692ae14b0567e5cc446054083219b56e89895117f69f786e6183f6c67d03d1f8404f7ba9632
-DIST cd-hit-v4.5.1-2011-01-31.tgz 368740 SHA256 c1c3a3a772fc683fec3ff1763fdeec62a0a2a3925124f7a723fe3b271da35281 SHA512 84beba384eb6e9bcf94c7e2ca63f862493fc0d058ad186752524a09016e01274229ca9b7a5275cd5454f54488235a6949e17090ffbf68ff441a613dbe5cf05a8 WHIRLPOOL 698d72f347b92091ade411bdbf540f4b4eeea6c742d3766e891bede7f1aa03024bd2f611a4235a6dec0ed9b9b5e06b3d69a7b8e6a7ab7d8139297b5a8b0da9d2
-DIST cd-hit-v4.5.4-2011-03-07.tgz 370264 SHA256 6de9074fada3c5f8109b670b8bdf96679dab45b841d36270d6c5e61a34284f6a SHA512 a093d15e26d6e226e5b37e43ed36affe58c0ee265bd43fd2098a39eafb54c7154ee1a7585da785324dc57532abe3401d48ad5a4a2de080fa6e1422091083683a WHIRLPOOL 3e2ea2db07ecc553d5f03f13a1092e85211257fb4a681629be0350d9cc3f3cc384d24bdb8b3e31d3f469fbc93070363afee608904b9ce3956ca24a8fa6d4d8e5
-DIST cd-hit-v4.6-2012-04-25.tgz 652228 SHA256 aa91e57bba61f04db39e83cdd6c8cdf082a006ea8c4c818b956b7531e4bcc2e9 SHA512 1004a4190643b6f5f1da067a4b911abc068d0bf7d909edd84f45d5fe9a1b17eb3276c0ddde391cbc5053a9ab979d09cbbe832615b7cce4fc2aeefce1d1bec52c WHIRLPOOL 1c7a50e40e9753c035a2920af09b024e9403f4a7cf1a801b998afd5b64189256857a236439f5b2935603fd4a691a722a9d74c3a373ab66c79faee9d8335834b4

diff --git a/sci-biology/cd-hit/cd-hit-4.5.1.ebuild b/sci-biology/cd-hit/cd-hit-4.5.1.ebuild
deleted file mode 100644
index e1eeac9a03..0000000000
--- a/sci-biology/cd-hit/cd-hit-4.5.1.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=3
-
-inherit eutils flag-o-matic toolchain-funcs
-
-RELDATE="2011-01-31"
-RELEASE="${PN}-v${PV}-${RELDATE}"
-
-DESCRIPTION="Clustering Database at High Identity with Tolerance"
-HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
-SRC_URI="https://cdhit.googlecode.com/files/${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} || die
-}
-
-src_install() {
-	dobin cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div *.pl || die
-	dodoc ChangeLog cdhit-user-guide.pdf || die
-}

diff --git a/sci-biology/cd-hit/cd-hit-4.5.4.ebuild b/sci-biology/cd-hit/cd-hit-4.5.4.ebuild
deleted file mode 100644
index 032aafc43b..0000000000
--- a/sci-biology/cd-hit/cd-hit-4.5.4.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils flag-o-matic toolchain-funcs
-
-RELDATE="2011-03-07"
-RELEASE="${PN}-v${PV}-${RELDATE}"
-
-DESCRIPTION="Clustering Database at High Identity with Tolerance"
-HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
-SRC_URI="https://cdhit.googlecode.com/files/${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/cd-hit-4.6.ebuild b/sci-biology/cd-hit/cd-hit-4.6.ebuild
deleted file mode 100644
index 73c8e48636..0000000000
--- a/sci-biology/cd-hit/cd-hit-4.6.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils flag-o-matic toolchain-funcs
-
-RELDATE="2012-04-25"
-RELEASE="${PN}-v${PV}-${RELDATE}"
-
-DESCRIPTION="Clustering Database at High Identity with Tolerance"
-HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
-SRC_URI="https://cdhit.googlecode.com/files/${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/4.5.1-gentoo.patch b/sci-biology/cd-hit/files/4.5.1-gentoo.patch
deleted file mode 100644
index c3eaf79cc8..0000000000
--- a/sci-biology/cd-hit/files/4.5.1-gentoo.patch
+++ /dev/null
@@ -1,85 +0,0 @@
-diff --git a/Makefile b/Makefile
-index f1eaa26..92d3130 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
- 
- .c++.o:
--	$(CC) $(CCFLAGS) -c $<
-+	$(CXX) $(CXXFLAGS) -c $<
- 
- all: $(PROGS)
- 
-@@ -37,39 +37,39 @@ 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
- 
- # 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
- 

diff --git a/sci-biology/cd-hit/files/4.5.4-gentoo.patch b/sci-biology/cd-hit/files/4.5.4-gentoo.patch
deleted file mode 100644
index 5aa9b79e02..0000000000
--- a/sci-biology/cd-hit/files/4.5.4-gentoo.patch
+++ /dev/null
@@ -1,98 +0,0 @@
- 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
- 

diff --git a/sci-biology/cd-hit/files/4.6-gentoo.patch b/sci-biology/cd-hit/files/4.6-gentoo.patch
deleted file mode 100644
index 7a376eb8e7..0000000000
--- a/sci-biology/cd-hit/files/4.6-gentoo.patch
+++ /dev/null
@@ -1,117 +0,0 @@
- 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
-