sci-biology/cd-hit: Remove old

Package-Manager: Portage-2.3.3, Repoman-2.3.1

3 files changed, 0 insertions, 300 deletions

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 c3eaf79cc8f2..000000000000
--- 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) $(CXXFLAGS) cdhit-div.c++ -c
- 
diff --git a/sci-biology/cd-hit/files/4.5.4-gentoo.patch b/sci-biology/cd-hit/files/4.5.4-gentoo.patch
deleted file mode 100644
index 5aa9b79e02ae..000000000000
--- a/sci-biology/cd-hit/files/4.5.4-gentoo.patch
+++ /dev/null
@@ -1,98 +0,0 @@
- Makefile |   36 ++++++++++++++++++------------------
- 1 files changed, 18 insertions(+), 18 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index e8bac1d..bd31093 100644
---- a/Makefile
-+++ b/Makefile
-@@ -10,7 +10,7 @@ CCFLAGS = -O2 -DNO_OPENMP
- # in command line: 
- # make openmp=yes
- ifeq ($(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) $(CXXFLAGS) cdhit-454.c++ -c
- 
- PREFIX ?= /usr/local/bin
- 
diff --git a/sci-biology/cd-hit/files/4.6-gentoo.patch b/sci-biology/cd-hit/files/4.6-gentoo.patch
deleted file mode 100644
index 7a376eb8e73c..000000000000
--- a/sci-biology/cd-hit/files/4.6-gentoo.patch
+++ /dev/null
@@ -1,117 +0,0 @@
- Makefile |   47 ++++++++++++++++++++++-------------------------
- 1 files changed, 22 insertions(+), 25 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index e9796a1..97dd72b 100644
---- a/Makefile
-+++ b/Makefile
-@@ -1,16 +1,13 @@
--
--CC = g++ -Wall -ggdb
--CC = g++ -pg
--CC = g++
-+CXX ?= g++
- 
- # without OpenMP
--CCFLAGS = -DNO_OPENMP
-+#CXXFLAGS = -DNO_OPENMP
- 
- # with OpenMP
- # in command line: 
- # make openmp=yes
- ifeq ($(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
-