1 files changed, 0 insertions, 135 deletions
diff --git a/sci-biology/seqclean/files/seqclean-110625-build.patch b/sci-biology/seqclean/files/seqclean-110625-build.patch
deleted file mode 100644
index b5797618f..000000000
--- a/sci-biology/seqclean/files/seqclean-110625-build.patch
+++ /dev/null
@@ -1,135 +0,0 @@
- mdust/Makefile    |   18 +++++++++---------
- mdust/fastafile.c |    3 ++-
- mdust/mdust.c     |    1 +
- trimpoly/Makefile |   16 ++++++++--------
- 4 files changed, 20 insertions(+), 18 deletions(-)
-
-diff --git a/mdust/Makefile b/mdust/Makefile
-index 81bf4e9..0c75e69 100644
---- a/mdust/Makefile
-+++ b/mdust/Makefile
-@@ -1,40 +1,40 @@
- # Useful directories
- 
- # Directories to search for header files
--SEARCHDIRS := -I. -I- 
-+SEARCHDIRS := -I. -iquote
- 
- 
- #SYSTYPE :=     $(shell uname)
- 
--CC      := gcc
--CFLAGS  = -O2 -Wall ${SEARCHDIRS} -D_REENTRANT
-+CC      ?= gcc
-+CFLAGS  += ${SEARCHDIRS} -D_REENTRANT
-+CXXFLAGS  += ${SEARCHDIRS} -D_REENTRANT
- 
- %.o : %.c
- 	${CC} ${CFLAGS} -c $< -o $@
- 
- %.o : %.cc
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.C
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.cpp
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.cxx
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- # C/C++ linker
- 
- LINKER    := gcc
--LDFLAGS    =
- LOADLIBES := 
- 
- .PHONY : all
- all:    mdust
- 
- mdust:  ./mdust.o ./dust.o ./fastafile.o
--	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
-+	${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
- 
- # target for removing all object files
- 
-diff --git a/mdust/fastafile.c b/mdust/fastafile.c
-index 6c14b99..5f70f14 100644
---- a/mdust/fastafile.c
-+++ b/mdust/fastafile.c
-@@ -1,7 +1,8 @@
- #include <stdio.h>
- #include <ctype.h>
- #include <malloc.h>
--
-+#include <string.h>
-+#include <stdlib.h>
- #include "fastafile.h"
- 
- 
-diff --git a/mdust/mdust.c b/mdust/mdust.c
-index f2bae99..c3ee686 100644
---- a/mdust/mdust.c
-+++ b/mdust/mdust.c
-@@ -1,6 +1,7 @@
- #include <stdlib.h>
- #include <stdio.h>
- #include <ctype.h>
-+#include <string.h>
- #include "dust.h"
- #include "fastafile.h"
- 
-diff --git a/trimpoly/Makefile b/trimpoly/Makefile
-index 84db22d..71145c2 100644
---- a/trimpoly/Makefile
-+++ b/trimpoly/Makefile
-@@ -3,28 +3,28 @@
- # Directories to search for header files
- SEARCHDIRS := -I.
- 
--CC      := gcc
--CFLAGS  = -O2 -Wall ${SEARCHDIRS} -D_REENTRANT
-+CC      ?= gcc
-+CFLAGS  += ${SEARCHDIRS} -D_REENTRANT
-+CXXFLAGS  += ${SEARCHDIRS} -D_REENTRANT
- 
- %.o : %.c
- 	${CC} ${CFLAGS} -c $< -o $@
- 
- %.o : %.cc
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.C
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.cpp
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- %.o : %.cxx
--	${CC} ${CFLAGS} -c $< -o $@
-+	${CXX} ${CXXFLAGS} -c $< -o $@
- 
- # C/C++ linker
- 
- LINKER    := gcc
--LDFLAGS    = 
- LOADLIBES =
- SYSTYPE :=     $(shell uname)
- #ifeq ($(SYSTYPE), Linux)
-@@ -37,7 +37,7 @@ SYSTYPE :=     $(shell uname)
- all:    trimpoly
- 
- trimpoly:  ./trimpoly.o color_c.o
--	${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
-+	${CXX} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LOADLIBES}
- 
- # target for removing all object files
-